Publications

2024

  • [DOI] M. McKinley, D. Sun, M. Kelly, K. G. Sabra, and A. Bracco, “Deep mesoscale and submesoscale circulations around the atlantis ii seamount,” Journal of geophysical research: oceans, vol. 129, iss. 11, p. e2024JC021233, 2024.
    [Bibtex] 
    @article{https://doi.org/10.1029/2024JC021233,
author = {McKinley, Matthew and Sun, Daoxun and Kelly, Mark and Sabra, Karim G. and Bracco, Annalisa},
title = {Deep Mesoscale and Submesoscale Circulations Around the Atlantis II Seamount},
journal = {Journal of Geophysical Research: Oceans},
volume = {129},
number = {11},
pages = {e2024JC021233},
keywords = {submesoscale, seamounts, north atlantic current, lee wave, ocean dynamics, topography},
doi = {https://doi.org/10.1029/2024JC021233},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2024JC021233},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2024JC021233},
note = {e2024JC021233 2024JC021233},
abstract = {Abstract This study investigates the complex interactions between the North Atlantic Current (NAC) and the New England Seamount chain, focusing on the Atlantis II seamount. Employing a high-resolution submesoscale permitting regional ocean circulation model nested within a basin-wide simulation, it explores three distinct periods, each 2 weeks long, showcasing varied deep mesoscale and submesoscale circulations around the seamount. The analysis includes Eulerian statistics and Lagrangian particle tracing experiments to explore the transport and mixing impacts of the highly dynamic flow around the seamount. The results reveal significant density variations across the water column, attributed to the seamount's influence on local ocean currents. Specifically, mesoscale and submesoscale vortices, a seamount wake, and lee waves form during periods of increased near-bottom current flow. These findings highlight the critical role of topographic features in modulating oceanic flows and ocean mixing, which have implications, among others, for nutrient distribution, acoustic propagation, and climate modeling. The variety and variability of the mesoscale and submesoscale circulations that arise in response to the variability in the NAC strength and position in relation to the New England Seamount Chain demonstrate the difficulty in extrapolating general behaviors from isolated observational campaigns.},
year = {2024}
}
  • [DOI] E. A. Flores, M. Ramos, B. Dewitte, O. Astudillo, and L. Glasner, “On the role of onshore geostrophic flow on larval retention in a permanent upwelling zone along north-central chile,” Frontiers in marine science, vol. 11, 2024.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2024.1449369,
AUTHOR = {Flores, Eduardo A. and Ramos, Marcel and Dewitte, Boris and Astudillo, Orlando and Glasner, Lucas },
TITLE = {On the role of onshore geostrophic flow on larval retention in a permanent upwelling zone along north-central Chile},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {11},
YEAR = {2024},
URL = {https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2024.1449369},
DOI = {10.3389/fmars.2024.1449369},
ISSN = {2296-7745},
ABSTRACT = {The Humboldt Archipelago (HAp), located off north-central Chile (~28° - 33° S) is one of the most productive marine zones of the Humboldt Current System (HCS). This area lies within a permanent upwelling zone, characterized by two upwelling centers, 100 km apart, that define the Coquimbo Bays System (CBS). The resulting increase in primary productivity and larval retention are mentioned as the main factors that explain the high biodiversity. However, how these upwelling centers interact remains unclear due to the interplay of various physical features such as the general circulation, the meso- and submeso-scale structures (e.g., eddies), and remote and local forcings (e.g., winds, topography) that affect larval transport in the HAp. In this study, we focus on the role played by geostrophic and Ekman currents in controlling the retention (and dispersion) of particles in these centers based on the analyses of satellite data and hydrodynamic model outputs. Lagrangian models are in particular carried out to document particles’ transport during selected oceanic conditions corresponding to whether Ekman transport or geostrophic recirculation prevails or are debilitated. The latitudinal variation of the Ekman transport reveals two maxima at each upwelling center with differences in spatial extent but not in intensity. Mean zonal geostrophic current occurs in alternating flow at each upwelling center. Results of the Lagrangian experiments highlight the importance of the cross-shore geostrophic flow on larval transport, where an increased transport of particles to the north and northwest occurs at the southern upwelling center, while the northern upwelling center (where HAp is located) received particles from the south and retained particles released in the same area, which is related to the cyclonic geostrophic recirculation and lower Ekman transport. Particle retention increased with depth and under the relaxation and downwelling scenarios revealing the importance of wind alternation for larval retention. The CBS could act as an upwelling shadow in the south and an upwelling trap in the north where the onshore flow of geostrophic current could enhance larval retention and recruitment over longer periods when compared with the Ekman transport timescale.}
}
  • [DOI] W. Podlejski, Léo. Berline, J. Jouanno, N. Barrier, and C. Lett, “Drivers of growth and decay of sargassum in the tropical atlantic: a lagrangian approach,” Progress in oceanography, vol. 229, p. 103364, 2024.
    [Bibtex] 
    @article{PODLEJSKI2024103364,
title = {Drivers of growth and decay of Sargassum in the Tropical Atlantic: A Lagrangian approach},
journal = {Progress in Oceanography},
volume = {229},
pages = {103364},
year = {2024},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2024.103364},
url = {https://www.sciencedirect.com/science/article/pii/S0079661124001708},
author = {Witold Podlejski and Léo Berline and Julien Jouanno and Nicolas Barrier and Christophe Lett},
keywords = {Lagrangian simulation, Growth model, Tropical North atlantic, Alternative Floating Algae Index, Time series, Nutrients},
abstract = {The proliferation of Sargassum in the Tropical Atlantic has occurred almost every year since 2011, but a strong variability of biomass is observed among years. Essential knowledge about the drivers of Sargassum growth and decay is still lacking to explain this interannual variability. Benefiting from accurate basin scale Sargassum detections provided by remote sensing, and from physical and biogeochemical ocean simulations, we developed a Lagrangian drift-growth model to simulate Sargassum distribution over the period 2016–2020. The resulting trajectories and biomass time series of Sargassum aggregates were analyzed to highlight the main limiting factors of growth and decay. The nitrogen and phosphorous concentrations are found to be weakly restrictive compared to physical limiting factors, especially the temperature. In particular, the warm waters found off northern Brazil appear to be instrumental in triggering the end of seasonal growth of Sargassum. The timing of the seasonal warming of this region strongly impacts the quantities of Sargassum simulated each year. This suggests that this region should be monitored to anticipate the development of Sargassum and resulting strandings.}
}
  • [DOI] G. Thompson-Saud, A. Grech, S. Choukroun, S. I. Vásquez, C. Salas, and A. Ospina-Alvarez, “The biophysical dynamics of giant kelp, macrocystis pyrifera: seasonal patterns and dispersal mechanisms in the southeast pacific,” Journal of biogeography, vol. 51, iss. 11, pp. 2198-2210, 2024.
    [Bibtex] 
    @article{https://doi.org/10.1111/jbi.14980,
author = {Thompson-Saud, G. and Grech, A. and Choukroun, S. and Vásquez, S. I. and Salas, C. and Ospina-Alvarez, A.},
title = {The biophysical dynamics of giant kelp, Macrocystis pyrifera: Seasonal patterns and dispersal mechanisms in the southeast Pacific},
journal = {Journal of Biogeography},
volume = {51},
number = {11},
pages = {2198-2210},
keywords = {biophysical modelling, dispersal, ENSO (El Niño-Southern Oscillation), Humboldt Current System, individual-based modelling, kelp, Macrocystis pyrifera},
doi = {https://doi.org/10.1111/jbi.14980},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.14980},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/jbi.14980},
abstract = {Abstract Aim Dispersal and connectivity play important roles in shaping the population structure of giant kelp, Macrocystis pyrifera, across the western coast of South America. Its high potential dispersal capacity suggests the existence of metapopulations, where discrete habitat patches or groups of patches form subpopulations that interact at some level. However, the dispersal patterns of giant kelp in this region have not been quantified. This study assesses the dispersal and settlement of Macrocystis pyrifera in the southeast Pacific, specifically focusing on the impact of environmental variables and ocean currents within the Humboldt Current System. Location Southeast Pacific (coast of Chile and Peru). Time Period 1997–2008. Major Taxa Studied Macrocystis pyrifera (giant kelp). Methods Using a combination of hydrodynamic and individual-based models, we analysed kelp fragment movements over 12 years, with a particular emphasis on the effects of the El Niño-Southern Oscillation (ENSO) and seasonal changes. Results Our results highlight a key settlement area in the southern Chilean region. We found that shorter travel distances of kelp fragments increased the likelihood of reaching a suitable habitat, underscoring the importance of local environmental conditions. We delineated intricate northward dispersal paths for kelp fragments, which appear to be governed by the interplay of wind and ocean current dynamics. Seasonal variations, notably in autumn and winter, favour the likelihood of reaching a settlement area due to favourable winds. Furthermore, ENSO events appear to influence dispersal distances, with fragments travelling the longest distances during El Niño phases. Main Conclusion These findings are essential for informing kelp conservation strategies in the context of climate change, emphasizing the necessity of considering local and seasonal environmental factors alongside ENSO impacts.},
year = {2024}
}
  • [DOI] E. G. Tosetto, C. Lett, S. Neumann-Leitão, A. Koch-Larrouy, N. Barrier, A. C. da Silva, J. Salvetat, and A. Bertrand, “Diel vertical migration and seamount stepping stones promote species connectivity from coastal to offshore insular systems in the tropical southwestern atlantic,” Limnology and oceanography, vol. 69, iss. 9, pp. 2071-2084, 2024.
    [Bibtex] 
    @article{https://doi.org/10.1002/lno.12648,
author = {Tosetto, Everton Giachini and Lett, Christophe and Neumann-Leitão, Sigrid and Koch-Larrouy, Ariane and Barrier, Nicolas and da Silva, Alex Costa and Salvetat, Julie and Bertrand, Arnaud},
title = {Diel vertical migration and seamount stepping stones promote species connectivity from coastal to offshore insular systems in the Tropical Southwestern Atlantic},
journal = {Limnology and Oceanography},
volume = {69},
number = {9},
pages = {2071-2084},
doi = {https://doi.org/10.1002/lno.12648},
url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.12648},
eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12648},
abstract = {Abstract The recruitment of marine species in isolated oceanic island systems can be challenged by prevailing currents, as exemplified by the Tropical Southwestern Atlantic. In this region, the Fernando de Noronha ridge hosts several seamounts, the Rocas Atoll and the Fernando de Noronha Archipelago, which are home to great marine biodiversity. However, along the ridge, the central branch of the South Equatorial Current (cSEC), flowing westward, poses a challenge to the recruitment of organisms toward Fernando de Noronha. To unveil critical insights into the intricate processes shaping biodiversity in these insular ecosystems, we use a dispersal Lagrangian tool to explore the role of diel vertical migration (DVM) to depth strata influenced by the South Equatorial Undercurrent (SEUC), which flows eastward bellow the cSEC, in shaping species dispersal and metacommunity dynamics. Our results show that while not a direct journey, the DVM into SEUC-influenced strata increases the possibility that the seamounts and the Rocas Atoll act as stepping stones between the continental shelf and Fernando de Noronha. Propagules of organisms originating primarily from the continental shelf are transported to the western seamounts of the ridge. Upon reaching the western seamounts, organisms can find suitable habitats to recruit. The progeny of these communities that migrate to SEUC-influenced strata have the opportunity to reach suitable habitats at the Rocas Atoll and the Eastern seamounts, ultimately connecting to the Fernando de Noronha archipelago. These results provide scientific fundaments for the development of a functional network of marine protected areas in the Tropical Southwestern Atlantic.},
year = {2024}
}
  • [DOI] A. Dupaix, M. Lengaigne, M. Andrello, N. Barrier, L. Dagorn, Q. Gusmai, G. Viennois, and M. Capello, “Floating objects in the open ocean: unveiling modifications of the pelagic habitat induced by forest cover change and climate variations,” Global environmental change, vol. 88, p. 102917, 2024.
    [Bibtex] 
    @article{DUPAIX2024102917,
title = {Floating objects in the open ocean: Unveiling modifications of the pelagic habitat induced by forest cover change and climate variations},
journal = {Global Environmental Change},
volume = {88},
pages = {102917},
year = {2024},
issn = {0959-3780},
doi = {https://doi.org/10.1016/j.gloenvcha.2024.102917},
url = {https://www.sciencedirect.com/science/article/pii/S0959378024001213},
author = {Amaël Dupaix and Matthieu Lengaigne and Marco Andrello and Nicolas Barrier and Laurent Dagorn and Quentin Gusmai and Gaëlle Viennois and Manuela Capello},
keywords = {Drifting fish aggregating device, Lagrangian simulation, Tropical tuna, Anthropogenic impacts},
abstract = {Natural floating objects (NLOGs) are a major component of the habitat of pelagic species. Since the 1990s, the number of floating objects in the open ocean has increased greatly as a result of the introduction of drifting fish aggregating devices (DFADs) by the industrial tropical tuna purse seine vessels. These changes, and their potential impacts on the species that associate with floating objects, remain poorly understood. If the habitat modifications induced by DFADs have been recently characterized and quantified, the impact of other human activities on the number of floating objects is poorly studied. Relying on lagrangian simulations at the scale of the whole Indian Ocean, from 2000 to 2019, we assess the potential modifications of the pelagic surface habitat that could originate from forest cover change and climate variations. We develop several scenarios, based on coastal and river forest cover, precipitations and river discharge, to simulate densities of NLOGs. Our results suggest no significant increase in average NLOG densities in the ocean and highlight important regional and seasonal variations of these densities driven by both forest cover change and precipitations. These preliminary findings underscore the limited understanding of this critical element of pelagic species habitat. Therefore, there is pressing need to intensify monitoring efforts for pelagic species habitat and raise awareness about potential impacts of habitat modifications on tuna and other pelagic species.}
}
  • [DOI] I. Laiz, N. Foletti, A. Teles-Machado, S. Plecha, Á. Peliz, R. F. Sánchez Leal, and M. Bolado-Penagos, “Spatial distribution of microplastics in the gulf of cadiz as a function of their density: a lagrangian modelling approach,” Science of the total environment, vol. 950, p. 175212, 2024.
    [Bibtex] 
    @article{LAIZ2024175212,
title = {Spatial distribution of microplastics in the Gulf of Cadiz as a function of their density: A Lagrangian modelling approach},
journal = {Science of The Total Environment},
volume = {950},
pages = {175212},
year = {2024},
issn = {0048-9697},
doi = {https://doi.org/10.1016/j.scitotenv.2024.175212},
url = {https://www.sciencedirect.com/science/article/pii/S0048969724053622},
author = {Irene Laiz and Nadine Foletti and Ana Teles-Machado and Sandra Plecha and Álvaro Peliz and Ricardo F. {Sánchez Leal} and Marina Bolado-Penagos},
keywords = {Microplastics transport, Buoyancy, Vertical distribution, CROCO, Ichthyop},
abstract = {Microplastics (MPs) are distributed throughout the world oceans and represent one of the greatest environmental concerns of marine pollution. In the Gulf of Cadiz (GoC), MPs are found throughout the water column, on the seafloor, and accumulated within commercial marine species, primarily due to discharges from the main estuaries. The aim of this study was to analyse the transport pathways, spatial distribution, and accumulation regions of MPs in the GoC based on their density and source. For this, a Lagrangian transport model was coupled to a high-resolution hydrodynamic model and four particle sources were considered: Cape San Vicente, Guadiana Estuary, Guadalquivir Estuary, and Bay of Cadiz/Guadalete River. To account for the diversity of plastics detected in the GoC, particles with ten different densities were used, from low-density to high-density polymers. This study indicates that a significant proportion of low-density MPs accumulate near their sources and within the top few centimetres of the water column due to local surface currents. The Guadalquivir and Guadiana estuaries are the primary contributors to the high accumulation of low-density MPs on the GoC eastern shelf, consistent with previous field studies identifying these estuaries as the main sources of MPs into the region, including polyethylene and polypropylene. In contrast, the Bay of Cadiz/Guadalete River seems to be the primary source of low-density MPs in offshore waters within the uppermost meter of the water column, influenced by local mesoscale features. The Guadalquivir Estuary seems to be the main source of high-density MPs into the continental shelves, such as polystyrene, polyamide, and polyvinyl chloride, followed by the Bay of Cadiz/Guadalete River, and to a lesser extent, the Guadiana estuary. These MPs accumulate near their sources at depths of 3.5 to 50 m due to their high sinking rates, but can also be transported offshore by deep currents, either northwards along the Portuguese offshore waters or westwards off the GoC offshore region.}
}
  • [DOI] J. Dauvin, A. Zarrouki, M. Boutet, and A. Bennis, “Numerical modelling of dispersal of ampelisca (amphipoda gammaridae) during their diel migration,” Ecological modelling, vol. 493, p. 110755, 2024.
    [Bibtex] 
    @article{DAUVIN2024110755,
title = {Numerical modelling of dispersal of Ampelisca (Amphipoda Gammaridae) during their diel migration},
journal = {Ecological Modelling},
volume = {493},
pages = {110755},
year = {2024},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2024.110755},
url = {https://www.sciencedirect.com/science/article/pii/S0304380024001431},
author = {Jean-Claude Dauvin and Assia Zarrouki and Martial Boutet and Anne-Claire Bennis},
keywords = {Diel migrations, Organism dispersal, Numerical modelling, Ampelisca, Bay of Morlaix, English Channel},
abstract = {The aim of this study is to analyse and model the dispersal of Ampelisca, a benthic genus of amphipod crustaceans, in the fine sand community of the Bay of Morlaix (western English Channel), during their nocturnal migration in the water column. Based on sampling of the suprabenthos (in the water column adjacent to the bottom) and surface plankton on 17 June 1994, Dauvin and Zouhiri (1996) studied the vertical distribution of Ampelisca during a spring swarming reproductive period. Statistical modelling techniques and specific numerical models were combined to simulate the effects of tidal currents, wind direction and speed on Ampelisca dispersal. As an illustration to constant pluriannual seasonal pattern, the dispersion of Ampelisca individuals considered as passive particles was studied at two reproductive periods, on a short night (17th-18th June 1994) during a neap tide, and on long night (7th-8th September 1994) during a spring tide. These models are used to investigate whether Ampelisca can be dispersed beyond the fine sand community in the immediate area of their small-scale benthic habitat (only 6 km²) during their diel vertical migration. According to the results, the speed and direction of currents will determine the trajectory of Ampelisca and the degree of dispersal outside their benthic habitat during a nighttime pelagic sortie. These simulations, particularly during spring tides, are incompatible with population stability, as they appear to be excessively dispersive. Short-term dispersal simulations for twenty minutes in the plankton allow the optimal return of individuals to the fine sand benthic habitats. We hypothesize there is an adaptative advantage for Ampelisca over time to short diel migrations. However, we currently do not know whether each individual makes a single migration, or several migrations in the water column during a night.}
}
  • [DOI] R. F. T. Pires, Á. Peliz, and A. dos Santos, “Dispersal and connectivity modelling simulations for invertebrate larvae passing through the Strait of Gibraltar,” Ices journal of marine science, p. fsae098, 2024.
    [Bibtex] 
    @article{10.1093/icesjms/fsae098,
author = {Pires, Rita F T and Peliz, Álvaro and dos Santos, Antonina},
title = "{Dispersal and connectivity modelling simulations for invertebrate larvae passing through the Strait of Gibraltar}",
journal = {ICES Journal of Marine Science},
pages = {fsae098},
year = {2024},
month = {07},
abstract = "{The link between the northeastern Atlantic and Mediterranean Sea created by the Strait of Gibraltar and the adjacent Iberian and Moroccan coasts marks remarkable transition areas between distinct environments that harbour a diverse mixture of species. The area is interesting regarding marine connectivity and the transport of pelagic invertebrate larvae, crucial knowledge to manage over-exploited populations, and minimize the impacts of climate change and anthropogenic activities. Biophysical models were developed, combining oceanic and particle-tracking Lagrangian simulations with in situ zooplankton distribution data. The conditions driving the larval exchange between the sub-basins and the connectivity throughout the region were explored, using crustacean decapod larvae as biological references. The potential exchange between both sub-basins was confirmed, although specific larval traits revealed contrasting scenarios. The simulations showed that slope-dwelling and mesopelagic larvae have advantage when crossing from the Alboran into the Atlantic, in comparison with shelf-dwelling and epipelagic larvae. Transport pathways and retention areas were identified, and passive drifts were shown to increase the dispersal range of the simulations. The spatial origin of the larval release, larval duration, vertical distribution, and the interaction of larvae with the oceanic features are presented as the main factors impacting the effective larval input into the Atlantic or Mediterranean basins.}",
issn = {1054-3139},
doi = {10.1093/icesjms/fsae098},
url = {https://doi.org/10.1093/icesjms/fsae098},
eprint = {https://academic.oup.com/icesjms/advance-article-pdf/doi/10.1093/icesjms/fsae098/58656488/fsae098.pdf},
}
  • [DOI] F. N. Amorim, M. Caetano, L. Bastos, and I. Iglesias, “Deep-sea mining rock-fragment dispersal scenarios associated with submesoscale forcings: a case study in the atlantic,” Heliyon, vol. 10, iss. 14, 2024.
    [Bibtex] 
    @article{amorim_deep-sea_2024,
title = {Deep-sea mining rock-fragment dispersal scenarios associated with submesoscale forcings: A case study in the Atlantic},
volume = {10},
issn = {2405-8440},
shorttitle = {Deep-sea mining rock-fragment dispersal scenarios associated with submesoscale forcings},
url = {https://www.cell.com/heliyon/abstract/S2405-8440(24)10205-8},
doi = {10.1016/j.heliyon.2024.e34174},
abstract = {In the last few years, the exploitation of deep-sea regions for minerals extraction raised international attention as an economically viable source for the mining industry. However, most of these minerals are found close to sensitive ecosystems that can be harmed by mining activities. Given the potential impact, there is a need for the establishment of best practices towards the adoption of preventive strategies for the sustainable management and exploitation of deep-sea environments. To accomplish this objective, numerical models have proven to be reliable tools to support decision-making. In the present study, a high-resolution eddy-resolving ocean numerical model was configured and integrated with a semi-Lagrangian model aiming to map the transport of rock-fragments associated with mining activities. The model was applied to an area rich in polymetallic sulphides at the Northern Mid-Atlantic Ridge (NMAR). Model results showed that local topography and circulation dynamics played an important role for the dispersion and settling of the rock-fragments. In the presence of local submesoscale processes, the residence time do not follow the neutral relation H/vs. It was demonstrated that, depending on the local hydrodynamics, rock-fragments released at sub-surface depth can impact wider areas, with a predicted impact on pelagic and benthic organisms.},
language = {English},
number = {14},
urldate = {2024-07-23},
journal = {Heliyon},
author = {Amorim, F. N. and Caetano, M. and Bastos, L. and Iglesias, I.},
month = jul,
year = {2024},
note = {Publisher: Elsevier},
}
  • [DOI] B. S. Malauene, C. Lett, F. Marsac, P. Penven, S. Abdula, C. L. Moloney, and M. J. Roberts, “Influence of mozambique channel eddies on larval loss of two shallow-water commercial shrimp species,” Plos climate, vol. 3, iss. 6, p. e0000414, 2024.
    [Bibtex] 
    @article{malauene_influence_2024,
title = {Influence of Mozambique Channel eddies on larval loss of two shallow-water commercial shrimp species},
volume = {3},
issn = {2767-3200},
url = {https://journals.plos.org/climate/article?id=10.1371/journal.pclm.0000414},
doi = {10.1371/journal.pclm.0000414},
abstract = {The shallow-water shrimp fishery is an important social and economic sector in Mozambique. However, catches of shrimps have been declining over the last decades, presumably due to poor recruitment. Climate change has been proposed as a potential cause of increased mesoscale eddy activity over the Mozambique Channel, which may have played a role in poor shrimp recruitment. Indeed, stronger eddies could transport matter, including increased numbers of shrimp larvae, from the coast to unfavourable offshore areas. In this study we used a biophysical model to investigate the influence of eddies on the dispersal of larvae of two commercial shrimp species (Penaeus indicus and Metapenaeus monoceros) from their spawning areas on the Sofala Bank. We found some 5 large events of offshore or southward transport loss ({\textgreater}10\% loss) from the Sofala Bank caused by eddies, occurring sporadically. The northern and central Sofala Bank areas were the most affected by larvae lost offshore. Simulations revealed that temperature-induced larval mortality, associated with cold-core cyclonic eddies, could also play a role in larval loss of up to 40\%, which is greater than the larval transport loss associated with the eddy circulation. However, when they survived, larvae transported offshore could travel long distances (600–1600 km in 15 days), potentially promoting connectivity with other stocks in the region.},
language = {en},
number = {6},
urldate = {2024-06-17},
journal = {PLOS Climate},
author = {Malauene, Bernardino S. and Lett, Christophe and Marsac, Francis and Penven, Pierrick and Abdula, Silvia and Moloney, Coleen L. and Roberts, Michael J.},
month = jun,
year = {2024},
note = {Publisher: Public Library of Science},
keywords = {Biophysics, Body temperature, Eggs, Fisheries science, Larvae, Mozambique, Shrimp, Spawning},
pages = {e0000414},
}
  • [DOI] J. Dauvin, A. Zarrouki, M. Boutet, and A. Bennis, “Numerical modelling of dispersal of ampelisca (amphipoda gammaridae) during their diel migration,” Ecological modelling, vol. 493, p. 110755, 2024.
    [Bibtex] 
    @article{DAUVIN2024110755,
title = {Numerical modelling of dispersal of Ampelisca (Amphipoda Gammaridae) during their diel migration},
journal = {Ecological Modelling},
volume = {493},
pages = {110755},
year = {2024},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2024.110755},
url = {https://www.sciencedirect.com/science/article/pii/S0304380024001431},
author = {Jean-Claude Dauvin and Assia Zarrouki and Martial Boutet and Anne-Claire Bennis},
keywords = {Diel migrations, Organism dispersal, Numerical modelling, Ampelisca, Bay of Morlaix, English Channel},
abstract = {The aim of this study is to analyse and model the dispersal of Ampelisca, a benthic genus of amphipod crustaceans, in the fine sand community of the Bay of Morlaix (western English Channel), during their nocturnal migration in the water column. Based on sampling of the suprabenthos (in the water column adjacent to the bottom) and surface plankton on 17 June 1994, Dauvin and Zouhiri (1996) studied the vertical distribution of Ampelisca during a spring swarming reproductive period. Statistical modelling techniques and specific numerical models were combined to simulate the effects of tidal currents, wind direction and speed on Ampelisca dispersal. As an illustration to constant pluriannual seasonal pattern, the dispersion of Ampelisca individuals considered as passive particles was studied at two reproductive periods, on a short night (17th-18th June 1994) during a neap tide, and on long night (7th-8th September 1994) during a spring tide. These models are used to investigate whether Ampelisca can be dispersed beyond the fine sand community in the immediate area of their small-scale benthic habitat (only 6 km²) during their diel vertical migration. According to the results, the speed and direction of currents will determine the trajectory of Ampelisca and the degree of dispersal outside their benthic habitat during a nighttime pelagic sortie. These simulations, particularly during spring tides, are incompatible with population stability, as they appear to be excessively dispersive. Short-term dispersal simulations for twenty minutes in the plankton allow the optimal return of individuals to the fine sand benthic habitats. We hypothesize there is an adaptative advantage for Ampelisca over time to short diel migrations. However, we currently do not know whether each individual makes a single migration, or several migrations in the water column during a night.}
}
  • [DOI] M. C. I. M. Jéssica Fernanda Ramos Coelho Luis Enrique Angeles-Gonzalez and S. M. Q. Lima, “Larval dispersal and climate models provide insights into present and future distribution of a tropical sardine,” Marine biology research, vol. 20, iss. 1-2, p. 1–14, 2024.
    [Bibtex] 
    @article{doi:10.1080/17451000.2024.2309562,
author = {Jéssica Fernanda Ramos Coelho, Luis Enrique Angeles-Gonzalez, Miguel Cahuich-López, Ismael Mariño-Tapia and Sergio Maia Queiroz Lima},
title = {Larval dispersal and climate models provide insights into present and future distribution of a tropical sardine},
journal = {Marine Biology Research},
volume = {20},
number = {1-2},
pages = {1--14},
year = {2024},
publisher = {Taylor \& Francis},
doi = {10.1080/17451000.2024.2309562},
URL = {https://doi.org/10.1080/17451000.2024.2309562},
eprint = {https://doi.org/10.1080/17451000.2024.2309562}
}
  • [DOI] A. Alcaïno, L. Vidal, L. Licari, C. Paillès, S. Conrod, J. Dauvier, C. Chevalier, C. Pinazo, M. Grelaud, and P. Ziveri, “Influence of the rhone river intrusion on microplastic distribution in the bay of marseille,” Regional studies in marine science, vol. 73, p. 103457, 2024.
    [Bibtex] 
    @article{ALCAINO2024103457,
title = {Influence of the Rhone River intrusion on microplastic distribution in the Bay of Marseille},
journal = {Regional Studies in Marine Science},
volume = {73},
pages = {103457},
year = {2024},
issn = {2352-4855},
doi = {https://doi.org/10.1016/j.rsma.2024.103457},
url = {https://www.sciencedirect.com/science/article/pii/S2352485524000902},
author = {A. Alcaïno and L. Vidal and L. Licari and C. Paillès and S. Conrod and J. Dauvier and C. Chevalier and C. Pinazo and M. Grelaud and P. Ziveri},
keywords = {Microplastics, Extraction protocol, Rhone River intrusion, Modelling, Mediterranean Sea},
abstract = {We present the spatiotemporal distribution of microplastics (MP) in surface waters and sediments between 2020 and 2022 in the Bay of Marseille. Microplastics were extracted with an improved, ecological protocol from 27 surface water and 16 sediment samples. The hydrodynamical circulation model MARS3D-RHOMA was used with in-situ data to test the influence of meteorological and hydrodynamic forcing on the concentration of MPs during the study period. The reported concentrations are analogous to abundances previously found in the Bay of Marseille, as well as in similar coastal systems. Average MP concentrations are 5.79 ± 12.71 MP.m−3 in surface water and 855 ± 413 MP.kg−1 dw in sediments. Simulations revealed hydrodynamic features associated with several episodes of Rhone intrusion in the Bay of Marseille. The observed MP concentrations and distribution in February 2020 suggest that the Rhone River’s plume entered the Bay of Marseille.}
}
  • [DOI] C. Muller, C. Lett, F. Porri, P. Pattrick, D. Bailey, H. Denis, N. Barrier, W. Potts, and D. M. Kaplan, “Coastal connectivity of an abundant inshore fish species: model-data comparison along the southern coast of south africa,” Marine ecology progress series, vol. 731, p. 89–104, 2024.
    [Bibtex] 
    @article{muller_coastal_2024,
title = {Coastal connectivity of an abundant inshore fish species: model-data comparison along the southern coast of South Africa},
volume = {731},
issn = {0171-8630, 1616-1599},
shorttitle = {Coastal connectivity of an abundant inshore fish species},
url = {https://www.int-res.com/abstracts/meps/v731/p89-104/},
doi = {10.3354/meps14272},
abstract = {Biophysical models are often used to estimate larval dispersal patterns for the assessment of marine metapopulation spatial structure. However, comparisons of these models with field observations are relatively rare, and the extent to which models reproduce true marine connectivity patterns is unclear. We developed a biophysical model for larvae of the blacktail seabream Diplodus capensis (Sparidae), an abundant recreational and subsistence fishery species along the south-east coast of South Africa, and compared outputs from various configurations of that model to results from a field study conducted in a large regional embayment (Algoa Bay). Seasonal patterns of dispersal and recruitment produced by the model agreed best with field observations when thermal constraints on spawners and larvae were included. Spatial gradients in settling larvae also matched well, with the model capturing observed high settler densities within the lee of a major headland. Nevertheless, stronger spatial gradients were observed in larval densities from the field study when compared with model results, which may be explained by behavioural post-settlement processes. Model-based dispersal patterns revealed up to 5 subpopulations along the southern coast, with barriers to connectivity between subpopulations generally linked to hydrographic features. Overall, our results suggest that thermally mediated spawning behaviour, physical transport and post-settlement processes all play important roles in determining marine connectivity for the blacktail seabream. Refining physiological larval constraints may be an important component that needs to be considered going forward.},
language = {en},
urldate = {2024-03-13},
journal = {Marine Ecology Progress Series},
author = {Muller, Cuen and Lett, Christophe and Porri, Francesca and Pattrick, Paula and Bailey, Dylan and Denis, Hugo and Barrier, Nicolas and Potts, Warren and Kaplan, David M.},
month = mar,
year = {2024},
keywords = {Biophysical model, Diplodus capensis, Larval dispersal, Population dynamics, Seabream},
pages = {89--104},
}
  • [DOI] E. Giachini Tosetto, C. Lett, A. Koch-Larrouy, A. Costa da Silva, S. Neumann-Leitão, M. Nogueira Junior, N. Barrier, A. N. Dossa, M. Tchilibou, P. Bauchot, G. Morvan, and A. Bertrand, “Identifying community assembling zones and connectivity pathways in the tropical southwestern atlantic ocean,” Ecography, vol. 2024, iss. 3, p. e07110, 2024.
    [Bibtex] 
    @article{https://doi.org/10.1111/ecog.07110,
author = {Giachini Tosetto, Everton and Lett, Christophe and Koch-Larrouy, Ariane and Costa da Silva, Alex and Neumann-Leitão, Sigrid and Nogueira Junior, Miodeli and Barrier, Nicolas and Dossa, Alina Nathanael and Tchilibou, Michel and Bauchot, Perrine and Morvan, Guillaume and Bertrand, Arnaud},
title = {Identifying community assembling zones and connectivity pathways in the Tropical Southwestern Atlantic Ocean},
journal = {Ecography},
volume = {2024},
number = {3},
pages = {e07110},
keywords = {community assembly, landscape ecology, mass effect, metacommunity, northeastern Brazil, species sorting},
doi = {https://doi.org/10.1111/ecog.07110},
url = {https://nsojournals.onlinelibrary.wiley.com/doi/abs/10.1111/ecog.07110},
eprint = {https://nsojournals.onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.07110},
abstract = {Dispersal is more intense in the ocean than on land because most marine taxa present planktonic life stages that are transported by currents even without specific morphological traits. Thus, species dispersal shapes the distribution of biodiversity along seascapes and drives the composition of biodiversity assemblages. To identify marine assembling zones which characterise spatial areas particularly prone to receive and retain similar animal assemblages from the regional pool of species through passive dispersal, we propose a community-based approach grounded on Lagrangian simulations of plankton dispersal. This novel approach was applied to communities (coast, outer shelf, slope, seamounts and islands; 0–80 m depth) of the Tropical Southwestern Atlantic and used to assess connectivity pathways. For that, we classified the modelled particles in 15 categories according to biological traits (planktonic life duration and spawning habitat) of representative planktonic communities. From the hierarchical clustering of the multivariate matrix containing the amount of arriving particles from each category in each cell we defined 14 assembling zones. Results highlighted that the assembling zones were mostly shaped by the degree of exposure to currents and the presence of mesoscale features (eddies, recirculation) derived from the interaction between these currents and coastlines. The boundaries, dispersal and connectivity patterns of these zones consistently align with local and regional in situ spatial distribution and abundance patterns of organisms, and provide an appropriate basis for the formulation of ecological hypotheses in the metacommunity framework to be tested in situ, such as the balance between species sorting and mass effect assembling archetypes. This approach, when coupled with the knowledge of other processes shaping communities' structure and distribution, provides important insights for regions and animal groups for which knowledge is limited or absent, and more generally allows for a comprehensive overview of the distribution of distinct communities and connectivity pathways along marine environments.},
year = {2024}
}
  • [DOI] R. L. Scott, N. F. Putman, R. Beyea, H. C. Repeta, and C. H. Ainsworth, “Modeling transport and feeding of juvenile kemp’s ridley sea turtles on the west florida shelf,” Ecological modelling, vol. 490, p. 110659, 2024.
    [Bibtex] 
    @article{SCOTT2024110659,
title = {Modeling transport and feeding of juvenile Kemp's ridley sea turtles on the West Florida shelf},
journal = {Ecological Modelling},
volume = {490},
pages = {110659},
year = {2024},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2024.110659},
url = {https://www.sciencedirect.com/science/article/pii/S0304380024000474},
author = {Rebecca L. Scott and Nathan F. Putman and R.Taylor Beyea and Hallie C. Repeta and Cameron H. Ainsworth},
keywords = {Atlantis ecosystem model, Kemp's ridley, Juvenile dispersal, Food availability, Gulf of Mexico, Circulation patterns},
abstract = {Survivorship during the juvenile oceanic phase likely acts as a bottleneck on the growth of sea turtle populations, and starvation mortality through this period is one potential factor influencing year class strength. We combined a simulation of juvenile Kemp's ridley (Lepidochelys kempii) sea turtle dispersal based on an ocean circulation model with an Atlantis ecosystem model to examine the spatial overlap of young sea turtles with their prey resources. We were particularly interested in whether ocean currents facilitated the movement of juveniles from western Gulf nesting beaches to areas in the eastern Gulf along the West Florida Shelf (WFS) with adequate food availability. We found that strong frontal gradients on the WFS may increase the potential for juveniles to remain offshore in areas of high per capita prey availability, allowing for more feeding opportunities during critical early life stages. Additionally, we found that multiple climatological indices are related to Gulf-wide patterns of juvenile dispersal, potentially via effects on the Loop Current. Findings from this study hold implications for continued population viability of protected sea turtle populations in the Gulf of Mexico, as well as other species with early life stages that disperse via ocean currents such as commercially important fishes.}
}
  • [DOI] M. M. Cintra, J. S. Silva-Cavalcanti, M. C. B. Araújo, P. L. F. Mazzini, M. Rollnic, and D. Mendes, “Sudden arrival of marine litter on the northeastern coast of brazil: physical forcings and associated transport,” Regional studies in marine science, vol. 71, p. 103382, 2024.
    [Bibtex] 
    @article{CINTRA2024103382,
title = {Sudden arrival of marine litter on the northeastern coast of Brazil: Physical forcings and associated transport},
journal = {Regional Studies in Marine Science},
volume = {71},
pages = {103382},
year = {2024},
issn = {2352-4855},
doi = {https://doi.org/10.1016/j.rsma.2024.103382},
url = {https://www.sciencedirect.com/science/article/pii/S235248552400015X},
author = {Marcio M. Cintra and Jacqueline S. Silva-Cavalcanti and Maria Christina {B. Araújo} and Piero L.F. Mazzini and Marcelo Rollnic and David Mendes},
keywords = {Marine pollution, Plastic accident, Lagrangian transport, Virtual particles},
abstract = {This study made use of four asynchronously coupled numerical simulations (four Eulerian and four Lagrangian) to investigate an event of a sudden arrival of more than 50 tons of marine litter on the northeastern Brazilian coast. This material mysteriously landed on several beaches, compromising water quality and impacting tourism, therefore raising serious concerns about its origin from local authorities. A total of 87,030 virtual particles were released and had their trajectories investigated, as well as their relationship with major physical forcings, including tides, winds and the North Brazil Under Current (NBUC). The virtual particles followed predominantly towards the north/northwest, mainly due to the presence of the NBUC and southeast trade winds. This pattern indicated that the flow of marine surface litter followed the continental shelf northwards, and the role of winds was key in providing the conditions for oceanic originated material to being deposit along the coastline. This study provided important insights about the regional circulation and main forcings that act in the transport and deposition of floating materials that reach the shallow shelf of the Brazilian northeast. Further investigation on the variability of these forcings along the seasonal cycle seems to be extremely important and should be undertaken soon.}
}
  • [DOI] C. Barrier, S. Ternengo, O. El Idrissi, L. Piacentini, N. Barrier, C. Lett, V. Pasqualini, and E. D. H. Durieux, “Edible sea urchin (paracentrotus lividus) larval dispersal and connectivity modelling in the northwestern mediterranean sea,” Journal of sea research, vol. 197, p. 102464, 2024.
    [Bibtex] 
    @article{BARRIER2024102464,
title = {Edible Sea urchin (Paracentrotus lividus) larval dispersal and connectivity modelling in the northwestern Mediterranean Sea},
journal = {Journal of Sea Research},
volume = {197},
pages = {102464},
year = {2024},
issn = {1385-1101},
doi = {https://doi.org/10.1016/j.seares.2023.102464},
url = {https://www.sciencedirect.com/science/article/pii/S1385110123001338},
author = {C. Barrier and S. Ternengo and O. {El Idrissi} and L. Piacentini and N. Barrier and C. Lett and V. Pasqualini and E.D.H. Durieux},
keywords = {Larval dispersal, Marine connectivity, Lagrangian model, Ichthyop, },
abstract = {The edible sea urchin (Paracentrotus lividus) is of significant economic importance due to high demand for its consumption in various Mediterranean countries. This echinoderm plays a crucial ecological role by regulating the dynamics of seaweed and seagrass through its grazing behaviour. The abundance of sea urchin is variable in time and space, but it is currently potentially declining in the Mediterranean Sea, and likely to be negatively affected by global change. Therefore, gaining a more comprehensive understanding of sea urchin larval dispersal patterns over an extended period could contribute to our understanding of how their dynamics relate to population connectivity. To investigate the trajectories of larval dispersal of this sea urchin in the Northwestern Mediterranean Sea, we combined a Lagrangian model (Ichthyop) with a hydrodynamic model (MARS3D). This study covered the years 2010–2018 and aimed to quantify the connectivity between the preferred habitats of the sea urchin (seagrasses and rocky substrates). The present study explores seasonal variations in dispersal routes and habitat connectivity relationships for two spawning scenarios identified in the literature (spring and autumn). The results enable us to identify dispersal routes, and their regularity over time. They highlight a consistent connection between Sardinia, Corsica, and the coastlines of the Ligurian and Tyrrhenian Seas, indicating a lack of genetic structuring within the edible sea urchin population in this area, particularly in Corsica. The connectivity matrices confirm the observed dispersal trajectories and highlight certain areas of significant and enduring local retention over time. The results also reveal minimal seasonal variability. Conversely, interannual variability appears pronounced, particularly in relation with trends in the warming of surface waters in the Mediterranean, which seem to impact the dispersal routes taken by P. lividus larvae. Lastly, a connectivity map was created to explore spatial resource management perspectives, aiming to identify frequent connections over an extended time period and assign varying levels of intensity to them. This approach can provide guidance with regard to resource management issues for different coastal areas that can be connected by larvae.}
}
  • [DOI] F. Rojas-Araos, N. Rojas-Hernández, S. Cornejo-Guzmán, B. Ernst, B. Dewitte, C. Parada, and D. Veliz, “Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster jasus frontalis inhabiting oceanic islands,” Marine environmental research, vol. 193, p. 106253, 2024.
    [Bibtex] 
    @article{ROJASARAOS2024106253,
title = {Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands},
journal = {Marine Environmental Research},
volume = {193},
pages = {106253},
year = {2024},
issn = {0141-1136},
doi = {https://doi.org/10.1016/j.marenvres.2023.106253},
url = {https://www.sciencedirect.com/science/article/pii/S0141113623003811},
author = {Felipe Rojas-Araos and Noemi Rojas-Hernández and Sebastián Cornejo-Guzmán and Billy Ernst and Boris Dewitte and Carolina Parada and David Veliz},
keywords = {Oceanic islands, Lobster, Population genetic analysis, Individual-based modeling, Population connectivity, Larval retention},
abstract = {Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.}
}

2023

  • [DOI] A. Villastrigo, V. Orenes-Salazar, A. J. García-Meseguer, J. M. Mirón-Gatón, B. Mourre, A. Millán, and J. Velasco, “Oceanic currents maintain the genetic structure of non-marine coastal taxa in the western Mediterranean Sea,” Npj biodiversity, vol. 2, iss. 1, p. 1–9, 2023.
    [Bibtex] 
    @article{villastrigo_oceanic_2023,
title = {Oceanic currents maintain the genetic structure of non-marine coastal taxa in the western {Mediterranean} {Sea}},
volume = {2},
copyright = {2023 The Author(s)},
issn = {2731-4243},
url = {https://www.nature.com/articles/s44185-023-00028-0},
doi = {10.1038/s44185-023-00028-0},
abstract = {Coastal habitats are amongst the most dynamic on Earth, due to their simultaneous exposure to terrestrial, oceanic and atmospheric processes. Coastal taxa are therefore often ecologically specialised and adapted to withstand frequent shifts in sea level, wave exposure, temperature or salinity. This specialisation often resulting in significant cryptic diversity. Previous molecular studies have suggested that genetic differentiation in non-marine coastal organisms may be influenced by oceanic currents and fronts, but the extent to which such processes affect dispersal and evolution of such taxa remains unclear. Here we explore whether population genetic structure in two supralittoral rockpool beetle species (genus Ochthebius) can be predicted from the general circulation pattern of the marine currents and associated oceanic fronts. We simulated dispersal using a Lagrangian particle tracking model and compared this with population genetic structure inferred from COI (mitochondrial) and wingless (nuclear) genes applying linear models and Mantel tests. We show that a biophysical model based on oceanic currents and fronts in the western Mediterranean Sea is a much better predictor of observed population genetic structure than isolation by distance in both species. Our results show that oceanic processes, besides shaping contemporary population connectivity in fully marine organisms, also exert a meaningful influence on terrestrially-derived coastal taxa such as supralittoral rockpool beetles — the first time this mode of dispersal has been demonstrated in an insect.},
language = {en},
number = {1},
urldate = {2023-11-27},
journal = {npj Biodiversity},
author = {Villastrigo, Adrián and Orenes-Salazar, Víctor and García-Meseguer, Antonio José and Mirón-Gatón, Juana María and Mourre, Baptiste and Millán, Andrés and Velasco, Josefa},
month = nov,
year = {2023},
note = {Number: 1
Publisher: Nature Publishing Group},
keywords = {Biodiversity, Biogeography, Evolutionary ecology},
pages = {1--9},
}
  • [DOI] S. Ajmi, M. Boutet, A. Bennis, J. Dauvin, and J. Pezy, “Numerical study of turbulent wake of offshore wind turbines and retention time of larval dispersion,” Journal of marine science and engineering, vol. 11, iss. 11, 2023.
    [Bibtex] 
    @Article{jmse11112152,
AUTHOR = {Ajmi, Souha and Boutet, Martial and Bennis, Anne-Claire and Dauvin, Jean-Claude and Pezy, Jean-Philippe},
TITLE = {Numerical Study of Turbulent Wake of Offshore Wind Turbines and Retention Time of Larval Dispersion},
JOURNAL = {Journal of Marine Science and Engineering},
VOLUME = {11},
YEAR = {2023},
NUMBER = {11},
ARTICLE-NUMBER = {2152},
URL = {https://www.mdpi.com/2077-1312/11/11/2152},
ISSN = {2077-1312},
ABSTRACT = {Offshore Wind Farm (OWF) foundations are considered to have a potential impact on the larval dispersion of benthic species. This study focused on OWFs’ impacts on larval dispersion, considering factors such as the foundation type, flow velocity, flow direction, and release type using numerical modelling. At the scale of monopile and gravity-based foundations, a combination of two numerical models was used: the Eulerian model (OpenFOAM), solving the 3D Navier–Stokes equations for computing the hydrodynamics, and the Lagrangian model (Ichthyop), solving the advection–diffusion equation for the larval dispersion simulations. The validation model tests were evaluated with experimental data as a first step of the study. Accurate results were achieved, yielding a Turbulent Kinetic Energy (TKE) Root-Mean-Squared Error (RMSE) in the range of 6.82–8.27 ×10−5kg/m·s2 within the refined mesh, with a coefficient of determination (R2) approaching unity. For the second phase, more-realistic simulations were modelled. Those simulations demonstrated turbulent wakes downstream of the foundations and horseshoe vortex formations near the bottom. A larval dispersion was simulated using passive particles’ motion. Vertical flumes in the wake with particles experiencing both upward and downward motions, impacting the fall velocities of the particles, were observed. The influence of gravity-based foundations might lead to a stepping-stone effect with a retention time of up to 9 min, potentially allowing the settlement of competent larvae. In a similar geometry with an angular spring tide velocity, 0.4% of particles were trapped.},
DOI = {10.3390/jmse11112152}
}
  • [DOI] P. Wilson, C. Pattiaratchi, S. Whiting, L. C. Ferreira, S. Fossette, K. Pendoley, and M. Thums, “Predicting core areas of flatback turtle hatchlings and potential exposure to threats,” Endangered species research, vol. 52, p. 129–147, 2023.
    [Bibtex] 
    @article{wilson_predicting_2023,
title = {Predicting core areas of flatback turtle hatchlings and potential exposure to threats},
volume = {52},
issn = {1863-5407, 1613-4796},
url = {https://www.int-res.com/abstracts/esr/v52/p129-147/},
doi = {10.3354/esr01269},
abstract = {The lack of data on distribution of juvenile marine species can limit conservation efforts. As hatchlings, marine turtles are too small to track using satellite telemetry, so their at-sea distribution remains unknown. This knowledge gap is critical, as hatchlings already experience high mortality in coastal zones. In addition, further risks to their survival may occur beyond these areas, linked to threats associated with in-water artificial infrastructure and/or attraction to artificial lights and thus increased mortality from higher risk of predation or exhaustion from disorientation. To fill this gap, we used particle tracking forced by an ocean circulation model to predict the dispersal of flatback turtle Natator depressus hatchlings from 12 nesting sites off the coast of Western Australia. We used the model outputs to calculate the distribution of these ‘virtual hatchlings’ and infer the core area of hatchling use over 3 dispersal phases (1-4, 10-15 and 25-30 d). We then calculated the overlap between core areas and 2 anthropogenic threats (in-water artificial infrastructure and light pollution). Core areas were predominately located on the continental shelf during all dispersal phases, supporting the hypothesis that flatback turtles remain in neritic areas. Most (70-80\%) of the core area during early dispersal (Days 1-4 and 10-15) contained at least one threat. However, less than half of the area used between Day 25 and 30 was exposed to threats. In the absence of empirical data on hatchling distribution, our results have predicted the core areas used by early life stage flatback turtles to assist in conservation management of these threatened species.},
language = {en},
urldate = {2023-10-17},
journal = {Endangered Species Research},
author = {Wilson, Phillipa and Pattiaratchi, Charitha and Whiting, Scott and Ferreira, Luciana C. and Fossette, Sabrina and Pendoley, Kellie and Thums, Michele},
month = oct,
year = {2023},
keywords = {Artificial light, Flatback turtle, In-water artificial infrastructure, Ocean circulation model, ozROMS, Particle tracking},
pages = {129--147}
}
  • [DOI] N. Al-Qattan, G. S. Herbert, H. J. Spero, S. McCarthy, R. McGeady, R. Tao, and A. Power, “A stable isotope sclerochronology-based forensic method for reconstructing debris drift paths with application to the mh370 crash,” Agu advances, vol. 4, iss. 4, p. e2023AV000915, 2023.
    [Bibtex] 
    @article{https://doi.org/10.1029/2023AV000915,
author = {Al-Qattan, Nasser and Herbert, Gregory S. and Spero, Howard J. and McCarthy, Sean and McGeady, Ryan and Tao, Ran and Power, Anne-Marie},
title = {A Stable Isotope Sclerochronology-Based Forensic Method for Reconstructing Debris Drift Paths With Application to the MH370 Crash},
journal = {AGU Advances},
volume = {4},
number = {4},
pages = {e2023AV000915},
keywords = {sclerochronology, isotope, Lepas, modeling, drift, MH370},
doi = {https://doi.org/10.1029/2023AV000915},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2023AV000915},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2023AV000915},
note = {e2023AV000915 2023AV000915},
abstract = {Abstract A flaperon belonging to Malaysian Airlines flight MH370 washed ashore on Réunion Island covered with the barnacle Lepas anatifera in July 2015, more than a year after the plane's disappearance. Here, we report the first high-precision δ18Ocalcite versus temperature relationship for L. anatifera reared under laboratory conditions to unlock clues to the flaperon's drift path and origin. Using this experimental relationship and known growth rates for L. anatifera, we also demonstrate a new method for (a) converting δ18O data for one of the MH370 barnacles into a dated time series of sea surface temperatures (SSTs) experienced during the last part of the flaperon's drift and (b) identifying best fits between the observed flaperon SST time series and 50,000 SST histories generated from a particle-tracking simulation. Our new method identifies a flaperon drift path far south of a previous isotope-based reconstruction. We conclude with specific recommendations for using our method to continue the search for MH370 and other applications.},
year = {2023}
}
  • [DOI] F. Santa Cruz, C. Parada, M. Haltuch, J. Wallace, S. Cornejo-Guzmán, and E. Curchitser, “Petrale sole transboundary connectivity and settlement success: a biophysical approach,” Frontiers in marine science, vol. 10, 2023.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2023.1155227,
AUTHOR = {Santa Cruz, Francisco and Parada, Carolina and Haltuch, Melissa and Wallace, John and Cornejo-Guzmán, Sebastián and Curchitser, Enrique},
TITLE = {Petrale sole transboundary connectivity and settlement success: a biophysical approach},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {10},
YEAR = {2023},
URL = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1155227},
DOI = {10.3389/fmars.2023.1155227},
ISSN = {2296-7745},
ABSTRACT = {Connectivity between inferred spawning areas and potential settlement areas of the petrale sole (Eopsetta jordani) was explored in the California Current System (CCS) using an individual-based model (IBM) coupled with the ROMS hydrodynamic model for the period 1988-2008. The IBM modeled pelagic early life stages, including egg and larval development, growth, natural mortality and settlement into benthos. Eggs were released within discrete spawning grounds identified from the winter fishery logbook data. Potential settlement areas were defined based on bathymetrical criteria and juvenile (2-year old) distribution from a groundfish bottom trawl survey. The influence of cross-shelf and alongshore advection on the transport and connectivity between spawning and benthic settlement areas was explored by identifying the location of juveniles (22 mm length) among the potential settlement areas. The most important spawning regions varied over time with between 4 and 19% of spawned individuals successfully settling, mostly ranging from off northern Washington to northern Oregon. The strong influence of northward alongshore transport resulted in transboundary transport of pelagic life stages from U.S. spawning grounds to inner shelf settlement areas in Canadian waters, with 33.9-70.4% (average 49.7 ± 9.6) of annual successful juveniles settling in Canada. Interannual variability in juvenile settlement success suggests that mesoscale (100-200 km) oceanographic structures play a major role defining pelagic juvenile transport trajectories. While, in some years, the presence of coastal cyclonic eddies can retain juveniles off Oregon, the strong northward transport supplies a large number of juveniles to Moresby and Vancouver island, clearly showing that petrale sole off the west coast of North America are a transboundary stock with important settlement areas off the coast of British Columbia, thus extension of this study into Canadian waters is particularly relevant.}
}
  • [DOI] E. Díaz-Cabrera, C. Vega-Retter, N. Roja-Hernández, E. Meerhoff, B. DeWitte, and D. Veliz, “Integrating genetic and biophysical approaches to estimate connectivity in an isolated, insular system: case of the culturally important marine gastropod monetaria caputdraconis,” Journal of the marine biological association of the united kingdom, vol. 103, p. e53, 2023.
    [Bibtex] 
    @article{díaz-cabrera_vega-retter_roja-hernández_meerhoff_dewitte_veliz_2023,
title = {Integrating genetic and biophysical approaches to estimate connectivity in an isolated, insular system: case of the culturally important marine gastropod Monetaria caputdraconis},
volume = {103},
DOI = {10.1017/S0025315423000437},
journal = {Journal of the Marine Biological Association of the United Kingdom},
author = {Díaz-Cabrera, Ernesto and Vega-Retter, Caren and Roja-Hernández, Noemi and Meerhoff, Erika and DeWitte, Boris and Veliz, David},
year = {2023},
pages = {e53}
}
  • [DOI] G. Marchessaux, C. Chevalier, M. C. Mangano, and G. Sarà, “Larval connectivity of the invasive blue crabs Callinectes sapidus and Portunus segnis in the Mediterranean Sea: A step toward improved cross border management,” Marine pollution bulletin, vol. 194, p. 115272, 2023.
    [Bibtex] 
    @article{marchessaux_larval_2023,
title = {Larval connectivity of the invasive blue crabs {Callinectes} sapidus and {Portunus} segnis in the {Mediterranean} {Sea}: {A} step toward improved cross border management},
volume = {194},
issn = {0025-326X},
shorttitle = {Larval connectivity of the invasive blue crabs {Callinectes} sapidus and {Portunus} segnis in the {Mediterranean} {Sea}},
url = {https://www.sciencedirect.com/science/article/pii/S0025326X23007063},
doi = {10.1016/j.marpolbul.2023.115272},
abstract = {The two invasive blue crabs, Callinectes sapidus and Portunus segnis have spread rapidly in the Mediterranean and no data exists on the connectivity of populations. Determining the source and recruitment areas is crucial to prioritize where population control measures should be put into immediate action. We simulated the dispersal of blue crab larvae using a Lagrangian model coupled at high resolution to estimate the potential connectivity of blue crab populations over a 3-year period. Our results reveal that the main areas at risk are the Spanish, French, Italian Tyrrhenian and Sardinian coasts for Callinectes sapidus with high populations connectivity. Tunisia and Egypt represent high auto recruitment zones for Portunus segnis restricted to the central and western basins. This study provides an overview of the connectivity between populations and will help define priority areas that require the urgent implementation of management measures.},
language = {en},
urldate = {2023-07-17},
journal = {Marine Pollution Bulletin},
author = {Marchessaux, Guillaume and Chevalier, Cristèle and Mangano, Maria Cristina and Sarà, Gianluca},
month = sep,
year = {2023},
keywords = {Mediterranean Sea, Connectivity, Blue crabs, Cross-border management, Invasion risk, Larval stage},
pages = {115272},
}
  • [DOI] J. Flores-Valiente, C. Lett, F. Colas, L. Pecquerie, A. Aguirre-Velarde, F. Rioual, J. Tam, A. Bertrand, P. Ayón, S. Sall, N. Barrier, and T. Brochier, “Influence of combined temperature and food availability on peruvian anchovy (engraulis ringens) early life stages in the northern humboldt current system: a modelling approach,” Progress in oceanography, vol. 215, p. 103034, 2023.
    [Bibtex] 
    @article{FLORESVALIENTE2023103034,
title = {Influence of combined temperature and food availability on Peruvian anchovy (Engraulis ringens) early life stages in the northern Humboldt Current system: A modelling approach},
journal = {Progress in Oceanography},
volume = {215},
pages = {103034},
year = {2023},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2023.103034},
url = {https://www.sciencedirect.com/science/article/pii/S0079661123000770},
author = {Jorge Flores-Valiente and Christophe Lett and François Colas and Laure Pecquerie and Arturo Aguirre-Velarde and Fanny Rioual and Jorge Tam and Arnaud Bertrand and Patricia Ayón and Saidou Sall and Nicolas Barrier and Timothée Brochier},
keywords = {Ichthyop-DEB model, Early life stages survival, Peruvian anchovy, Larval drift, Larval growth}
}
  • [DOI] C. de Mello, M. Barreiro, E. Hernandez-Garcia, R. Trinchin, and G. Manta, “A lagrangian study of summer upwelling along the uruguayan coast,” Continental shelf research, vol. 258, p. 104987, 2023.
    [Bibtex] 
    @article{DEMELLO2023104987,
title = {A Lagrangian study of summer upwelling along the Uruguayan coast},
journal = {Continental Shelf Research},
volume = {258},
pages = {104987},
year = {2023},
issn = {0278-4343},
doi = {https://doi.org/10.1016/j.csr.2023.104987},
url = {https://www.sciencedirect.com/science/article/pii/S027843432300064X},
author = {Camila de Mello and Marcelo Barreiro and Emilio Hernandez-Garcia and Romina Trinchin and Gaston Manta},
keywords = {Coastal upwelling, Uruguay, Finite size Lyapunov exponents},
abstract = {This study focuses on the surface transport in the Uruguayan coastal zone during summertime under favorable wind upwelling conditions. The surface transport in the area was investigated for the first time with the application of a Lagrangian technique computing the backward-in-time Finite Size Lyapunov Exponents (FSLE) using the current velocity field derived from a high resolution numerical model (CROCO, 1/36° horizontal grid). Intense summer upwellings were studied focusing on surface stirring characterized by FSLE temporal averages. Subsequently, the analysis of the attracting FSLE field maxima allowed the detection of Lagrangian Coherent Structures (LCS), providing information on the location of the upwelling frontal regions and on the transport patterns associated with the flow. The FSLE analysis during summertime revealed an intense mixing activity concentrated in the oceanic coastal area, concordant with the location of the summer climatological upwelling, while during the most intense upwelling dates an increase in the mixing activity was found in the estuarine coastal region. When concentrating on the FSLE maxima during intense upwelling dates, we identified attractive LCS in the estuarine region locating retention fronts. The identified structures' location coincided with the frontal regions observed from both, simulated SST and satellite Chlorophyll-a distribution, highlighting the Lagrangian approximation's importance in locating retention fronts with different origins. Finally, the LCS evolution analyzed for two particular upwelling events, together with the simulated dispersion of synthetic Lagrangian particles, evidenced the importance of this approximation to study the transport processes in the area.}
}
  • [DOI] Apriansyah, A. S. Atmadipoera, D. Nugroho, I. Jaya, and M. F. Akhir, “Simulated seasonal oceanographic changes and their implication for the small pelagic fisheries in the java sea, indonesia,” Marine environmental research, vol. 188, p. 106012, 2023.
    [Bibtex] 
    @article{apriansyah_simulated_2023,
title = {Simulated seasonal oceanographic changes and their implication for the small pelagic fisheries in the Java Sea, Indonesia},
volume = {188},
issn = {0141-1136},
url = {https://www.sciencedirect.com/science/article/pii/S014111362300140X},
doi = {10.1016/j.marenvres.2023.106012},
abstract = {Small pelagic fisheries in the Java Sea (JS) contributes to about 26.6\% of the total marine fisheries resources, where their spatial-temporal variation is controlled by seasonal oceanographic changes. This study aims to investigate a relationship between seasonal reversal circulation and number of light-fishing vessels (VBD) dispersion that capture small pelagic fishes, using multi-datasets from a regional ocean circulation model, satellite-derived datasets, and pelagic fish landing datasets between 2010 and 2020. The model demonstrates that main axis of eastward (westward) monsoon current that brings warmer and fresher (cooler and saltier) water, confines much closer along the northern Java (southern Kalimantan) during the northwest (southeast) monsoon period. These changes are followed unprecedentedly by southward (northward) shift of VBD and high abundance of euryhaline (stenohaline) fish species. This new evidence implies that reversal monsoon current and surface component of Makassar Throughflow play a significant role on delineating potential small pelagic fishing ground and fish productions.},
language = {en},
urldate = {2023-05-10},
journal = {Marine Environmental Research},
author = {Apriansyah and Atmadipoera, Agus S. and Nugroho, Dwiyoga and Jaya, Indra and Akhir, Mohd Fadzil},
month = jun,
year = {2023},
keywords = {CROCO model, Java sea, Monsoon current, Satellite-derived dataset, Small pelagic fishery},
pages = {106012},
}
  • [DOI] N. Henschke, B. Espinasse, C. A. Stock, X. Liu, N. Barrier, and E. A. Pakhomov, “The role of water mass advection in staging of the southern ocean salpa thompsoni populations,” Scientific reports, vol. 13, 2023.
    [Bibtex] 
    @article{Henschke2023,
title = {The role of water mass advection in staging of the Southern Ocean Salpa thompsoni populations},
journal = {Scientific Reports},
volume = {13},
author = {Henschke, Natasha and Espinasse, Boris and Stock, Charles A. and Liu, Xiao and Barrier, Nicolas and Pakhomov, Evgeny A.},
year = {2023},
doi = {10.1038/s41598-023-34231-7}
}
  • [DOI] F. D. Lima, L. E. Angeles-Gonzalez, H. Maia, T. S. Leite, M. Cahuich-López, I. Mariño-Tapia, M. L. Santana-Cisneros, P. Ardisson, and S. M. Q. Lima, “Molecular data, ecological niche, and dispersal models reveal a trans-Atlantic shallow-water octopus species,” Progress in oceanography, vol. 213, p. 103019, 2023.
    [Bibtex] 
    @article{lima_molecular_2023,
title = {Molecular data, ecological niche, and dispersal models reveal a trans-{Atlantic} shallow-water octopus species},
volume = {213},
issn = {0079-6611},
url = {https://www.sciencedirect.com/science/article/pii/S0079661123000629},
doi = {10.1016/j.pocean.2023.103019},
abstract = {The tropical Octopus insularis is a shallow-water species widely distributed in the western Atlantic. Recent studies of niche models have identified suitable habitats for its settlement also on the east coast of the Atlantic. Considering the pelagic larval period and the high tolerance of this species to environmental variations, this study aimed to analyze the possibility of O. insularis occurrence in the West Atlantic (São Tomé Island) through molecular analyses, dispersion, and niche models. The molecular analyses were performed using fragments of 481 bp of the mitochondrial gene (cox1) from three muscle samples collected in São Tomé Island. The O. insularis long-range connectivity between South America and Western Africa was analyzed using a Lagrangian particle tracking model. Additionally, O. insularis records across its entire known distribution were applied to run the ecological niche model (ENM) using the Maxent algorithm. The Bayesian phylogenetic reconstruction showed that two of the three octopus sequences from São Tomé island (Central-Western Africa) belong to a monophyletic and well-supported O. insularis clade. The third octopus sample revealed a new species related to the clade with the Octopus vulgaris species complex. The dispersal models pointed out that passive particles could potentially reach the seamounts region at Africa coast via oceanic currents (mainly the North Equatorial Countercurrent) from São Pedro and São Paulo archipelago (Central-Western Region of the Atlantic) in a period of ∼30–60 days. This suggests that São Pedro and São Paulo archipelago could act as a potential source of paralarvae to Western Africa, although we hypothesize that this connection was more common during the Pleistocene, when sea level was around 120 m lower. In addition to the already known areas of O. insularis occurrence, the ENM pointed suitable habitats to the octopus settlement from Guinea-Bissau down to Equatorial Guinea and Gabon, and African Islands, such as São Tomé and Príncipe. The new record of O. insularis in Africa raises important questions regarding regional fisheries management. Considering that O. insularis is highly tolerant to environmental variations and very adapted to warm shallow waters, there is a possibility that octopus fisheries stocks on the African coast have a mixed composition (O. vulgaris, O. insularis, and Octopus sp.) and therefore the fisheries must follow management measures suitable for each species. In addition, further studies should be carried out in order to characterize and describe the potential new octopus species found only in São Tomé Island according to our genetic survey.},
language = {en},
urldate = {2023-04-17},
journal = {Progress in Oceanography},
author = {Lima, Françoise D. and Angeles-Gonzalez, Luis Enrique and Maia, Hugulay and Leite, Tatiana S. and Cahuich-López, Miguel and Mariño-Tapia, Ismael and Santana-Cisneros, Mariana L. and Ardisson, Pedro-Luis and Lima, Sergio M. Q.},
month = apr,
year = {2023},
keywords = {Dispersion, Molecular genetics, Niche modeling, Oceanic currents},
pages = {103019},
}
  • [DOI] T. Imzilen, D. M. Kaplan, N. Barrier, and C. Lett, “Simulations of drifting fish aggregating device (dfad) trajectories in the atlantic and indian oceans,” Fisheries research, vol. 264, p. 106711, 2023.
    [Bibtex] 
    @article{IMZILEN2023106711,
title = {Simulations of drifting fish aggregating device (dFAD) trajectories in the Atlantic and Indian Oceans},
journal = {Fisheries Research},
volume = {264},
pages = {106711},
year = {2023},
issn = {0165-7836},
doi = {https://doi.org/10.1016/j.fishres.2023.106711},
url = {https://www.sciencedirect.com/science/article/pii/S0165783623001042},
author = {Taha Imzilen and David M. Kaplan and Nicolas Barrier and Christophe Lett},
keywords = {Marine pollution, Fishing debris, Coral reefs, Fish aggregating device (FAD), Ocean currents, Lagrangian transport, Simulation of trajectories},
abstract = {Tropical tuna purse-seine fisheries deploy thousands of human-made drifting fish aggregating devices (dFADs) annually, raising a number of concerns regarding ecosystem impacts. In this study, we explored the use of a Lagrangian particle-tracking model to simulate the drift of dFADs in the Atlantic and Indian Oceans. We simulated more than 100,000 dFADs trajectories using the Lagrangian tool Ichthyop forced with velocity fields from an ocean model output (GLORYS12V1) and two satellite-derived ocean currents products (OSCAR and GEKCO). Importantly, through a collaborative agreement with the French frozen tuna producers’ organization we had access to the true locations of all dFADs along their drift and could therefore evaluate the accuracy of our simulations. The accuracy was assessed by comparing the observed and simulated trajectories in terms of spatial distribution, separation distance, and a non-dimensional skill score (an index based on separation distances normalized by net displacements of dFADs). In the two oceans, simulations forced with GLORYS12V1 were more accurate than with OSCAR and GEKCO, probably due to the differences in the spatio-temporal resolution of the forcing products. When we compared multiple depths for GLORYS12V1, the model performed better at 0 m in the Indian Ocean and at 5 m in the Atlantic Ocean, which could be related to the longer vertical structure of dFADs in the Atlantic Ocean. We showed that including a windage factor did not improve the accuracy of modeled dFADs trajectories. We found that mean model-data separation distances were similar in both oceans, exceeding 100 km after 6–8 days of drift. While separation distances between simulated and observed trajectories show that model errors were similar in the two oceans, the generally longer distances traveled by dFADs in the Indian Ocean than in the Atlantic Ocean lead to considerably higher skill scores in the former than in the latter. This explains the relatively good predictive ability of the model to represent mean dFAD densities at the basin scale in both oceans, while at the same time indicates higher prediction skills for the movements of individual dFADs in the Indian Ocean than in the Atlantic Ocean.}
}
  • [DOI] S. Mavruk, C. Toslak, F. B. Yalım, A. E. Ütük, Ö. Aktaş, Ş. S. Yılmaz, A. Kara, and A. Yüksek, “Contribution of integrative taxonomy of ichthyoplankton to knowledge on mesopelagic fish biodiversity in the Northeastern Mediterranean,” Marine biodiversity, vol. 53, iss. 1, p. 7, 2023.
    [Bibtex] 
    @article{mavruk_contribution_2023,
title = {Contribution of integrative taxonomy of ichthyoplankton to knowledge on mesopelagic fish biodiversity in the {Northeastern} {Mediterranean}},
volume = {53},
issn = {1867-1624},
url = {https://doi.org/10.1007/s12526-022-01312-1},
doi = {10.1007/s12526-022-01312-1},
abstract = {Ichthyoplankton surveys hold much potential for studying fish biodiversity, but challenges and uncertainties in identification of early life stages and the drifting of planktonic eggs and larvae limit the efficacy of this method. In this study, we investigate mesopelagic fish biodiversity in Antalya Bay in the Northeastern Mediterranean Sea, based on ichthyoplankton samplings in combination with integrative taxonomy and particle backtracking simulations to overcome the forementioned limitations. We morphologically identified early life stages of 26 mesopelagic species and the identification of 17 of them was validated using DNA barcoding. With 13 species identified, Myctophidae was the most diverse family. Larvae of Cyclothone braueri Jespersen \& Tåning, 1926, Diaphus holti Tåning, 1918, Ceratoscopelus maderensis (Lowe, 1839) and Cyclothone pygmea Jespersen \& Tåning, 1926, constituted the most dominant species in the study area. Based on larval samples, we provided the first record of Paralepis coregonoides Risso, 1820, the first substantiated records of Vinciguerria poweriae (Cocco, 1838) and Hygophum hygomii (Lütken, 1892) and the second record of Evermannella balbo (Risso, 1820) off the Turkish coasts of the Mediterranean Sea. Particle backtracking simulations revealed that the spawning grounds of these species were in Antalya Bay, suggesting that there were reproducing populations of these species off the Mediterranean coast of Turkey, although these were not properly documented before the present study. Our results demonstrate that ichthyoplankton surveys can provide a reliable practice to study the biodiversity of understudied and difficult to access fish groups when combined with molecular identification techniques and particle backtracking simulations.},
language = {en},
number = {1},
urldate = {2023-02-13},
journal = {Marine Biodiversity},
author = {Mavruk, Sinan and Toslak, Cihan and Yalım, Fatma Banu and Ütük, Armağan Erdem and Aktaş, Özgür and Yılmaz, Şakire Serap and Kara, Alpaslan and Yüksek, Ahsen},
month = jan,
year = {2023},
keywords = {DNA barcoding, Larvae, Levant basin, Particle backtracking, The Eastern Mediterranean Sea},
pages = {7}
}
  • [DOI] E. Ramirez-Romero, A. Amores, D. Diaz, A. Muñoz, I. A. Catalan, J. C. Molinero, and A. Ospina-Alvarez, “Atmospheric–ocean coupling drives prevailing and synchronic dispersal patterns of marine species with long pelagic durations,” Scientific reports, vol. 13, iss. 1, p. 2366, 2023.
    [Bibtex] 
    @article{ramirez-romero_atmosphericocean_2023,
title = {Atmospheric–ocean coupling drives prevailing and synchronic dispersal patterns of marine species with long pelagic durations},
volume = {13},
copyright = {2023 The Author(s)},
issn = {2045-2322},
url = {https://www.nature.com/articles/s41598-023-29543-7},
doi = {10.1038/s41598-023-29543-7},
abstract = {Dispersal shapes population connectivity and plays a critical role in marine metacommunities. Prominent species for coastal socioecological systems, such as jellyfish and spiny lobsters, feature long pelagic dispersal phases (LPDPs), which have long been overlooked. Here, we use a cross-scale approach combining field surveys of these species with a high-resolution hydrodynamic model to decipher the underlying mechanisms of LPDP patterns in northwestern Mediterranean shores. We identified basin-scale prevailing dispersal routes and synchronic year-to-year patterns tightly linked to prominent circulation features typical of marginal seas and semienclosed basins, with an outstanding role of a retentive source area replenishing shores and potentially acting as a pelagic nursery area. We show how the atmospheric forcing of the ocean, a marked hydrological driver of the Mediterranean Sea, modulates dispersal routes and sources of LPDP at interannual scales. These findings represent a crucial advance in our understanding of the functioning of metapopulations of species with LPDP in marginal seas and may contribute to the effective management of coastal ecosystem services in the face of climate change.},
language = {en},
number = {1},
urldate = {2023-02-13},
journal = {Scientific Reports},
author = {Ramirez-Romero, Eduardo and Amores, Angel and Diaz, David and Muñoz, Anabel and Catalan, Ignacio A. and Molinero, Juan Carlos and Ospina-Alvarez, Andres},
month = feb,
year = {2023},
note = {Number: 1
Publisher: Nature Publishing Group},
keywords = {Animal migration, Ecological modelling, Ecosystem services, Marine biology, Physical oceanography, Population dynamics},
pages = {2366}
}
  • [DOI] N. F. Putman, P. M. Richards, S. G. Dufault, E. Scott-Dention, K. McCarthy, T. R. Beyea, C. W. Caillouet, W. D. Heyman, E. E. Seney, K. L. Mansfield, and B. J. Gallaway, “Modeling juvenile sea turtle bycatch risk in commercial and recreational fisheries,” Iscience, vol. 26, iss. 2, p. 105977, 2023.
    [Bibtex] 
    @article{putman_modeling_2023,
title = {Modeling juvenile sea turtle bycatch risk in commercial and recreational fisheries},
volume = {26},
issn = {2589-0042},
url = {https://www.sciencedirect.com/science/article/pii/S2589004223000548},
doi = {10.1016/j.isci.2023.105977},
abstract = {Understanding the drivers of fisheries bycatch is essential for limiting its impacts on vulnerable species. Here we present a model to estimate the relative magnitude of sea turtle bycatch in major coastal fisheries across the southeastern US based on spatiotemporal variation in fishing effort and the simulated distributions of juvenile Kemp’s ridley (Lepidochelys kempii) and green (Chelonia mydas) sea turtles recruiting from oceanic to nearshore habitats. Over the period modeled (1996–2017), bycatch in recreational fisheries was estimated to be greater than the sum of bycatch that occurred in commercial fisheries that have historically been considered high risks to turtles (e.g., those using trawls, gillnets, and bottom longlines). Prioritizing engagement with recreational anglers to reduce bycatch could be especially beneficial to sea turtle populations. Applying lessons learned from efforts to protect turtles in commercial fisheries may help meet the challenges that arise from the large, diffuse recreational fishing sector.},
language = {en},
number = {2},
urldate = {2023-02-13},
journal = {iScience},
author = {Putman, Nathan F. and Richards, Paul M. and Dufault, Susan G. and Scott-Dention, Elizabeth and McCarthy, Kevin and Beyea, R. Taylor and Caillouet, Charles W. and Heyman, William D. and Seney, Erin E. and Mansfield, Katherine L. and Gallaway, Benny J.},
month = feb,
year = {2023},
keywords = {Biological sciences, Ecology, Environmental science, Nature conservation},
pages = {105977}
}

2022

  • S. Ajmi, M. Boutet, A. C. Bennis, J. P. Pezy, and J. C. Dauvin, “Impact of the turbulent wake downstream offshore wind turbines on larval dispersal,” in Trends in Renewable Energies Offshore, Crc press, 2022.
    [Bibtex] 
    @incollection{ajmi_impact_2022,
title = {Impact of the turbulent wake downstream offshore wind turbines on larval dispersal},
isbn = {978-1-00-336077-3},
abstract = {France challenge is currently to install Offshore Wind Farms (OWFs). OWFs structures will be colonised by numerous fouling species which emitted large number of planktonic larvae, and they are considered as stepping stones which probably impact the dispersal of larvae and therefore the connectivity of species. This work highlight this possible impact using numerical modeling at local scale of OWFs foundations. This modelling combines two models: Eulerian model, OpenFoam, for computing the hydrodynamics, and Lagrangian model, Ichthyop, for simulating the larval dispersal. The hydrodynamic turbulence is represented using RANS turbulence model, k-omega SST. The influence of two different foundations, monopile and gravity base, on hydrodynamics were studied from realistic conditions. Then, the larval dispersal by the hydrodynamic is simulated using passive particles. Main findings are: 1) transport of particles follows the 3D turbulence with a release of few larvae outside the wake. 2) a retention is observed close to the structures.},
booktitle = {Trends in {Renewable} {Energies} {Offshore}},
publisher = {CRC Press},
author = {Ajmi, S. and Boutet, M. and Bennis, A. C. and Pezy, J. P. and Dauvin, J. C.},
year = {2022},
note = {Num Pages: 6}
}
  • [DOI] J. Kolbusz, C. Pattiaratchi, S. Wijeratne, T. Langlois, S. de Lestang, J. Kolbusz, C. Pattiaratchi, S. Wijeratne, T. Langlois, and S. de Lestang, “Finding lobsters: investigating a period of unusually low settlement of Panulirus cygnus by using larval dispersal modelling,” Marine and freshwater research, vol. 74, iss. 1, p. 20–38, 2022.
    [Bibtex] 
    @article{kolbusz_finding_2022,
title = {Finding lobsters: investigating a period of unusually low settlement of {Panulirus} cygnus by using larval dispersal modelling},
volume = {74},
issn = {1448-6059, 1448-6059},
shorttitle = {Finding lobsters},
url = {https://www.publish.csiro.au/mf/MF22117},
doi = {10.1071/MF22117},
abstract = {Context Spiny lobsters are critically affected by ocean current movements over their long journey from hatching to swimming post-larvae (puerulus).Methods Isolating three different larval stages of the Western rock lobster (Panulirus cygnus), we have applied three-dimensional larval-dispersal modelling techniquesAims To better understand a period of unusually low puerulus settlement in the late 2000s.Key results Model results showed that transport mechanisms assisting pueruli in reaching nearshore habitats may have been inhibited by a strengthening of the southward-flowing Leeuwin Current over the austral summer at the settlement stage. As a result, modelled pueruli were transported significantly less northward, in some cases southward, during and after the period of unusually low settlement. Hatching-stage trajectories also suggest increased dispersal off the coast during 2007 and 2008, transporting modelled larvae further offshore and possibly contributing to decreased recruits into the fishery.Conclusions Our study distinguishes the influence that ocean circulation patterns off Western Australia have on three different larval stages.Implications Larval dispersal modelling of pueruli, therefore, provides a possible explanation for the changes in puerulus settlement over the past two decades and future considerations.},
language = {en},
number = {1},
urldate = {2023-02-13},
journal = {Marine and Freshwater Research},
author = {Kolbusz, Jessica and Pattiaratchi, Charitha and Wijeratne, Sarath and Langlois, Tim and Lestang, Simon de and Kolbusz, Jessica and Pattiaratchi, Charitha and Wijeratne, Sarath and Langlois, Tim and Lestang, Simon de},
month = nov,
year = {2022},
note = {Publisher: CSIRO PUBLISHING},
pages = {20--38}
}
  • [DOI] S. M. Lombardo, L. M. Chérubin, A. J. Adams, J. M. Shenker, P. S. Wills, A. J. Danylchuk, and M. J. Ajemian, “Biophysical larval dispersal models of observed bonefish (albula vulpes) spawning events in abaco, the bahamas: an assessment of population connectivity and ocean dynamics,” Plos one, vol. 17, iss. 10, p. e0276528, 2022.
    [Bibtex] 
    @article{lombardo_biophysical_2022,
title = {Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics},
volume = {17},
issn = {1932-6203},
shorttitle = {Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276528},
doi = {10.1371/journal.pone.0276528},
abstract = {Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. Albula vulpes is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten-thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for A. vulpes. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a parks in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.},
language = {en},
number = {10},
urldate = {2022-11-07},
journal = {PLOS ONE},
author = {Lombardo, Steven M. and Chérubin, Laurent M. and Adams, Aaron J. and Shenker, Jonathan M. and Wills, Paul S. and Danylchuk, Andy J. and Ajemian, Matthew J.},
month = {oct},
year = {2022},
note = {Publisher: Public Library of Science},
keywords = {Animal migration, Conservation science, Hydrodynamics, Islands, Larvae, Shores, Spawning, Statistical dispersion},
pages = {e0276528}
}
  • [DOI] S. Hariri, M. Plus, M. Le Gac, V. Séchet, M. Revilla, and M. Sourisseau, “Advection and composition of dinophysis spp. populations along the european atlantic shelf,” Frontiers in marine science, vol. 9, 2022.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2022.914909,
AUTHOR = {Hariri, Saeed and Plus, Martin and Le Gac, Mickael and Séchet, Véronique and Revilla, Marta and Sourisseau, Marc},
TITLE = {Advection and Composition of Dinophysis spp. Populations Along the European Atlantic Shelf},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {9},
YEAR = {2022},
URL = {https://www.frontiersin.org/articles/10.3389/fmars.2022.914909},
DOI = {10.3389/fmars.2022.914909},
ISSN = {2296-7745},
ABSTRACT = {The main objective was to study relationships between the regional biogeography of Dinophysis species and water masses circulation along the European Atlantic coast. Hydrodynamic connectivities were estimated with a Lagrangian approach. Available and validated physical hindcasts from regional hydrodynamical models, with different resolutions were used. The target area is the Bay of Biscay (NE Atlantic) and connectivity was evaluated between a set of spatially distributed stations and during temporally specified periods. Different indexes related to connectivity properties such as mean, median, most frequent transit times were calculated. To illustrate the dispersion pattern, a molecular approach was jointly set-up to describe the species composition of this genus. At the seasonal scale, a high connectivity within the Bay of Biscay was observed with a slight northward connectivity from Galicia coastal waters to the Shelf of the Bay of Biscay. By comparison to the connectivity between shelf waters of French Brittany and English Channel waters, a higher connectivity between shelf waters of French Brittany and the Celtic Sea shelf was observed. The species mixing in the Bay of Biscay from Galicia waters to the Celtic Sea was confirmed by the genetic analyses despite the absence of Dinophysis sacculus in natural samples. The molecular methodology developed for this work, permitting at least the description of the species composition, also highlights, at the European scale, an unexpected low genetic variability which echoes the complex taxonomic classification inside the genus and the difficulties encountered by national monitoring programs to reach a taxonomic resolution at species level. It is now necessary to start some monitoring at the species level before realizing mid- or long-term forecasts.}
}
  • [DOI] M. Bedington, L. M. García-García, M. Sourisseau, and M. Ruiz-Villarreal, “Assessing the performance and application of operational lagrangian transport hab forecasting systems,” Frontiers in marine science, vol. 9, 2022.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2022.749071,
AUTHOR = {Bedington, Michael and García-García, Luz María and Sourisseau, Marc and Ruiz-Villarreal, Manuel},
TITLE = {Assessing the Performance and Application of Operational Lagrangian Transport HAB Forecasting Systems},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {9},
YEAR = {2022},
URL = {https://www.frontiersin.org/articles/10.3389/fmars.2022.749071},
DOI = {10.3389/fmars.2022.749071},
ISSN = {2296-7745},
ABSTRACT = {Availability of operational regional hydrodynamic models and near real time Harmful Algal Bloom (HAB) alerts from monitoring stations and remote sensing products have allowed the proliferation of short term advective HAB forecasts. However, their predictive ability in simulating HAB transport needs to be continuously evaluated in events of different HAB species to assess their applicability to different domains and the impacts of the choices made in model setup. Here we review the performance of three different modelling systems which were part of the PRIMROSE project against historical bloom events in different regions in the European Atlantic Area. The objectives are to understand their predictive ability and to demonstrate some aspects of Lagrangian model setup that are relevant to HAB early warning systems; in particular the use of advection-diffusion only models (without a biological component) and the effects of model configuration, especially model resolution. Hindcast and forecast simulations have been run in examples of high biomass blooms detected in satellite imagery; in the western English Channel, several events of potentially toxic species like Karenia mikimotoi and Prorocentrum cordatum (minimum) were simulated and in Western France a bloom of Mesodinium rubrum, prey of the toxic Dinophysis spp. Additionally, some simulations for studying the evolution of low biomass Dinophysis spp. blooms in Galicia-North Portugal were undertaken with models of different setup. Several metrics have been used to quantify the model performance and to compare the results of the different model configurations, showing that differences in hydrodynamical model configuration (initiation, resolution, forcing, and simulation domain) result in differences in the predicted transport of HABs. We find that advection only is a reasonable approximation but that it may do worse in an early (onset) phase than later on, and we find transport is generally increases with increasing resolution. Our results confirm that Lagrangian particle tracking tools can be integrated operationally in HAB early warning systems providing useful information on potential HAB evolution to users.}
}
  • [DOI] S. Ben Ismail, E. Costa, H. Jaziri, S. Morgana, M. Boukthir, M. A. Ben Ismail, R. Minetti, A. Montarsolo, R. Narizzano, C. Sammari, M. Faimali, and F. Garaventa, “Evolution of the distribution and dynamic of microplastic in water and biota: a study case from the gulf of gabes (southern mediterranean sea),” Frontiers in marine science, vol. 9, 2022.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2022.786026,
AUTHOR = {Ben Ismail, Sana and Costa, Elisa and Jaziri, Hela and Morgana, Silvia and Boukthir, Moncef and Ben Ismail, Mohamed Anis and Minetti, Roberta and Montarsolo, Alessio and Narizzano, Riccardo and Sammari, Cherif and Faimali, Marco and Garaventa, Francesca},
TITLE = {Evolution of the Distribution and Dynamic of Microplastic in Water and Biota: A Study Case From the Gulf of Gabes (Southern Mediterranean Sea)},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {9},
YEAR = {2022},
URL = {https://www.frontiersin.org/article/10.3389/fmars.2022.786026},
DOI = {10.3389/fmars.2022.786026},
ISSN = {2296-7745},
ABSTRACT = {Marine plastic pollution represents a major problem owing to its increasing presence in the environment, persistence and ability to spread in every compartment in the form of small plastic particles, namely microplastics (MPs). Studies concerning MPs abundance in the Mediterranean Sea are growing, but their occurrence in the Southern regions remains largely unexplored. In this study, distribution, abundance, size, and polymer type of microplastics were investigated in surface water samples collected with a Manta net (200 μm mesh size) and in 118 marine specimens of commercial interests, including fishes, crustaceans, and mollusks, during Spring and Autumn 2019 EU H2020 Claim Project sampling Campaigns in the Gulf of Gabes (Southern Mediterranean Sea). Laboratory characterization showed significant plastic pollution concentrations, with an average abundance of 312,887 and 77,110 items/km2 in surface water samples collected in Spring and Autumn, respectively. A 3D hydrodynamic and Tracking Model was used to identify dispersal and transport pathways of the floating plastics, reporting a seasonal variability observed in MPs distribution between I (Spring) and II Campaign (Autumn). Despite the high values of MPs abundance found in surface water samples, an overall low frequency of ingestion among studied species was observed, with a maximum value of 20% of individuals (in Scomber scombrus) found with ingested MPs. The present study contributes to expand our state of knowledge regarding MPs pollution level in water and biota samples collected in the Gulf of Gabes, an area of particular interest for its biological resources, but still little investigated.}
}
  • [DOI] D. Macias, A. Stips, and G. Hanke, “Model based estimate of transboundary litter pollution on mediterranean coasts,” Marine pollution bulletin, vol. 175, p. 113121, 2022.
    [Bibtex] 
    @article{MACIAS2022113121,
title = {Model based estimate of transboundary litter pollution on Mediterranean coasts},
journal = {Marine Pollution Bulletin},
volume = {175},
pages = {113121},
year = {2022},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2021.113121},
url = {https://www.sciencedirect.com/science/article/pii/S0025326X21011553},
author = {Diego Macias and Adolf Stips and Georg Hanke},
keywords = {Mediterranean Sea, Litter modelling, Cross-boundary pollution, Plastic in the ocean},
abstract = {Plastic litter pollution is one of the major concerns for the health of marine ecosystems worldwide. This pervasive form of pollution affects all oceans and seas and it's interacting with multiple levels of the marine food webs. In the European context, several pieces of legislation try to fight against this pervasive and ubiquitous form of pollution. Recently, EU Member States have agreed to a maximum threshold of litter items per coast length (20 items/100 m coastline). One major concern among stakeholders to reach this consensus was the transboundary litter, as measures need to be implemented in the country of origin. Henceforth, a solid method to estimate the amounts of the transboundary litter to a given Member State's coasts is needed. In this contribution, we use a combination of hydrodynamic and Lagrangian models for the Mediterranean Sea in order to understand the origin of coastal litter. Simulations show that the amount of transboundary litter in Mediterranean countries could be as large as 30% although both regional and seasonal differences could be significant.}
}
  • [DOI] R. McGeady, C. Lordan, and A. M. Power, “Long-term interannual variability in larval dispersal and connectivity of the norway lobster (nephrops norvegicus) around ireland: when supply-side matters,” Fisheries oceanography, vol. 31, iss. 3, pp. 255-270, 2022.
    [Bibtex] 
    @article{https://doi.org/10.1111/fog.12576,
author = {McGeady, Ryan and Lordan, Colm and Power, Anne Marie},
title = {Long-term interannual variability in larval dispersal and connectivity of the Norway lobster (Nephrops norvegicus) around Ireland: When supply-side matters},
journal = {Fisheries Oceanography},
volume = {31},
number = {3},
pages = {255-270},
keywords = {connectivity, dispersal, larvae, Nephrops norvegicus, Norway lobster, recruitment, supply-side ecology},
doi = {https://doi.org/10.1111/fog.12576},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12576},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12576},
abstract = {Abstract Dispersal of meroplankton larvae in the ocean is a key process which determines larval supply to areas of suitable habitat and enables connectivity between populations, particularly for nonmigratory species. Our objective was to use a biophysical larval transport model to create a time series (2000–2019) of larval retention, dispersal distance and connectivity estimates for the commercially important Norway lobster (Nephrops norvegicus) on mud grounds off Ireland. Where time series of population estimates were sufficiently long to conduct analysis, we also investigated if larval dispersal indices could be used to predict variations in adult density, after a lag period, hypothesising that this would only apply to grounds with consistently low larval supply. Grounds off Ireland had varying characteristics related to their ability to retain and exchange larvae which was influenced by the local hydrodynamic regime and spatial isolation from other grounds. Larval supply was consistently low on the Aran grounds to the west of Ireland, which have experienced abundance declines in the past. The time series of modelled larval dispersal indices at the Aran grounds was linked to empirical adult burrow densities with a 3-year lag. Whereas the western Irish Sea, which has consistently high larval supply, showed no such relationship. Models can provide important larval recruitment information early in the life cycle for species of commercial or conservation importance.},
year = {2022}
}
  • [DOI] G. A. Gibson, M. R. Baker, W. T. Stockhausen, S. Hinckley, C. Parada, K. Aydin, K. O. Coyle, A. J. Hermann, T. P. Hurst, and A. E. Punt, “Modeling in an integrated ecosystem research framework to explore recruitment in gulf of alaska groundfish – applications to management and lessons learned,” Deep sea research part ii: topical studies in oceanography, vol. 197, p. 105048, 2022.
    [Bibtex] 
    @article{GIBSON2022105048,
title = {Modeling in an integrated ecosystem research framework to explore recruitment in Gulf of Alaska groundfish – Applications to management and lessons learned},
journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
volume = {197},
pages = {105048},
year = {2022},
issn = {0967-0645},
doi = {https://doi.org/10.1016/j.dsr2.2022.105048},
url = {https://www.sciencedirect.com/science/article/pii/S0967064522000339},
author = {Georgina A. Gibson and Matthew R. Baker and William T. Stockhausen and Sarah Hinckley and Carolina Parada and Kerim Aydin and Kenneth O. Coyle and Albert J. Hermann and Thomas P. Hurst and André E. Punt},
keywords = {Mathematical models, Fishery management, Ecosystem management, Recruitment, Research programmes},
abstract = {The Gulf of Alaska Integrated Ecosystem Research Program (GOAIERP) supported multi-disciplinary analyses integrating physical and biological oceanography and modeling to examine how the environment influences survival and recruitment of early life stages of select commercially and ecologically important groundfish species. Recruitment is an important component of population variability, and understanding the processes influencing recruitment is central to fishery management and ecosystem planning. Determining the relative impact of advection and the environmental conditions experienced during transport between spawning and nursery areas is an inherently interdisciplinary problem. It requires consideration of physical and lower trophic level environments in concert with early life history dynamics. Here we discuss how Eulerian ecosystem models and Lagrangian Individual-Based Models for groundfish were integrated within the framework of an interdisciplinary observational program. Metrics (e.g. regionally-based averaged water temperature, integrated primary production, probability of juvenile settlement) were derived from model outputs as proxies for recruitment success. The recruitment indices were then correlated to estimated recruitment from stock assessments. Using the GOAIERP as a case study, we discuss the value that modeling can add to a field program and fisheries management planning, the challenges faced, and steps that can be taken to maximize program success. Coordination of model development, experimentation, and field sampling is necessary but can be challenging. Consideration of the appropriate sequence during data analyses and model development is critical. Careful consideration must be given to ensure that data collected in the field will inform, improve, or validate models. Sufficient time must be allocated within the program to incorporate field data collected during the program and mechanistic understandings into the models. Model outputs should be designed to have utility to management decisions and value to regional stakeholders. Collectively, the studies in this modeling program provide insight as to how models might be used to better understand recruitment processes and lead to recommendations to support the integration of ecosystem models into fisheries management.}
}
  • [DOI] S. C. C. Coelho, D. F. M. Gherardi, M. B. Gouveia, and M. V. Kitahara, “Western boundary currents drive sun-coral (Tubastraea spp.) coastal invasion from oil platforms,” Scientific reports, vol. 12, iss. 1, p. 5286, 2022.
    [Bibtex] 
    @article{coelho_western_2022,
title = {Western boundary currents drive sun-coral ({Tubastraea} spp.) coastal invasion from oil platforms},
volume = {12},
copyright = {2022 The Author(s)},
issn = {2045-2322},
url = {https://www.nature.com/articles/s41598-022-09269-8},
doi = {10.1038/s41598-022-09269-8},
abstract = {Most marine species have a planktonic larval phase that benefit from the surface oceanic flow to enhance their dispersion potential. For invasive species, the interaction of environmentally resistant larvae with different flow regimes and artificial substrates can lead to complex larval dispersion patterns and boost geographic expansion. In the Southwest Atlantic, the invasive corals Tubastraea spp. (sun-coral) have been recorded biofouling on oil platforms since the late 1980s. These platforms are considered important vectors for the established populations throughout the Brazilian coast. However, we still do not know how the position of these structures relative to regional flow contribute to the natural dispersion potential of these invaders on a regional scale. Herein, we used an eddy-resolving ocean model (ROMS) and an Individual Based Model (IBM-Ichthyop) to simulate the natural dispersion patterns of sun-coral larvae from all oil platforms on Brazilian oil-producing basins, for the austral summer and winter along 6 years (2010–2015) in 90-day simulations. We found that mortality rates by advection were significantly higher during the winter (p = 0.001) and when sources of larvae were compared throughout this season (p = 1.9 × 10–17). The influence of two western boundary currents and persistent eddy activity contribute to the dispersal of larvae to distances up to 7000 km. The effectiveness of each oil-producing basin as vectors for the entire Brazilian coastline, measured as the percentage of larval supply, highlights the importance of the northern Ceará (59.89\%) and Potiguar (87.47\%) basins and the more central Camamu (44.11\%) and Sergipe-Alagoas (39.20\%) basins. The poleward shift of the Southern branch of the South Equatorial Current during the winter causes larvae released from the Sergipe-Alagoas and Camamu basins to enter the North Brazil Current, expanding their dispersion towards the north. The Brazil Current disperses larvae southwards, but strong mesoscale activity prevents their dispersion to the coast, especially for those released from the oil platforms on Campos and Santos basins. Within this complex hydrodynamic setting, a few source areas, like those in the Sergipe-Alagoas and Camamu basins, can potentially contribute to the spread of larvae along nearly all the Brazilian coast. Therefore, oil platforms act as possible chronic sources of sun-coral propagules to the coast, emphasizing the urgency for a more detailed set of actions to control and monitor these invasive exotic species.},
language = {en},
number = {1},
urldate = {2022-04-05},
journal = {Scientific Reports},
author = {Coelho, Stella Correia Cesar and Gherardi, Douglas Francisco Marcolino and Gouveia, Mainara Biazati and Kitahara, Marcelo Visentini},
month = mar,
year = {2022},
note = {Number: 1
Publisher: Nature Publishing Group},
keywords = {Coral reefs, Ecological modelling, Ocean sciences},
pages = {5286}
}
  • [DOI] R. Díaz-Gamboa, C. Tamayo-Millán, G. Poot-López, C. González-Salas, H. Villegas-Hernández, and S. Guillén-Hernández, “First stranding record of fin whale (balaenoptera physalus) in the mexican waters of the gulf of mexico,” Aquatic mammals, vol. 48, pp. 92-96, 2022.
    [Bibtex] 
    @article{article,
author = {Díaz-Gamboa, Raúl and Tamayo-Millán, Carlos and Poot-López, Gaspar and González-Salas, Carlos and Villegas-Hernández, Harold and Guillén-Hernández, Sergio},
year = {2022},
month = {01},
pages = {92-96},
title = {First Stranding Record of Fin Whale (Balaenoptera physalus) in the Mexican Waters of the Gulf of Mexico},
volume = {48},
journal = {Aquatic Mammals},
doi = {10.1578/AM.48.1.2022.92}
}
  • [DOI] E. Meerhoff, V. Combes, R. Matano, N. Barrier, B. Franco, A. Piola, F. Hernández-Vaca, and O. Defeo, “Large-scale connectivity of the sandy beach clam mesodesma mactroides along the atlantic coast of south america, and climate change implications,” Marine environmental research, p. 105591, 2022.
    [Bibtex] 
    @article{MEERHOFF2022105591,
title = {Large-scale connectivity of the sandy beach clam Mesodesma mactroides along the Atlantic coast of South America, and climate change implications},
journal = {Marine Environmental Research},
pages = {105591},
year = {2022},
issn = {0141-1136},
doi = {https://doi.org/10.1016/j.marenvres.2022.105591},
url = {https://www.sciencedirect.com/science/article/pii/S0141113622000368},
author = {Erika Meerhoff and Vincent Combes and Ricardo Matano and Nicolas Barrier and Barbara Franco and Alberto Piola and Freddy Hernández-Vaca and Omar Defeo},
keywords = {Yellow clam, Larval connectivity, Individual-based model, Salinity-dependent larval mortality, Temperature-dependent larval mortality, Warming hotspot},
abstract = {The yellow clam Mesodesma mactroides is a cool-water species that typifies sandy beaches of the Southwestern Atlantic Ocean (SAO), which embraces one of the strongest ocean warming hotspots. The region is influenced by the Rio de la Plata (RdlP), which represents a zoogeographic barrier that restricts its larval exchange. We investigated yellow clam larval connectivity patterns using an individual based model (IBM). The IBM combined outputs from a 3D hydrodynamic model with a clam submodel that considered salinity- and temperature-dependent mortality for the planktonic larvae. Connectivity across the RdlP estuary occurred only for larvae released in spring during a strong La Niña event. Mortality due to freshwater precluded larval transport across the RdlP, whereas larval mortality induced by warmer waters reduced connectivity, leading to self-recruitment in most areas. Warming acceleration in this hotspot could further restrict larval connectivity between populations in the SAO, with conservation implications for this threatened species.}
}
  • [DOI] S. Schembri, I. Deschepper, P. G. Myers, P. Sirois, L. Fortier, C. Bouchard, and F. Maps, “Arctic cod (boreogadus saida) hatching in the hudson bay system: testing of the freshwater winter refuge hypothesis,” Elementa: science of the anthropocene, vol. 9, iss. 1, 2022.
    [Bibtex] 
    @article{10.1525/elementa.2021.00042,
author = {Schembri, Sarah and Deschepper, Inge and Myers, Paul G. and Sirois, Pascal and Fortier, Louis and Bouchard, Caroline and Maps, Frédéric},
title = {Arctic cod (Boreogadus saida) hatching in the Hudson Bay system: Testing of the freshwater winter refuge hypothesis},
journal = {Elementa: Science of the Anthropocene},
volume = {9},
number = {1},
year = {2022},
month = {01},
abstract = {Buoyant Arctic cod (Boreogadus saida) eggs are found at the surface or at the ice-water interface in winter. While winter temperatures in saline waters fall below 0°C, the temperature in areas affected by under-ice river plumes is slightly higher. Under-ice river plumes may therefore provide thermal refuges favoring the survival of the vulnerable early life stages of Arctic cod. Thermal refuges would allow early hatchers to survive, benefit from a long growing period, and add to the number of individuals recruiting to the adult population: These expectations define the freshwater winter refuge hypothesis. More than 42 rivers drain into Hudson Bay making it particularly well suited to test this hypothesis. Whereas the bulk of Arctic cod observed in Hudson Bay hatch between mid-April and June, some larvae hatch as early as January. We used two independent but complementary methods to test the hypothesis: (1) Lagrangian model simulations that traced back the planktonic trajectories of the sampled larvae and (2) measurements of the concentration of strontium-88 in the otolith cores. Throughout the Hudson Bay system, Lagrangian simulations revealed that early hatchers were more likely to hatch in lower surface salinities and that larvae reaching larger prewinter lengths were likely to have hatched near or within estuaries. Analysis of otolith microchemistry showed that larvae with low strontium-88 concentration in the otolith core, indicating a low salinity hatch location, had hatched earlier and thus had a longer growth period before freeze-up. These results show the potential for Arctic cod persistence in the Arctic where freshwater input is projected to increase and the ice regime is predicted to become more seasonal, provided that the surface temperatures remain below embryonic and larval lethal limits.},
issn = {2325-1026},
doi = {10.1525/elementa.2021.00042},
url = {https://doi.org/10.1525/elementa.2021.00042},
note = {00042},
eprint = {https://online.ucpress.edu/elementa/article-pdf/9/1/00042/487536/elementa.2021.00042.pdf}
}
  • [DOI] C. Patterson, C. Laing, and R. Early, “The range expansion of Clibanarius erythropus to the UK suggests that other range-shifting intertidal species may not follow,” Marine biology, vol. 169, iss. 2, p. 30, 2022.
    [Bibtex] 
    @article{patterson_range_2022,
title = {The range expansion of {Clibanarius} erythropus to the {UK} suggests that other range-shifting intertidal species may not follow},
volume = {169},
issn = {1432-1793},
url = {https://doi.org/10.1007/s00227-021-04008-5},
doi = {10.1007/s00227-021-04008-5},
abstract = {The ranges of species are shifting as a consequence of anthropogenic climate change. In the marine realm biogeographic transition zones could form barriers to dispersal and inhibit range-shift, but little is known about this potential effect. The hermit crab Clibanarius erythropus appeared in the UK in 2016 with the nearest reproducing population being on the northern coast of Brittany. This raises questions of which conditions may have permitted C. erythropus to cross the English Channel (7.25°W, 49.00°N) and whether this barrier could be overcome by other intertidal species. Dispersal simulations suggest the larvae of C. erythropus arrived in 2014, originated from North Brittany, experienced a mean temperature of around 16 °C, and took longer than 20 days to be transported across the channel. The transportation of larvae from Brittany to the southwest UK appears to be rare and driven by occasional, unusual ocean currents. The English Channel may continue to prevent species with pelagic larvae that settle within 20 days, such as many species of gastropod, annelids, and macroalgae, from successfully range expanding to the UK. North Brittany was the only landmass from which it is feasible the UK population of C. erythropus could have originated. Therefore, species with long-lived pelagic larvae but without reproducing populations in North Brittany may not appear in the southwest UK until the species are established in North Brittany. The English Channel could continue to limit the ability of many intertidal species to shift their range with climate change.},
language = {en},
number = {2},
urldate = {2022-01-26},
journal = {Marine Biology},
author = {Patterson, Christophe and Laing, Chris and Early, Regan},
month = jan,
year = {2022},
pages = {30}
}
  • [DOI] L. Fontoura, S. D’Agata, M. Gamoyo, D. R. Barneche, O. J. Luiz, E. M. P. Madin, L. Eggertsen, and J. M. Maina, “Protecting connectivity promotes successful biodiversity and fisheries conservation,” Science, vol. 375, iss. 6578, pp. 336-340, 2022.
    [Bibtex] 
    @article{doi:10.1126/science.abg4351,
author = {Luisa Fontoura and Stephanie D’Agata and Majambo Gamoyo and Diego R. Barneche and Osmar J. Luiz and Elizabeth M. P. Madin and Linda Eggertsen and Joseph M. Maina },
title = {Protecting connectivity promotes successful biodiversity and fisheries conservation},
journal = {Science},
volume = {375},
number = {6578},
pages = {336-340},
year = {2022},
doi = {10.1126/science.abg4351},
URL = {https://www.science.org/doi/abs/10.1126/science.abg4351},
eprint = {https://www.science.org/doi/pdf/10.1126/science.abg4351},
abstract = { The global decline of coral reefs has led to calls for strategies that reconcile biodiversity conservation and fisheries benefits. Still, considerable gaps in our understanding of the spatial ecology of ecosystem services remain. We combined spatial information on larval dispersal networks and estimates of human pressure to test the importance of connectivity for ecosystem service provision. We found that reefs receiving larvae from highly connected dispersal corridors were associated with high fish species richness. Generally, larval “sinks” contained twice as much fish biomass as “sources” and exhibited greater resilience to human pressure when protected. Despite their potential to support biodiversity persistence and sustainable fisheries, up to 70\% of important dispersal corridors, sinks, and source reefs remain unprotected, emphasizing the need for increased protection of networks of well-connected reefs. Coral reefs are highly threatened by climate change and human pressure. Recent research has focused extensively on how to protect reefs from these impacts, but a fact that is often missed is that reefs are not isolated systems. Fish and coral larvae are actively exchanged across regions, and some reefs supply more whereas others receive more. Fontoura et al. looked at the source/sink dynamics of reefs globally and found that maintaining these networks, including dispersal corridors, is essential for biodiversity conservation and sustainable fisheries. Furthermore, they found that the majority of key source reefs and corridors remain unprotected. —SNV Coral reefs receiving larvae from highly connected dispersal corridors are associated with high fish species richness. }
}
  • [DOI] C. Pattiaratchi, M. van der Mheen, C. Schlundt, B. E. Narayanaswamy, A. Sura, S. Hajbane, R. White, N. Kumar, M. Fernandes, and S. Wijeratne, “Plastics in the indian ocean – sources, transport, distribution, and impacts,” Ocean science, vol. 18, iss. 1, p. 1–28, 2022.
    [Bibtex] 
    @Article{os-18-1-2022,
AUTHOR = {Pattiaratchi, C. and van der Mheen, M. and Schlundt, C. and Narayanaswamy, B. E. and Sura, A. and Hajbane, S. and White, R. and Kumar, N. and Fernandes, M. and Wijeratne, S.},
TITLE = {Plastics in the Indian Ocean -- sources, transport, distribution, and impacts},
JOURNAL = {Ocean Science},
VOLUME = {18},
YEAR = {2022},
NUMBER = {1},
PAGES = {1--28},
URL = {https://os.copernicus.org/articles/18/1/2022/},
DOI = {10.5194/os-18-1-2022}
}

2021

  • [DOI] G. Liu, A. Bracco, A. M. Quattrini, and S. Herrera, “Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for paramuricea biscaya in the northern gulf of mexico,” Frontiers in marine science, vol. 8, 2021.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2021.790927,
AUTHOR = {Liu, Guangpeng and Bracco, Annalisa and Quattrini, Andrea M. and Herrera, Santiago},
TITLE = {Kilometer-Scale Larval Dispersal Processes Predict Metapopulation Connectivity Pathways for Paramuricea biscaya in the Northern Gulf of Mexico},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {8},
YEAR = {2021},
URL = {https://www.frontiersin.org/article/10.3389/fmars.2021.790927},
DOI = {10.3389/fmars.2021.790927},
ISSN = {2296-7745},
ABSTRACT = {Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1,000 and 3,000 m. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1,000 to 2,000-m isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.}
}
  • [DOI] A. G. López, R. G. Najjar, M. A. M. Friedrichs, M. A. Hickner, and D. H. Wardrop, “Estuaries as filters for riverine microplastics: simulations in a large, coastal-plain estuary,” Frontiers in marine science, vol. 8, p. 1200, 2021.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2021.715924,
AUTHOR = {López, Alexander G. and Najjar, Raymond G. and Friedrichs, Marjorie A. M. and Hickner, Michael A. and Wardrop, Denice H.},
TITLE = {Estuaries as Filters for Riverine Microplastics: Simulations in a Large, Coastal-Plain Estuary},
JOURNAL = {Frontiers in Marine Science},
VOLUME = {8},
PAGES = {1200},
YEAR = {2021},
URL = {https://www.frontiersin.org/article/10.3389/fmars.2021.715924},
DOI = {10.3389/fmars.2021.715924},
ISSN = {2296-7745},
}
  • [DOI] A. Dupaix, M. Capello, C. Lett, M. Andrello, N. Barrier, G. Viennois, and L. Dagorn, “Surface habitat modification through industrial tuna fishery practices,” Ices journal of marine science, vol. 78, iss. 9, pp. 3075-3088, 2021.
    [Bibtex] 
    @article{10.1093/icesjms/fsab175,
author = {Dupaix, Amaël and Capello, Manuela and Lett, Christophe and Andrello, Marco and Barrier, Nicolas and Viennois, Gaëlle and Dagorn, Laurent},
title = "{Surface habitat modification through industrial tuna fishery practices}",
journal = {ICES Journal of Marine Science},
volume = {78},
number = {9},
pages = {3075-3088},
year = {2021},
month = {09},
abstract = "{Natural floating objects (FOBs) have always been a major component of the habitat of pelagic species. Since the 1990s, the number of FOBs in the open ocean has increased greatly as a result of the introduction of fish aggregating devices (FADs) by the industrial tropical tuna purse seine vessels. These changes, and their potential impacts on the species that associate with FOBs, remain poorly understood. Using fisheries observer data, data from satellite-linked tracking buoys attached to FOBs and Lagrangian simulations, this study quantifies the temporal changes in the density and spatial distribution of FOBs due to the use of FADs in the Indian Ocean (IO) between 2006 and 2018. From 2012 to 2018, the entire western IO is impacted, with FADs representing more than 85\\% of the overall FOBs, natural FOBs less than 10\\%, and objects originating from pollution 5\\%. Results also suggest that both FADs and natural FOBs densities are lower in the eastern IO, but this initial investigation highlights the need for further studies. Our study confirms that FADs have greatly modified the density and spatial distribution of FOBs, which highlights the need to investigate potential consequences on the ecology of associated species.}",
issn = {1054-3139},
doi = {10.1093/icesjms/fsab175},
url = {https://doi.org/10.1093/icesjms/fsab175},
eprint = {https://academic.oup.com/icesjms/article-pdf/78/9/3075/41324394/fsab175.pdf},
}
  • [DOI] M. L. Santana-Cisneros, P. Ardisson, Á. F. González, I. Mariño-Tapia, M. Cahuich-López, L. E. Ángeles-González, U. Ordoñez-López, and I. Velázquez-Abunader, “Dispersal modeling of octopoda paralarvae in the gulf of mexico,” Fisheries oceanography, vol. 30, iss. 6, pp. 726-739, 2021.
    [Bibtex] 
    @article{https://doi.org/10.1111/fog.12555,
author = {Santana-Cisneros, Mariana L. and Ardisson, Pedro-Luis and González, Ángel F. and Mariño-Tapia, Ismael and Cahuich-López, Miguel and Ángeles-González, Luis Enrique and Ordoñez-López, Uriel and Velázquez-Abunader, Iván},
title = {Dispersal modeling of octopoda paralarvae in the Gulf of Mexico},
journal = {Fisheries Oceanography},
volume = {30},
number = {6},
pages = {726-739},
keywords = {fertility, Gulf of Mexico, Lagrangian model, larval transport, MaxEnt, octopus, settlement},
doi = {https://doi.org/10.1111/fog.12555},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12555},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12555},
abstract = {Abstract The dynamics and population structure of octopus species in the Gulf of Mexico (GoM) can be studied by analyzing dispersal paralarvae mechanisms. Accordingly, this study focused on understanding octopus paralarval dispersal using numerical modeling. A Lagrangian approach was implemented using the transport model ICHTHYOP and surface currents from a GoM simulation of the HYbrid Coordinate Ocean Model (HYCOM). We modeled the dispersal of four octopus species from the GoM (Octopus “vulgaris”, Octopus insularis, Macrotritopus defilippi, and Amphioctopus burryi), considering two regions as the source of larvae in the southern GoM, namely the Yucatan shelf and the Veracruz coastal waters. Additionally, an environmental suitability analysis was incorporated using the maximum entropy (MaxEnt) model to establish potential settlement areas under the influence of the water masses’ thermal conditions. The simulation results supported the hypothesis that the abundances recorded in the GoM were influenced by the fertility (egg-laying) of each species, surface water circulation (the Loop Current, eddies, and wind), and sea surface temperature. Greater dispersal was obtained throughout the GoM for Yucatan species O. “vulgaris”, registering the highest settlement rates. In contrast, in Veracruz, O. insularis dispersed and settled only in the western portion of the GoM. The relevance of the ecological descriptors proposed to influence the dispersal and abundance of octopods throughout the GoM's coastal waters are discussed.},
year = {2021}
}
  • [DOI] K. Drouet, C. Jauzein, D. Herviot-Heath, S. Hariri, A. Laza-Martinez, C. Lecadet, M. Plus, S. Seoane, M. Sourisseau, R. Lemée, and R. Siano, “Current distribution and potential expansion of the harmful benthic dinoflagellate ostreopsis cf. siamensis towards the warming waters of the bay of biscay, north-east atlantic,” Environmental microbiology, vol. 23, iss. 9, pp. 4956-4979, 2021.
    [Bibtex] 
    @article{https://doi.org/10.1111/1462-2920.15406,
author = {Drouet, Kévin and Jauzein, Cécile and Herviot-Heath, Dominique and Hariri, Saeed and Laza-Martinez, Aitor and Lecadet, Cyrielle and Plus, Martin and Seoane, Sergio and Sourisseau, Marc and Lemée, Rodolphe and Siano, Raffaele},
title = {Current distribution and potential expansion of the harmful benthic dinoflagellate Ostreopsis cf. siamensis towards the warming waters of the Bay of Biscay, North-East Atlantic},
journal = {Environmental Microbiology},
volume = {23},
number = {9},
pages = {4956-4979},
doi = {https://doi.org/10.1111/1462-2920.15406},
url = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15406},
eprint = {https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15406},
abstract = {Summary In a future scenario of increasing temperatures in North-Atlantic waters, the risk associated with the expansion of the harmful, benthic dinoflagellate Ostreopsis cf. siamensis has to be evaluated and monitored. Microscopy observations and spatio-temporal surveys of environmental DNA (eDNA) were associated with Lagrangian particle dispersal simulations to: (i) establish the current colonization of the species in the Bay of Biscay, (ii) assess the spatial connectivity among sampling zones that explain this distribution, and (iii) identify the sentinel zones to monitor future expansion. Throughout a sampling campaign carried out in August to September 2018, microscope analysis showed that the species develops in the south-east of the bay where optimal temperatures foster blooms. Quantitative PCR analyses revealed its presence across almost the whole bay to the western English Channel. An eDNA time-series collected on plastic samplers showed that the species occurs in the bay from April to September. Due to the water circulation, colonization of the whole bay from the southern blooming zones is explained by inter-site connectivity. Key areas in the middle of the bay permit continuous dispersal connectivity towards the north. These key areas are proposed as sentinel zones to monitor O. cf. siamensis invasions towards the presumably warming water of the North-East Atlantic.},
year = {2021}
}
  • [DOI] L. A. Gray, A. G. Bisonó León, F. E. Rojas, S. S. Veroneau, and A. H. Slocum, “Caribbean-wide, negative emissions solution to sargassum spp. low-cost collection device and sustainable disposal method,” Phycology, vol. 1, iss. 1, p. 49–75, 2021.
    [Bibtex] 
    @Article{phycology1010004,
AUTHOR = {Gray, Luke A. and Bisonó León, Andres G. and Rojas, Folkers E. and Veroneau, Samuel S. and Slocum, Alexander H.},
TITLE = {Caribbean-Wide, Negative Emissions Solution to Sargassum spp. Low-Cost Collection Device and Sustainable Disposal Method},
JOURNAL = {Phycology},
VOLUME = {1},
YEAR = {2021},
NUMBER = {1},
PAGES = {49--75},
URL = {https://www.mdpi.com/2673-9410/1/1/4},
ISSN = {2673-9410},
ABSTRACT = {Sargassum spp. blooms exacerbated by climate change and agricultural runoff are inundating Caribbean beaches, emitting toxic fumes and greenhouse gases through decomposition. This hurts tourism, artisanal fishing, shore-based industry, human health, standards-of-living, coastal ecology, and the global climate. Barriers, collection machinery, and Sargassum valorization have been unable to provide sufficient, sustainable, or widespread relief. This article presents a total Sargassum management system that is effective, low-impact, and economically scalable across the Caribbean. Littoral Collection Modules (LCMs), attached to artisanal fishing boats, collect Sargassum in nets which are brought to a barge. When full, the barge is towed to the deep ocean where Sargassum is pumped to ~150–200 m depth, whereafter it continues sinking (Sargassum Ocean Sequestration of Carbon; “SOS Carbon”). Costing and negative emissions calculations for this system show cleanup costs <$1/m3 and emissions reduction potential up to 1.356 → 3.029 tCO2e/dmt Sargassum. COVID-19 decimated Caribbean tourism, adding to the pressures of indebtedness and natural disasters facing the region. The “SOS Carbon strategy” could help the Caribbean “build back better” by establishing a negative emissions industry that builds resilience against Sargassum and flight shame (“flygskam”). Employing fishermen to operate LCMs achieves socioeconomic goals while increasing Sargassum cleanup and avoiding landfilling achieves sustainable development goals.},
DOI = {10.3390/phycology1010004}
}
  • [DOI] M. Bouzaiene, M. Menna, D. Elhmaidi, A. F. Dilmahamod, and P. Poulain, “Spreading of lagrangian particles in the black sea: a comparison between drifters and a high-resolution ocean model,” Remote sensing, vol. 13, iss. 13, 2021.
    [Bibtex] 
    @Article{rs13132603,
AUTHOR = {Bouzaiene, Maher and Menna, Milena and Elhmaidi, Dalila and Dilmahamod, Ahmad Fehmi and Poulain, Pierre-Marie},
TITLE = {Spreading of Lagrangian Particles in the Black Sea: A Comparison between Drifters and a High-Resolution Ocean Model},
JOURNAL = {Remote Sensing},
VOLUME = {13},
YEAR = {2021},
NUMBER = {13},
ARTICLE-NUMBER = {2603},
URL = {https://www.mdpi.com/2072-4292/13/13/2603},
ISSN = {2072-4292},
ABSTRACT = {The Lagrangian dispersion statistics of the Black Sea are estimated using satellite-tracked drifters, satellite altimeter data and a high-resolution ocean model. Comparison between the in-situ measurements and the model reveals good agreement in terms of the surface dispersion. The mean sub-basin coherent structures and currents of the Black Sea are well reproduced by the model. Seasonal variability of the dispersion in the upper (15 m), intermediate (150 m) and deep (750 m) layers are discussed with a special focus of the role of sub-basin scale structures and currents on the turbulent dispersion regimes. In terms of the surface relative dispersion, the results show the presence of the three known turbulent exponential, Richardson and diffusive-like regimes. The non-local exponential regime is only detected by the model for scales <10 km, while the local Richardson regime occurs between 10 and 100 km in all cases due to the presence of an inverse energy cascade range, and the diffusive-like regime is well detected for the largest distance by drifters (100–300 km) in winter/spring. Regarding the surface absolute dispersion, it reflects the occurrence of both quasi-ballistic and random-walk regimes at small and large times, respectively, while the two anomalous hyperbolic (5/4) and elliptic (5/3) regimes, which are related to the topology of the Black Sea, are detected at intermediate times. At depth, the signatures of the relative and absolute dispersion regimes shown in the surface layer are still valid in most cases. The absolute dispersion is anisotropic; the zonal component grows faster than the meridional component in any scenario.},
DOI = {10.3390/rs13132603}
}
  • [DOI] D. Macías, L. Prieto, and E. García-Gorriz, “A model-based management tool to predict the spread of physalia physalis in the mediterranean sea. minimizing risks for coastal activities,” Ocean & coastal management, vol. 212, p. 105810, 2021.
    [Bibtex] 
    @article{MACIAS2021105810,
title = {A model-based management tool to predict the spread of Physalia physalis in the Mediterranean Sea. Minimizing risks for coastal activities},
journal = {Ocean \& Coastal Management},
volume = {212},
pages = {105810},
year = {2021},
issn = {0964-5691},
doi = {https://doi.org/10.1016/j.ocecoaman.2021.105810},
url = {https://www.sciencedirect.com/science/article/pii/S0964569121002933},
author = {Diego Macías and Laura Prieto and Elisa García-Gorriz},
keywords = {, Mediterranean sea, Lagrangian modeling, Coastal management, Risk assessment},
abstract = {During recent years, the oceanic siphonophore Physalia physalis has repeatedly entered the Mediterranean Sea through the Strait of Gibraltar, being successively transported and distributed to different regions of that basin. When these floating colonies arrive to coastal areas during peak tourism periods there are large economic and health costs. Their highly venomous nature causes the closure of beaches and coastal attractions, creating a myriad of problems for local and regional authorities throughout the Mediterranean Sea. Many of these problems could be minimized or totally avoided if early warning of P. physalis arrivals to Mediterranean coasts could be issued. In this work, advanced particle tracking Lagrangian models were applied to simulate the dispersion and beaching of P. physalis colonies within the Mediterranean. Observations from two high-presence years (2010 and 2013) were used as calibration dataset and an additional high-abundance record (2018) was employed as validation for the models. The calibrated and validated model set-up was used to construct a statistical inference dataset and extraction tool (Physalia-SIM) that allowed assessing the likelihood of P. physalis arrival to any given coastal region of the Mediterranean Sea (with 97% accuracy) only by knowing their entrance time through the Strait of Gibraltar. The Physalia-SIM is a free-access, easily-useable tool by any stakeholder interested in knowing the probability for P. physalis presence in their particular region of interest. Moreover, this tool can help to provide warning as early as 3–4 months before the actual P. physalis presence is likely to occur. By making use of this prognosis tool, local and regional managers and stakeholders could take the necessary actions in order to minimize the economic and health impacts of the presence of these organisms in their coastlines.}
}
  • [DOI] H. Cabral, H. Drouineau, A. Teles-Machado, M. Pierre, M. Lepage, J. Lobry, P. Reis-Santos, and S. E. Tanner, “Contrasting impacts of climate change on connectivity and larval recruitment to estuarine nursery areas,” Progress in oceanography, vol. 196, p. 102608, 2021.
    [Bibtex] 
    @article{CABRAL2021102608,
title = {Contrasting impacts of climate change on connectivity and larval recruitment to estuarine nursery areas},
journal = {Progress in Oceanography},
volume = {196},
pages = {102608},
year = {2021},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2021.102608},
url = {https://www.sciencedirect.com/science/article/pii/S0079661121000951},
author = {Henrique Cabral and Hilaire Drouineau and Ana Teles-Machado and Maud Pierre and Mario Lepage and Jérémy Lobry and Patrick Reis-Santos and Susanne E. Tanner},
keywords = {Connectivity, Larval dispersal, Marine-estuarine opportunist fishes, Estuarine recruitment, Climate change, Nurseries, North Atlantic, Iberian coast},
abstract = {Connectivity between spawning grounds and recruitment areas of marine fish species drives population structure and dynamics, and may be affected by climate-induced changes in oceanographic processes. We analysed the variability in recruitment success of larvae to estuarine nursery areas along the Iberian Atlantic coast of four fish species with distinct spawning grounds and periods (Solea solea, Solea senegalensis, Platichthys flesus and Dicentrarchus labrax). Concomitantly, we explored the variations in connectivity patterns between “cold” and “warm” year archetypes. We used a three-dimensional Lagrangian transport particle-tracking model integrating time series of velocity, temperature and salinity fields archived from the Regional Ocean Modelling System. We simulated individual larval dispersal, over extended spawning periods, from multiple coastal spawning areas to estuarine recruitment areas over 20 years (1989–2008). Overall, high inter- and intra-annual variation were found for all species. Nonetheless, highest overall average recruitment estimates were obtained for S. solea and D. labrax (with 7.3% and 5.7% of the particles released in spawning areas reaching a recruitment area, respectively) compared to S. senegalensis and P. flesus (3.4% and 1.7%, respectively). Recruitment estimates were overall higher at earlier spawning dates but peak values occurred at later spawning events. Regarding spawning origin, particles that recruited to the northern part of the Iberian coast were mainly from southern source areas. For estuarine systems located in southern Portugal, the relative contributions of northern and southern coastal spawning areas were more balanced, or with a preponderance of northern spawning areas (namely for S. senegalensis and D. labrax). Recruitment was higher in “warm” years compared to “cold” years, except for P. flesus for which nil recruitment was registered in the southern Iberian coast during “warm” years. Larvae also travelled farther in “warm” years compared to “cold” years. Ultimately, understanding how oceanographic conditions govern larval recruitment to estuarine nursery areas is pivotal to forecast the potential impacts of climate change on species with segregated life histories, and will underpin long term management and safeguarding of estuarine nursery role.}
}
  • [DOI] M. Tiedemann, A. Slotte, R. D. M. Nash, E. K. Stenevik, and O. S. Kjesbu, “Drift indices confirm that rapid larval displacement is essential for recruitment success in high-latitude oceans,” Frontiers in marine science, vol. 8, p. 602, 2021.
    [Bibtex] 
    @article{10.3389/fmars.2021.679900,
title = {Drift Indices Confirm That Rapid Larval Displacement Is Essential for Recruitment Success in High-Latitude Oceans},
journal = {Frontiers in Marine Science},
volume = {8},
pages = {602},
year = {2021},
url = {https://www.frontiersin.org/article/10.3389/fmars.2021.679900},
author = {Tiedemann, Maik and Slotte, Aril and Nash, Richard D. M. and Stenevik, Erling K. and Kjesbu, Olav S.},
doi = {10.3389/fmars.2021.679900},
issn = {2296-7745},
abstract = {Larval drift is a key process for successful fish recruitment. We used Norwegian spring-spawning herring (Clupea harengus) as model species to investigate the relationship between larval drift and recruitment. Larval drift indices were derived from simulations based on survey observations between 1993 and 2016. We show that forward simulated larval drift indices have an important positive relation to recruitment success. The relationship demonstrates elevated recruitment when larvae relocate rapidly northwards toward the Barents Sea. Negative or low larval drift indices coincide with only weak recruitment emphasizing limited survival in years with enhanced larval retention. Hence, with this work we combine drift model outcomes refined with survey data indicating that more extensive larval drift is an important component in population dynamics for high-latitude small pelagic fishes. However, larval displacement alone represents only one among many controlling factors but may offer possible predictions of the probability of higher or lower recruitment in the short term. The applicability of the drift indices is adaptable in all world oceans and all marine organisms that occupy planktonic life stages exposed to dynamic ocean currents. The study demonstrates how larval drift indices help to identify larval transport or retention to be crucial for population replenishment.}
}
  • [DOI] L. S. Lima, D. F. M. Gherardi, L. P. Pezzi, L. G. dos Passos, C. A. K. Endo, and J. P. Quimbayo, “Potential changes in the connectivity of marine protected areas driven by extreme ocean warming,” Scientific reports, vol. 11, p. 10339, 2021.
    [Bibtex] 
    @article{lima_potential_2021,
title = {Potential changes in the connectivity of marine protected areas driven by extreme ocean warming},
volume = {11},
issn = {2045-2322},
url = {https://www.nature.com/articles/s41598-021-89192-6},
doi = {10.1038/s41598-021-89192-6},
abstract = {Projected future climate scenarios anticipate a warmer tropical ocean and changes in surface currents that will likely influence the survival of marine organisms and the connectivity of marine protected areas (MPAs) networks. We simulated the regional effects of climate change on the demographic connectivity of parrotfishes in nine MPAs in the South Atlantic through downscaling of the HadGEM2-ES Earth System Model running the RCP 8.5 greenhouse gas trajectory. Results indicate a tropicalization scenario over the tropical southwest Atlantic following an increase of sea surface temperature (SST) between 1.8 and 4.5 °C and changes in mean surface currents between − 0.6 to 0.5 m s−1 relative to present conditions. High mortality rates will reduce demographic connectivity and increase the isolation of oceanic islands. The simulation of organismal response to ocean warming shows that acclimation can significantly improve (p {\textless} 0.001) particle survival, promoting connectivity and tropicalization of MPAs, with potential impacts on their functional integrity and long-term resilience.},
journal = {Scientific Reports},
author = {Lima, Luciana Shigihara and Gherardi, Douglas Francisco Marcolino and Pezzi, Luciano Ponzi and Passos, Leilane Gonçalves dos and Endo, Clarissa Akemi Kajiya and Quimbayo, Juan Pablo},
year = {2021},
pages = {10339}
}
  • [DOI] C. Jordan, C. Cusack, M. C. Tomlinson, A. Meredith, R. McGeady, R. Salas, C. Gregory, and P. L. Croot, “Using the red band difference algorithm to detect and monitor a karenia spp. bloom off the south coast of ireland, june 2019,” Frontiers in marine science, vol. 8, p. 436, 2021.
    [Bibtex] 
    @article{10.3389/fmars.2021.638889,
title = {Using the Red Band Difference Algorithm to Detect and Monitor a Karenia spp. Bloom Off the South Coast of Ireland, June 2019},
journal = {Frontiers in Marine Science},
volume = {8},
pages = {436},
year = {2021},
url = {https://www.frontiersin.org/article/10.3389/fmars.2021.638889},
author = {Jordan, Catherine and Cusack, Caroline and Tomlinson, Michelle C. and Meredith, Andrew and McGeady, Ryan and Salas, Rafael and Gregory, Clynton and Croot, Peter L.},
doi = {10.3389/fmars.2021.638889},
issn = {2296-7745},
abstract = {During the months of May, June, July and August 2019 the Red Band Difference algorithm was tested over Irish waters to assess its suitability for the Irish harmful algal bloom alert system. Over the 4 weeks of June an extensive localised surface phytoplankton bloom formed in the Celtic Sea, south of Ireland. Satellite imagery from the Sentinel-3a’s Ocean and Land Colour Instrument, processed using the Red Band Difference algorithm detected the bloom in surface shelf waters and helped monitor its movement. Daily satellite images indicated that the bloom appeared at the sea surface on the 2nd June 2019 and peaked in size and surface abundance in offshore shelf waters within 4 weeks, remnants remained at the surface into July. A particle tracking approach was used to replicate oceanic circulation patterns in the vicinity of the observed algal bloom and estimate its trajectory. The initial horizontal distribution of particles in the tracking model were based on a satellite imagery polygon of the bloom when it first appeared in surface waters. Good agreement was observed between satellite imagery of the bloom and the particle tracking model. In situ sampling efforts from a research cruise and the national inshore phytoplankton monitoring programme confirmed that Karenia mikimotoi was the causative organism of the bloom. This pilot study shows great potential to use the Red Band Difference algorithm in the existing Irish harmful algal bloom alert system. In addition, satellite ocean colour data combined with particle tracking model estimates can be a useful tool to monitor high biomass harmful algal bloom forming species, such as Karenia mikimotoi, in surface coastal waters around Ireland and elsewhere.}
}
  • [DOI] R. F. T. Pires, Á. Peliz, and A. dos Santos, “Into the deep – dispersal models for deep-water decapod shrimp larvae: the case of parapenaeus longirostris,” Progress in oceanography, vol. 194, p. 102568, 2021.
    [Bibtex] 
    @article{PIRES2021102568,
title = {Into the deep – Dispersal models for deep-water decapod shrimp larvae: The case of Parapenaeus longirostris},
journal = {Progress in Oceanography},
volume = {194},
pages = {102568},
year = {2021},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2021.102568},
url = {https://www.sciencedirect.com/science/article/pii/S0079661121000550},
author = {Rita F.T. Pires and \'{A}lvaro Peliz and Antonina dos Santos},
keywords = {Decapoda, Penaeidae, Deep-water rose shrimp, ROMS, Ichthyop, Gulf of Cadiz, Western Iberian Margin},
abstract = {Deep-water shrimps remain some of the less understood decapod crustacean taxa, despite the high commercial and ecological importance. The lack of knowledge on adults and larval stages of many species rsults in an incomplete view of the biology, distribution, dispersal and connectivity, essential knowledge for conservation and stock management. In zooplankton samples, larvae of deep-water shrimps are usually found in low abundances. Here, we address the insufficiently studied topics of distribution and transport of deep-water shrimp larvae, providing information on potential pathways and mechanisms of dispersal. The work focuses on southern Portuguese waters, giving important indications for deep-water shrimp species worldwide. Physical-ecological modelling was used to examine the dispersal of larvae of the deep-water rose shrimp, Parapenaeus longirostris, that were found distributed over shelf waters in the study region. In situ spatial abundances were examined, and ontogenetic vertical distributions and sites of larval release were included in the models. The circulation in the vicinity of submarine canyons and deep moats promoted relatively shallower positions of simulated particles. Passive drifts were insufficient for larvae to reach the uppermost water layers, while the vertical distribution adopted, in the upper or lower water layers, was highly important, dictating the direction of the transport and the retention over shelf waters. Slope or shelf larval releases influenced the dispersal patterns and the concentration of particles over productive waters, suggesting that the onshore movement of females during spawning may benefit the larval retention over shelf waters.}
}
  • [DOI] M. J. DuBois, N. F. Putman, and S. E. Piacenza, “A global assessment of the potential for ocean-driven transport in hatchling sea turtles,” Water, vol. 13, iss. 6, 2021.
    [Bibtex] 
    @article{w13060757,
author = {DuBois, Morgan J. and Putman, Nathan F. and Piacenza, Susan E.},
title = {A Global Assessment of the Potential for Ocean-Driven Transport in Hatchling Sea Turtles},
journal = {Water},
volume = {13},
year = {2021},
number = {6},
article-number = {757},
url = {https://www.mdpi.com/2073-4441/13/6/757},
issn = {2073-4441},
abstract = {Ocean circulation models are an essential tool for use in estimating the movements of drifting marine species. Across the world, hatchling sea turtle transport to the pelagic ocean is facilitated by the local currents off their natal beaches. It is difficult, if not impossible, to observe this transport reliably for any lengthy period, and, as such, ocean circulation models are an essential tool for studying sea turtles during this vulnerable time. Here, we use the ocean circulation model HYCOM and the particle simulator Ichthyop to model the first month of hatchling transport across all sea turtle species from nesting sites across the world from 25 cohorts of hatchlings at 67 nesting sites. We evaluated transport as a function of spatiotemporal factors that could influence turtle movement, using generalized linear models and the information theoretic approach to model selection. We found that multiple physical factors influence transport across the first month of movement and that annual variability is an important factor in hatchling transport. Our findings suggest that the beaches turtles hatch from and the year in which they hatch may shape their early life and the speed of transport into the relative safety of the open ocean. An increased understanding of the likely survival of a cohort may aid in designating funds and planning conservation strategies for individual beaches to either compensate for or take advantage of the local currents.},
doi = {10.3390/w13060757}
}
  • [DOI] S. Huang, Z. Deng, G. Tang, H. Li, and T. Yu, “Numerical study on blue mackerel larval transport in east china sea,” Journal of marine systems, vol. 217, p. 103515, 2021.
    [Bibtex] 
    @article{HUANG2021103515,
title = {Numerical study on blue mackerel larval transport in East China Sea},
journal = {Journal of Marine Systems},
volume = {217},
pages = {103515},
year = {2021},
issn = {0924-7963},
doi = {https://doi.org/10.1016/j.jmarsys.2021.103515},
url = {https://www.sciencedirect.com/science/article/pii/S0924796321000142},
author = {Shan Huang and Zengan Deng and Guoqin Tang and Haoqian Li and Ting Yu},
keywords = {Blue mackerel, Early life history, Diel vertical migration, Individual based model},
abstract = {An Individual-based model (IBM) for studying the blue mackerel larval transport in East China Sea (ECS), for the first time, is developed based on Ichthyop model. Coastal and Regional Ocean Community model (CROCO), a typical hydrodynamic model, is configured as well to provide Ichthyop with the physical variables (e.g. temperature, salinity, current). Effects of physical environments (current and temperature), spawning ground/depth/time and diel vertical migration (DVM) on aspects of the early life stage of blue mackerel, including connectivity between spawning ground and nursery area, temperature-dependent mortality, transportation and dispersal distance, are discussed in detail for the first time based on IBM. Two transport scenarios are considered in our simulations: (1) passive Lagrangian transport and (2) DVM. The experimental results show that the transport of the blue mackerel in ECS is principally controlled by the Kuroshio Current (KC) and Tsushima Warm Current (TSWC). Most of the larvae that affected by TSWC are mainly remained in ECS stock, while those controlled by KC are generally confined in the Pacific stock. In passive Lagrangian transport, the larvae from the largest spawning ground do not only remain in ECS stock but also drift to the Pacific stock in February. In travelling to the Pacific stock, the larvae will experience a long-distance trip and may spread away from the suitable growth area, which is not conducive to their survival. Whereas in DVM scenario, cases with different vertical migration mechanisms all have shorter dispersal distances comparing to the first scenario, the long-distance movement is significantly reduced during the simulating period, particularly in February. DVM tends to prevent the larvae entering the Pacific stock from the largest spawning ground in ECS, thus could increase the recruitment and survival for ECS stock.}
}
  • [DOI] E. Valencia, E. Meerhoff, E. Díaz-Cabrera, F. Guerrero, N. Roja-Hernández, C. Vega-Retter, and D. Veliz, “Weak connectivity and population cohesiveness in rudderfish kyphosus sandwicensis (teleostei: kyphosidae) inhabiting remote oceanic islands,” Aquatic conservation: marine and freshwater ecosystems, vol. 31, iss. 2, pp. 356-366, 2021.
    [Bibtex] 
    @article{https://doi.org/10.1002/aqc.3438,
author = {Valencia, Evelyn and Meerhoff, Erika and Díaz-Cabrera, Ernesto and Guerrero, Felipe and Roja-Hernández, Noemi and Vega-Retter, Caren and Veliz, David},
title = {Weak connectivity and population cohesiveness in rudderfish Kyphosus sandwicensis (Teleostei: Kyphosidae) inhabiting remote oceanic islands},
journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
volume = {31},
number = {2},
pages = {356-366},
keywords = {marine protected areas, population connectivity, Rapa Nui ecoregion, reef-associated fish},
doi = {https://doi.org/10.1002/aqc.3438},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3438},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/aqc.3438},
abstract = {Abstract Population connectivity has a fundamental role in metapopulation dynamics, with important implications in conservation. Easter Island (EI) and Salas y Gómez Island (SG) in the Pacific Ocean are ideal for the study of population connectivity because they are separated by 415 km and isolated from other islands in the Pacific Ocean by >2,000 km. Considering that dispersal processes could play a critical role in the persistence of its populations, the connectivity pattern of the rudderfish Kyphosus sandwicensis was evaluated between EI and SG using both a population genetics and a biophysical modelling approach. The variability in the control region of the mitochondrial DNA did not show a significant phylogeographical pattern, and the variability in 16 microsatellite loci suggested that individuals of K. sandwicensis located at EI and SG belong to the same genetic population. However, historical migration showed that 0.2\% of the recruits at EI come from SG and that 0.15\% at SG come from EI per year. Using simulated larval release during September and a larval development of 30 days in the plankton, biophysical modelling did not detect migration between the islands. Furthermore, self-recruitment shows interannual variation ranging from 5 to 10\% of the total released larvae. Whereas the genetic data showed a lack of population genetic structure but low connectivity of K. sandwicensis between EI and SG, the biophysical modelling showed null movement of particles between the islands. Stochastic movement of larvae or adults could explain the pattern observed, with rafting as an example. These low-frequency and stochastic movements may be important in maintaining the cohesiveness between EI and SG.},
year = {2021}
}
  • [DOI] R. McGeady, C. Lordan, and A. M. Power, “Shift in the larval phenology of a marine ectotherm due to ocean warming with consequences for larval transport,” Limnology and oceanography, vol. 66, iss. 2, pp. 543-557, 2021.
    [Bibtex] 
    @article{https://doi.org/10.1002/lno.11622,
author = {McGeady, Ryan and Lordan, Colm and Power, Anne Marie},
title = {Shift in the larval phenology of a marine ectotherm due to ocean warming with consequences for larval transport},
journal = {Limnology and Oceanography},
volume = {66},
number = {2},
pages = {543-557},
doi = {https://doi.org/10.1002/lno.11622},
url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11622},
eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11622},
abstract = {Abstract Because environmental temperature has an important influence on developmental rate and physiology, marine ectotherms are vulnerable to phenology changes due to ocean warming. Identifying changes to phenology, the timing of biological events, and understanding their effect on recruitment and abundance is of critical importance to establish potential population effects. We examined the larval phenology of the commercially important Norway lobster (Nephrops norvegicus) and used a larval transport model to examine its effect on simulated transport patterns. Using a model to estimate annual larval release dates based on temperature-dependent embryo incubation, an earlier shift of 17.2 d occurred between 1982–1995 and 2000–2010 in the Irish Sea, similar to an observed empirical shift in phenology of 19.1 d using historical zooplankton data sets. Despite this earlier phenology, temperature-dependent pelagic larval durations were unchanged because the water column to which larvae were released earlier had also warmed. Larval transport simulations in the western Irish Sea indicated that the phenology shift had minimal effects on larval retention and advection distance overall, because major variations were observed only at very early or late stages of the larval season, that is, times when lower proportions of larvae were present. As the western Irish Sea grounds exports small but consistent quantities of larvae to nearby populations, especially off Scotland, it may act as an important source of larvae, especially when retention of native larvae is low. Overall, larval transport tools may indicate grounds that are periodically vulnerable to recruitment failures and offer potentially valuable information in fishery management.},
year = {2021}
}
  • [DOI] L. Bonnin, C. Lett, L. Dagorn, J. D. Filmalter, F. Forget, P. Verley, and M. Capello, “Can drifting objects drive the movements of a vulnerable pelagic shark?,” Aquatic conservation: marine and freshwater ecosystems, vol. 31, iss. 1, pp. 74-82, 2021.
    [Bibtex] 
    @article{https://doi.org/10.1002/aqc.3420,
author = {Bonnin, Lucas and Lett, Christophe and Dagorn, Laurent and Filmalter, John David and Forget, Fabien and Verley, Philippe and Capello, Manuela},
title = {Can drifting objects drive the movements of a vulnerable pelagic shark?},
journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
volume = {31},
number = {1},
pages = {74-82},
keywords = {bycatch, fish aggregating devices, Lagrangian drift model, pop-up satellite archival telemetry, silky shark, vulnerability},
doi = {https://doi.org/10.1002/aqc.3420},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3420},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/aqc.3420},
abstract = {Abstract Juvenile silky sharks (Carcharhinus falciformis) regularly associate with floating objects yet the reasons driving this behaviour remain uncertain. Understanding the proportion of time that silky sharks spend associated with floating objects is essential for assessing the impacts of the extensive use of fish aggregating devices (FADs) in the tropical tuna purse-seine fisheries, including increased probability of incidental capture and the potential of an ecological trap. Previous studies provided insight into the amount of time that silky sharks spent at an individual FAD but were unable to assess neither the time spent between two associations nor the proportion of time spent associated/unassociated. The percentage of time that juvenile silky sharks spend unassociated with floating objects was estimated through the analysis of horizontal movements of 26 silky sharks monitored with pop-up archival tags. Under the assumption that a high association rate with drifting FADs would align the trajectories of tracked sharks with ocean surface currents, a novel methodology is proposed, based on the comparison of shark trajectories with simulated trajectories of passively drifting particles derived using a Lagrangian model. Results revealed that silky shark trajectories were divergent from surface currents, and thus unassociated with FADs, for at least 30\% of their time. The potential of the methodology and the results are discussed in the context of increasing FAD densities in the Indian Ocean.},
year = {2021}
}

2020

  • N. S. Suhaimi, N. R. Daud, M. F. Akhir, and M. U. Rusli, “Oceanic dispersal model of green turtle hatchlings in the south china sea,” Malaysian applied biology, vol. 49, iss. 4, pp. 41-55, 2020.
    [Bibtex] 
    @article{suhaimi_oceanic_nodate,
title = {Oceanic dispersal model of green turtle hatchlings in the South China Sea},
journal = {Malaysian Applied Biology},
volume = {49},
number = {4},
pages = {41-55},
year = {2020},
url = {http://www.mabjournal.com/images/49_4_December_2020/49_04_06.pdf},
author = {Suhaimi, Nadhirah Syafiqah and Daud, Nurul Rabitah and Akhir, Mohd Fadzil and Rusli, Mohd Uzair},
abstract = {High-resolution ocean circulation models have increased our understanding of the movement and distribution of worldwide ocean currents, which were previously unknown and difficult to study. The metabolic expenditure data obtained through open-flow respirometric analysis was put into an energy budget context by comparing it to their available reserved energy in the body upon entering the swimming life phase. We modeled the dispersal range of green turtle hatchling from Chagar Hutang in various monsoon season using the particle-tracking program Ichthyop v3.2 and ocean surface current output from HYCOM (Hybrid Coordinate Ocean Model). The prediction distribution suggests that ocean current variability determines their movements into different dispersal areas. The simulated hatchlings are distributed north into the Gulf of Thailand during the Southwest monsoon, while during the Northeast monsoon, the simulated hatchlings travel south into the Java Sea. By quantifying hatchlings potential energy, they can swim a distance of 116 km and can last up to 7 days. Green turtle hatchlings from Chagar Hutang reached offshore water of Kelantan State and Terengganu waters near Tenggol Island on Day 7. These findings highlight areas of high priority for conservation, as habitat crucial for an endangered sea turtle species during a critical period of early development.}
}
  • [DOI] E. Cuevas, N. F. Putman, A. Uribe-Martínez, M. C. López-Castro, V. Guzmán-Hernández, S. A. Gallegos-Fernández, M. Á. de los Liceaga-Correa, J. A. Trujillo-Córdova, R. J. de González-Díaz-Mirón, A. Negrete-Phillipe, H. H. Acosta-Sánchez, R. C. Martínez-Portugal, M. López-Hernández, P. Huerta-Rodríguez, and J. Silver, “First spatial distribution analysis of male sea turtles in the southern gulf of mexico,” Frontiers in marine science, vol. 7, p. 962, 2020.
    [Bibtex] 
    @article{10.3389/fmars.2020.561846,
author = {Cuevas, Eduardo and Putman, Nathan F. and Uribe-Martínez, Abigail and López-Castro, Melania C. and Guzmán-Hernández, Vicente and Gallegos-Fernández, Sandra A. and Liceaga-Correa, María de los Ángeles and Trujillo-Córdova, Jorge A. and González-Díaz-Mirón, Raúl de Jesús and Negrete-Phillipe, Ana and Acosta-Sánchez, Héctor H. and Martínez-Portugal, Rosa C. and López-Hernández, Martha and Huerta-Rodríguez, Patricia and Silver, Jim},
title = {First Spatial Distribution Analysis of Male Sea Turtles in the Southern Gulf of Mexico},
journal = {Frontiers in Marine Science},
volume = {7},
pages = {962},
year = {2020},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.561846},
doi = {10.3389/fmars.2020.561846},
issn = {2296-7745},
}
  • [DOI] V. Michotey, A. Blanfuné, C. Chevalier, M. Garel, F. Diaz, Léo. Berline, L. Le Grand, F. Armougom, S. Guasco, S. Ruitton, T. Changeux, B. Belloni, J. Blanchot, F. Ménard, and T. Thibaut, “In situ observations and modelling revealed environmental factors favouring occurrence of vibrio in microbiome of the pelagic sargassum responsible for strandings,” Science of the total environment, vol. 748, p. 141216, 2020.
    [Bibtex] 
    @article{MICHOTEY2020141216,
title = "In situ observations and modelling revealed environmental factors favouring occurrence of Vibrio in microbiome of the pelagic Sargassum responsible for strandings",
journal = "Science of The Total Environment",
volume = "748",
pages = "141216",
year = "2020",
issn = "0048-9697",
doi = "https://doi.org/10.1016/j.scitotenv.2020.141216",
url = "http://www.sciencedirect.com/science/article/pii/S0048969720347458",
author = "Valérie Michotey and Aurélie Blanfuné and Cristèle Chevalier and Marc Garel and Frédéric Diaz and Léo Berline and Louis {Le Grand} and Fabrice Armougom and Sophie Guasco and Sandrine Ruitton and Thomas Changeux and Bruno Belloni and Jean Blanchot and Frédéric Ménard and Thierry Thibaut",
keywords = "s, Copepod, Microbiome, Nutrient, growth rate, Wind",
abstract = "Historically, pelagic Sargassum were only found in the Sargasso Sea. Since 2011, blooms were regularly observed in warmer water, further south. Their developments in Central Atlantic are associated with mass strandings on the coasts, causing important damages and potentially dispersion of new bacteria. Microbiomes associated with pelagic Sargassum were analysed at large scale in Central Atlantic and near Caribbean Islands with a focus on pathogenic bacteria. Vibrio appeared widely distributed among pelagic Sargassum microbiome of our samples with higher occurrence than previously found in Mexico Gulf. Six out the 16 Vibrio-OTUs (Operational Taxonomic Unit), representing 81.2 ± 13.1% of the sequences, felt in cluster containing pathogens. Among the four different microbial profiles of pelagic Sargassum microbiome, Vibrio attained about 2% in two profiles whereas it peaked, in the two others, at 6.5 and 26.8% respectively, largely above the concentrations found in seawater surrounding raft (0.5%). In addition to sampling and measurements, we performed backward Lagrangian modelling of trajectories of rafts, and rebuilt the sampled rafts environmental history allowing us to estimate Sargassum growth rates along raft displacements. We found that Vibrio was favoured by high Sargassum growth rate and in situ ammonium and nitrite, modelled phosphate and nitrate concentrations, whereas zooplankters, benthic copepods, and calm wind (proxy of raft buoyancy near the sea surface) were less favourable for them. Relations between Vibrio and other main bacterial groups identified a competition with Alteromonas. According to forward Lagrangian tracking, part of rafts containing Vibrio could strand on the Caribbean coasts, however the strong decreases of modelled Sargassum growth rates along this displacement suggest unfavourable environment for Vibrio. For the conditions and areas observed, the sanitary risk seemed in consequence minor, but in other areas or conditions where high Sargassum growth rate occurred near coasts, it could be more important."
}
  • [DOI] J. Soto-Navarro, G. Jordá, S. Deudero, C. Alomar, Á. Amores, and M. Compa, “3d hotspots of marine litter in the mediterranean: a modeling study,” Marine pollution bulletin, vol. 155, p. 111159, 2020.
    [Bibtex] 
    @article {478,
title = {3D hotspots of marine litter in the Mediterranean: A modeling study},
journal = {Marine Pollution Bulletin},
volume = {155},
year = {2020},
pages = {111159},
abstract = {
    The 3D dispersion of marine litter (ML) over the Mediterranean basin has been simulated using the velocity fields from a high resolution circulation model as base to run a 3D Lagrangian model. Three simulations have been performed to mimic the evolution of ML with density lower, similar, or higher than seawater. In all cases a realistic distribution of ML sources was used. Our results show that the accumulation/dispersion areas of the floating and buoyancy neutral particles are practically the same, although the latter are distributed in the water column, 80\% of them found in the photic layer (average depth of 35m). Regarding to the densest particles, they rapidly sink and reach the seafloor close to their source. The regions of higher temporal variability mostly coincide with the ML accumulation regions. Weak seasonal variability occurs at a sub-basin scale as a result of the particles redistribution induced by the seasonal variability of the current field.
    
},
keywords = {3D circulation, Lagrangian models, Marine litter, Marine pollution, Mediterranean Sea, Plastic pollution},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2020.111159},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X20302770},
author = {Javier Soto-Navarro and Gabriel Jord{\'a} and Salud Deudero and Carme Alomar and {\'A}ngel Amores and Montserrat Compa}
}
  • [DOI] J. M. Maina, M. Gamoyo, V. M. Adams, S. D’agata, J. Bosire, J. Francis, and D. Waruinge, “Aligning marine spatial conservation priorities with functional connectivity across maritime jurisdictions,” Conservation science and practice, vol. 2, p. e156, 2020.
    [Bibtex] 
    @article {458,
title = {Aligning marine spatial conservation priorities with functional connectivity across maritime jurisdictions},
journal = {Conservation Science and Practice},
volume = {2},
year = {2020},
pages = {e156},
abstract = {
    Globally, maritime boundaries on oceans form the basis of governance and management of natural resources, yet the fish, and other marine resources neither conform nor confine to these artificial boundaries. As goods and services from marine life continue to retrogress under the intense human exploitation and changing global environment, resilience could be supported through establishment of a functionally connected network of marine reserves across maritime jurisdictions. While the establishment of protected areas within the exclusive economic zones (EEZ) is expanding, mechanisms that would allow governments to conserve marine areas beyond national jurisdictions are currently inadequate. Consequently, implementing marine reserves is largely confined within territorial waters, high connectivity among contiguous maritime zones notwithstanding. As the global focus shifts toward achieving sustainable development goals for the oceans, there is a need for region-specific approaches to area-based biodiversity conservation that extends the scope of protection to areas in the high seas beyond the EEZ. Using simulations of functional connectivity and seafloor geomorphology, we present and apply in the Western Indian Ocean (WIO) region a contextual approach to regional marine conservation planning to inform a more effective regional marine conservation across maritime zones.
    
},
keywords = {areas beyond national jurisdiction, fisheries management, functional connectivity, high seas, larval dispersal, marine conservation planning, marine protected areas, ocean governance, regional MPA, seafloor geomorphic habitats, Western Indian Ocean},
issn = {2578-4854},
doi = {10.1111/csp2.156},
url = {https://conbio.onlinelibrary.wiley.com/doi/abs/10.1111/csp2.156},
author = {Maina, Joseph M. and Gamoyo, Majambo and Adams, Vanessa M. and D'agata, Stephanie and Bosire, Jared and Francis, Julius and Waruinge, Dixon}
}
  • [DOI] H. Amemou, V. Koné, A. Aman, and C. Lett, “Assessment of a lagrangian model using trajectories of oceanographic drifters and fishing devices in the tropical atlantic ocean,” Progress in oceanography, vol. 188, p. 102426, 2020.
    [Bibtex] 
    @article {498,
title = {Assessment of a Lagrangian model using trajectories of oceanographic drifters and fishing devices in the Tropical Atlantic Ocean},
journal = {Progress in Oceanography},
volume = {188},
year = {2020},
pages = {102426},
abstract = {
    In the Tropical Atlantic Ocean, we assessed the accuracy of a Lagrangian model (Ichthyop) forced with velocity fields from a hydrodynamical model (CROCO) and two different remote sensing products (GlobCurrent and OSCAR) using trajectories of oceanographic drifters. Additionally, we evaluated the possibility to expand the drifters data using trajectories of GPS-buoy equipped drifting Fish Aggregating Devices (FADs). The observed and simulated trajectories were compared in terms of spatial distribution, velocity distribution and a nondimensional skill score. For the drifters and FADs, the GlobCurrent and OSCAR products lead to similar performances as the CROCO model-ouputs in the broad studied domain. In the Gulf of Guinea, however, the CROCO model performed significantly better than the other two because the parent solution of CROCO benefited from its communication with a child grid of finer resolution in this region. On average, the simulations lead to an underestimation of the drifter and FAD velocities, likely because the spatial resolutions of the forcing products were insufficient and the time frequency at which they were produced were too low to resolve the relevant oceanic processes properly. We found a low skill for all models to simulate FAD trajectories, possibly because of the devices vertical structure that prevent FADs from drifting like water parcels. Our results therefore suggest that in the Tropical Atlantic the FAD dataset may not be appropriate to use for corroborating Lagrangian simulations.
    
},
keywords = {Drifter, Fish aggregating device, Model performance, Particle, Trajectory, Velocity},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2020.102426},
url = {http://www.sciencedirect.com/science/article/pii/S0079661120301658},
author = {H. Amemou and V. Kon{\'e} and A. Aman and C. Lett}
}
  • [DOI] E. Meerhoff, O. Defeo, V. Combes, B. C. Franco, R. P. Matano, A. R. Piola, F. H. Vaca, and E. Celentano, “Assessment of larval connectivity in a sandy beach mole crab through a coupled bio-oceanographic model,” Estuarine, coastal and shelf science, vol. 246, p. 107035, 2020.
    [Bibtex] 
    @article {501,
title = {Assessment of larval connectivity in a sandy beach mole crab through a coupled bio-oceanographic model},
journal = {Estuarine, Coastal and Shelf Science},
volume = {246},
year = {2020},
pages = {107035},
abstract = {
    The biophysical mechanisms influencing larval distribution and their impacts on the metapopulation dynamics of sandy beaches, particularly the connectivity patterns associated with larval dispersal, are poorly understood. Here, we identify larval connectivity patterns of the mole crab Emerita brasiliensis in the coast of Uruguay. A biophysical individual based model (IBM) of larval transport was coupled to a regional high-resolution physical model to estimate the monthly and interannual variation of larval connectivity, as well as the impact of the length of the reproductive period on it. Larval connectivity showed marked interannual variations, which were mainly related to interannual changes in seasonal winds and associated ocean circulation patterns, particularly during La Ni{\~n}a years. The southernmost area where E. brasiliensis occurs only received larvae from the nearest release area in November and January spawning events during a strong La Ni{\~n}a year, characterized by intense northeasterly winds. The Uruguayan coast constitutes the leading (poleward) edge of the distribution of E. brasiliensis, where climate change effects are projected to intensify. Extrapolation of these results to a climate change scenario with stronger La Ni{\~n}a events, suggest that larval transport to southernmost beaches will become more probable.
    
},
keywords = {Individual based model, Larval connectivity, Mole crab, Sandy beach},
issn = {0272-7714},
doi = {https://doi.org/10.1016/j.ecss.2020.107035},
url = {http://www.sciencedirect.com/science/article/pii/S0272771420307666},
author = {Erika Meerhoff and Omar Defeo and Vincent Combes and Barbara C. Franco and Ricardo P. Matano and Alberto R. Piola and Freddy Hern{\'a}ndez Vaca and Eleonora Celentano}
}
  • [DOI] I. Deschepper, K. Lyons, O. Lyashevska, and D. Brophy, “Biophysical models reveal the role of tides, wind, and larval behaviour in early transport and retention of atlantic herring (clupea harengus) in the celtic sea,” Canadian journal of fisheries and aquatic sciences, vol. 77, p. 90{–}107, 2020.
    [Bibtex] 
    @article {453,
title = {Biophysical models reveal the role of tides, wind, and larval behaviour in early transport and retention of Atlantic herring (Clupea harengus) in the Celtic Sea},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
volume = {77},
year = {2020},
pages = {90{\textendash}107},
abstract = {
    Fish are adapted to spawn where their larvae will be retained in, or transported to, suitable juvenile habitat. Variability in circulation and behaviour produces variation in larval transport with consequences for recruitment. A biophysical model was used to simulate early larval dispersal of Celtic Sea herring (Clupea harengus) during wintertime in 6 years (2002, 2003, 2004, 2005, 2008, 2010). After 30 days, particles occurred in three areas: inshore Celtic Sea, offshore Celtic Sea, and southern Irish Sea, with the majority (70\%\–78\% on average) of particles retained in the Celtic Sea. Inclusion of tidal forcing increased transport to the Irish Sea and decreased transport offshore, as did release during a spring tide. Retention in the Celtic Sea was increased by diel vertical migration and decreased by horizontal diffusion. Strong and frequent west to southwest winds increased transport offshore, while strong and frequent east to south-southeast winds increased inshore retention in the Celtic Sea and transport into the Irish Sea. The study shows how tides, winds, and behaviour influence larval transport and retention and highlights potential impacts of climate change on population persistence.
    
},
issn = {0706-652X},
doi = {10.1139/cjfas-2018-0491},
url = {https://www.nrcresearchpress.com/doi/10.1139/cjfas-2018-0491},
author = {Deschepper, Inge and Lyons, Kieran and Lyashevska, Olga and Brophy, Deirdre}
}
  • [DOI] L. Lopera, Y. Cardona, and P. A. Zapata-Ramírez, “Circulation in the seaflower reserve and its potential impact on biological connectivity,” Frontiers in marine science, vol. 7, p. 385, 2020.
    [Bibtex] 
    @article {484,
title = {Circulation in the Seaflower Reserve and Its Potential Impact on Biological Connectivity},
journal = {Frontiers in Marine Science},
volume = {7},
year = {2020},
pages = {385},
abstract = {
    The influence of ocean currents on marine population connectivity is critical to territory planning, and such phenomena should be considered in the design and implementation of marine protected areas (MPAs), marine spatial planning strategies, and restoration plans, among other developments. Knowledge of the influence of currents is also vital in understanding the relationship between oceanographic drivers and ecosystem configurations. However, despite their importance, ocean currents and their role in coral connectivity remain poorly constrained in the Seaflower Marine Reserve, an area that hosts the most productive open-ocean coral reef system in the Caribbean and that was declared a biosphere reserve in 2000. We herein characterize the larva transport patterns associated with surface currents that control connectivity in the reserve. To achieve this aim, we simulated the advection of buoyant coral larvae of Acropora palmata during nine spawning events. Larval dispersal patterns were obtained through offline coupling of a high-spatiotemporal resolution hydrodynamic field and a biophysical Lagrangian model for particle dispersion. Ocean current fields were generated using a Regional Ocean Modeling System (ROMS) that was appropriately configured for the region. Larval dispersion was simulated using an Individual-Based Model (Ichthyop). Our results show that there are heterogeneous connectivity patterns during the spawning events at seasonal and inter-annual scales. This seems to be associated with high spatiotemporal dynamic variability in the region, such as the Caribbean Current bifurcation close to the Nicaraguan Rise, the intrusion-formation of mesoscale and sub-mesoscale eddies, and the semi-permanent presence of the Panama-Colombia Gyre. We also found that Serranilla, Providencia, Quitasue\ño, and Serrana act as the most important sinks. In contrast, the northernmost reefs, Serranilla, B. Alicia, and B. Nuevo, seem to be the most important sources of larvae, highlighting that these areas need to be incorporated into the current MPA zonification and that this could lead to the improvement of MPA effectiveness. Our findings also suggest the need to implement MPA networks between Jamaica and Colombia to allow biological populations to become resilient to environmental changes and less prone to local extinctions.
    
},
issn = {2296-7745},
doi = {10.3389/fmars.2020.00385},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00385},
author = "Lopera, Luisa and Cardona, Yuley and Zapata-Ram\'irez, Paula A."
}
  • [DOI] E. Crochelet, N. Barrier, M. Andrello, F. Marsac, A. Spadone, and C. Lett, “Connectivity between seamounts and coastal ecosystems in the southwestern indian ocean,” Deep sea research part ii: topical studies in oceanography, vol. 176, p. 104774, 2020.
    [Bibtex] 
    @article {493,
title = {Connectivity between seamounts and coastal ecosystems in the Southwestern Indian Ocean},
journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
volume = {176},
year = {2020},
pages = {104774},
abstract = {Understanding larval connectivity patterns is critical for marine spatial planning, particularly for designing marine protected areas and managing fisheries. Patterns of larval dispersal and connectivity can be inferred from numerical transport models at large spatial and temporal scales. We assess model-based connectivity patterns between seamounts of the Southwestern Indian Ocean (SWIO) and the coastal ecosystems of Mauritius, La R{\'e}union, Madagascar, Mozambique and South Africa, with emphasis on three shallow seamounts (La P{\'e}rouse [LP], MAD-Ridge [MR] and Walters Shoal [WS]). Using drifter trajectory and a Lagrangian model of ichthyoplankton dispersal, we show that larvae can undertake very long dispersion, with larval distances increasing with pelagic larval duration (PLD). There are three groups of greater connectivity: the region between the eastern coast of Madagascar, Mauritius and La R{\'e}union islands; the seamounts of the South West Indian Ridge; and the pair formed by WS and a nearby un-named seamount. Connectivity between these three groups is evident only for the longest PLD examined (360~d). Connectivity from seamounts to coastal ecosystems is weak, with a maximum of 2\% of larvae originating from seamounts reaching coastal ecosystems. Local retention at the three focal seamounts (LP, MR and WS) peaks at about 11\% for the shortest PLD considered (15~d) at the most retentive seamount (WS) and decreases sharply with increasing PLD. Information on PLD and age of larvae collected at MR and LP are used to assess their putative origin. These larvae are likely self-recruits but it is also plausible that they immigrate from nearby coastal sites, i.e. the southern coast of Madagascar for MR and the islands of La R{\'e}union and Mauritius for LP.},
keywords = {Biophysical model, Connectivity, Ichthyop, Lagrangian modelling, Larval drift, Larval duration, Seamounts, Southwestern indian ocean, Surface drifters},
issn = {0967-0645},
doi = {https://doi.org/10.1016/j.dsr2.2020.104774},
url = {http://www.sciencedirect.com/science/article/pii/S0967064519301080},
author = {Estelle Crochelet and Nicolas Barrier and Marco Andrello and Francis Marsac and Aur{\'e}lie Spadone and Christophe Lett}
}
  • [DOI] E. A. Flores, C. Parada, L. R. Castro, D. A. Narváez, and H. H. Sepúlveda, “Connectivity in early life stages of the southern hake, merluccius australis, in northern chilean patagonia,” Journal of marine systems, vol. 212, p. 103452, 2020.
    [Bibtex] 
    @article {506,
title = {Connectivity in early life stages of the southern hake, Merluccius australis, in northern Chilean Patagonia},
journal = {Journal of Marine Systems},
volume = {212},
year = {2020},
pages = {103452},
abstract = {
    The southern hake, Merluccius australis, is one of the most important marine fishery resources in Chilean Patagonia. However, little is known about its early life history, especially the transport of eggs and larvae and the connectivity between spawning and nursery areas. An individual-based model (IBM) of the early life stages of M. australis, coupled to a hydrodynamic model, was used to track virtual individuals released from known spawning locations and identify potential nursery areas. The simulations were used to assess connectivity and retention of M. australis eggs and yolk-sac larvae within (and between) the continental shelf (offshore) and the inner sea (inshore) zones. The inshore zone included two spawning and nursery areas (Inner Sea of Chilo{\'e} (ISCh), Inner Sea of Moraleda Channel ISM)) and the offshore zone included three spawning and nursery areas (Guafo Island, Guamblin Island, and the Taitao Peninsula). The hydrodynamic model was validated using available observations (oceanographic surveys and the World Ocean Atlas 2018) for winter and spring, periods during which M. australis reproductive activity peaks. The IBM reproduced well the observed seasonal variability of egg and larval distributions. Individuals from the offshore spawning areas had low connectivity with those in the inshore nursery areas in winter and spring. However, individuals from the inshore spawning areas showed a high degree of connectivity with one of the offshore nursery areas (Guafo) during winter and spring, but low connectivity between the inshore ones (ISCh and ISM). Guamblin (in winter) and ISCh (in spring) were the most important retention areas. A conceptual model is proposed to represent the connectivity in early developmental stages between the spawning and nursery areas of M. australis: ichthyoplankton is transported from inshore to offshore in winter when little spawning occurs inshore, but not in spring when spawning and retention increases inshore. Retention in the offshore zone in winter is significant, with almost no connectivity with the inshore zone. Since the main spawning of the species occurs in winter in the offshore zone and secondarily in the inshore zone in spring, the seasonal differences in dispersal patterns seem to be part of the reproductive strategy of the species, which apparently confers advantages for the offspring by promoting development in the most advantageous feeding environment for each season (offshore in winter and inshore in spring).
    
},
keywords = {Connectivity, early life stages, Individual-based model, Patagonia},
issn = {0924-7963},
doi = {https://doi.org/10.1016/j.jmarsys.2020.103452},
url = {http://www.sciencedirect.com/science/article/pii/S0924796320301482},
author = {Eduardo A. Flores and Carolina Parada and Leonardo R. Castro and Diego A. Narv{\'a}ez and H{\'e}ctor H. Sep{\'u}lveda}
}
  • [DOI] R. S. Martins, R. de Camargo, and M. A. de los Gasalla, “Effect of retention processes on the recruitment of tropical arrow squid (doryteuthis pleii): an individual-based modeling case study in southeastern brazil,” Fisheries research, vol. 224, p. 105455, 2020.
    [Bibtex] 
    @article {449,
title = {Effect of retention processes on the recruitment of tropical arrow squid (Doryteuthis pleii): An individual-based modeling case study in southeastern Brazil},
journal = {Fisheries Research},
volume = {224},
year = {2020},
pages = {105455},
abstract = {
    Squid recruitment depends on paralarvae survival, as the parental stock dies following reproduction. Therefore, the biotic and abiotic environmental conditions experienced by paralarvae control recruitment strength. To benefit from the favorable environments (i.e. nursery grounds) in the dynamic pelagic domain, paralarvae rely on passive retention by currents to remain in suitable nursery habitat. To evaluate the retention conditions for tropical arrow squid (Doryteuthis pleii) paralarvae off the South Brazil Bight (SBB, 22\–29 \°S), we ran a series of particle-tracking Individual-Based Models (IBM) coupled to a 3D Princeton Ocean Model (POM). We forced the hydrodynamic model with observed satellite data obtained from January 2000 to December 2010. The IBM-POM models considered two transport scenarios: (1) passive Lagrangian transport and (2) Diel Vertical Migration (DVM). The results show a high retention on actual and putative nursery grounds that could retain paralarvae in a suitable environment for survival, growth, and ultimately to recruit to the adult population. Moreover, model outputs showed high correlation between autumn-winter retention indexes and spring-summer commercial and artisanal landings in the following year. Considering the nine-month post-hatching lifespan of the species, autumn-winter retention indexes potentially provide forthcoming adult biomass predictions.
    
},
keywords = {paralarvae, Retention index, SE Brazil, Squid recruitment},
issn = {0165-7836},
doi = {https://doi.org/10.1016/j.fishres.2019.105455},
url = {http://www.sciencedirect.com/science/article/pii/S0165783619303108},
author = {Rodrigo Silvestre Martins and Ricardo de Camargo and Maria de los Angeles Gasalla}
}
  • [DOI] E. M. Johns, R. Lumpkin, N. F. Putman, R. H. Smith, F. E. Muller-Karger, D. T. Rueda-Roa, C. Hu, M. Wang, M. T. Brooks, L. J. Gramer, and F. E. Werner, “The establishment of a pelagic sargassum population in the tropical atlantic: biological consequences of a basin-scale long distance dispersal event,” Progress in oceanography, vol. 182, p. 102269, 2020.
    [Bibtex] 
    @article {455,
title = {The establishment of a pelagic Sargassum population in the tropical Atlantic: Biological consequences of a basin-scale long distance dispersal event},
journal = {Progress in Oceanography},
volume = {182},
year = {2020},
pages = {102269},
abstract = {
    Starting in 2011, coastal areas of the Caribbean Sea and tropical Atlantic Ocean began to experience extraordinary yearly accumulations of pelagic Sargassum brown alga. Historical reports place large quantities of Sargassum only in the North Atlantic (mostly in the Gulf of Mexico and the Sargasso Sea). Accumulations of Sargassum in the tropical Atlantic have continued. We used a numerical particle-tracking system, wind and current reanalysis data, drifting buoy trajectories, and satellite imagery to determine the origin of the Sargassum that is now found persistently in the tropical Atlantic. Our analyses suggest that during the extreme negative phase of the winter 2009\–2010 North Atlantic Oscillation (NAO), unusually strong and southward-shifted westerly winds explain the transport of Sargassum from the Sargasso Sea (\∼20\–40\°N, 80\–20\°W) into the far eastern North Atlantic. Our hindcast Sargassum distributions agree with surface current simulations with the inclusion of \“windage\”. Windage is the additional, wind-induced drift of material floating at the free surface resulting from direct wind forcing on the sea surface, as well as on floating or partially-submerged objects. In our simulations, windage is included as an added vector (speed and direction) to the model-computed surface ocean currents equivalent to 1\% of surface wind velocities. Lagrangian analysis of the regional circulation suggests that (1) part of the Sargassum subsequently drifted to the southwest in the North Equatorial Current (NEC) and entered the central tropical Atlantic, arriving in the Caribbean by the spring of 2011, with (2) another portion continuing southward along the coast of Africa in the Canary Current, eventually joining the seasonally-varying system of tropical Atlantic currents and thereby delivering a large Sargassum population to the tropical Atlantic. Since then, Sargassum patches aggregate from March to September in massive windrows along the Inter-Tropical Convergence Zone (ITCZ) under the action of converging winds. The windrows follow the ITCZ in its seasonal northward migration in the central tropical Atlantic. They are stretched across the central tropical Atlantic as the ITCZ crosses the latitude of the seasonal formation of the North Equatorial Counter Current (NECC). These patches and windrows are exposed to high sunlight and open-ocean upward flux of nutrients due to eddy and wind-driven mixing in the central tropical Atlantic. During the northern spring and summer, as the Sargassum drifts farther north with the ITCZ, large portions of the population are advected into the eastern Caribbean Sea. Some of these patches remain dispersed as the ITCZ migrates southward, and re-aggregate into new windrows as the ITCZ intensifies the following March-April. If wind mixing is strong and the mixed layer is deeper than about 50\–60 m in the southern tropical Atlantic at this time, the Sargassum will bloom and form a massive windrow. Otherwise, the bloom will be inhibited. The extreme 2009\–2010 NAO wind anomaly could be considered as triggering a biosphere \“tipping point\” that caused important ocean-scale ecosystem changes in the tropical Atlantic, with significant recurrent social and economic consequences. Understanding whether this new expanded geographic range of massive Sargassum blooms is temporary or whether it will revert to its pre-2009 distribution requires sustained monitoring and research.
    
},
keywords = {Caribbean Sea, Ekman pumping, Inter-Tropical Convergence Zone (ITCZ), Mixed layer depth, North Atlantic Ocean, North Atlantic Oscillation (NAO), Sargasso Sea, Tropical Atlantic, Windage},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2020.102269},
url = {http://www.sciencedirect.com/science/article/pii/S0079661120300070},
author = {Elizabeth M. Johns and Rick Lumpkin and Nathan F. Putman and Ryan H. Smith and Frank E. Muller-Karger and Digna T. Rueda-Roa and Chuanmin Hu and Mengqiu Wang and Maureen T. Brooks and Lewis J. Gramer and Francisco E. Werner}
}
  • [DOI] Léo. Berline, A. Ody, J. Jouanno, C. Chevalier, J. André, T. Thibaut, and F. Ménard, “Hindcasting the 2017 dispersal of sargassum algae in the tropical north atlantic,” Marine pollution bulletin, vol. 158, p. 111431, 2020.
    [Bibtex] 
    @article {490,
title = {Hindcasting the 2017 dispersal of Sargassum algae in the Tropical North Atlantic},
journal = {Marine Pollution Bulletin},
volume = {158},
year = {2020},
pages = {111431},
abstract = {Since 2011, huge amounts of Sargassum algae are detected in the equatorial Atlantic, causing large strandings events on the coasts of the West Indies, Brazil and West Africa. The distribution of this stock shows strong annual and interannual variability, whose drivers are not settled yet. Here we use satellite Sargassum observations from MODIS and currents from an ocean reanalysis to simulate the passive transport of algae in 2017. Wind effect was necessary to fit the observed distribution. Simulations reasonably reproduce the satellite monthly distribution for up to seven months, confirming the prominent role of transport in the distribution cycle. Annual cycle appears as a zonal exchange between eastern (EAR) and western accumulation regions (WAR). EAR is well explained by advection alone, with sharp meridional distribution controlled by converging currents below the inter-tropical Convergence Zone. Instead, WAR is not explained by advection alone, suggesting local growth.},
keywords = {AFAI, Aggregation, Annual cycle, distribution, Forecast, Lagrangian transport, MODIS},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2020.111431},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X2030549X},
author = {L{\'e}o Berline and Anouck Ody and Julien Jouanno and Cristele Chevalier and Jean-Michel Andr{\'e} and Thierry Thibaut and Fr{\'e}d{\'e}ric M{\'e}nard}
}
  • [DOI] M. J. DuBois, N. F. Putman, and S. E. Piacenza, “Hurricane frequency and intensity may decrease dispersal of kemp’s ridley sea turtle hatchlings in the gulf of mexico,” Frontiers in marine science, vol. 7, p. 301, 2020.
    [Bibtex] 
    @article {482,
title = {Hurricane Frequency and Intensity May Decrease Dispersal of Kemp's Ridley Sea Turtle Hatchlings in the Gulf of Mexico},
journal = {Frontiers in Marine Science},
volume = {7},
year = {2020},
pages = {301},
abstract = {
    Environmental variability can be an important factor in the population dynamics of many species. In marine systems, for instance, whether environmental conditions facilitate or impede the movements of juvenile animals to nursery habitat can have a large influence on subsequent population abundance. Both subtle differences in the position of oceanographic features (such as meandering currents) and major disturbances (such as hurricanes) can greatly alter dispersal outcomes. Here, we use an ocean circulation model to explore seasonal and annual variation in the dispersal of post-hatchling Kemp\’s ridley sea turtles (Lepidochelys kempii). We simulated the transport of 24 cohorts of young-of-the-year Kemp\’s ridley sea turtles dispersing from the three primary nesting areas in the western Gulf of Mexico to describe variability in transport during the main hatching season and across years. We examined whether differences in transport distance among Kemp\’s ridley cohorts could be explained by hurricane events. We found that years with high numbers of hurricanes corresponded to shorter dispersal distances and less variance within the first 6 months. Our findings suggest that differences in dispersal among sites and the impact of hurricane frequency and intensity could influence the survivorship and somatic growth rates of turtles from different nesting sites and hatching cohorts, either improving survival by encouraging retention in optimal pelagic habitat or decreasing survival by pushing hatchlings into dangerous shallow habitats. Considering such factors in future population assessments may aid in predicting how the potential for increasing tropical storms, a phenomenon linked to climate change, could affect Kemp\’s ridley and other populations of sea turtles in the Atlantic Ocean.
    
},
issn = {2296-7745},
doi = {10.3389/fmars.2020.00301},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00301},
author = {DuBois, Morgan J. and Putman, Nathan F. and Piacenza, Susan E.}
}
  • [DOI] S. Miladinova, D. Macias, A. Stips, and E. Garcia-Gorriz, “Identifying distribution and accumulation patterns of floating marine debris in the black sea,” Marine pollution bulletin, vol. 153, p. 110964, 2020.
    [Bibtex] 
    @article {456,
title = {Identifying distribution and accumulation patterns of floating marine debris in the Black Sea},
journal = {Marine Pollution Bulletin},
volume = {153},
year = {2020},
pages = {110964},
abstract = {
    The distribution and accumulation of floating marine debris in the Black Sea during the last few decades are analysed by the help of numerical modelling. An approach based on a mesoscale circulation model combined with a particle tracking model is applied. It is established that the litter distribution is nearly independent of the source location and is mainly controlled by the basin circulation system. The western gyre predominantly accumulates floating debris in summer. After the integration of the main cyclonic current in winter, the debris in the inner basin moves east. Retention zones along the south-western coast persist in time. The mean particle stranding time is estimated at about 200\ days. Accumulation zones along the south-eastern and eastern coast are abundant in summer, and then move further northeast and north. Simulations demonstrate an increasing litter accumulation in summer on the North Western Shelf and shelf break.
    
},
keywords = {Black Sea, Floating litter, Mesoscale circulation, Numerical modelling},
issn = {0025-326X},
doi = {10.1016/j.marpolbul.2020.110964},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X20300825},
author = {Miladinova, S. and Macias, D. and Stips, A. and Garcia-Gorriz, E.}
}
  • [DOI] N. F. Putman, R. Lumpkin, M. J. Olascoaga, J. Trinanes, and G. J. Goni, “Improving transport predictions of pelagic sargassum,” Journal of experimental marine biology and ecology, vol. 529, p. 151398, 2020.
    [Bibtex] 
    @article {481,
title = {Improving transport predictions of pelagic Sargassum},
journal = {Journal of Experimental Marine Biology and Ecology},
volume = {529},
year = {2020},
pages = {151398},
abstract = {
    A mechanistic understanding of organismal movement provides context for existing biogeographic and ecological patterns and improves our ability to predict changing patterns in dynamic environments. Here, we examined the movement ecology of pelagic Sargassum in the northern Caribbean Sea, where major inundation events of this brown algae have become increasingly problematic to coastal communities. We used GPS-trackers affixed to Sargassum mats, standard oceanographic drifters, and \“pseudo-Sargassum\” drifters to acquire empirical data on the movement of Sargassum and ocean currents. We related these observed movements to ocean surface velocity fields from a global ocean circulation model and wind velocities derived from models and satellite observations. Specifically, we assessed whether adding a windage component to ocean surface velocities improved predictions generated by synthetic particles tracked within an ocean circulation model. We found that the inclusion of a windage factor of 1 to 3\% reduced separation distances between synthetic particles and the tracks of Sargassum mats, pseudo-Sargassum drifters, and un-drogued oceanographic drifters. When similar analyses were conducted for oceanographic drifters with drogues centered at 15\ m depth (which are designed to minimize the influence of winds and waves and thus served as a control for this technique), inclusion of a windage factor did not improve particle-tracking predictions. These findings indicate that adding a windage calculated from satellite-derived winds to the surface layer of an ocean circulation model produces particle-tracking results that are more relevant to Sargassum, likely by accounting for the buoyant nature of the algae and the influence of the direct forcing of wind (and waves, implicitly) on the part of the object extending above the surface. However, the estimates of an appropriate windage coefficient for Sargassum may differ depending on the wind and surface current products used as well as the particular oceanic region being studied. Future work to identify and resolve systematic biases in the representation of winds and currents will be an important step toward eventually forecasting Sargassum movement and coastal inundation events.
    
},
keywords = {Caribbean Sea, Dispersal, movement ecology, ocean circulation model},
issn = {0022-0981},
doi = {https://doi.org/10.1016/j.jembe.2020.151398},
url = {http://www.sciencedirect.com/science/article/pii/S0022098120300125},
author = {Nathan F. Putman and Rick Lumpkin and Maria J. Olascoaga and Joaquin Trinanes and Gustavo J. Goni}
}
  • [DOI] J. L. Headlam, K. Lyons, J. Kenny, E. S. Lenihan, D. T. G. Quigley, W. Helps, M. M. Dugon, and T. K. Doyle, “Insights on the origin and drift trajectories of portuguese man of war (physalia physalis) over the celtic sea shelf area,” Estuarine, coastal and shelf science, vol. 246, p. 107033, 2020.
    [Bibtex] 
    @article {504,
title = {Insights on the origin and drift trajectories of Portuguese man of war (Physalia physalis) over the Celtic Sea shelf area},
journal = {Estuarine, Coastal and Shelf Science},
volume = {246},
year = {2020},
pages = {107033},
abstract = {
    Many marine animals are difficult to study because they are widely dispersed across oceans and are not captured by traditional sampling methodologies such as fishery surveys. A case in point is the Portuguese man of war (Physalia physalis) (Linn{\ae}us, 1758), which despite being pleustonic and remarkably conspicuous, is one of the least studied and understood gelatinous zooplankton species, especially in terms of its ecology. During August to October 2016, the Irish coastline experienced the largest mass stranding of P. physalis in over 150 years. At the same time, P. physalis were recorded offshore in the Porcupine Seabight. Here we used these stranded and offshore observations of P. physalis to inform a Lagrangian particle-tracking model forced by wind to 1) hindcast the backwards drift of this species for three months to determine their likely origin and provide some insights on likely pathways to Irish shores and, 2) forecast the drift of this species towards the Irish coastline. Hindcasting stranded P. physalis from the Irish coastline suggested that they most likely originated from an extensive source area located over the European basin but ultimately from the North Atlantic Current. Our forecast model indicated that particles released from the Porcupine Seabight stranded on Irish shores, in fact, stranding patterns were 82\% similar to actual strandings. Both models combined suggested that the Porcupine Seabight was an important source area, but that many P. physalis likely originated from further south and took a more tortuous trajectory towards Ireland determined by wind. This study also highlights the value of collecting routine beach strandings data and opportunistic offshore visual observations to inform future coastal and shelf modelling studies.
    
},
keywords = {-5.0{\textdegree}E, 10.0{\textdegree}E, 40.0{\textdegree}N, 64.0{\textdegree}N, Continental shelf, Lagrangian drifters, Mathematical model, zooplankton},
issn = {0272-7714},
doi = {https://doi.org/10.1016/j.ecss.2020.107033},
url = {http://www.sciencedirect.com/science/article/pii/S0272771420307642},
author = {Jasmine L. Headlam and Kieran Lyons and Jon Kenny and Eamonn S. Lenihan and Declan T.G. Quigley and William Helps and Michel M. Dugon and Thomas K. Doyle}
}
  • [DOI] A. Ospina-Alvarez, S. de Juan, K. J. Davis, C. González, M. Fernández, and S. A. Navarrete, “Integration of biophysical connectivity in the spatial optimization of coastal ecosystem services,” Science of the total environment, vol. 733, p. 139367, 2020.
    [Bibtex] 
    @article {486,
title = {Integration of biophysical connectivity in the spatial optimization of coastal ecosystem services},
journal = {Science of The Total Environment},
volume = {733},
year = {2020},
pages = {139367},
abstract = {
    Ecological connectivity in coastal oceanic waters is mediated by dispersion of the early life stages of marine organisms and conditions the structure of biological communities and the provision of ecosystem services. Integrated management strategies aimed at ensuring long-term service provision to society do not currently consider the importance of dispersal and larval connectivity. A spatial optimization model is introduced to maximise the potential provision of ecosystem services in coastal areas by accounting for the role of dispersal and larval connectivity. The approach combines a validated coastal circulation model that reproduces realistic patterns of larval transport along the coast, which ultimately conditions the biological connectivity and productivity of an area, with additional spatial layers describing potential ecosystem services. The spatial optimization exercise was tested along the coast of Central Chile, a highly productive area dominated by the Humboldt Current. Results show it is unnecessary to relocate existing management areas, as increasing no-take areas by 10\% could maximise ecosystem service provision, while improving the spatial representativeness of protected areas and minimizing social conflicts. The location of protected areas was underrepresented in some sections of the study domain, principally due to the restriction of the model to rocky subtidal habitats. Future model developments should encompass the diversity of coastal ecosystems and human activities to inform integrative spatial management. Nevertheless, the spatial optimization model is innovative not only for its integrated ecosystem perspective, but also because it demonstrates that it is possible to incorporate time-varying biophysical connectivity within the optimization problem, thereby linking the dynamics of exploited populations produced by the spatial management regime.
    
},
keywords = {Aichi targets, Benthic communities, Coastal users, Ecological connectivity, Integrated management, Protected areas, Social-ecological systems, Spatial management},
issn = {0048-9697},
doi = {https://doi.org/10.1016/j.scitotenv.2020.139367},
url = {http://www.sciencedirect.com/science/article/pii/S0048969720328849},
author = {Andr{\'e}s Ospina-Alvarez and Silvia de Juan and Katrina J. Davis and Catherine Gonz{\'a}lez and Miriam Fern{\'a}ndez and Sergio A. Navarrete}
}
  • [DOI] A. M. McGrath, J. C. Hermes, C. L. Moloney, C. Roy, G. Cambon, S. Herbette, and C. D. Van Der Lingen, “Investigating connectivity between two sardine stocks off south africa using a high-resolution ibm: retention and transport success of sardine eggs,” Fisheries oceanography, vol. 29, pp. 137-151, 2020.
    [Bibtex] 
    @article {457,
title = {Investigating connectivity between two sardine stocks off South Africa using a high-resolution IBM: Retention and transport success of sardine eggs},
journal = {Fisheries Oceanography},
volume = {29},
year = {2020},
pages = {137-151},
abstract = {
    Abstract This study applied a previously used Lagrangian individual-based model (IBM) for sardine in the Southern Benguela to an improved and more robust hydrodynamic model to investigate whether a more representative spatial coverage, greater horizontal and vertical resolution, more realistic winds and improved representation of mesoscale features such as eddies and filaments would give different results for transport and retention of early life stages. Despite major differences between the old and new hydrodynamic models, overall the IBM results were quite similar to the previous southern Benguela sardine IBM study. This surprising result indicates that it is the macroscale circulation features resolved by the two hydrodynamic models that are controlling transport and retention of sardine early life stages. The contribution of transient mesoscale features such as eddies and filaments appears to be less important when transport patterns are averaged over the 21-year-long experiment. Another aim of this study was to better estimate the contribution of south coast spawning to west coast sardine recruitment. This was possible because of an eastward extension of the geographical domain of the new hydrodynamic model which provided a more realistic representation of the south coast spawning ground. Three main spawning and nursery area systems, similar to those identified in the previous sardine IBM, were identified: west coast and west coast (WC-WC), south coast and west coast (SC-WC), and south coast and south coast (SC-SC). Spawning area proved to be an important determinant of modelled retention and transport success, with spawning depth also playing an important role on the west coast. The main difference observed from the previous study was an increase in the average percentage of particles released on the south coast and transported to the west coast (P0, 17.4\%). This indicates more connectivity between the southern and western sardine stocks than previously thought and is therefore important for fishery management. Standardized anomalies from the modelled retention/transport were compared with recruitment estimates from stock assessment models but there was no correlation between the two sets of anomalies. However, a significant correlation was observed between the modelled retention/transport anomalies for the west coast and total cumulative upwelling anomalies for the Southern Benguela (r\ =\ \−0.67, p\ \<\ .001).
    
},
keywords = {fisheries management, Hydrodynamics, individual-based models, retention, sardine, Southern Benguela, Transport},
doi = {10.1111/fog.12460},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12460},
author = {McGrath, Alice M. and Hermes, Juliet C. and Moloney, Coleen L. and Roy, Claude and Cambon, Gildas and Herbette, Steven and Van Der Lingen, Carl D.}
}
  • [DOI] A. Zayen, S. Sayadi, C. Chevalier, M. Boukthir, S. B. Ismail, and M. Tedetti, “Microplastics in surface waters of the gulf of gabes, southern mediterranean sea: distribution, composition and influence of hydrodynamics,” Estuarine, coastal and shelf science, vol. 242, p. 106832, 2020.
    [Bibtex] 
    @article {483,
title = {Microplastics in surface waters of the Gulf of Gabes, southern Mediterranean Sea: Distribution, composition and influence of hydrodynamics},
journal = {Estuarine, Coastal and Shelf Science},
volume = {242},
year = {2020},
pages = {106832},
abstract = {
    The Mediterranean Sea has been described as one of the most affected areas by marine litter in the world. Although microplastics and their effects have been investigated in this area, most of the currently available studies have been limited to the northwestern part of the basin. This study constitutes a first attempt to determine the abundance, characteristics and composition of microplastics in near surface waters of the Gulf of Gabes (southern Mediterranean Sea, Tunisia). Samples were collected using a 200\ \μm-mesh size trawl net along two transects. The study revealed an average concentration of 63,739 items/km2 where fragments and films were the most frequent microplastics. Polyethylene, reformulated polyethylene and polypropylene were the most abundant plastics identified among the samples (86\–100\%). The influence of hydrodynamics on microplastics in the Gulf of Gabes was investigated through the use of a Lagrangian tracking model to simulate the dispersion of particles in water. Modelling results seem to be in agreement with the reported distribution and characteristics of microplastics in this area.
    
},
keywords = {Gulf of gabes, Hydrodynamics, Mediterranean Sea, Microplastics, Modelling},
issn = {0272-7714},
doi = {https://doi.org/10.1016/j.ecss.2020.106832},
url = {http://www.sciencedirect.com/science/article/pii/S0272771419310777},
author = {Amal Zayen and Sami Sayadi and Cristele Chevalier and Moncef Boukthir and Sana Ben Ismail and Marc Tedetti}
}
  • [DOI] M. Stelfox, C. Lett, G. Reid, G. Souch, and M. Sweet, “Minimum drift times infer trajectories of ghost nets found in the maldives,” Marine pollution bulletin, vol. 154, p. 111037, 2020.
    [Bibtex] 
    @article {471,
title = {Minimum drift times infer trajectories of ghost nets found in the Maldives},
journal = {Marine Pollution Bulletin},
volume = {154},
year = {2020},
pages = {111037},
abstract = {
    This study explores methods to estimate minimum drift times of ghost nets found in the Maldives with the aim of identifying a putative origin. We highlight that percentage cover of biofouling organisms and capitulum length of Lepas anatifera are two methods that provide these estimates. Eight ghost nets were collected in the Maldives and estimated drift times ranged between 7.5 and 101\ days. Additionally, Lagrangian simulations identified drift trajectories of 326 historical ghost nets records. Purse seine fisheries (associated with Korea, Mauritius, the Philippines, Spain, France and Seychelles) and gill nets from Sri Lanka were identified as \&$\#$39;high risk\&$\#$39; fisheries with regard to likley origins of ghost nets drifting into the Maldives. These fisheries are active in areas where dense particle clusters occured (drift trajectories between 30 and 120\ days). Interestingly, ghost nets drifting less than 30\ days however, remained inside the exclusive economic zone of the Maldivian archipelago highlighting potential illegal, unreported and unregulated fishing activity is occuring in this area. This study therefore points to the urgent need for gear loss reporting to be undertaken, especially by purse seine and gill net fisheries in order to ascertain the source of this major threat to marine life. This should also be coupled with an improvment in the data focused on spatial distribution of the abandoned, lost or discarded fishing gear originating from both large- and small-scale fisheries.
    
},
keywords = {Biofouling, Drift trajectories, Ghost nets, Gill nets, Lagrangian, Plastics, Plastisphere, Pollution, Purse seine},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2020.111037},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X20301557},
author = {Martin Stelfox and Christophe Lett and Geraldine Reid and Graham Souch and Michael Sweet}
}
  • [DOI] A. F. Dilmahamod, P. Penven, B. Aguiar-González, C. J. C. Reason, and J. C. Hermes, “A model investigation of the influences of the south-east madagascar current on the south-east madagascar bloom,” Journal of geophysical research: oceans, vol. 125, p. e2019JC015761, 2020.
    [Bibtex] 
    @article {485,
title = {A Model Investigation of the Influences of the South-East Madagascar Current on the South-East Madagascar Bloom},
journal = {Journal of Geophysical Research: Oceans},
volume = {125},
year = {2020},
pages = {e2019JC015761},
abstract = {
    The South-East Madagascar Bloom, one of the most compelling biogeochemical features of the Indian Ocean, occurs sporadically during austral summer in the oligotrophic waters south-east of Madagascar, where it can cover up to 1\% of the global ocean surface area. Its spatial extension and its timing are highly variable. A high-resolution biophysical model is used to investigate a previous hypothesis that the onset of a particular circulation of the South-East Madagascar Current advects fresher and nutrient-rich waters eastward, feeding the bloom. The model is able to reproduce an intermittent phytoplankton bloom with large spatial variability but in the subsurface layers, as well as the presence of an irregular retroflection of the South-East Madagascar Current. The simulated bloom occurs within a shallow stratified mixed layer, with fresher waters at the surface, parallel to the water mass in an observed bloom. The model results suggest, from a nutrient flux analysis, that horizontal advection of low-salinity nutrient-rich Madagascan coastal waters can indeed trigger a phytoplankton bloom. The coupled model is also able to resolve a bloom that is atmospherically forced by cyclonic activity.
    
},
keywords = {Biogeochemical Modeling, Phytoplankton Bloom, South-East Madagascar Bloom, South-East Madagascar Current, South-West Indian Ocean},
issn = {2169-9291},
doi = {10.1029/2019JC015761},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JC015761},
author = {Dilmahamod, A. F. and Penven, P. and Aguiar-Gonz{\'a}lez, B. and Reason, C. J. C. and Hermes, J. C.}
}
  • [DOI] N. F. Putman, E. E. Seney, P. Verley, D. J. Shaver, M. C. López-Castro, M. Cook, V. Guzmán, B. Brost, S. A. Ceriani, R. J. G. D. de Mirón, L. J. Peña, M. Tzeek, R. A. Valverde, C. C. G. Cantón, L. Howell, J. A. Ravell Ley, M. C. Tumlin, W. G. Teas, C. W. Caillouet Jr, E. Cuevas, B. J. Gallaway, P. M. Richards, and K. L. Mansfield, “Predicted distributions and abundances of the sea turtle “lost years” in the western north atlantic ocean,” Ecography, vol. 43, pp. 506-517, 2020.
    [Bibtex] 
    @article {500,
title = {Predicted distributions and abundances of the sea turtle "lost years" in the western North Atlantic Ocean},
journal = {Ecography},
volume = {43},
year = {2020},
pages = {506-517},
abstract = {
    Oceanic dispersal characterizes the early juvenile life-stages of numerous marine species of conservation concern. This early stage may be a {\textquoteleft}critical period{\textquoteright} for many species, playing an overriding role in population dynamics. Often, relatively little information is available on their distribution during this period, limiting the effectiveness of efforts to understand environmental and anthropogenic impacts on these species. Here we present a simple model to predict annual variation in the distribution and abundance of oceanic-stage juvenile sea turtles based on species{\textquoteright} reproductive output, movement and mortality. We simulated dispersal of 25 cohorts (1993{\textendash}2017) of oceanic-stage juveniles by tracking the movements of virtual hatchling sea turtles released in a hindcast ocean circulation model. We then used estimates of annual hatchling production from Kemp{\textquoteright}s ridley Lepidochelys kempii (n = 3), green Chelonia mydas (n = 8) and loggerhead Caretta caretta (n = 5) nesting areas in the northwestern Atlantic (inclusive of the Gulf of Mexico, Caribbean Sea and eastern seaboard of the U.S.) and their stage-specific mortality rates to weight dispersal predictions. The model{\textquoteright}s predictions indicate spatial heterogeneity in turtle distribution across their marine range, identify locations of increasing turtle abundance (notably along the U.S. coast), and provide valuable context for temporal variation in the stranding of young sea turtles across the Gulf of Mexico. Further effort to collect demographic, distribution and behavioral data that refine, complement and extend the utility of this modeling approach for sea turtles and other dispersive marine taxa is warranted. Finally, generating these spatially-explicit predictions of turtle abundance required extensive international collaboration among scientists; our findings indicate that continued conservation of these sea turtle populations and the management of the numerous anthropogenic activities that operate in the northwestern Atlantic Ocean will require similar international coordination.
    
},
keywords = {green turtle, Kemp{\textquoteright}s ridley turtle, loggerhead turtle, movement ecology, ontogenetic shift, stranding},
doi = {10.1111/ecog.04929},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.04929},
author = {Putman, Nathan F. and Seney, Erin E. and Verley, Phlippe and Shaver, Donna J. and L{\'o}pez-Castro, Melania C. and Cook, Melissa and Guzm{\'a}n, Vicente and Brost, Beth and Ceriani, Simona A. and Mir{\'o}n, Ra{\'u}l de Jes{\'u}s Gonz{\'a}lez D\'iaz and Pe{\~n}a, Luis Jaime and Tzeek, Miriam and Valverde, Rold{\'a}n A. and Cant{\'o}n, Crist{\'o}bal C{\'a}ceres G. and Howell, Lyndsey and Ravell Ley, Jonathan A. and Tumlin, Mandy C. and Teas, Wendy G. and Caillouet Jr, Charles W. and Cuevas, Eduardo and Gallaway, Benny J. and Richards, Paul M. and Mansfield, Katherine L.}
}
  • [DOI] B. Daly, C. Parada, T. Loher, S. Hinckley, A. J. Hermann, and D. Armstrong, “Red king crab larval advection in bristol bay: implications for recruitment variability,” Fisheries oceanography, vol. 29, pp. 505-525, 2020.
    [Bibtex] 
    @article {503,
title = {Red king crab larval advection in Bristol Bay: Implications for recruitment variability},
journal = {Fisheries Oceanography},
volume = {29},
year = {2020},
pages = {505-525},
abstract = {
    Abstract Recruitment variability is poorly understood for Bering Sea crab stocks. The nearshore area in southwest Bristol Bay (Alaska, USA) is hypothesized as having historically (i.e., prior to\  \ 1980) been the most important spawning ground for Bristol Bay red king crab (Paralithodes camtschaticus) because post-larvae are thought to have been most likely to reach optimal settlement habitat along the Alaska Peninsula when hatched from this area as part of an endless-belt reproductive strategy. We coupled a biophysical and oceanographic circulation model to test this hypothesis, investigate larval connectivity of more recent female spatial distributions, and evaluate the importance of climate variability on larval advection trajectories. Predicted settlement success varied through changes in larval pelagic duration and oceanographic circulation patterns: Shorter advective distance was associated with warmer conditions, causing higher rates of local retention relative to cold conditions. Contrary to earlier models, most larvae hatched in southwest Bristol Bay were advected offshore away from good habitat, whereas larvae hatched in central and nearshore Bristol Bay were retained in or advected to good habitat along the Alaska Peninsula. Our results suggest contemporary spatial distributions can supply settlement-competent larvae to nurseries along the Alaska Peninsula and that under certain conditions, larvae may reach the Pribilof Islands when hatched from southwest Bristol Bay. Our study informs the role of environmental variability on larval transport and provides context within which to structure future investigations of recruitment mechanisms.
    
},
keywords = {Bristol Bay, Connectivity, larval advection, Paralithodes camtschaticus, Recruitment, red king crab, retention},
doi = {10.1111/fog.12492},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12492},
author = {Daly, Benjamin and Parada, Carolina and Loher, Timothy and Hinckley, Sarah and Hermann, Albert J. and Armstrong, David}
}
  • [DOI] G. Marchessaux, V. Faure, C. Chevalier, and D. Thibault, “Refugia area for the ctenophore mnemiopsis leidyi a. agassiz 1865 in the berre lagoon (southeast france): the key to its persistence,” Regional studies in marine science, vol. 39, p. 101409, 2020.
    [Bibtex] 
    @article {496,
title = {Refugia area for the ctenophore Mnemiopsis leidyi A. Agassiz 1865 in the Berre Lagoon (southeast France): The key to its persistence},
journal = {Regional Studies in Marine Science},
volume = {39},
year = {2020},
pages = {101409},
abstract = {
    The invasive ctenophore,\ Mnemiopsis leidyi\ has been proliferating in lagoons and coastal areas around Europe for almost 20 years but the role and the impact of its presence in sink ecosystems is still not completely understood. In France, Mnemiopsis leidyi is present in Mediterranean lagoons and estuaries along La Manche Sea. Mnemiopsis was first recorded in the Berre Lagoon in early 2000. This lagoon has been highly perturbated for years, with a large volume of freshwater inflow through natural rivers and a succession of large hydroelectric power plants, inducing important eutrophication. Legislation has been implemented to improve the health status of the lagoon since 1994. A long-term study was undertaken in 2010 to measure Mnemiopsis population dynamics, and to identify the main drivers of its persistence in this highly anthropogenic lagoon. In 2011 and 2012, during extreme winter conditions, populations of this ctenophore were not observed for months. Its re-appearance later in year could be linked to either a new introduction from the Mediterranean Sea or the existence of retention areas where individuals sought refugia. Following measurement of biochemical conditions (i.e. chlorophyll a), plankton biomass and Mnemiopsis populations structure (eggs, cydippid larvae/transitional phase and adult) in different areas of the lagoon, as well as the lagrangian modelling of {\textquotedblleft}particles{\textquotedblright} distribution (i.e. Ichthyop), we highlighted the seasonal patterns in the population structure, the level of available carbon always above the minimal for the survival of Mnemiopsis (24 μgC L-1) and the potential refugia area role the Vaine sub-basin could play. Populations from the Vaine sub-basin probably serve as source populations for the rest of the lagoon by advective transport in spring.
    
},
keywords = {Invasive species, Lagrangian transport, Long-term monitoring, Mediterranean lagoon},
issn = {2352-4855},
doi = {https://doi.org/10.1016/j.rsma.2020.101409},
url = {http://www.sciencedirect.com/science/article/pii/S2352485520305375},
author = {Guillaume Marchessaux and Vincent Faure and Cristele Chevalier and Delphine Thibault}
}
  • [DOI] R. F. T. Pires, Á. Peliz, M. Pan, and A. dos Santos, “”there and back again” – how decapod megalopae find the way home: a modelling exercise for pachygrapsus marmoratus,” Progress in oceanography, vol. 184, p. 102331, 2020.
    [Bibtex] 
    @article {476,
title = {"There and back again" - How decapod megalopae find the way home: A modelling exercise for Pachygrapsus marmoratus},
journal = {Progress in Oceanography},
volume = {184},
year = {2020},
pages = {102331},
abstract = {
    Pachygrapsus marmoratus is a common coastal crab occurring in rocky shores of the northeastern Atlantic. The species presents a planktonic larval phase, constituting an interesting subject for dispersal studies, given the larval release in intertidal areas, followed by the exportation to shelf waters where larval development takes place. Onshore migration to the adult habitats is thought to be performed by the megalopa stage. Observations obtained during a summer zooplankton survey showed P. marmoratus larvae gradually farther from the coast throughout larval development, with early larval stages found in surface layers and megalopae occurring closer to the coast. The vertical migration mechanisms for larval dispersal and the return to settlement habitats were tested through physical-ecological models where the vertical distributions changed through the larval development. Ecological data, such as the ontogenetic vertical distribution of each larval stage, larval duration, and time and sites of spawning, were integrated in an oceanic model. Simulations tested different vertical distributions and periods, covering the entire larval development from intertidal areas to shelf and back to shore. The distribution of the early stages in surface layers promoted cross- and alongshore transport. Differences in the initial advection determined the positions where the more advanced stages were found later in the development. The subsurface distribution of advanced stages facilitated the transport to the inner shelf, limiting the cross-shore upwelling transport and promoting higher return to the adult habitats. Different periods of larval release resulted in contrasting dispersal patterns that could influence larval survival and recruitment to adult populations.
    
},
keywords = {Decapoda, Grapsidae, Ichthyop, larval dispersal, ROMS, Western Iberian Margin},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2020.102331},
url = {http://www.sciencedirect.com/science/article/pii/S0079661120300707},
author = {Rita F.T. Pires and {\'A}lvaro Peliz and Maria Pan and Antonina dos Santos}
}

2019

  • [DOI] N. Schmidt, V. Fauvelle, A. Ody, J. Castro-Jiménez, J. Jouanno, T. Changeux, T. Thibaut, and R. Sempéré, “The amazon river: a major source of organic plastic additives to the tropical north atlantic?,” Environmental science & technology, vol. 53, p. 7513{–}7521, 2019.
    [Bibtex] 
    @article {429,
title = {The Amazon River: A major source of organic plastic additives to the Tropical North Atlantic?},
journal = {Environmental Science \& Technology},
volume = {53},
year = {2019},
pages = {7513{\textendash}7521},
abstract = {
    The release of emerging organic contaminants is identified among the most critical hazards to the marine environment, and plastic additives have received growing attention due to their worldwide distribution and potential deleterious effects. Here, we report dissolved surface water concentrations of two important families of plastic additives (organophosphate esters (OPEs) and bisphenols) and other related organic compounds (perfluorinated chemicals) measured in the North Atlantic from Cape Verde to the West Indies. We found that OPEs were the most abundant contaminants, reaching remarkably high concentrations in open ocean waters (1200 km offshore of the American Coast, at the location of the Amazon river plume during the sampling period), with up to 1.3 \μg L\–1 (\Σ9OPEs). A Lagrangian analysis confirmed that these high concentrations of contaminants originated from the Amazon River plume and were transported more than 3000 km by the North Brazil Current and its retroflection. We thus consider the Amazon River as a major source of organic contaminants of emerging concern to the tropical North Atlantic Ocean and suggest that medium-/long-range contaminant transport occurs, most certainly facilitated by the highly stratified conditions offered by the river plume.
    
},
issn = {0013-936X},
doi = {10.1021/acs.est.9b01585},
url = {https://doi.org/10.1021/acs.est.9b01585},
author = {Schmidt, Natascha and Fauvelle, Vincent and Ody, Anouck and Castro-Jim{\'e}nez, Javier and Jouanno, Julien and Changeux, Thomas and Thibaut, Thierry and Semp{\'e}r{\'e}, Richard}
}
  • [DOI] E. C. Atwood, F. M. Falcieri, S. Piehl, M. Bochow, M. Matthies, J. Franke, S. Carniel, M. Sclavo, C. Laforsch, and F. Siegert, “Coastal accumulation of microplastic particles emitted from the po river, northern italy: comparing remote sensing and hydrodynamic modelling with in situ sample collections,” Marine pollution bulletin, vol. 138, pp. 561-574, 2019.
    [Bibtex] 
    @article {401,
title = {Coastal accumulation of microplastic particles emitted from the Po River, Northern Italy: Comparing remote sensing and hydrodynamic modelling with in situ sample collections},
journal = {Marine Pollution Bulletin},
volume = {138},
year = {2019},
pages = {561 - 574},
abstract = {
    Microplastic research has mainly concentrated on open seas, while riverine plumes remain largely unexplored despite their hypothesized importance as a microplastic source to coastal waters. This work aimed to model coastal accumulation of microplastic particles (1\–5 mm) emitted by the Po River over 1.5 years. We posit that river-induced microplastic accumulation on adjacent coasts can be predicted using (1) hydrodynamic-based and (2) remote sensing-based modelling. Model accumulation maps were validated against sampling at nine beaches, with sediment microplastic concentrations up to 78 particles/kg (dry weight). Hydrodynamic modelling revealed that discharged particle amount is only semi-coupled to beaching rates, which are strongly mouth dependent and occur within the first ten days. Remote sensing modelling was found to better capture river mouth relative strength, and accumulation patterns were found consistent with hydrodynamic modelling. This methodology lays groundwork for developing an operational monitoring system to assess microplastic pollution emitted by a major river.
    
},
keywords = {Beach sediment, FT-IR, Landsat-8, River plume, ROMS, Sentinel-2},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2018.11.045},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X18308300},
author = {Elizabeth C. Atwood and Francesco M. Falcieri and Sarah Piehl and Mathias Bochow and Michael Matthies and Jonas Franke and Sandro Carniel and Mauro Sclavo and Christian Laforsch and Florian Siegert}
}
  • [DOI] M. F. A. Ismail and J. Ribbe, “On the cross-shelf exchange driven by frontal eddies along a western boundary current during austral winter 2007,” Estuarine, coastal and shelf science, vol. 227, p. 106314, 2019.
    [Bibtex] 
    @article {438,
title = {On the cross-shelf exchange driven by frontal eddies along a western boundary current during austral winter 2007},
journal = {Estuarine, Coastal and Shelf Science},
volume = {227},
year = {2019},
pages = {106314},
abstract = {
    Western boundary currents are characterised by high mesoscale eddy activity including that of cyclonic frontal eddies (CFEs). These form frequently adjacent to the shelf-break, export coastal water and affect biological productivity. Here, we study the physical properties of eddies identified within the intensification zone of the East Australian Current (EAC) through the analysis of remotely sensed data, the application of an ocean circulation model and the evaluation of Lagrangian simulations during austral winter 2007. We examine the spatial and temporal evolution of identified eddies, investigate their formation mechanism, and quantify the contribution made to cross-shelf exchanges. The mesoscale eddies are tracked from generation to decay using an eddy detection and tracking method. In this case study, we identify two CFEs referred to as C1 and C2 with lifetimes of 11 and 38 days and radii of 45 and 70 km, respectively, and one anticyclonic eddy (ACE) with a lifetime of 62 days and a radius of 60 km. Both CFEs interact with the ACE leading to quasi-stationary dipole-eddies located in the vicinity of the shelf. This is the first time dipole-eddies are reported for the intensification zone of the EAC. The location of CFEs characterised by negative sea surface height anomaly (SSHA) and clockwise rotation coincides with remotely-sensed sea surface temperature (SST) and chlorophyll-a (Chl-a) anomalies. CFEs C1 and C2 appear to contribute in different ways to the cross-shelf transport along the shelf-break. CFE C1 drives a stronger onshore transport, while CFE C2 appears to enhance the offshore transport. The estimated export of shelf water associated with CFE C2 is estimated with about 1.23 Sv (\ 106 km3 day\−1). It renews the regional shelf water in about 7 days. The lifetime of CFE C2 is about 38 days, thus the eddy had the potential to flush the shelf at least five times. The CFEs intensify the cross-shelf exchange that is due to the wind-driven cyclonic circulation of the Fraser Gyre. This seasonally occurring gyre dominates the local shelf during austral autumn and winter. The results from this study demonstrate the importance of CFEs in exporting cooler and Chl-a enriched shelf water into the warmer and oligotrophic waters of the southward-flowing EAC.
    
},
keywords = {Cross-shelf transport, Cyclonic frontal eddies, Dipole-eddies, East australian current, Sea surface height anomaly},
issn = {0272-7714},
doi = {https://doi.org/10.1016/j.ecss.2019.106314},
url = {http://www.sciencedirect.com/science/article/pii/S0272771419300307},
author = {Mochamad Furqon Azis Ismail and Joachim Ribbe}
}
  • [DOI] C. L. Lopes, L. Bastos, M. Caetano, I. Martins, M. M. Santos, and I. Iglesias, “Development of physical modelling tools in support of risk scenarios: a new framework focused on deep-sea mining,” Science of the total environment, vol. 650, pp. 2294-2306, 2019.
    [Bibtex] 
    @article {380,
title = {Development of physical modelling tools in support of risk scenarios: A new framework focused on deep-sea mining},
journal = {Science of The Total Environment},
volume = {650},
year = {2019},
pages = {2294 - 2306},
abstract = {
    Deep-sea mining has gained international interest to provide materials for the worldwide industry. European oceans and, particularly, the Portuguese Exclusive Economic Zone present a recognized number of areas with polymetallic sulphides rich in metals used in high technology developments. A large part of these resources are in the vicinity of sensitive ecosystems, where the mineral extraction can potentially damage deep-ocean life services. In this context, technological research must be intensified, towards the implementation of environmental friendly solutions that mitigate the associated impacts. To reproduce deep-sea dynamics and evaluate the effects of the mining activities, reliable numerical modelling tools should be developed. The present work highlights the usefulness of a new framework for risk and impact assessment based on oceanographic numerical models to support the adoption of good management practices for deep-sea sustainable exploitation. This tool integrates the oceanic circulation model ROMS-Agrif with the semi-Lagrangian model ICHTHYOP, allowing the representation of deep-sea dynamics and particles trajectories considering the sediments physical properties. Numerical simulations for the North Mid-Atlantic Ridge region, revealed the ability of ROMS-Agrif to simulate real deep-sea dynamics through validation with in situ data. Results showed a strong diversity in the particle residence time, with a dependency on their density and size but also on local ocean conditions and bottom topography. The highest distances are obtained for the smaller and less dense particles, although they tend to be confined by bathymetric constrains and deposited in deepest regions. This work highlights the potential of this modelling tool to forecast laden plume trajectories, allowing the definition of risk assessment scenarios for deep-sea mining activities and the implementation of sustainable exploitation plans. Furthermore, the coupling of this numerical solution with models of biota inhabiting deep-sea vent fields into ecosystem models is discussed and outlined as cost-effective tools for the management of these remote ecosystems.
    
},
keywords = {Adaptive management, Biological communities, Deep-sea technologies, Hazard assessment, Numerical modelling, Precautionary principles},
issn = {0048-9697},
doi = {https://doi.org/10.1016/j.scitotenv.2018.09.351},
url = {http://www.sciencedirect.com/science/article/pii/S004896971833852X},
author = {Carina L. Lopes and Lu\'isa Bastos and Miguel Caetano and Irene Martins and Miguel M. Santos and Isabel Iglesias}
}
  • [DOI] M. Gamoyo, D. Obura, and C. J. C. Reason, “Estimating connectivity through larval dispersal in the western indian ocean,” Journal of geophysical research: biogeosciences, vol. 124, pp. 2446-2459, 2019.
    [Bibtex] 
    @article {439,
title = {Estimating Connectivity Through Larval Dispersal in the Western Indian Ocean},
journal = {Journal of Geophysical Research: Biogeosciences},
volume = {124},
year = {2019},
pages = {2446-2459},
abstract = {
    Abstract The health and functioning of coral reef ecosystems in the Western Indian Ocean are in decline due to anthropogenic stress, and the rate of decline is set to accelerate. Marine reserves have become important tools in mitigating these pressures, and one of the most critical factors in determining their spatial design is the degree of connectivity among populations. However, the spatial scale and strength at which populations are potentially connected by dispersal remain uncertain. In this paper, the potential connectivity of corals was assessed through a Lagrangian particle-tracking algorithm coupled offline with an ocean circulation numerical model. Connectivity metrics and graph theory were used to analyze the networks and highlight those reefs that are critical for maintaining the connectivity of corals across the region. Western Indian Ocean coral reefs formed about 13 clusters for larvae with short pelagic larval duration (PLD; 5 days) but grouped into stable larger clusters at 15, 30, and 60 days PLDs, with strong westward dispersal from the northern tip of Madagascar and Comoro Islands toward the East African coast. Reefs at Mafia-Latham Island (Tanzania), Angoche-Nacala and Pemba-Mucufi (Mozambique), Anjouan and Ngazidja (Comoros), and Glorieuses (France) were the most significant for multigenerational connectivity, as measured by betweenness centrality. The small islands Agalega and Tromelin were completely disconnected from other sites at all PLDs. These findings identify priority conservation areas and actions to help support coral reef resilience through a connected network of marine protected areas.
    
},
keywords = {Biophysical model, Connectivity, coral reef larvae, Dispersal, graph theory analysis},
doi = {10.1029/2019JG005128},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JG005128},
author = {Gamoyo, Majambo and Obura, David and Reason, Chris J. C.}
}
  • [DOI] J. Porobic, E. A. Fulton, C. Parada, S. Frusher, B. Ernst, and P. Manríquez, “The impact of fishing on a highly vulnerable ecosystem, the case of juan fernández ridge ecosystem,” Plos one, vol. 14, p. e0212485, 2019.
    [Bibtex] 
    @article {405,
title = {The impact of fishing on a highly vulnerable ecosystem, the case of Juan Fern{\'a}ndez Ridge ecosystem},
journal = {PLOS ONE},
volume = {14},
year = {2019},
pages = {e0212485},
abstract = {
    The Juan Fern\ández Ridge (JFRE) is a vulnerable marine ecosystem (VME) located off the coast of central Chile formed by the Juan Fern\ández Archipelago and a group of seamounts. This ecosystem has unique biological and oceanographic features, characterized by: small geographical units, high degree of endemism with a high degree of connectivity within the system. Two fleets have historically operated in this system: a long term coastal artisanal fishery associated with the Islands, focused mainly on lobster, and a mainland based industrial demersal finfish fishery operating on the seamounts which is currently considered overexploited. The management of these fisheries has been based on a classical single-species approach to determine output controls (industrial fleet) and a mixed management system with formal and informal components (artisanal fleet). There has been growing interest in increasing the exploitation of fisheries, and modernization of the fishing fleet already operating in the JFRE. Under this scenario of increased levels of fishing exploitation and the high level of interrelation of species it might be necessary to understand the impact of these fisheries from a holistic perspective based on a ecosystem-based modeling approach. To address these challenges we developed an Atlantis end-to-end model was configured for this ecosystem. The implemented model has a high degree of skill in representing the observed trends and fluctuations of the JFRE. The model shows that the industrial fishing has a localized impact and the artisanal fisheries have a relatively low impact on the ecosystem, mainly via the lobster fishery. The model indicates that the depletion of large sized lobster has leads to an increase in the population of sea urchins. Although this increase is not sufficient, as yet, to cause substantial flow-on effects to other groups, caution is advised in case extra pressure leads the ecosystem towards a regime shift.
    
},
keywords = {Biomass, Crustaceans, Ecosystems, Fisheries science, Lobsters, Marine ecosystems, marine fish, Seamounts},
issn = {1932-6203},
doi = {10.1371/journal.pone.0212485},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212485},
author = {Porobic, Javier and Fulton, Elizabeth A. and Parada, Carolina and Frusher, Stewart and Ernst, Billy and Manr\'iquez, Pablo}
}
  • [DOI] M. Blanco, A. Ospina-Álvarez, S. A. Navarrete, and M. Fernández, “Influence of larval traits on dispersal and connectivity patterns of two exploited marine invertebrates in central chile,” Marine ecology progress series, vol. 612, p. 43{–}64, 2019.
    [Bibtex] 
    @article {406,
title = {Influence of larval traits on dispersal and connectivity patterns of two exploited marine invertebrates in central Chile},
journal = {Marine Ecology Progress Series},
volume = {612},
year = {2019},
pages = {43{\textendash}64},
abstract = {
    Environmental variability can influence larval development rates and affect critical processes in the dynamics of natural populations, such as dispersal distances and connectivity, when modulated by different larval traits. Knowledge of connectivity patterns in marine populations is fundamental for defining population viability and progressing with management and conservation goals. Here, we developed a biophysical, individual-based larval dispersal model to assess the effect of oceanographic variability and biological traits (i.e. larval diel vertical migration [DVM] and temperature-dependent larval development [PLD]) on recruitment success, dispersal distance, and alongshore connectivity patterns. We selected 2 species exploited by Chilean artisanal fisheries: Loxechinus albus (PLD: 20 d) and Fissurella latimarginata (PLD: 5 d). A sensitivity analysis was used to examine the effect of intrinsic (DVM and PLD) and extrinsic (release depth, latitude, and timing) processes. Release location and timing of release explained respectively 24.30 and 5.54\% (F. latimarginata) and 34.8 and 4.19\% (L. albus) of the variability observed in recruitment success, and 23.80 and 6.94\% (F. latimarginata) and 26.10 and 19.60\% (L. albus) of the variability observed in dispersal distance. Most recruitment to local populations was allochthonous, presenting low levels of self-recruitment and local retention, including species with short PLD. Similar geographic patterns of source and destination strengths were observed in both species, showing a geographic mosaic of source and sink populations with relatively higher importance towards the northern region of the study area. Our findings allow us to identify primary determinants of recruitment success and dispersal distance for 2 important exploited species in Chile.
    
},
keywords = {Individual-based model, Larval behavior, Larval migration, Management, Numerical model, Source-sink dynamics},
issn = {0171-8630, 1616-1599},
doi = {10.3354/meps12870},
url = {https://www.int-res.com/abstracts/meps/v612/p43-64/},
author = {Blanco, Marta and Ospina-{\'A}lvarez, Andr{\'e}s and Navarrete, Sergio A. and Fern{\'a}ndez, Miriam}
}
  • [DOI] M. Clavel-Henry, J. Solé, M. -Á. Ahumada-Sempoal, N. Bahamon, F. Briton, G. Rotllant, and J. B. Company, “Influence of the summer deep-sea circulations on passive drifts among the submarine canyons in the northwestern mediterranean sea,” Ocean science, vol. 15, p. 1745{–}1759, 2019.
    [Bibtex] 
    @article {447,
title = {Influence of the summer deep-sea circulations on passive drifts among the submarine canyons in the northwestern Mediterranean Sea},
journal = {Ocean Science},
volume = {15},
year = {2019},
pages = {1745{\textendash}1759},
doi = {10.5194/os-15-1745-2019},
url = {https://www.ocean-sci.net/15/1745/2019/},
author = {Clavel-Henry, M. and Sol{\'e}, J. and Ahumada-Sempoal, M.-{\'A}. and Bahamon, N. and Briton, F. and Rotllant, G. and Company, J. B.}
}
  • [DOI] J. Flores-Valiente, J. Tam, T. Brochier, F. Colas, L. Pecquerie, A. Aguirre-Velarde, J. Mendo, and C. Lett, “Larval supply of peruvian scallop to the marine reserve of lobos de tierra island: a modeling approach,” Journal of sea research, vol. 144, pp. 142-155, 2019.
    [Bibtex] 
    @article {399,
title = {Larval supply of Peruvian scallop to the marine reserve of Lobos de Tierra Island: A modeling approach},
journal = {Journal of Sea Research},
volume = {144},
year = {2019},
month = {FEB},
pages = {142-155},
type = {Article},
abstract = {
    The Peruvian scallop (Argopecten purpuratus) is the second main contributor to the total catch of mollusks in Peru, after jumbo squid. There are two main scallop banks populations in northern Peru: Lobos de Tierra Island (LTI) and Sechura Bay (SB). Despite a continuous, intense relocation of seeds from LTI, the natural bank population still persists there. To understand this, we studied larval connectivity between LTI and SB using the first invertebrate larval transport biophysical model developed in the region. Larval local retention were 2.4\% and 1.57\% on average at LTI and SB respectively, while larval transport from SB to LTI was 0.02\% on average and 0.07\% in the opposite direction. Both larval retention and larval transport increased with spawning depth and were highest in austral summer. Two main larval transport paths from SB to LTI were identified, resulting from a combination of horizontal mesoscale circulation patterns and vertical flows. Potential management implications for these natural banks are discussed.
    
},
keywords = {Biophysical model, Humboldt current system, larval transport, Marine connectivity, Marine reserve, Peruvian scallop},
issn = {1385-1101},
doi = {10.1016/j.seares.2018.12.003},
author = {Flores-Valiente, Jorge and Tam, Jorge and Brochier, Timoth{\'e}e and Colas, Francois and Pecquerie, Laure and Aguirre-Velarde, Arturo and Mendo, Jaime and Lett, Christophe}
}
  • [DOI] C. A. K. Endo, D. F. M. Gherardi, L. P. Pezzi, and L. N. Lima, “Low connectivity compromises the conservation of reef fishes by marine protected areas in the tropical south atlantic,” Scientific reports, vol. 9, p. 8634, 2019.
    [Bibtex] 
    @article {422,
title = {Low connectivity compromises the conservation of reef fishes by marine protected areas in the tropical South Atlantic},
journal = {Scientific Reports},
volume = {9},
year = {2019},
pages = {8634},
abstract = {
    The total spatial coverage of Marine Protected Areas (MPAs) within the Brazilian Economic Exclusive Zone (EEZ) has recently achieved the quantitative requirement of the Aichii Biodiversity Target 11. However, the distribution of MPAs in the Brazilian EEZ is still unbalanced regarding the proportion of protected ecosystems, protection goals and management types. Moreover, the demographic connectivity between these MPAs and their effectiveness regarding the maintenance of biodiversity are still not comprehensively understood. An individual-based modeling scheme coupled with a regional hydrodynamic model of the ocean is used to determine the demographic connectivity of reef fishes based on the widespread genus Sparisoma found in the oceanic islands and on the Brazilian continental shelf between 10\° N and 23\° S. Model results indicate that MPAs are highly isolated due to extremely low demographic connectivity. Consequently, low connectivity and the long distances separating MPAs contribute to their isolation. Therefore, the current MPA design falls short of its goal of maintaining the demographic connectivity of Sparisoma populations living within these areas. In an extreme scenario in which the MPAs rely solely on protected populations for recruits, it is unlikely that they will be able to effectively contribute to the resilience of these populations or other reef fish species sharing the same dispersal abilities. Results also show that recruitment occurs elsewhere along the continental shelf indicating that the protection of areas larger than the current MPAs would enhance the network, maintain connectivity and contribute to the conservation of reef fishes.
    
},
issn = {2045-2322},
doi = {10.1038/s41598-019-45042-0},
url = {https://www.nature.com/articles/s41598-019-45042-0},
author = {Endo, Clarissa Akemi Kajiya and Gherardi, Douglas Francisco Marcolino and Pezzi, Luciano Ponzi and Lima, Leonardo Nascimento}
}
  • [DOI] C. Lett, N. Barrier, Y. Ourmières, C. Petit, M. Labonne, J. Bourjea, and A. M. Darnaude, “Modeling larval dispersal for the gilthead seabream in the northwestern mediterranean sea,” Marine environmental research, vol. 152, p. 104781, 2019.
    [Bibtex] 
    @article {444,
title = {Modeling larval dispersal for the gilthead seabream in the northwestern Mediterranean Sea},
journal = {Marine Environmental Research},
volume = {152},
year = {2019},
pages = {104781},
abstract = {
    To investigate dispersal and connectivity between spawning and lagoon nursery habitats of the gilthead seabream, Sparus aurata, in the Gulf of Lions (northwestern Mediterranean Sea), we modeled the potential transport of the species\’ larvae between its supposed main spawning site in the region (the Planier Island) and two of its main local nursery areas (the coastal lagoons of Thau and Salses-Leucate). Passive larval drift simulations using a dispersal biophysical model showed a large variability in the possible trajectories from spawning to nursery areas and in the predicted ages for larvae arrival on the two nursery sites. The most common ages at arrival obtained in the simulations (20\–60 days) are broadly consistent with previous modeling studies but contrast with the actual ages of the S. aurata post-larvae collected in 2016 and 2017 at time of the lagoon entrances (60\–90 days, from otolith readings). The period between 25 and 70 days being critical for gilthead seabream larvae to acquire sufficient swimming, osmoregulatory, and olfactory abilities to enter coastal lagoons, we argue that ontogenic development plays a crucial role in the transport and local retention of S. aurata larvae in the studied region, explaining the discrepancy between simulation results and observed data.
    
},
keywords = {Biophysical model, Connectivity, Fish, Gulf of Lions, larvae, Models-hydrodynamic, Otolith},
issn = {0141-1136},
doi = {https://doi.org/10.1016/j.marenvres.2019.104781},
url = {http://www.sciencedirect.com/science/article/pii/S014111361930340X},
author = {Christophe Lett and Nicolas Barrier and Yann Ourmi{\`e}res and C{\'e}cile Petit and Maylis Labonne and J{\'e}r{\^o}me Bourjea and Audrey M. Darnaude}
}
  • [DOI] C. Collins and J. C. Hermes, “Modelling the accumulation and transport of floating marine micro-plastics around south africa,” Marine pollution bulletin, vol. 139, pp. 46-58, 2019.
    [Bibtex] 
    @article {394,
title = {Modelling the accumulation and transport of floating marine micro-plastics around South Africa},
journal = {Marine Pollution Bulletin},
volume = {139},
year = {2019},
pages = {46 - 58},
abstract = {
    Plastic pollution of South Africa\&$\#$39;s marine environment is widespread, yet limited research exists on the distribution, accumulation and transport of plastic debris around South Africa. In this paper, numerical modelling is used to provide a first approximation of the pathways and accumulation of marine micro-plastics around South Africa. To account for a range of plastic classes, particles with two different densities are considered. Low-density (LD) particles represent low- and high-density polyethylene while high-density (HD) particles are representative of Polyethylene terephthalate and Polyvinyl chloride. While the majority of micro-plastic particles that enter the ocean from the five major coastal urban-industrialised centers beach along the coastline of South Africa, a third is exported to the open ocean. LD and HD particles are primarily exported to the South Atlantic and South Indian Ocean, respectively. Particles that beach along South Africa\&$\#$39;s coastline tend to accumulate in close proximity to the coastal urban-industrialised centers.
    
},
keywords = {Accumulation, Micro-plastic, South Africa, Transport},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2018.12.028},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X18308798},
author = {C. Collins and J.C. Hermes}
}
  • [DOI] I. Segura-García, L. Garavelli, M. Tringali, T. Matthews, L. M. Chérubin, J. Hunt, and S. J. Box, “Reconstruction of larval origins based on genetic relatedness and biophysical modeling,” Scientific reports, vol. 9, p. 7100, 2019.
    [Bibtex] 
    @article {417,
title = {Reconstruction of larval origins based on genetic relatedness and biophysical modeling},
journal = {Scientific Reports},
volume = {9},
year = {2019},
pages = {7100},
abstract = {
    The assessment of the mechanisms and patterns of larval connectivity between geographically separated populations leads to a better understanding of benthic marine population dynamics, especially in commercially valuable species. This study investigated for the first time the fine-scale temporal genetic variability of new settlers and their origins in a benthic marine organism with one of the longest pelagic larval phases, the Caribbean spiny lobster (Panulirus argus). We genotyped newly settled postlarvae in the Florida Keys and adults of spiny lobster from the Florida Keys and throughout the Caribbean Sea. We identified strong larval connectivity between Dominican Republic, Belize, Nicaragua, the Florida Keys, and West-Florida. The larval dispersal modeling suggests that Florida\’s lobster population could receive recruits from within and from other areas outside its state and national maritime boundaries. The genetic analyses refine the oceanographic model indicating that the connectivity patterns described could also result from unknown parental populations sourcing adults and postlarvae in different spawning seasons to the Florida Keys. We discuss the importance of small temporal scales to identify patterns in larval export. Our findings are significant on two levels. From the larval dispersal perspective, genetic results and biophysical modeling identify patterns of gene flow enhancing persistence of local populations. From an economic and fishery perspective, P. argus is the most important commercial species in the Caribbean and our results inform how considering larval source and sink dynamics across international boundaries could improve management plans at local, national, and regional levels.
    
},
issn = {2045-2322},
doi = {10.1038/s41598-019-43435-9},
url = {https://www.nature.com/articles/s41598-019-43435-9},
author = {Segura-Garc\'ia, I. and Garavelli, L. and Tringali, M. and Matthews, T. and Ch{\'e}rubin, L. M. and Hunt, J. and Box, S. J.}
}
  • [DOI] I. Žužul, T. Šegvić-Bubić, I. Talijančić, T. Džoić, I. L. Pleić, G. B. Paklar, S. Ivatek-Šahdan, I. Katavić, and L. Grubišić, “Spatial connectivity pattern of expanding gilthead seabream populations and its interactions with aquaculture sites: a combined population genetic and physical modelling approach,” Scientific reports, vol. 9, p. 1{–}14, 2019.
    [Bibtex] 
    @article {440,
title = {Spatial connectivity pattern of expanding gilthead seabream populations and its interactions with aquaculture sites: a combined population genetic and physical modelling approach},
journal = {Scientific Reports},
volume = {9},
year = {2019},
pages = {1{\textendash}14},
abstract = {
    In gilthead seabream the number of domesticated individuals increased annually, and escape events occur regularly in the Adriatic Sea. Still there is a lack of population genetic characteristics and evidence of the extent and geographic scale of interbreeding resulting from fish-farm escapees. We screened 1586 individuals using a panel of 21 neutral microsatellite loci in several consecutive years and here report on the medium-scale detection of hybrid and farmed seabream in the natural environment. Wild adults showed a lack of genetic structure within basin and sampling years and reduced connectivity with wild offspring collection, suggesting their temporal residency within the Adriatic. On the contrary, by linking the results of multiannual genetic analyses with the results of coupled hydrodynamic and individual based models (IBM-Ichthyop), we observed a strong connection of wild seabream associated with tuna-aquaculture sites and offspring from the nursery grounds, indicating that the surroundings of tuna sea-cage farms can function as a spawning grounds. The study results present the genetic baseline of wild and farmed strains from the eastern Adriatic Sea, as a first step toward development of a mitigation strategy for fish escapees aimed at controlling further erosion of genetic integrity.
    
},
issn = {2045-2322},
doi = {10.1038/s41598-019-51256-z},
url = {https://www.nature.com/articles/s41598-019-51256-z},
author = {{\v Z}u{\v z}ul, Iva and {\v S}egvi{\'c}-Bubi{\'c}, Tanja and Talijan{\v c}i{\'c}, Igor and D{\v z}oi{\'c}, Tomislav and Plei{\'c}, Ivana Lepen and Paklar, Gordana Beg and Ivatek-{\v S}ahdan, Stjepan and Katavi{\'c}, Ivan and Grubi{\v s}i{\'c}, Leon}
}
  • [DOI] M. H. Schleyer, N. J. Downey-Breedt, and Y. Benayahu, “Species composition of alcyonacea (octocorallia) on coral reefs at europa island and associated connectivity across the mozambique channel,” Marine biodiversity, 2019.
    [Bibtex] 
    @article {427,
title = {Species composition of Alcyonacea (Octocorallia) on coral reefs at Europa Island and associated connectivity across the Mozambique Channel},
journal = {Marine Biodiversity},
year = {2019},
month = {Jul},
abstract = {
    The soft coral fauna (Octocorallia: Alcyonacea) on reefs around Europa Island (Western Indian Ocean) were surveyed in 2016. The species richness was rather low for a protected, relatively pristine environment in the region. While certain {\textquoteleft}fugitive\&$\#$39; alcyonacean species were noticeably abundant, other soft corals were rare or absent. Since Europa Island is remote and isolated, connectivity was thus investigated with other alcyonacean communities in the Mozambique Channel by particle transport modelling. This revealed that, while the north-west coast of Madagascar appears well-connected with the northern Mozambique coast, the most likely source of soft coral recruits at Europa Island would be the Tulear region further south in Madagascar.
    
},
issn = {1867-1624},
doi = {10.1007/s12526-019-00975-7},
url = {https://doi.org/10.1007/s12526-019-00975-7},
author = {Schleyer, M. H. and Downey-Breedt, N. J. and Benayahu, Y.}
}
  • [DOI] D. Macias, A. Cózar, E. Garcia-Gorriz, D. González-Fernández, and A. Stips, “Surface water circulation develops seasonally changing patterns of floating litter accumulation in the mediterranean sea. a modelling approach,” Marine pollution bulletin, vol. 149, p. 110619, 2019.
    [Bibtex] 
    @article {442,
title = {Surface water circulation develops seasonally changing patterns of floating litter accumulation in the Mediterranean Sea. A modelling approach},
journal = {Marine Pollution Bulletin},
volume = {149},
year = {2019},
pages = {110619},
abstract = {
    Marine litter and, particularly, plastics are a growing concern at global scale. The Mediterranean Sea is among the zones in the world with the highest concentration of floating plastic debris. However, our knowledge remains limited on the spatial distribution of litter across this basin. Here, a set of different numerical model simulations were conducted to examine the dynamic conditions of the surface layer of the Mediterranean and how this drives the circulation and accumulation of floating litter. Seasonal dynamics of surface water circulation led to contrasting distribution patterns of floating litter along the year. Multiple hot spots of litter zones appeared across the basin in summer, while litter disperses and moves towards the Eastern Mediterranean and nearshore waters in winter. Taking into account such seasonal variability in the spatial patterns of litter in the Mediterranean seems to be key in the design of further sampling surveys and management strategies.
    
},
keywords = {Floating litter, Mediterranean Sea, Numerical modelling, Surface circulation},
issn = {0025-326X},
doi = {https://doi.org/10.1016/j.marpolbul.2019.110619},
url = {http://www.sciencedirect.com/science/article/pii/S0025326X19307672},
author = {D. Macias and A. C{\'o}zar and E. Garcia-Gorriz and D. Gonz{\'a}lez-Fern{\'a}ndez and A. Stips}
}
  • [DOI] R. McGeady, C. Lordan, and A. M. Power, “Twilight migrators: factors determining larval vertical distribution in nephrops norvegicus with implications for larval retention,” Marine ecology progress series, vol. 631, p. 141{–}155, 2019.
    [Bibtex] 
    @article {446,
title = {Twilight migrators: factors determining larval vertical distribution in Nephrops norvegicus with implications for larval retention},
journal = {Marine Ecology Progress Series},
volume = {631},
year = {2019},
pages = {141{\textendash}155},
abstract = {
    The vertical distribution of pelagic marine larvae can greatly influence their dispersal due to depth-varying currents, which can determine larval retention or transport away from critical habitat. Vertical distribution of commercially important lobster Nephrops norvegicus larvae was examined over fishing grounds off the west and east coasts of Ireland. Larval vertical distribution for both grounds was significantly influenced by the temperature differential between the surface and 60 m depth, zooplankton biomass and, to a lesser extent, stratification, measured using the potential energy anomaly. Fixed station sampling was conducted over 3 d in the western Irish Sea (WIS) to investigate the occurrence and extent of a diel vertical migration (DVM). Larvae performed twilight DVM with an ~10 m ascent prior to sunset and sunrise and a descent at midnight and after sunrise. Particle-tracking model simulations were used to examine the effect of DVM behaviour on larval retention over mud habitat. The presence of a DVM actually reduced the likelihood of retention on both the Aran and WIS grounds. Predicted larval retention was unusually low over the Aran grounds in 2018, which is potentially significant in the context of historic stock fluctuations in this area. These findings suggest that understanding larval dynamics could be crucial in managing N. norvegicus stocks on fishing grounds, in particular those with variable interannual oceanography and a low rate of larval donation from other grounds.
    
},
keywords = {Diel vertical migration, larvae, larval retention, Nephrops norvegicus, Particle tracking, Vertical distribution},
issn = {0171-8630, 1616-1599},
doi = {10.3354/meps13142},
url = {https://www.int-res.com/abstracts/meps/v631/p141-155/},
author = {McGeady, Ryan and Lordan, Colm and Power, Anne Marie}
}

2018

  • [DOI] E. Meerhoff, B. Yannicelli, B. Dewitte, E. Díaz-Cabrera, C. Vega-Retter, M. Ramos, L. Bravo, E. Concha, F. Hernández-Vaca, and D. Véliz, “Asymmetric connectivity of the lobster panulirus pascuensis in remote islands of the southern pacific: importance for its management and conservation,” Bulletin of marine science, vol. 94, iss. 3, pp. 753-774, 2018.
    [Bibtex] 
    @article {Meerhoff:2018:0007-4977:753,
title = {Asymmetric connectivity of the lobster Panulirus pascuensis in remote islands of the southern Pacific: importance for its management and conservation},
journal = {Bulletin of Marine Science},
year = {2018},
volume = {94},
number = {3},
pages = {753-774},
issn = {0007-4977},
url = {https://www.ingentaconnect.com/content/umrsmas/bullmar/2018/00000094/00000003/art00016},
doi = {doi:10.5343/bms.2017.1114},
author = {Meerhoff, Erika and Yannicelli, Beatriz and Dewitte, Boris and Díaz-Cabrera, Ernesto and Vega-Retter, Caren and Ramos, Marcel and Bravo, Luis and Concha, Emilio and Hernández-Vaca, Freddy and Véliz, David},
}
  • [DOI] S. Crickenberger and D. S. Wethey, “Annual temperature variation as a time machine to understand the effects of long-term climate change on a poleward range shift,” Global change biology, vol. 24, pp. 3804-3819, 2018.
    [Bibtex] 
    @article {366,
title = {Annual temperature variation as a time machine to understand the effects of long-term climate change on a poleward range shift},
journal = {Global Change Biology},
volume = {24},
year = {2018},
month = {08/2018},
pages = {3804-3819},
abstract = {
    Abstract Range shifts due to annual variation in temperature are more tractable than range shifts linked to decadal to century long temperature changes due to climate change, providing natural experiments to determine the mechanisms responsible for driving long-term distributional shifts. In this study we couple physiologically grounded mechanistic models with biogeographic surveys in 2 years with high levels of annual temperature variation to disentangle the drivers of a historical range shift driven by climate change. The distribution of the barnacle Semibalanus balanoides has shifted 350 km poleward in the past half century along the east coast of the United States. Recruits were present throughout the historical range following the 2015 reproductive season, when temperatures were similar to those in the past century, and absent following the 2016 reproductive season when temperatures were warmer than they have been since 1870, the earliest date for temperature records. Our dispersal dependent mechanistic models of reproductive success were highly accurate and predicted patterns of reproduction success documented in field surveys throughout the historical range in 2015 and 2016. Our mechanistic models of reproductive success not only predicted recruitment dynamics near the range edge but also predicted interior range fragmentation in a number of years between 1870 and 2016. All recruits monitored within the historical range following the 2015 colonization died before 2016 suggesting juvenile survival was likely the primary driver of the historical range retraction. However, if 2016 is indicative of future temperatures mechanisms of range limitation will shift and reproductive failure will lead to further range retraction in the future. Mechanistic models are necessary for accurately predicting the effects of climate change on ranges of species.
    
},
keywords = {climate change, climate variability, competency window, Dispersal, interior range fragmentation, range shift, Semibalanus balanoides},
doi = {10.1111/gcb.14300},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14300},
author = {Crickenberger, Sam and Wethey, David S.}
}
  • [DOI] L. Garavelli, M. S. Studivan, J. D. Voss, A. Kuba, J. Figueiredo, and L. M. Chérubin, “Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest gulf of mexico: larval dynamics,” Frontiers in marine science, vol. 5, p. 174, 2018.
    [Bibtex] 
    @article {357,
title = {Assessment of Mesophotic Coral Ecosystem Connectivity for Proposed Expansion of a Marine Sanctuary in the Northwest Gulf of Mexico: Larval Dynamics},
journal = {Frontiers in Marine Science},
volume = {5},
year = {2018},
pages = {174},
abstract = {
    In coral reef ecosystems, mesophotic coral habitat (\>30m to the end of the photic zone) are extensions of shallow reefs and contribute to the persistence of coral reef populations. In the North West Gulf of Mexico (NW GOM), the Flower Garden Banks National Marine Sanctuary (FGBNMS) is an isolated reef ecosystem comprising contiguous shallow and mesophotic reefs habitats on two central banks along the margin of the continental shelf. A future expansion of the sanctuary is proposed to include additional mesophotic banks and aims at building a network of protected areas in the NW GOM to ensure the persistence of the coral reef populations inhabiting the sanctuary. To evaluate the feasibility of this expansion and investigate the overall dynamics of coral species in the region, we studied the patterns of larval connectivity of Montastraea cavernosa, a common depth generalist coral species, using a larval dispersal modelling approach. Our results highlighted larval exports from the NW GOM banks to the northeastern and southwestern GOM larval connectivity between all banks investigated in this study, and the potential for exporting larvae from mesophotic to shallower reefs. Our study associated with Studivan and Voss (2018; associate manuscript) demonstrates the relevance of combining modeling and genetic methods to consider both demographic and genetic timescales for the evaluation of the connectivity dynamics of marine populations. In the case of the NW GOM, both studies support the future management plan for expanding FGBNMS.
    
},
issn = {2296-7745},
doi = {10.3389/fmars.2018.00174},
url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00174},
author = {Garavelli, Lysel and Studivan, Michael S. and Voss, Joshua D. and Kuba, Alyson and Figueiredo, Joana and Ch{\'e}rubin, Laurent M.}
}
  • [DOI] R. A. Magris, M. Andrello, R. L. Pressey, D. Mouillot, A. Dalongeville, M. N. Jacobi, and S. Manel, “Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning,” Conservation letters, vol. 11, p. e12439, 2018.
    [Bibtex] 
    @article {376,
title = {Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning},
journal = {Conservation Letters},
volume = {11},
year = {2018},
pages = {e12439},
abstract = {
    Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing persistence of small-ranged species, which are most in need of conservation, while the representation objective benefited only wide-ranging species. Our approach provides a more comprehensive appraisal of planning applications than approaches focusing on either representation or connectivity, and will hopefully contribute to build more effective reserve networks for the persistence of biodiversity.
    
},
keywords = {biodiversity conservation, larval dispersal, marine protected areas, marine reserve design, spatial planning, spatial prioritization},
issn = {1755-263X},
doi = {10.1111/conl.12439},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/conl.12439},
author = {Magris, Rafael A. and Andrello, Marco and Pressey, Robert L. and Mouillot, David and Dalongeville, Alicia and Jacobi, Martin N. and Manel, St{\'e}phanie}
}
  • [DOI] T. Brochier, P. Auger, L. Pecquerie, E. Machu, X. Capet, M. Thiaw, B. C. Mbaye, C. Braham, O. Ettahiri, N. Charouki, O. N. Sène, F. Werner, and P. Brehmer, “Complex small pelagic fish population patterns arising from individual behavioral responses to their environment,” Progress in oceanography, vol. 164, pp. 12-27, 2018.
    [Bibtex] 
    @article {435,
title = {Complex small pelagic fish population patterns arising from individual behavioral responses to their environment},
journal = {Progress in Oceanography},
volume = {164},
year = {2018},
pages = {12 - 27},
abstract = {
    Small pelagic fish (SPF) species are heavily exploited in eastern boundary upwelling systems (EBUS) as their transformation products are increasingly used in the world\’s food chain. Management relies on regular monitoring, but there is a lack of robust theories for the emergence of the populations\’ traits and their evolution in highly variable environments. This work aims to address existing knowledge gaps by combining physical and biogeochemical modelling with an individual life-cycle based model applied to round sardinella (Sardinella aurita) off northwest Africa, a key species for regional food security. Our approach focused on the processes responsible for seasonal migrations, spatio-temporal size-structure, and interannual biomass fluctuations. Emergence of preferred habitat resulted from interactions between natal homing behavior and environmental variability that impacts early life stages. Exploration of the environment by the fishes was determined by swimming capabilities, mesoscale to regional habitat structure, and horizontal currents. Fish spatio-temporal abundance variability emerged from a complex combination of distinct life-history traits. An alongshore gradient in fish size distributions is reported and validated by in situ measurements. New insights into population structure are provided, within an area where the species is abundant year-round (Mauritania) and with latitudinal migrations of variable (300\–1200 km) amplitude. Interannual biomass fluctuations were linked to modulations of fish recruitment over the Sahara Bank driven by variability in alongshore current intensity. The identified processes constitute an analytical framework that can be implemented in other EBUS and used to explore impacts of regional climate change on SPF.
    
},
keywords = {Dynamic energy budget, Eastern boundary upwelling system, Fish migration, Individual based biophysical models, small pelagic fish},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2018.03.011},
url = {http://www.sciencedirect.com/science/article/pii/S0079661117303737},
author = {Timoth{\'e}e Brochier and Pierre-Ama{\"e}l Auger and Laure Pecquerie and Eric Machu and Xavier Capet and Modou Thiaw and Baye Cheikh Mbaye and Cheikh-Baye Braham and Omar Ettahiri and Najib Charouki and Ousseynou Ndaw S{\`e}ne and Francisco Werner and Patrice Brehmer}
}
  • [DOI] R. L. Rognstad, D. S. Wethey, H. Oliver, and T. J. Hilbish, “Connectivity modeling and graph theory analysis predict recolonization in transient populations,” Journal of marine systems, vol. 183, pp. 13-22, 2018.
    [Bibtex] 
    @article {347,
title = {Connectivity modeling and graph theory analysis predict recolonization in transient populations},
journal = {Journal of Marine Systems},
volume = {183},
year = {2018},
pages = {13 - 22},
abstract = {
    Population connectivity plays a major role in the ecology and evolution of marine organisms. In these systems, connectivity of many species occurs primarily during a larval stage, when larvae are frequently too small and numerous to track directly. To indirectly estimate larval dispersal, ocean circulation models have emerged as a popular technique. Here we use regional ocean circulation models to estimate dispersal of the intertidal barnacle Semibalanus balanoides at its local distribution limit in Southwest England. We incorporate historical and recent repatriation events to provide support for our modeled dispersal estimates, which predict a recolonization rate similar to that observed in two recolonization events. Using graph theory techniques to describe the dispersal landscape, we identify likely physical barriers to dispersal in the region. Our results demonstrate the use of recolonization data to support dispersal models and how these models can be used to describe population connectivity.
    
},
keywords = {Barnacle, Connectivity, Dispersal, larvae, Marine environment, Recolonization, Recruitment},
issn = {0924-7963},
doi = {https://doi.org/10.1016/j.jmarsys.2018.03.002},
url = {http://www.sciencedirect.com/science/article/pii/S0924796317304372},
author = {Rhiannon L. Rognstad and David S. Wethey and Hilde Oliver and Thomas J. Hilbish}
}
  • [DOI] B. S. Santos, D. M. Kaplan, M. A. M. Friedrichs, S. G. Barco, K. L. Mansfield, and J. P. Manning, “Consequences of drift and carcass decomposition for estimating sea turtle mortality hotspots,” Ecological indicators, vol. 84, pp. 319-336, 2018.
    [Bibtex] 
    @article {323,
title = {Consequences of drift and carcass decomposition for estimating sea turtle mortality hotspots},
journal = {Ecological Indicators},
volume = {84},
year = {2018},
pages = {319 - 336},
abstract = {
    Abstract Sea turtle strandings provide important mortality information, yet knowledge of turtle carcass at-sea drift and decomposition characteristics are needed to better understand and manage where these mortalities occur. We used empirical sea turtle carcass decomposition and drift experiments in the Chesapeake Bay, Virginia, \{USA\} to estimate probable carcass oceanic drift times and quantify the impact of direct wind forcing on carcass drift. Based on the time period during which free-floating turtle carcasses tethered nearshore were buoyant, we determined that oceanic drift duration of turtle carcasses was highly dependent on water temperature and varied from 2 to 15 days during typical late spring to early fall Bay water conditions. The importance of direct wind forcing for turtle carcass drift was assessed based on track divergence rates from multiple simultaneous deployments of three types of surface drifters: bucket drifters, artificial turtles and turtle carcass drifters. Turtle drift along-wind leeway was found to vary from 1 to 4\% of wind speed, representing an added drift velocity of approximately 0.030.2 m/s), suggesting wind is important for carcass drift. Estimated carcass drift parameters were integrated into a Chesapeake Bay oceanographic drift model to predict carcass drift to terrestrial stranding locations. Increased drift duration (e.g., due to low temperatures) increases mean distance between expected mortality events and stranding locations, as well as decreases overall likelihood of retention in the Bay. Probable mortality hotspots for the peak month of strandings (June) were identified off coastal southeastern Virginia and within the lower Bay, including the Bay mouth and lower James River. Overall, results support that sea turtle drift time is quite variable, and varies greatly depending on water and air temperature as well as oceanic conditions. Knowledge of these parameters will improve our ability to interpret stranding events around the globe.
    
},
keywords = {Conservation},
issn = {1470-160X},
doi = {https://doi.org/10.1016/j.ecolind.2017.08.064},
url = {http://www.sciencedirect.com/science/article/pii/S1470160X17305563},
author = {Bianca S. Santos and David M. Kaplan and Marjorie A.M. Friedrichs and Susan G. Barco and Katherine L. Mansfield and James P. Manning}
}
  • [DOI] B. D. Lequeux, M. Ahumada-Sempoal, A. López-Pérez, and C. Reyes-Hernández, “Coral connectivity between equatorial eastern pacific marine protected areas: a biophysical modeling approach,” Plos one, vol. 13, p. e0202995, 2018.
    [Bibtex] 
    @article {371,
title = {Coral connectivity between equatorial eastern Pacific marine protected areas: A biophysical modeling approach},
journal = {PLOS ONE},
volume = {13},
year = {2018},
pages = {e0202995},
abstract = {
    There are many marine protected areas (MPAs) containing coral reef aggregations in the eastern Pacific region. However, the connectivity of corals between MPAs is still poorly known, especially in the Marine Conservation Corridor of the Eastern Tropical Pacific (MCCETP). Here, we assess the potential connectivity of corals across equatorial eastern Pacific MPAs through a Lagrangian particle-tracking algorithm coupled offline with an ocean-circulation numerical model. Connectivity metrics and graph theory were used to analyze the networks and highlight those MPAs that are critical for maintaining the connectivity of corals across the region. Our results show that the equatorial eastern Pacific MPAs form a relatively well-connected network, at least 40\% of coral larvae released per year end up within the boundaries of an MPA. MPAs like Malpelo and Gorgona islands included in the MCCETP were found to be critical for connectivity of corals because of their high betweenness centrality and potential role as stepping-stones between coastal MPAs and offshore MPAs such as the Galapagos Islands. Two pelagic larval duration (PLD) scenarios (40 and 130 days) indicate a quasi-unidirectional larval flow from coastal MPAs toward oceanic MPAs, where the only resilient MPAs (Coiba and Malpelo islands) depend mostly on subsidiary recruitment from MPAs located along the coast of Costa Rica, Panama and Colombia. In the two PLD scenarios, Cocos Island maintains a very low resilience potential. Our results indicate the imperative need to include coastal MPAs in the MCCETP network initiative, since connectivity and resilience of coral reefs in the equatorial eastern Pacific region rely heavily on coastal MPAs.
    
},
keywords = {Centrality, Cocos, Coral reefs, Costa Rica, Islands, larvae, Marine conservation, Panama},
issn = {1932-6203},
doi = {10.1371/journal.pone.0202995},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202995},
author = {Lequeux, Bertrand D. and Ahumada-Sempoal, Miguel-Angel and L{\'o}pez-P{\'e}rez, Andr{\'e}s and Reyes-Hern{\'a}ndez, Crist{\'o}bal}
}
  • [DOI] C. Medel, C. Parada, C. E. Morales, O. Pizarro, B. Ernst, and C. Conejero, “How biophysical interactions associated with sub- and mesoscale structures and migration behavior affect planktonic larvae of the spiny lobster in the juan fernández ridge: a modeling approach,” Progress in oceanography, vol. 162, pp. 98-119, 2018.
    [Bibtex] 
    @article {346,
title = {How biophysical interactions associated with sub- and mesoscale structures and migration behavior affect planktonic larvae of the spiny lobster in the Juan Fern{\'a}ndez Ridge: A modeling approach},
journal = {Progress in Oceanography},
volume = {162},
year = {2018},
pages = {98 - 119},
abstract = {
    The Juan Fern\ández Ridge (JFR) is a chain of topographical elevations in the eastern South Pacific (\∼33\–35\°S, 76\–81.5\°W). Rich in endemic marine species, this ridge is frequently affected by the arrival of mesoscale eddies originating in the coastal upwelling zone off central-southern Chile. The impacts of these interactions on the structure and dynamics of the JFR pelagic system have, however, not been addressed yet. The present model-based study is focused on the coupled influence of mesoscale-submesoscale processes and biological behavior (i.e., diel vertical migration) on the horizontal distribution of planktonic larvae of the spiny lobster (Jasus frontalis) around the JFR waters. Two case studies were selected from a hydrodynamic Regional Ocean Modeling System to characterize mesoscale and submesoscale structures and an Individual-based model (IBM) to simulate diel vertical migration (DVM) and its impact on the horizontal distribution and the patchiness level. DVM behavior of these larvae has not been clearly characterized, therefore, three types of vertical mechanisms were assessed on the IBM: (1) no migration (LG), (2) a short migration (0\–50 m depth, DVM1), and (3) a long migration (10\–200 m depth, DVM2). The influence of physical properties (eddy kinetic energy, stretching deformation and divergence) on larval aggregation within meso and submesoscale features was quantified. The patchiness index assessed for mesoscale and submesoscale structures showed higher values in the mesoscale than in the submesoscale. However, submesoscale structures revealed a higher accumulation of particles by unit of area. Both vertical migration mechanisms produced larger patchiness indices compared to the no migration experiment. DVM2 was the one that showed by far the largest aggregation of almost all the aggregation zones. Larval concentrations were highest in the submesoscale structures; these zones were characterized by low eddy kinetic energy, negative stretching deformation, and slight convergence. Stretching deformation flow appeared to be triggered by the eddy-eddy interactions and the Robinson Island barrier effect, and it likely promotes the aggregation of the spiny lobster larvae in the Juan Fern\ández system. These results highlighted the importance of the coupled effect of physical (mesoscale and submesoscale oceanographic features) and biological processes (DVM) in the generation of larval patchiness and concentration of spiny lobster larvae around the JFR, which could be key for their survival and retention in those waters.
    
},
keywords = {Diel vertical migration, Juan Fernandez Ridge, Mesoscale and submesoscale features, Patchiness, Regional Ocean Modeling System and Individual-based models, Spiny lobster larval dispersion},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2018.02.017},
url = {http://www.sciencedirect.com/science/article/pii/S0079661116302373},
author = {Carolina Medel and Carolina Parada and Carmen E. Morales and Oscar Pizarro and Billy Ernst and Carlos Conejero}
}
  • C. C. Tchamabi, M. Araujo, M. Silva, B. Bourlès, and P. Travassos, “Ichthyoplankton transport around the brazilian fernando de noronha archipelago and rocas atoll: are there any connectivity patterns?,” Indian journal of geo marine sciences, vol. 47, p. 812{–}818, 2018.
    [Bibtex] 
    @article {349,
title = {Ichthyoplankton transport around the Brazilian Fernando de Noronha archipelago and Rocas Atoll: Are there any connectivity patterns?},
journal = {Indian Journal of Geo Marine Sciences},
volume = {47},
year = {2018},
pages = {812{\textendash}818},
abstract = {
    To investigate the influence of environmental conditions on ichthyoplankton transport in the FN and AR system, the outputs of a hydrodynamic simulation have been used as inputs to force an Individual-Based Model (IBM) around islands. The results show larval retention over the entire year. This retention is highly correlated with the intensity of the zonal current. Lagrangian analysis reveals connectivity between FN and AR, represented here by larval transport success, which would be important for the conservation of the species in these tropical Brazilian islands.
    
},
issn = {0975-1033 (Online); 0379-5136 (Print)},
url = {http://nopr.niscair.res.in/handle/123456789/44247},
author = {Tchamabi, Christine C. and Araujo, Moacyr and Silva, Marcus and Bourl{\`e}s, Bernard and Travassos, Paulo}
}
  • [DOI] A. Ospina-Alvarez, N. Weidberg, C. M. Aiken, and S. A. Navarrete, “Larval transport in the upwelling ecosystem of central chile: the effects of vertical migration, developmental time and coastal topography on recruitment,” Progress in oceanography, 2018.
    [Bibtex] 
    @article {374,
title = {Larval transport in the upwelling ecosystem of central Chile: The effects of vertical migration, developmental time and coastal topography on recruitment},
journal = {Progress in Oceanography},
year = {2018},
abstract = {
    Several empirical plankton studies and realistic numerical models of the coastal ocean have clearly shown the dramatic effects that larval behaviour and coastal topography can have on effective alongshore dispersal, population connectivity, successful recruitment and cross-shore distribution of the larval stages of benthic coastal invertebrates and fish. All these are essentially distinct and ecologically important aspects of the dispersal process, but which are correlated to a greater or lesser extent through the interaction of larval attributes (e.g. behaviour, pelagic larval duration, PLD) and specific velocity fields of a region of the ocean. Vertical positioning in the water column and ontogenetic and diel vertical migration (DVM) have been identified as the most efficient behavioural mechanisms that can modulate larval transport in the ocean, especially in stratified, baroclinic water columns such as those typically found in upwelling ecosystems. The large seasonal variability in circulation within most upwelling ecosystems is therefore expected to deeply influence all aspects of the larval dispersal process, but it has been less researched. Here we use a realistic representation of velocity fields across a section of the Humboldt Current Upwelling Ecosystem (HCUE) to evaluate the relative effects of variation in PLD, geographic position, DVM and the timing of larval release on successful onshore recruitment, alongshore dispersal distances, cross-shore retention and persistence of recruitment spatial patterns. Our results show that an increase in pelagic larval duration exponentially increase larval waste, consequently reducing onshore recruitment, regardless of whether larvae perform DVM or not during their development. For any given larval duration, season of the year and location along the shore (topography) had the largest effects on recruitment variability, explaining over 8.49\% and over 11.47\% of the temporal and spatial variation, respectively. In contrast, while DVM had a highly consistent positive effect on recruitment along the shore, PLD\’s and seasons, it only explained about 3\% of recruitment variability. Thus, while performing DVM appears to be a safe strategy to increase recruitment, selective forces for such behaviour maybe weak when only oceanic transport is considered. Neither season of the year, nor larval behaviour altered the broad spatial pattern of recruitment across the study region. Pelagic larval durations of over 20 days did not significantly alter this spatial pattern either, suggesting the existence of persistent sources and sinks for benthic populations across the region, although the connectivity matrices must be examined in more detail. Interestingly, in the section of the HCUE, the DVM behaviour led to significantly higher mean dispersal distances along the shore during the upwelling season, as compared to passively advected particles. Such a behavioural effect on dispersal distances have all but disappeared when larvae were released in winter time. These results demonstrate that onshore recruitment, dispersal and connectivity among populations are not correlated across the different larval behaviours, as it has often been implied in the literature and that timing of peak larval release must receive more attention within the HCUE. Results also illustrate the importance of examining fundamental questions of the dispersal process, distance, recruitment, retention, connectivity, in different regions of the world\’s costal ocean.
    
},
keywords = {Biophysical model, DVM, Hydrodynamic model, IBM, larval dispersal, larval transport, upwelling system, zooplankton},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2018.09.016},
url = {http://www.sciencedirect.com/science/article/pii/S0079661117300800},
author = {Andr{\'e}s Ospina-Alvarez and Nicolas Weidberg and Christopher M. Aiken and Sergio A. Navarrete}
}
  • [DOI] B. S. Santos, M. A. M. Friedrichs, S. A. Rose, S. G. Barco, and D. M. Kaplan, “Likely locations of sea turtle stranding mortality using experimentally-calibrated, time and space-specific drift models,” Biological conservation, vol. 226, pp. 127-143, 2018.
    [Bibtex] 
    @article {365,
title = {Likely locations of sea turtle stranding mortality using experimentally-calibrated, time and space-specific drift models},
journal = {Biological Conservation},
volume = {226},
year = {2018},
pages = {127 - 143},
abstract = {
    Sea turtle stranding events provide an opportunity to study drivers of mortality, but causes of strandings are poorly understood. A general sea turtle carcass oceanographic drift model was developed to estimate likely mortality locations from coastal sea turtle stranding records. Key model advancements include realistic direct wind forcing on carcasses, temperature driven carcass decomposition and the development of mortality location predictions for individual strandings. We applied this model to 2009\–2014 stranding events within the Chesapeake Bay, Virginia. Predicted origin of vessel strike strandings were compared to commercial vessel data, and potential hazardous turtle-vessel interactions were identified in the southeastern Bay and James River. Commercial fishing activity of gear types with known sea turtle interactions were compared to predicted mortality locations for stranded turtles with suggested fisheries-induced mortality. Probable mortality locations for these strandings varied seasonally, with two distinct areas in the southwest and southeast portions of the lower Bay. Spatial overlap was noted between potential mortality locations and gillnet, seine, pot, and pound net fisheries, providing important information for focusing future research on mitigating conflict between sea turtles and human activities. Our ability to quantitatively assess spatial and temporal overlap between sea turtle mortality and human uses of the habitat were hindered by the low resolution of human use datasets, especially those for recreational vessel and commercial fishing gear distributions. This study highlights the importance of addressing these data gaps and provides a meaningful conservation tool that can be applied to stranding data of sea turtles and other marine megafauna worldwide.
    
},
keywords = {Chesapeake Bay, Drift simulations, Endangered species, Fisheries and vessel interactions, Marine conservation, Protected species management, Sea turtle mortality, Sea turtle strandings},
issn = {0006-3207},
doi = {https://doi.org/10.1016/j.biocon.2018.06.029},
url = {http://www.sciencedirect.com/science/article/pii/S0006320718302441},
author = {Bianca S. Santos and Marjorie A.M. Friedrichs and Sarah A. Rose and Susan G. Barco and David M. Kaplan}
}
  • [DOI] F. Bernardi Aubry, F. M. Falcieri, J. Chiggiato, A. Boldrin, G. M. Luna, S. Finotto, E. Camatti, F. Acri, M. Sclavo, S. Carniel, and L. Bongiorni, “Massive shelf dense water flow influences plankton community structure and particle transport over long distance,” Scientific reports, vol. 8, p. 4554, 2018.
    [Bibtex] 
    @article {344,
title = {Massive shelf dense water flow influences plankton community structure and particle transport over long distance},
journal = {Scientific Reports},
volume = {8},
year = {2018},
pages = {4554},
abstract = {
    Dense waters (DW) formation in shelf areas and their cascading off the shelf break play a major role in ventilating deep waters, thus potentially affecting ecosystem functioning and biogeochemical cycles. However, whether DW flow across shelves may affect the composition and structure of plankton communities down to the seafloor and the particles transport over long distances has not been fully investigated. Following the 2012 north Adriatic Sea cold outbreak, DW masses were intercepted at ca. 460\ km south the area of origin and compared to resident ones in term of plankton biomass partitioning (pico to micro size) and phytoplankton species composition. Results indicated a relatively higher contribution of heterotrophs in DW than in deep resident water masses, probably as result of DW-mediated advection of fresh organic matter available to consumers. DWs showed unusual high abundances of Skeletonema sp., a diatom that bloomed in the north Adriatic during DW formation. The Lagrangian numerical model set up on this diatom confirmed that DW flow could be an important mechanism for plankton/particles export to deep waters. We conclude that the predicted climate-induced variability in DW formation events could have the potential to affect the ecosystem functioning of the deeper part of the Mediterranean basin, even at significant distance from generation sites.
    
},
issn = {2045-2322},
doi = {10.1038/s41598-018-22569-2},
url = {https://www.nature.com/articles/s41598-018-22569-2},
author = {Bernardi Aubry, Fabrizio and Falcieri, Francesco Marcello and Chiggiato, Jacopo and Boldrin, Alfredo and Luna, Gian Marco and Finotto, Stefania and Camatti, Elisa and Acri, Francesco and Sclavo, Mauro and Carniel, Sandro and Bongiorni, Lucia}
}
  • [DOI] L. Garavelli, W. J. White, I. Chollett, and L. M. Chérubin, “Population models reveal unexpected patterns of local persistence despite widespread larval dispersal in a highly exploited species,” Conservation letters, vol. 11, 2018.
    [Bibtex] 
    @article {379,
title = {Population models reveal unexpected patterns of local persistence despite widespread larval dispersal in a highly exploited species},
journal = {Conservation Letters},
volume = {11},
year = {2018},
abstract = {
    Nearshore marine populations are structured in metapopulations that are connected through larval dispersal across national boundaries. One of the main challenges for effective management of these metapopulations is the need for partnerships between nations that share the same resource. By coupling large-scale connectivity information to a dynamic population model, we analyzed the patterns of connectivity and population persistence for the Caribbean spiny lobster (Panulirus argus) metapopulation both within and across national boundaries. Although spiny lobster subpopulations are highly connected at the basin scale, several nations located in the northern Caribbean and ecoregional networks could persist independently of the larger basin-wide metapopulation. Based on these results, we propose transnational neighborhoods for spiny lobster management. Our analysis suggests that the dynamics and management of those subpopulations neighborhoods are not intrinsically dependent on \“upstream\” connectivity even though current rates of upstream larval supply are very high.
    
},
issn = {1755-263X},
doi = {10.1111/conl.12567},
url = {https://doi.org/10.1111/conl.12567},
author = {Garavelli, Lysel and White, J. Wilson and Chollett, Iliana and Ch{\'e}rubin, Laurent Marcel}
}
  • [DOI] S. T. M., Y. P. H., B. B. R., T. Martin, H. G. C., S. van Erik, P. N. F., M. P. I., S. C. D. H., and S. Brody, “Rare long-distance dispersal of a marine angiosperm across the pacific ocean,” Global ecology and biogeography, vol. 27, p. 487{–}496, 2018.
    [Bibtex] 
    @article {345,
title = {Rare long-distance dispersal of a marine angiosperm across the Pacific Ocean},
journal = {Global Ecology and Biogeography},
volume = {27},
year = {2018},
pages = {487{\textendash}496},
abstract = {
    Abstract Aim Longd-istance dispersal (LDD) events occur rarely but play a fundamental role in shaping species biogeography. Lying at the heart of island biogeography theory, LDD relies on unusual events to facilitate colonization of new habitats and range expansion. Despite the importance of LDD, it is inherently difficult to quantify due to the rarity of such events. We estimate the probability of LDD of the seagrass Heterozostera nigricaulis, a common Australian species, across the Pacific Ocean to colonize South America. Location Coastal Chile, Australia and the Pacific Ocean. Methods Genetic analyses of H.\ nigricaulis collected from Chile and Australia were used to assess the relationship between the populations and levels of clonality. Ocean surface current models were used to predict the probability of propagules dispersing from south-east Australia to central Chile and shipping data used to determine the likelihood of anthropogenic dispersal. Results Our study infers that the seagrass H.\ nigricaulis dispersed from Australia across the entire width of the Pacific (c.\ 14,000 km) to colonize South America on two occasions. Genetic analyses reveal that these events led to two large isolated clones, one of which covers a combined area of 3.47 km2. Oceanographic models estimate the arrival probability of a dispersal propagule within 3 years to be at most 0.00264\%. Early shipping provides a potential alternative dispersal vector, yet few ships sailed from SE Australia to Chile prior to the first recording of H.\ nigricaulis and the lack of more recent and ongoing introductions demonstrate the rarity of such dispersal. Main conclusions These findings demonstrate LDD does occur over extreme distances despite very low probabilities. The large number of propagules (100s of millions) produced over 100s of years suggests that the arrival of propagules in Chile was inevitable and confirms the importance of LDD for species distributions and community ecology.
    
},
keywords = {biogeography, clonal organisms, long distance dispersal, Oceanography, seagrass},
issn = {1466-822X},
doi = {10.1111/geb.12713},
url = {https://onlinelibrary.wiley.com/doi/full/10.1111/geb.12713},
author = {Smith Timothy M. and York Paul H. and Broitman Bernardo R. and Thiel Martin and Hays Graeme C. and van Sebille Erik and Putman Nathan F. and Macreadie Peter I. and Sherman Craig D. H. and Sandel Brody}
}
  • [DOI] A. M. P. Santos, A. -E. Nieblas, P. Verley, A. Teles-Machado, S. Bonhommeau, C. Lett, S. Garrido, and A. Peliz, “Sardine (sardina pilchardus) larval dispersal in the iberian upwelling system, using coupled biophysical techniques,” Progress in oceanography, vol. 162, p. 83{–}97, 2018.
    [Bibtex] 
    @article {341,
title = {Sardine (Sardina pilchardus) larval dispersal in the Iberian upwelling system, using coupled biophysical techniques},
journal = {Progress in Oceanography},
volume = {162},
year = {2018},
pages = {83{\textendash}97},
abstract = {
    The European sardine (Sardina pilchardus) is the most important small pelagic fishery of the Western Iberia Upwelling Ecosystem (WIUE). Recently, recruitment of this species has declined due to changing environmental conditions. Furthermore, controversies exist regarding its population structure with barriers thought to exist between the Atlantic-Iberian Peninsula, Northern Africa, and the Mediterranean. Few studies have investigated the transport and dispersal of sardine eggs and larvae off Iberia and the subsequent impact on larval recruitment variability. Here, we examine these issues using a Regional Ocean Modeling System climatology (1989\–2008) coupled to the Lagrangian transport model, Ichthyop. Using biological parameters from the literature, we conduct simulations that investigate the effects of spawning patchiness, diel vertical migration behaviors, and egg buoyancy on the transport and recruitment of virtual sardine ichthyoplankton on the continental shelf. We find that release area, release depth, and month of release all significantly affect recruitment. Patchiness has no effect and diel vertical migration causes slightly lower recruitment. Egg buoyancy effects are significant and act similarly to depth of release. As with other studies, we find that recruitment peaks vary by latitude, explained here by the seasonal variability of offshore transport. We find weak, continuous alongshore transport between release areas, though a large proportion of simulated ichthyoplankton transport north to the Cantabrian coast (up to 27\%). We also show low level transport into Morocco (up to 1\%) and the Mediterranean (up to 8\%). The high proportion of local retention and low but consistent alongshore transport supports the idea of a series of metapopulations along this coast.
    
},
keywords = {Iberian Peninsula, Ichthyop, Lagrangian transport, larval dispersal, Regional Ocean Modeling System},
issn = {0079-6611},
doi = {10.1016/j.pocean.2018.02.011},
url = {http://www.sciencedirect.com/science/article/pii/S0079661117300125},
author = {Santos, A. M. P. and Nieblas, A. -E. and Verley, P. and Teles-Machado, A. and Bonhommeau, S. and Lett, C. and Garrido, S. and Peliz, A.}
}
  • [DOI] J. Veitch, J. Hermes, T. Lamont, P. Penven, and F. Dufois, “Shelf-edge jet currents in the southern benguela: a modelling approach,” Journal of marine systems, vol. 188, pp. 27-38, 2018.
    [Bibtex] 
    @article {373,
title = {Shelf-edge jet currents in the southern Benguela: A modelling approach},
journal = {Journal of Marine Systems},
volume = {188},
year = {2018},
pages = {27 - 38},
abstract = {
    The dynamics and seasonal variability of jet currents on the southern Benguela shelf-edge are investigated using a climatologically forced Regional Ocean Modelling System (ROMS) model. The jet is primarily forced by the intense horizontal gradients that exist across the southern Benguela shelf. These gradients are set up by nearshore cooling via the strongly seasonal upwelling regime and variable offshore warming by the advection of Agulhas waters. While the nearshore cooling is prevalent only during the spring and summer upwelling season, the offshore warming exists throughout the year. As a result intensified geostrophically adjusted currents exist throughout the year, particularly off the Cape Peninsula and Cape Columbine. However, the distinct shelf-edge jet features are most intense during upwelling seasons and extend, more or less continuously, from Cape Agulhas, the southern-tip of the continent, to Cape Columbine. The spring and summer jet off the Cape Peninsula reaches speeds of at least 0.7m.s\−1, bifurcates as it moves northward. The branch that continues northward over the shelf goes on to feed the offshore branch of the Cape Columbine jet (over the 500m isobath) and to a less extent the nearshore branch (over the 200m isobath) that is locally enhanced by upwelling processes. During winter, the Cape Peninsula jet is more confined to the shelf region and goes on to feed the whole outer-shelf (200\–500m) region off and beyond Cape Columbine. An ageostrophic component associated with offshore non-linearities related to Agulhas influx causes the mean manifestation of the Cape Peninsula jet to broaden slightly (60km) compared to its 40km-wide geostrophic core which is situated over the 350m isobath. The ageostrophic component is related to the generation of eddies that cause the isopycnals to flatten out.
    
},
keywords = {Numerical model, Shelf-edge jet, Southern Benguela},
issn = {0924-7963},
doi = {https://doi.org/10.1016/j.jmarsys.2017.09.003},
url = {http://www.sciencedirect.com/science/article/pii/S0924796317300118},
author = {Jennifer Veitch and Juliet Hermes and Tarron Lamont and Pierrick Penven and Fran{\c c}ois Dufois}
}
  • [DOI] N. F. Putman, G. J. Goni, L. J. Gramer, C. Hu, E. M. Johns, J. Trinanes, and M. Wang, “Simulating transport pathways of pelagic sargassum from the equatorial atlantic into the caribbean sea,” Progress in oceanography, vol. 165, pp. 205-214, 2018.
    [Bibtex] 
    @article {362,
title = {Simulating transport pathways of pelagic Sargassum from the Equatorial Atlantic into the Caribbean Sea},
journal = {Progress in Oceanography},
volume = {165},
year = {2018},
pages = {205 - 214},
abstract = {
    Since 2011, beach inundation of massive amounts of pelagic Sargassum algae has occurred around the Caribbean nations and islands. Previous studies have applied satellite ocean color to determine the origins of this phenomenon. These techniques, combined with complementary approaches, suggest that, rather than blooms originating in the Caribbean, they arrive from the Equatorial Atlantic. However, oceanographic context for these occurrences remains limited. Here, we present results from synthetic particle tracking experiments that characterize the interannual and seasonal dynamics of ocean currents and winds likely to influence the transport of Sargassum from the Equatorial Atlantic into the Caribbean Sea. Our findings suggest that Sargassum present in the western Equatorial Atlantic (west of longitude 50\°W) has a high probability of entering the Caribbean Sea within a year\’s time. Transport routes include the Guiana Current, North Brazil Current Rings, and the North Equatorial Current north of the North Brazil Current Retroflection. The amount of Sargassum following each route varies seasonally. This has important implications for the amount of time it takes Sargassum to reach the Caribbean Sea. By weighting particle transport predictions with Sargassum concentrations at release sites in the western Equatorial Atlantic, our simulations explain close to 90\% of the annual variation in observed Sargassum abundance entering the Caribbean Sea. Additionally, results from our numerical experiments are in good agreement with observations of variability in the timing of Sargassum movement from the Equatorial Atlantic to the Caribbean, and observations of the spatial extent of Sargassum occurrence throughout the Caribbean. However, this work also highlights some areas of uncertainty that should be examined, in particular the effect of \“windage\” and other surface transport processes on the movement of Sargassum. Our results provide a useful launching point to predict Sargassum beaching events along the Caribbean islands well in advance of their occurrence and, more generally, to understand the movement ecology of a floating ecosystem that is essential habitat to numerous marine species.
    
},
keywords = {movement ecology, ocean circulation model, Remote sensing},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2018.06.009},
url = {http://www.sciencedirect.com/science/article/pii/S0079661118300259},
author = {Nathan F. Putman and Gustavo J. Goni and Lewis J. Gramer and Chuanmin Hu and Elizabeth M. Johns and Joaquin Trinanes and Mengqiu Wang}
}
  • [DOI] B. Millet, C. Pinazo, D. Banaru, R. Pagès, P. Guiart, and I. Pairaud, “Unexpected spatial impact of treatment plant discharges induced by episodic hydrodynamic events: modelling lagrangian transport of fine particles by northern current intrusions in the bays of marseille (france),” Plos one, vol. 13, p. e0195257, 2018.
    [Bibtex] 
    @article {348,
title = {Unexpected spatial impact of treatment plant discharges induced by episodic hydrodynamic events: Modelling Lagrangian transport of fine particles by Northern Current intrusions in the bays of Marseille (France)},
journal = {PLOS ONE},
volume = {13},
year = {2018},
pages = {e0195257},
abstract = {
    Our study highlights the Lagrangian transport of solid particles discharged at the Marseille Wastewater Treatment Plant (WWTP), located at Cortiou on the southern coastline. We focused on episodic situations characterized by a coastal circulation pattern induced by intrusion events of the Northern Current (NC) on the continental shelf, associated with SE wind regimes. We computed, using MARS3D-RHOMA and ICHTHYOP models, the particle trajectories from a patch of 5.104 passive and conservative fine particles released at the WWTP outlet, during 2 chosen representative periods of intrusion of the NC in June 2008 and in October 2011, associated with S-SE and E-SE winds, respectively. Unexpected results highlighted that the amount of particles reaching the vulnerable shorelines of both northern and southern bays accounted for 21.2\% and 46.3\% of the WWTP initial patch, in June 2008 and October 2011, respectively. Finally, a conceptual diagram is proposed to highlight the mechanisms of dispersion within the bays of Marseille of the fine particles released at the WWTP outlet that have long been underestimated.
    
},
keywords = {Effluent, Hydrodynamics, Phytoplankton, Sea water, Shores, Stable isotopes, Water pollution, Wind},
issn = {1932-6203},
doi = {10.1371/journal.pone.0195257},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195257},
author = {Millet, Bertrand and Pinazo, Christel and Banaru, Daniela and Pag{\`e}s, R{\'e}mi and Guiart, Pierre and Pairaud, Ivane}
}
  • [DOI] A. Calò, C. Lett, B. Mourre, Á. Pérez-Ruzafa, and J. A. Garcia-Charton, “Use of lagrangian simulations to hindcast the geographical position of propagule release zones in a mediterranean coastal fish,” Marine environmental research, vol. 134, p. 16{–}27, 2018.
    [Bibtex] 
    @article {338,
title = {Use of Lagrangian simulations to hindcast the geographical position of propagule release zones in a Mediterranean coastal fish},
journal = {Marine Environmental Research},
volume = {134},
year = {2018},
pages = {16{\textendash}27},
abstract = {
    The study of organism dispersal is fundamental for elucidating patterns of connectivity between populations, thus crucial for the design of effective protection and management strategies. This is especially challenging in the case of coastal fish, for which information on egg release zones (i.e. spawning grounds) is often lacking. Here we assessed the putative location of egg release zones of the saddled sea bream (Oblada melanura) along the south-eastern coast of Spain in 2013. To this aim, we hindcasted propagule (egg and larva) dispersal using Lagrangian simulations, fed with species-specific information on early life history traits (ELTs), with two approaches: 1) back-tracking and 2) comparing settler distribution obtained from simulations to the analogous distribution resulting from otolith chemical analysis. Simulations were also used to assess which factors contributed the most to dispersal distances. Back-tracking simulations indicated that both the northern sector of the Murcia region and some traits of the North-African coast were hydrodynamically suitable to generate and drive the supply of larvae recorded along the coast of Murcia in 2013. With the second approach, based on the correlation between simulation outputs and field results (otolith chemical analysis), we found that the oceanographic characteristics of the study area could have determined the pattern of settler distribution recorded with otolith analysis in 2013 and inferred the geographical position of main O. melanura spawning grounds along the coast. Dispersal distance was found to be significantly affected by the geographical position of propagule release zones. The combination of methods used was the first attempt to assess the geographical position of propagule release zones in the Mediterranean Sea for O. melanura, and can represent a valuable approach for elucidating dispersal and connectivity patterns in other coastal species.
    
},
keywords = {Dispersal distance, Lagrangian simulations, Mediterranean Sea, Propagule release zones, Sea bream},
issn = {0141-1136},
doi = {10.1016/j.marenvres.2017.12.011},
url = {http://www.sciencedirect.com/science/article/pii/S0141113617305834},
author = {Cal{\`o}, Antonio and Lett, Christophe and Mourre, Baptiste and P{\'e}rez-Ruzafa, {\'A}ngel and Garcia-Charton, Jos{\'e} Antonio}
}

2017

  • [DOI] L. Bray, D. Kassis, and J. M. Hall-Spencer, “Assessing larval connectivity for marine spatial planning in the adriatic,” Marine environmental research, vol. 125, pp. 73-81, 2017.
    [Bibtex] 
    @article {298,
title = {Assessing larval connectivity for marine spatial planning in the Adriatic},
journal = {Marine Environmental Research},
volume = {125},
year = {2017},
pages = {73 - 81},
abstract = {
    Abstract There are plans to start building offshore marine renewable energy devices throughout the Mediterranean and the Adriatic has been identified as a key location for wind farm developments. The development of offshore wind farms in the area would provide hard substrata for the settlement of sessile benthos. Since the seafloor of the Adriatic is predominantly sedimentary this may alter the larval connectivity of benthic populations in the region. Here, we simulated the release of larvae from benthic populations along the coasts of the Adriatic Sea using coupled bio-physical models and investigated the effect of pelagic larval duration on dispersal. Our model simulations show that currents typically carry particles from east to west across the Adriatic, whereas particles released along western coasts tend to remain there with the Puglia coast of Italy acting as a sink for larvae from benthic populations. We identify areas of high connectivity, as well as areas that are much more isolated, and discuss how these results can be used to inform marine spatial planning and the licensing of offshore marine renewable energy developments.
    
},
keywords = {Marine spatial planning},
issn = {0141-1136},
doi = {https://doi.org/10.1016/j.marenvres.2017.01.006},
url = {http://www.sciencedirect.com/science/article/pii/S0141113617300430},
author = {L. Bray and D. Kassis and J.M. Hall-Spencer}
}
  • [DOI] V. Koné, C. Lett, P. Penven, B. Bourlès, and S. Djakouré, “A biophysical model of s. aurita early life history in the northern gulf of guinea,” Progress in oceanography, vol. 151, p. 83{–}96, 2017.
    [Bibtex] 
    @article {285,
title = {A biophysical model of S. aurita early life history in the northern Gulf of Guinea},
journal = {Progress in Oceanography},
volume = {151},
year = {2017},
pages = {83{\textendash}96},
abstract = {
    S. aurita is the most abundant small pelagic fish in the northern Gulf of Guinea. Its reproduction and recruitment depend crucially on environmental conditions. We developed a biophysical model of S. aurita early life history by coupling offline an individual-based model with the regional oceanic modeling system (ROMS). We used this model to investigate the main factors driving variability in eggs and larval dispersal and survival in the northern Gulf of Guinea. Precisely, individuals were released from different spawning areas along the coast and tracked for a period of 28 days corresponding to their planktonic phase. Individuals that remained in the coastal recruitment areas at an age more than 7 days, at which they can supposedly actively retain themselves in a favorable area, were considered as recruited. Simulation results show the importance of the spawning areas around Cape Palmas and Cape Three Points where cyclonic eddies trap eggs and larvae along the coast, preventing their advection offshore by the Guinea Current. The spawning period also plays a key role in the recruitment success, with highest coastal retention obtained during the major upwelling period (July\–September). We find that a second retention peak can occur during the minor upwelling period (February\–March) when larval mortality due to temperature is included in the model. These results are in general agreement with knowledge of S. aurita reproduction in the northern Gulf of Guinea.
    
},
keywords = {Hydrodynamic model, Individual-based model, Northern Gulf of Guinea, Recruitment, S. aurita early life stage, upwelling},
issn = {0079-6611},
doi = {10.1016/j.pocean.2016.10.008},
url = {http://www.sciencedirect.com/science/article/pii/S0079661116300477},
author = {Kon{\'e}, Vamara and Lett, Christophe and Penven, Pierrick and Bourl{\`e}s, Bernard and Djakour{\'e}, Sandrine}
}
  • [DOI] E. Naro-Maciel, K. M. Hart, R. Cruciata, and N. F. Putman, “Dna and dispersal models highlight constrained connectivity in a migratory marine megavertebrate,” Ecography, vol. 40, p. 586{–}597, 2017.
    [Bibtex] 
    @article {305,
title = {DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate},
journal = {Ecography},
volume = {40},
year = {2017},
pages = {586{\textendash}597},
abstract = {
    Population structure and spatial distribution are fundamentally important fields within ecology, evolution, and conservation biology. To investigate pan-Atlantic connectivity of globally endangered green turtles Chelonia mydas from two National Parks in Florida, USA, we applied a multidisciplinary approach comparing genetic analysis and ocean circulation modeling. The Everglades (EP) is a juvenile feeding ground, whereas the Dry Tortugas (DT) is used for courtship, breeding, and feeding by adults and juveniles. We sequenced two mitochondrial segments from 138 turtles sampled there from 2006\–2015, and simulated oceanic transport to estimate their origins. Genetic and ocean connectivity data revealed northwestern Atlantic rookeries as the major natal sources, while southern and eastern Atlantic contributions were negligible. However, specific rookery estimates differed between genetic and ocean transport models. The combined analyses suggest that post-hatchling drift via ocean currents poorly explains the distribution of neritic juveniles and adults, but juvenile natal homing and population history likely play important roles. DT and EP were genetically similar to feeding grounds along the southern US coast, but highly differentiated from most other Atlantic groups. Despite expanded mitogenomic analysis and correspondingly increased ability to detect genetic variation, no significant differentiation between DT and EP, or among years, sexes or stages was observed. This first genetic analysis of a North Atlantic green turtle courtship area provides rare data supporting local movements and male philopatry. The study highlights the applications of multidisciplinary approaches for ecological research and conservation.
    
},
issn = {1600-0587},
doi = {10.1111/ecog.02056},
url = {http://dx.doi.org/10.1111/ecog.02056},
author = {Naro-Maciel, Eugenia and Hart, Kristen M. and Cruciata, Rossana and Putman, Nathan F.}
}
  • [DOI] M. B. Gouveia, D. F. M. Gherardi, C. A. D. Lentini, D. F. Dias, and P. C. Campos, “Do the brazilian sardine commercial landings respond to local ocean circulation?,” Plos one, vol. 12, 2017.
    [Bibtex] 
    @article {303,
title = {Do the Brazilian sardine commercial landings respond to local ocean circulation?},
journal = {PLoS ONE},
volume = {12},
year = {2017},
abstract = {
    It has been reported that sea surface temperature (SST) anomalies, flow intensity and mesoscale ocean processes, all affect sardine production, both in eastern and western boundary current systems. Here we tested the hypothesis whether extreme high and low commercial landings of the Brazilian sardine fisheries in the South Brazil Bight (SBB) are sensitive to different oceanic conditions. An ocean model (ROMS) and an individual based model (Ichthyop) were used to assess the relationship between oceanic conditions during the spawning season and commercial landings of the Brazilian sardine one year later. Model output was compared with remote sensing and analysis data showing good consistency. Simulations indicate that mortality of eggs and larvae by low temperature prior to maximum and minimum landings are significantly higher than mortality caused by offshore advection. However, when periods of maximum and minimum sardine landings are compared with respect to these causes of mortality no significant differences were detected. Results indicate that mortality caused by prevailing oceanic conditions at early life stages alone can not be invoked to explain the observed extreme commercial landings of the Brazilian sardine. Likely influencing factors include starvation and predation interacting with the strategy of spawning \“at the right place and at the right time\”.
    
},
issn = {1932-6203},
doi = {10.1371/journal.pone.0176808},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425177/},
author = {Gouveia, Mainara B. and Gherardi, Douglas F. M. and Lentini, Carlos A. D. and Dias, Daniela F. and Campos, Paula C.}
}
  • [DOI] C. Parada, A. Gretchina, S. Vásquez, A. Belmadani, V. Combes, B. Ernst, E. Di Lorenzo, J. Porobic, A. Sepúlveda, and C. Paris, “Expanding the conceptual framework of the spatial population structure and life history of jack mackerel in the eastern south pacific: an oceanic seamount region as potential spawning/nursery habitat,” Ices journal of marine science, vol. 74, p. 2398{–}2414, 2017.
    [Bibtex] 
    @article {333,
title = {Expanding the conceptual framework of the spatial population structure and life history of jack mackerel in the eastern South Pacific: an oceanic seamount region as potential spawning/nursery habitat},
journal = {ICES Journal of Marine Science},
volume = {74},
year = {2017},
pages = {2398{\textendash}2414},
abstract = {
    Juvenile jack mackerel were found in 2009 in the Challenger break and the East Pacific ridge (CHAEPR). This seamount region is \∼3500\ km from the coastal historic jack mackerel nursery grounds off Chile (north of 30\°S). We reviewed historic evidence of juveniles around this seamount and data on several local environmental conditions: sea surface temperature, chlorophyll-a, wind, turbulence levels, and Eddy kinetic energy (EKE). A Lagrangian model for the early life stages of jack mackerel in the eastern South Pacific was used to assess the potential of the seamount region as a permanent nursery ground. Transport/retention mechanisms were assessed by releasing virtual particles coupled to a growth model into the flow simulated by an eddy-resolving ocean model. Model simulations showed high inter-annual variability for particle retention in the seamount region; high retention levels were associated with low EKE such that the particles were retained for several months. Satellite altimetry has shown a local minimum in eddy activity in the region where the juveniles were observed; this minimum was consistent with the above temporal relationship. The inclusion of the CHAEPR oceanic seamount region as a potential nursery ground for jack mackerel expands the current conceptual framework for the spatial population structure of this species in the South Pacific off central Chile proposed by Arcos et al. (The jack mackerel fishery and El Ni\ño 1997\–98 effects off Chile. Progress in Oceanography 49: 597\–617, 2001). Finally, we discuss the relevance of seamounts playing a double role (spawning and nursery grounds) from the standpoint of conservation and biodiversity.
    
},
issn = {1054-3139},
doi = {10.1093/icesjms/fsx065},
url = {https://academic.oup.com/icesjms/article/74/9/2398/3831740},
author = {Parada, Carolina and Gretchina, Alexandre and V{\'a}squez, Sebasti{\'a}n and Belmadani, Ali and Combes, Vincent and Ernst, Billy and Di Lorenzo, Emanuele and Porobic, Javier and Sep{\'u}lveda, Aquiles and Paris, Claire}
}
  • [DOI] K. L. Mansfield, M. L. Mendilaharsu, N. F. Putman, M. A. G. dei Marcovaldi, A. E. Sacco, G. Lopez, T. Pires, and Y. Swimmer, “First satellite tracks of south atlantic sea turtle “lost years”: seasonal variation in trans-equatorial movement,” Proceedings of the royal society of london b: biological sciences, vol. 284, 2017.
    [Bibtex] 
    @article {330,
title = {First satellite tracks of South Atlantic sea turtle "lost years": seasonal variation in trans-equatorial movement},
journal = {Proceedings of the Royal Society of London B: Biological Sciences},
volume = {284},
year = {2017},
abstract = {
    In the South Atlantic Ocean, few data exist regarding the dispersal of young oceanic sea turtles. We characterized the movements of laboratory-reared yearling loggerhead turtles from Brazilian rookeries using novel telemetry techniques, testing for differences in dispersal during different periods of the sea turtle hatching season that correspond to seasonal changes in ocean currents. Oceanographic drifters deployed alongside satellite-tagged turtles allowed us to explore the mechanisms of dispersal (passive drift or active swimming). Early in the hatching season turtles transited south with strong southward currents. Late in the hatching season, when currents flowed in the opposite direction, turtles uniformly moved northwards across the Equator. However, the movement of individuals differed from what was predicted by surface currents alone. Swimming velocity inferred from track data and an ocean circulation model strongly suggest that turtles\’ swimming plays a role in maintaining their position within frontal zones seaward of the continental shelf. The long nesting season of adults and behaviour of post-hatchlings exposes young turtles to seasonally varying ocean conditions that lead some individuals further into the South Atlantic and others into the Northern Hemisphere. Such migratory route diversity may ultimately buffer the population against environmental changes or anthropologic threats, fostering population resiliency.
    
},
issn = {0962-8452},
doi = {10.1098/rspb.2017.1730},
url = {http://rspb.royalsocietypublishing.org/content/284/1868/20171730},
author = {Mansfield, Katherine L. and Mendilaharsu, Milagros L. and Putman, Nathan F. and dei Marcovaldi, Maria A. G. and Sacco, Alexander E. and Lopez, Gustave and Pires, Thais and Swimmer, Yonat}
}
  • [DOI] M. Andrello, F. Guilhaumon, C. Albouy, V. Parravicini, J. Scholtens, P. Verley, M. Barange, R. U. Sumaila, S. Manel, and D. Mouillot, “Global mismatch between fishing dependency and larval supply from marine reserves,” Nature communications, vol. 8, p. ncomms16039, 2017.
    [Bibtex] 
    @article {315,
title = {Global mismatch between fishing dependency and larval supply from marine reserves},
journal = {Nature Communications},
volume = {8},
year = {2017},
pages = {ncomms16039},
abstract = {
    Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems.
    
},
issn = {2041-1723},
doi = {10.1038/ncomms16039},
url = {https://www.nature.com/articles/ncomms16039},
author = {Andrello, Marco and Guilhaumon, Fran{\c c}ois and Albouy, Camille and Parravicini, Valeriano and Scholtens, Joeri and Verley, Philippe and Barange, Manuel and Sumaila, U. Rashid and Manel, St{\'e}phanie and Mouillot, David}
}
  • [DOI] L. Frère, I. Paul-Pont, E. Rinnert, S. Petton, J. Jaffré, I. Bihannic, P. Soudant, C. Lambert, and A. Huvet, “Influence of environmental and anthropogenic factors on the composition, concentration and spatial distribution of microplastics: a case study of the bay of brest (brittany, france),” Environmental pollution, vol. 225, pp. 211-222, 2017.
    [Bibtex] 
    @article {294,
title = {Influence of environmental and anthropogenic factors on the composition, concentration and spatial distribution of microplastics: A case study of the Bay of Brest (Brittany, France)},
journal = {Environmental Pollution},
volume = {225},
year = {2017},
pages = {211 - 222},
abstract = {
    Abstract The concentration and spatial distribution of microplastics in the Bay of Brest (Brittany, France) was investigated in two surveys. Surface water and sediment were sampled at nine locations in areas characterized by contrasting anthropic pressures, riverine influences or water mixing. Microplastics were categorized by their polymer type and size class. Microplastic contamination in surface water and sediment was dominated by polyethylene fragments (PE, 53\–67\%) followed by polypropylene (PP, 16\–30\%) and polystyrene (PS, 16\–17\%) microparticles. The presence of buoyant microplastics (PE, \{PP\} and PS) in sediment suggests the existence of physical and/or biological processes leading to vertical transfer of lightweight microplastics in the bay. In sediment (upper 5\ cm), the percentage of particles identified by Raman micro-spectroscopy was lower (41\%) than in surface water (79\%) and may explain the apparent low concentration observed in this matrix (0.97\ \±\ 2.08\ MP\ kg\−1 dry sediment). Mean microplastic concentration was 0.24\ \±\ 0.35\ MP\ m\−3 in surface water. We suggest that the observed spatial \{MP\} distribution is related to proximity to urbanized areas and to hydrodynamics in the bay. A particle dispersal model was used to study the influence of hydrodynamics on surface microplastic distribution. The outputs of the model showed the presence of a transitional convergence zone in the centre of the bay during flood tide, where floating debris coming from the northern and southern parts of the bay tends to accumulate before being expelled from the bay. Further modelling work and observations integrating (i) the complex vertical motion of microplastics, and (ii) their point sources is required to better understand the fate of microplastics in such a complex coastal ecosystem.
    
},
keywords = {Dispersal particle modelling},
issn = {0269-7491},
doi = {http://doi.org/10.1016/j.envpol.2017.03.023},
url = {http://www.sciencedirect.com/science/article/pii/S0269749117309831},
author = {L. Fr{\`e}re and I. Paul-Pont and E. Rinnert and S. Petton and J. Jaffr{\'e} and I. Bihannic and P. Soudant and C. Lambert and A. Huvet}
}
  • [DOI] L. C. Naisbett-Jones, N. F. Putman, J. F. Stephenson, S. Ladak, and K. A. Young, “A magnetic map leads juvenile european eels to the gulf stream,” Current biology, vol. 27, p. 1236{–}1240, 2017.
    [Bibtex] 
    @article {304,
title = {A Magnetic Map Leads Juvenile European Eels to the Gulf Stream},
journal = {Current Biology},
volume = {27},
year = {2017},
pages = {1236{\textendash}1240},
abstract = {
    Summary Migration allows animals to track the environmental conditions that maximize growth, survival, and reproduction [1\–3]. Improved understanding of the\ mechanisms underlying migrations allows for improved management of species and ecosystems [1\–4]. For centuries, the catadromous European eel (Anguilla anguilla) has provided one of Europe\’s most important fisheries and has sparked considerable scientific inquiry, most recently owing to the dramatic collapse of juvenile recruitment [5]. Larval eels are transported by ocean currents associated with the Gulf Stream System from Sargasso Sea breeding grounds to coastal and freshwater habitats from North Africa to Scandinavia [6, 7]. After a decade or more, maturing adults migrate back to the Sargasso Sea, spawn, and die [8]. However, the migratory mechanisms that bring juvenile eels to Europe and return adults to the Sargasso Sea remain equivocal [9, 10]. Here, we used a \“magnetic displacement\” experiment [11, 12] to show that the\ orientation of juvenile eels varies in response to subtle differences in magnetic field intensity and inclination angle along their marine migration route. Simulations using an ocean circulation model revealed that even weakly swimming in the experimentally observed directions at the locations corresponding to the magnetic displacements would increase entrainment of juvenile eels into the Gulf Stream System. These findings provide new insight into the migration ecology and recruitment dynamics of eels and suggest that an adaptive magnetic map, tuned to large-scale features of ocean circulation, facilitates the vast oceanic migrations of the Anguilla genus [7, 13, 14].
    
},
keywords = {Anguilla anguilla, animal migration, animal navigation, Magnetic orientation, ocean currents, Sargasso Sea, sensory ecology},
issn = {0960-9822},
doi = {10.1016/j.cub.2017.03.015},
url = {http://www.sciencedirect.com/science/article/pii/S0960982217302841},
author = {Naisbett-Jones, Lewis C. and Putman, Nathan F. and Stephenson, Jessica F. and Ladak, Sam and Young, Kyle A.}
}
  • [DOI] B. Espinasse, V. Tverberg, S. L. Basedow, T. Hattermann, O. A. Nøst, J. Albretsen, J. SkarDhamar, and K. Eiane, “Mechanisms regulating inter-annual variability in zooplankton advection over the lofoten shelf, implications for cod larvae survival,” Fisheries oceanography, vol. 26, p. 299{–}315, 2017.
    [Bibtex] 
    @article {295,
title = {Mechanisms regulating inter-annual variability in zooplankton advection over the Lofoten shelf, implications for cod larvae survival},
journal = {Fisheries Oceanography},
volume = {26},
year = {2017},
pages = {299{\textendash}315},
abstract = {
    Variability in the availability of suitable prey (mainly nauplii stages of Calanus spp.) in the early life stages of cod is likely a significant contributor to the fluctuations in the year-class strength in the Arcto Norwegian cod stock. We have investigated the origin of the Lofoten shelf population of Calanus using a particle tracking model approach based on velocity fields simulated from 2002 to 2012. By performing backwards simulations of trajectories from particles released on the Lofoten shelf in early spring, we assessed the relative contribution of potential Calanus sources, such as the Lofoten Basin, the local overwintering on the continental shelf and the adjacent fjords. This analysis revealed significant interannual differences in advection patterns mainly driven by changes in wind conditions and variable strength of the Norwegian Coastal Current. Most of the particles advected into our study area originated on the shelf, and contrary to expectations, only a few originated from the Lofoten Basin where Calanus abundances tend to be high. These results suggest that contribution from the Lofoten Basin to the early spring shelf Calanus population may be overestimated and that contribution from more local sources, especially from adjacent fjords, may play a more important role than what has been previously anticipated. Our results highlight the necessity to improve quantification of shelf-fjord exchange processes, as these may contribute more to the regulation of spring zooplankton stocks on the northern Norwegian shelf, and, as a result, may affect the survival of cod larvae in this area.
    
},
keywords = {Calanus finmarchicus, Norwegian Coastal Current, offshelf-shelf exchanges, Particle tracking, Vestfjorden},
issn = {1365-2419},
doi = {10.1111/fog.12193},
url = {http://dx.doi.org/10.1111/fog.12193},
author = {Espinasse, Boris and Tverberg, Vigdis and Basedow, S{\"u}nnje L. and Hattermann, Tore and Nøst, Ole Anders and Albretsen, Jon and SkarDhamar, Jofrid and Eiane, Ketil}
}
  • [DOI] B. M. Shamblin, P. H. Dutton, D. J. Shaver, D. A. Bagley, N. F. Putman, K. L. Mansfield, L. M. Ehrhart, L. J. Peña, and C. J. Nairn, “Mexican origins for the texas green turtle foraging aggregation: a cautionary tale of incomplete baselines and poor marker resolution,” Journal of experimental marine biology and ecology, vol. 488, pp. 111-120, 2017.
    [Bibtex] 
    @article {314,
title = {Mexican origins for the Texas green turtle foraging aggregation: A cautionary tale of incomplete baselines and poor marker resolution},
journal = {Journal of Experimental Marine Biology and Ecology},
volume = {488},
year = {2017},
pages = {111 - 120},
keywords = {Migratory connectivity},
issn = {0022-0981},
doi = {http://dx.doi.org/10.1016/j.jembe.2016.11.009},
url = {http://www.sciencedirect.com/science/article/pii/S0022098116302520},
author = {Brian M. Shamblin and Peter H. Dutton and Donna J. Shaver and Dean A. Bagley and Nathan F. Putman and Katherine L. Mansfield and Llewellyn M. Ehrhart and Luis Jaime Pe{\~n}a and Campbell J. Nairn}
}
  • [DOI] F. Palmas, A. Olita, P. Addis, R. Sorgente, and A. Sabatini, “Modelling giant red shrimp larval dispersal in the sardinian seas: density and connectivity scenarios,” Fisheries oceanography, vol. 26, p. 364{–}378, 2017.
    [Bibtex] 
    @article {296,
title = {Modelling giant red shrimp larval dispersal in the Sardinian seas: density and connectivity scenarios},
journal = {Fisheries Oceanography},
volume = {26},
year = {2017},
pages = {364{\textendash}378},
abstract = {
    The connectivity and three-dimensional (3D) dispersion of the larvae of giant red shrimp, potentially released from known spawning areas along the Sardinia slope in the western Mediterranean Sea, were assessed using Lagrangian simulations forced by a 3D submesoscale permitting a regional ocean model. Biophysical simulations using the hydrodynamic conditions of the year 2012 were run to track propagules released from known spawning areas during the spawning period (May to September). Passive transport (PT) and vertical migration (VM) scenarios were tested, each with two possible pelagic larval durations (PLDs) of 21 or 42\ days. Dispersion of propagules in the PT and VM scenarios differed in terms of travelled distance, export out of the domain (larger for VM), and depth distribution (shallower and bimodal for VM due to the larger variability of encountered currents). Connectivity patterns were investigated among eight release areas, and four predetermined Eco-Regions, and results showed strong connectivity among the North-Western (NW), Western (W), and Southern (S) regions of Sardinia, whereas the Eastern region was more segregated. Differences in connectivity patterns among scenarios were related mainly to the tendency of greater retention of propagules in the release area for the PT scenarios. This finding, together with existing hypotheses of vertical migration likely occurring during first egg-larval phases, suggest that the VM scenarios are the most probable of the two hypotheses tested. Strong connectivity between the W and S sides of Sardinia and the relative isolation of the E side could have significant implications for the protection of this important resource.
    
},
keywords = {Aristeidae, behavioural scenarios, Connectivity, deep sea, giant red shrimp, larval dispersal},
issn = {1365-2419},
doi = {10.1111/fog.12199},
url = {http://dx.doi.org/10.1111/fog.12199},
author = {Palmas, Francesco and Olita, Antonio and Addis, Piero and Sorgente, Roberto and Sabatini, Andrea}
}
  • [DOI] S. E. Tanner, A. Teles-Machado, F. Martinho, Á. Peliz, and H. N. Cabral, “Modelling larval dispersal dynamics of common sole (solea solea) along the western iberian coast,” Progress in oceanography, vol. 156, pp. 78-90, 2017.
    [Bibtex] 
    @article {321,
title = {Modelling larval dispersal dynamics of common sole (Solea solea) along the western Iberian coast},
journal = {Progress in Oceanography},
volume = {156},
year = {2017},
pages = {78 - 90},
abstract = {
    Individual-based coupled physical-biological models have become the standard tool for studying ichthyoplankton dynamics and assessing fish recruitment. Here, common sole (Solea solea L.), a flatfish of high commercial importance in Europe was used to evaluate transport of eggs and larvae and investigate the connectivity between spawning and nursery areas along the western Iberian coast as spatio-temporal variability in dispersal and recruitment patterns can result in very strong or weak year-classes causing large fluctuations in stock size. A three-dimensional particle tracking model coupled to Regional Ocean Modelling System model was used to investigate variability of sole larvae dispersal along the western Iberian coast over a five-year period (2004\–2009). A sensitivity analysis evaluating: (1) the importance of diel vertical migrations of larvae and (2) the size of designated recruitment areas was performed. Results suggested that connectivity patterns of sole larvae dispersal and their spatio-temporal variability are influenced by the configuration of the coast with its topographical structures and thus the suitable recruitment area available as well as the wind-driven mesoscale circulation along the Iberian coast.
    
},
issn = {0079-6611},
doi = {http://dx.doi.org/10.1016/j.pocean.2017.06.005},
url = {http://www.sciencedirect.com/science/article/pii/S0079661116302518},
author = {Susanne E. Tanner and Ana Teles-Machado and Filipe Martinho and {\'A}lvaro Peliz and Henrique N. Cabral}
}
  • M. Vodopivec, Á. J. Peliz, and A. Malej, “Offshore marine constructions as propagators of moon jellyfish dispersal,” Environmental research letters, vol. 12, p. 84003, 2017.
    [Bibtex] 
    @article {318,
title = {Offshore marine constructions as propagators of moon jellyfish dispersal},
journal = {Environmental Research Letters},
volume = {12},
year = {2017},
pages = {084003},
abstract = {
    We have studied the influence of offshore marine constructions on the moon jellyfish population in the Adriatic sea, where the newly set up substrates enable the formation of a new population based in the formerly unpopulated open waters. Our five-year long computer simulation uses a high resolution coupled bio-physical individual-based model to track the dispersal of the offspring from subpopulations originating from offshore and shore-based sources. According to our study, the platforms enhance connectivity between subpopulations of jellyfish polyps, help sustain existing shore-based subpopulations, contribute to jellyfish blooms in some areas, and play an important role in establishing connection with the rest of the Mediterranean, in addition to representing substantial amounts of available substrate. This is an aspect that is usually overlooked when evaluating the ecological impact of existing and future wind farms, oil and gas platforms, etc. Our approach could serve as a role model in future studies of ecological impacts of planned offshore constructions.
    
},
url = {http://stacks.iop.org/1748-9326/12/i=8/a=084003},
author = {Martin Vodopivec and {\'A}lvaro J Peliz and Alenka Malej}
}
  • [DOI] T. Džoić, G. B. Paklar, B. Grbec, S. Ivatek-Šahdan, B. Zorica, T. Šegvić-Bubić, V. Č. Keč, I. L. Pleić, I. Mladineo, L. Grubišić, and P. Verley, “Spillover of the atlantic bluefin tuna offspring from cages in the adriatic sea: a multidisciplinary approach and assessment,” Plos one, vol. 12, p. e0188956, 2017.
    [Bibtex] 
    @article {328,
title = {Spillover of the Atlantic bluefin tuna offspring from cages in the Adriatic Sea: A multidisciplinary approach and assessment},
journal = {PLOS ONE},
volume = {12},
year = {2017},
pages = {e0188956},
abstract = {
    During routine monitoring of commercial purse seine catches in 2011, 87 fingerling specimens of scombrids were collected in the southern Adriatic Sea. Sequencing of the mitochondrial DNA control region locus inferred that specimens belonged to the Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758) (N = 29), bullet tuna, Auxis rochei (Risso, 1810) (N = 30) and little tunny, Euthynnus alletteratus, Rafinesque, 1810 (N = 28). According to previously published growth parameters, the age of the collected specimens was estimated at approximately 30\–40 days, suggesting they might have been spawned in the Adriatic Sea, contrary to the current knowledge. A coupled modelling system with hydrodynamic (ROMS) and individual based model (IBM\—Ichthyop) was set up to determine the location of the spawning event. Numerical simulations with the IBM model, both backward and forward in time, indicate commercial tuna cages in the middle Adriatic coastal area as possible spawning location. The two other non-commercial species likely opportunistically use the positive environmental (abiotic and biotic) conditions to spawn in the same area.
    
},
keywords = {Fish farming, Haplotypes, Hydrodynamics, Islands, Simulation and modeling, Spawning, Swimming, Tuna},
issn = {1932-6203},
doi = {10.1371/journal.pone.0188956},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188956},
author = {D{\v z}oi{\'c}, Tomislav and Paklar, Gordana Beg and Grbec, Branka and Ivatek-{\v S}ahdan, Stjepan and Zorica, Barbara and {\v S}egvi{\'c}-Bubi{\'c}, Tanja and Ke{\v c}, Vanja {\v C}ike{\v s} and Plei{\'c}, Ivana Lepen and Mladineo, Ivona and Grubi{\v s}i{\'c}, Leon and Verley, Philippe}
}
  • [DOI] J. M. Landeira, T. Brochier, E. Mason, F. Lozano-Soldevilla, S. Hernández-León, and E. D. Barton, “Transport pathways of decapod larvae under intense mesoscale activity in the canary-african coastal transition zone: implications for population connectivity,” Scientia marina, vol. 81, pp. 299-315, 2017.
    [Bibtex] 
    @article {322,
title = {Transport pathways of decapod larvae under intense mesoscale activity in the Canary-African coastal transition zone: implications for population connectivity},
journal = {SCIENTIA MARINA},
volume = {81},
year = {2017},
month = {SEP},
pages = {299-315},
abstract = {
    We investigate the transport dynamics of decapod larvae in the Canary-African coastal transition zone (C-ACTZ), where larval assemblages are poorly known. In August 1999, during the FAX99 cruise, the waters downstream of the Canary Island archipelago displayed intense mesoscale activity, with numerous cyclonic and anticyclonic eddies as well as upwelling filaments. Our results illustrate a close relationship between these mesoscale oceanographic structures and the distribution of decapod larvae, using both field observations and Lagrangian transport modelling. Analysis of plankton samples shows that larvae of pelagic species were excluded from filament waters, whereas larvae of neritic species were heterogeneously distributed, suggesting that the C-ACTZ is a mixing area where larvae originating from both the Canary Islands and the African coast may be present at the same time. This finding was supported by the simulations, which suggested that the larvae collected in the offshore waters south of Gran Canaria came mainly from the African population (between Cape Bojador and Cape Juby) during early August, whereas during the second half of August the targeted area was dominated by larvae released from Fuerteventura populations. Our observations introduce new insights into our understanding of marine population connectivity, the dispersal pathways of the terrestrial biota, and general biogeography in the region.
    
},
issn = {0214-8358},
doi = {10.3989/scimar.04599.06A},
author = {Landeira, Jose M. and Brochier, Timoth{\'e}e and Mason, Evan and Lozano-Soldevilla, Fernando and Hern{\'a}ndez-Le{\'o}n, Santiago and Barton, Eric D.}
}
  • [DOI] N. A. Robson, Y. Hetzel, S. Whiting, S. Wijeratne, C. B. Pattiaratchi, P. Withers, and M. Thums, “Use of particle tracking to determine optimal release dates and locations for rehabilitated neonate sea turtles,” Frontiers in marine science, vol. 4, p. 173, 2017.
    [Bibtex] 
    @article {313,
title = {Use of Particle Tracking to Determine Optimal Release Dates and Locations for Rehabilitated Neonate Sea Turtles},
journal = {Frontiers in Marine Science},
volume = {4},
year = {2017},
pages = {173},
issn = {2296-7745},
doi = {10.3389/fmars.2017.00173},
url = {http://journal.frontiersin.org/article/10.3389/fmars.2017.00173},
author = {Robson, Natalie A. and Hetzel, Yasha and Whiting, Scott and Wijeratne, Sarath and Pattiaratchi, Charitha B. and Withers, Philip and Thums, Michele}
}

2016

  • [DOI] D. K. Briscoe, D. M. Parker, G. H. Balazs, M. Kurita, T. Saito, H. Okamoto, M. Rice, J. J. Polovina, and L. B. Crowder, “Active dispersal in loggerhead sea turtles (caretta caretta) during the “lost years”,” Proc. r. soc. b, vol. 283, p. 20160690, 2016.
    [Bibtex] 
    @article {260,
title = {Active dispersal in loggerhead sea turtles (Caretta caretta) during the "lost years"},
journal = {Proc. R. Soc. B},
volume = {283},
year = {2016},
pages = {20160690},
abstract = {
    Highly migratory marine species can travel long distances and across entire ocean basins to reach foraging and breeding grounds, yet gaps persist in our knowledge of oceanic dispersal and habitat use. This is especially true for sea turtles, whose complex life history and lengthy pelagic stage present unique conservation challenges. Few studies have explored how these young at-sea turtles navigate their environment, but advancements in satellite technology and numerical models have shown that active and passive movements are used in relation to open ocean features. Here, we provide the first study, to the best of our knowledge, to simultaneously combine a high-resolution physical forcing ocean circulation model with long-term multi-year tracking data of young, trans-oceanic North Pacific loggerhead sea turtles during their \‘lost years\’ at sea. From 2010 to 2014, we compare simulated trajectories of passive transport with empirical data of 1\–3 year old turtles released off Japan (29.7\–37.5 straight carapace length cm). After several years, the at-sea distribution of simulated current-driven trajectories significantly differed from that of the observed turtle tracks. These results underscore current theories on active dispersal by young oceanic-stage sea turtles and give further weight to hypotheses of juvenile foraging strategies for this species. Such information can also provide critical geographical information for spatially explicit conservation approaches to this endangered population.
    
},
issn = {0962-8452, 1471-2954},
doi = {10.1098/rspb.2016.0690},
url = {http://rspb.royalsocietypublishing.org/content/283/1832/20160690},
author = {Briscoe, D. K. and Parker, D. M. and Balazs, G. H. and Kurita, M. and Saito, T. and Okamoto, H. and Rice, M. and Polovina, J. J. and Crowder, L. B.}
}
  • [DOI] L. M. García-García, M. Ruiz-Villarreal, and M. Bernal, “A biophysical model for simulating early life stages of sardine in the iberian atlantic stock,” Fisheries research, vol. 173, Part 3, p. 250{–}272, 2016.
    [Bibtex] 
    @article {234,
title = {A biophysical model for simulating early life stages of sardine in the Iberian Atlantic stock},
journal = {Fisheries Research},
volume = {173, Part 3},
year = {2016},
pages = {250{\textendash}272},
abstract = {
    The Iberian sardine (Sardina pilchardus) is a traditional fishery in western Iberia that is economically important in Portugal and in Galicia (NW Spain). The International Council for the Exploration of the Seas (ICES) advice for the sardine in regions VIII and IXa in 2013 indicated that the biomass has decreased since 2006 and recruitment has been below the long term average since 2005. Recruitment is very variable, so it is important to understand the underlying processes driving this variation in order to manage the fishery effectively. In this study, a biophysical model was used to simulate the early life (egg and larval) stages of sardine. A high resolution hydrodynamic model for North and Northwest Iberia was used to force a Lagrangian Individually-Based Model (IBM) that simulated advection and dispersion (both horizontal and vertical) and included some biological behaviour. A Lower Trophic Level (LTL) model coupled to the hydrodynamic model was also used to get some insight on recruitment for years 2006\–2007. Additionally, since in this area there are two different spawning grounds that could be associated with two eventually different populations, we have tried to show how the model can be used for giving insight on stock connectivity and therefore can contribute to stock delineation.
    
},
keywords = {Atlanto-Iberian sardine stock, Biophysical model, early life stages, Individual based model, Recruitment, sardine},
issn = {0165-7836},
doi = {10.1016/j.fishres.2015.10.002},
url = {http://www.sciencedirect.com/science/article/pii/S0165783615300990},
author = {Garc\'ia-Garc\'ia, Luz Mar\'ia and Ruiz-Villarreal, Manuel and Bernal, Miguel}
}
  • [DOI] S. Hinckley, C. Parada, J. K. Horne, M. Mazur, and M. Woillez, “Comparison of individual-based model output to data using a model of walleye pollock early life history in the gulf of alaska,” Understanding ecosystem processes in the gulf of alaska: volume 1, vol. 132, p. 240{–}262, 2016.
    [Bibtex] 
    @article {279,
title = {Comparison of individual-based model output to data using a model of walleye pollock early life history in the Gulf of Alaska},
journal = {Understanding Ecosystem Processes in the Gulf of Alaska: Volume 1},
volume = {132},
year = {2016},
pages = {240{\textendash}262},
abstract = {
    Biophysical individual-based models (IBMs) have been used to study aspects of early life history of marine fishes such as recruitment, connectivity of spawning and nursery areas, and marine reserve design. However, there is no consistent approach to validating the spatial outputs of these models. In this study, we hope to rectify this gap. We document additions to an existing individual-based biophysical model for Alaska walleye pollock (Gadus chalcogrammus), some simulations made with this model and methods that were used to describe and compare spatial output of the model versus field data derived from ichthyoplankton surveys in the Gulf of Alaska. We used visual methods (e.g. distributional centroids with directional ellipses), several indices (such as a Normalized Difference Index (NDI), and an Overlap Coefficient (OC), and several statistical methods: the Syrjala method, the Getis-Ord Gi* statistic, and a geostatistical method for comparing spatial indices. We assess the utility of these different methods in analyzing spatial output and comparing model output to data, and give recommendations for their appropriate use. Visual methods are useful for initial comparisons of model and data distributions. Metrics such as the NDI and OC give useful measures of co-location and overlap, but care must be taken in discretizing the fields into bins. The Getis-Ord Gi* statistic is useful to determine the patchiness of the fields. The Syrjala method is an easily implemented statistical measure of the difference between the fields, but does not give information on the details of the distributions. Finally, the geostatistical comparison of spatial indices gives good information of details of the distributions and whether they differ significantly between the model and the data. We conclude that each technique gives quite different information about the model-data distribution comparison, and that some are easy to apply and some more complex. We also give recommendations for a multistep process to validate spatial output from IBMs.
    
},
keywords = {individual-based models, marine fish, Mathematical models, Spatial analysis, Spatial distributions, Statistical analysis, USA gulf of alaska, Walleye pollock},
issn = {0967-0645},
doi = {10.1016/j.dsr2.2016.04.007},
url = {http://www.sciencedirect.com/science/article/pii/S0967064516300790},
author = {Hinckley, Sarah and Parada, Carolina and Horne, John K. and Mazur, Michael and Woillez, Mathieu}
}
  • [DOI] T. Thibaut, L. Bottin, D. Aurelle, C. Boudouresque, A. Blanfuné, M. Verlaque, I. Pairaud, and B. Millet, “Connectivity of populations of the seaweed cystoseira amentacea within the bay of marseille (mediterranean sea): genetic structure and hydrodynamic connections,” Cryptogamie, algologie, vol. 37, p. 233{–}255, 2016.
    [Bibtex] 
    @article {283,
title = {Connectivity of Populations of the Seaweed Cystoseira amentacea within the Bay of Marseille (Mediterranean Sea): Genetic Structure and Hydrodynamic Connections},
journal = {Cryptogamie, Algologie},
volume = {37},
year = {2016},
pages = {233{\textendash}255},
abstract = {
    The brown alga Cystoseira amentacea (Phaeophyceae, kingdom Stramenopiles) constitutes an extensive belt in the shallowest horizon of the infralittoral (the infralittoral fringe), in the Mediterranean Sea. Hydrodynamic modelling was used to infer connectivity between populations of C. amentacea of the Bay of Marseille (Provence, France, NW Mediterranean) and to test the correlation between genetic and hydrodynamic connectivity. We genotyped 183 individuals from six populations at six microsatellite loci. Current fields were computed at a fine resolution by a 3D numerical model simultaneously utilizing the local winds, the Rhone River inputs and offshore circulation. The Lagrangian trajectories of the propagules (zygotes, or rafts) were computed with the ICHTHYOP software, for both NW and SE strong wind forcing (11\–12 m\·s-1). Cystoseira amentacea displayed a strong and significant genetic structure, not correlated with the geographic distance, i.e. a lack of isolation by distance (IBD). The pairs of sites with the lowest FST were those connected by the current patterns. The time needed for a zygote or a raft to travel from one location to another ranged from 4 to 18 h (i.e. within the survival time of a zygote) and for distances of up to 23 km. Despite the very low dispersal capability of the zygotes, long-distance dispersal is therefore possible. Several non-exclusive processes can account for the genetic structure of C. amentacea populations, such as step-by-step local dispersal, long-distance dispersal of zygotes and rafts by currents, during storms, and the \“priority effect\”, i.e. the importance of the timing of arrival of the propagules.
    
},
issn = {0181-1568},
doi = {10.7872/crya/v37.iss4.2016.233},
url = {http://www.bioone.org/doi/abs/10.7872/crya/v37.iss4.2016.233},
author = {Thibaut, Thierry and Bottin, Lorraine and Aurelle, Didier and Boudouresque, Charles-Fran{\c c}ois and Blanfun{\'e}, Aur{\'e}lie and Verlaque, Marc and Pairaud, Ivane and Millet, Bertrand}
}
  • [DOI] L. M. Chérubin and L. Garavelli, “Eastern caribbean circulation and island mass effect on st. croix, us virgin islands: a mechanism for relatively consistent recruitment patterns,” Plos one, vol. 11, p. e0150409, 2016.
    [Bibtex] 
    @article {252,
title = {Eastern Caribbean Circulation and Island Mass Effect on St. Croix, US Virgin Islands: A Mechanism for Relatively Consistent Recruitment Patterns},
journal = {PloS One},
volume = {11},
year = {2016},
pages = {e0150409},
abstract = {
    The northeastern Caribbean Sea is under the seasonal influence of the Trade Winds but also of the Orinoco/Amazon freshwater plume. The latter is responsible for intensification of the Caribbean Current in general and of its eddy activity in the northern part of the Caribbean Sea. More importantly, we show in this study that the front of the freshwater plume drives a northward flow that impinges directly on the island of St. Croix in the United States Virgin Islands. The angle of incidence of the incoming flow controls the nature of the wake on both sides and ends of the island, which changes from cyclonic to anticylonic wake flow, with either attached or shed eddies. Using an off-line bio-physical model, we simulated the dispersal and recruitment of an abundant Caribbean coral reef fish, the bluehead wrasse (Thalassoma bifasciatum) in the context of the wake flow variability around St. Croix. Our results revealed the role played by the consistent seasonal forcing of the wake flow on the recruitment patterns around the island at the interannual scale. The interannual variability of the timing of arrival and northward penetration of the plume instead controls the nature of the wake, hence the regional spatial recruitment patterns.
    
},
issn = {1932-6203},
doi = {10.1371/journal.pone.0150409},
author = {Ch{\'e}rubin, Laurent Marcel and Garavelli, Lysel}
}
  • [DOI] Z. K. Klouch, F. Caradec, M. Plus, T. Hernández-Fariñas, L. Pineau-Guillou, A. Chapelle, S. Schmitt, J. Quéré, L. Guillou, and R. Siano, “Heterogeneous distribution in sediments and dispersal in waters of alexandrium minutum in a semi-enclosed coastal ecosystem,” Harmful algae, vol. 60, p. 81{–}91, 2016.
    [Bibtex] 
    @article {280,
title = {Heterogeneous distribution in sediments and dispersal in waters of Alexandrium minutum in a semi-enclosed coastal ecosystem},
journal = {Harmful Algae},
volume = {60},
year = {2016},
pages = {81{\textendash}91},
abstract = {
    Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1\–3 cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species. Coherent estimations of ITS1rDNA copy numbers were obtained for the two sampling cruises, supporting the hypothesis of regular accumulation of A. minutum resting stages in the south-eastern, more confined embayments of the study area, where fine-muddy sediments are also more abundant. Higher ITS1rDNA copy numbers were detected in sediments of areas where blooms have been seasonally detected since 2012. This result suggests that specific genetic material estimations in superficial sediments of the bay may be a proxy of the cyst banks of A. minutum. The simulation of particle trajectory analyses by a Lagrangian physical model showed that blooms occurring in the south-eastern part of the bay are disconnected from those of the north-eastern zone. The heterogeneous distribution of A. minutum inferred from both water and sediment suggests the existence of potential barriers for the dispersal of this species in the Bay of Brest and encourages finer analyses at the population level for this species within semi-enclosed coastal ecosystems.
    
},
keywords = {Dinoflagellate cyst, Lagrangian model, Molecular ecology, Population Dynamics, Real-time PCR, spatial distribution},
issn = {1568-9883},
doi = {10.1016/j.hal.2016.11.001},
url = {http://www.sciencedirect.com/science/article/pii/S156898831630230X},
author = {Klouch, Z. K. and Caradec, F. and Plus, M. and Hern{\'a}ndez-Fari{\~n}as, T. and Pineau-Guillou, L. and Chapelle, A. and Schmitt, S. and Qu{\'e}r{\'e}, J. and Guillou, L. and Siano, R.}
}
  • [DOI] L. Garavelli, F. Colas, P. Verley, D. M. Kaplan, B. Yannicelli, and C. Lett, “Influence of biological factors on connectivity patterns for concholepas concholepas (loco) in chile,” Plos one, vol. 11, p. e0146418, 2016.
    [Bibtex] 
    @article {238,
title = {Influence of biological factors on connectivity patterns for Concholepas concholepas (loco) in Chile},
journal = {PLoS ONE},
volume = {11},
year = {2016},
pages = {e0146418},
abstract = {
    In marine benthic ecosystems, larval connectivity is a major process influencing the maintenance and distribution of invertebrate populations. Larval connectivity is a complex process to study as it is determined by several interacting factors. Here we use an individual-based, biophysical model, to disentangle the effects of such factors, namely larval vertical migration, larval growth, larval mortality, adults fecundity, and habitat availability, for the marine gastropod Concholepas concholepas (loco) in Chile. Lower transport success and higher dispersal distances are observed including larval vertical migration in the model. We find an overall decrease in larval transport success to settlement areas from northern to southern Chile. This spatial gradient results from the combination of current direction and intensity, seawater temperature, and available habitat. From our simulated connectivity patterns we then identify subpopulations of loco along the Chilean coast, which could serve as a basis for spatial management of this resource in the future.
    
},
doi = {10.1371/journal.pone.0146418},
url = {http://dx.doi.org/10.1371/journal.pone.0146418},
author = {Garavelli, Lysel and Colas, Francois and Verley, Philippe and Kaplan, David Michael and Yannicelli, Beatriz and Lett, Christophe}
}
  • [DOI] B. Espinasse, S. L. Basedow, V. Tverberg, T. Hattermann, and K. Eiane, “A major calanus finmarchicus overwintering population inside a deep fjord in northern norway: implications for cod larvae recruitment success,” Journal of plankton research, vol. 38, pp. 604-609, 2016.
    [Bibtex] 
    @article {266,
title = {A major Calanus finmarchicus overwintering population inside a deep fjord in northern Norway: implications for cod larvae recruitment success},
journal = {Journal of Plankton Research},
volume = {38},
year = {2016},
pages = {604-609},
abstract = {
    High Calanus finmarchicus abundances were recorded in wintertime in Vestfjorden, close to the main cod breeding grounds off Lofoten and Vester\ålen, northern Norway. The mean abundance for locations with water depth \>500 m was \∼37000 ind. m\−2 (range: 26700\–49000 ind. m\−2). To our knowledge, this is the first report of massive overwintering of C. finmarchicus on the Norwegian shelf. Because of the observed size and location of this population, we argue that local overwintering on the northern Norwegian shelf can contribute significantly to sustain a C. finmarchicus population on the shelf during the period of first feeding for cod larvae. This is supported by a particle tracking model.
    
},
doi = {10.1093/plankt/fbw024},
url = {http://plankt.oxfordjournals.org/content/38/3/604.abstract},
author = {Espinasse, Boris and Basedow, S{\"u}nnje L. and Tverberg, Vigdis and Hattermann, Tore and Eiane, Ketil}
}
  • [DOI] C. Parada, S. Hinckley, J. Horne, M. Mazur, A. Hermann, and E. Curchister, “Modeling connectivity of walleye pollock in the gulf of alaska: are there any linkages to the bering sea and aleutian islands?,” Deep sea research part ii: topical studies in oceanography, vol. 132, pp. 227-239, 2016.
    [Bibtex] 
    @article {299,
title = {Modeling connectivity of walleye pollock in the Gulf of Alaska: Are there any linkages to the Bering Sea and Aleutian Islands?},
journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
volume = {132},
year = {2016},
pages = {227 - 239},
abstract = {
    Abstract We investigated the connectivity of walleye pollock in the Gulf of Alaska (GOA) and linkages to the Bering Sea (BS) and Aleutian Island (AL) regions. We used a spatially-explicit Individual-based model (IBM) coupled to 6 years of a hydrodynamic model that simulates the early life history of walleye pollock in the \{GOA\} (eggs to age-0 juveniles). The processes modeled included growth, movement, mortality, feeding and the bioenergetics component for larvae and juveniles. Simulations were set to release particles on the 1st of the month (February to May) in fourteen historical spawning areas in the \{GOA\} up to the 1st of September each year. Model results reproduced the link between the Shelikof Strait spawning area and the Shumagin nursery region for March and April spawners, besides other Potential Nursery Areas (PNAs) found in the GOA. A prominent finding of this study was the appearance of the \{BS\} as important \{PNAs\} for several \{GOA\} spawning grounds, which is supported by a consistent flow into the \{BS\} through Unimak Pass. The simulations showed the highest density of simulated surviving pollock in the western Bering Sea (WBS) region with the lowest coefficients of variation of the whole domain. Three spawning sectors were defined, which aggregate multiple spawning areas in the eastern (EGOA), central (CGOA) and western Gulf of Alaska (WGOA). A connectivity matrix showed strong retention within the \{CGOA\} (25.9\%) and \{EGOA\} (23.8\%), but not in the \{WGOA\} (7.2\%). Within the GOA, the highest connectivity is observed from \{EGOA\} to \{CGOA\} (57.8\%) followed by the connection from \{CGOA\} to \{WGOA\} (24.3\%). Overall, one of the most prominent connections was from \{WGOA\} to \{WBS\} (62.8\%), followed by a connection from \{CGOA\} to \{WBS\} (29.2\%). In addition, scenarios of shifting spawning locations and nursery sectors of GOA, \{BS\} and \{AL\} are explored and implications for walleye pollock stock structure hypotheses are discussed.
    
},
keywords = {Stock structure},
issn = {0967-0645},
doi = {https://doi.org/10.1016/j.dsr2.2015.12.010},
url = {http://www.sciencedirect.com/science/article/pii/S0967064515004415},
author = {Carolina Parada and Sarah Hinckley and John Horne and Michael Mazur and Albert Hermann and Enrique Curchister}
}
  • [DOI] M. Ruiz-Villarreal, L. M. García-García, M. Cobas, P. A. Díaz, and B. Reguera, “Modelling the hydrodynamic conditions associated with dinophysis blooms in galicia (nw spain),” Harmful algae, vol. 53, pp. 40-52, 2016.
    [Bibtex] 
    @article {257,
title = {Modelling the hydrodynamic conditions associated with Dinophysis blooms in Galicia (NW Spain)},
journal = {Harmful Algae},
volume = {53},
year = {2016},
pages = {40 - 52},
abstract = {
    Abstract The northwestern Iberian coast (Galician R\ías and shelf) is frequently affected by toxic harmful algal blooms (HABs) (mainly Dinophysis spp.), leading to lengthy harvesting closures in a region where aquaculture has a strong socioeconomic impact. The project \{ASIMUTH\} (http://www.asimuth.eu) aimed to develop forecasting capabilities to warn of impending \{HABs\} along the European Atlantic coast. Simulations with the \{ROMS\} model (hydrodynamical and ecological simulations complemented with Lagrangian particle tracking simulations) of the Galician coastal circulation have been performed in the framework of the \{ASIMUTH\} project to characterize and forecast oceanographic conditions before and during \{HAB\} periods. In this work, we present the Galician \{ASIMUTH\} forecast system and demonstrate its skill in predicting \{HAB\} transport and its usefulness to provide assessment for the management of the areas affected by toxic outbreaks. Experience gained during \{DSP\} events in 2005 and 2013 is shown. We also describe the Galician pilot \{HAB\} bulletins, aimed at distributing forecasts of \{HAB\} events that might induce closures of harvesting areas or, when the areas are already closed, at giving information on forthcoming oceanographic conditions that could favour or hamper the opening of an area. Our results show that the model forecasts and the bulletins can provide early warning of the risk of Dinophysis spp. events and the risk of closures linked to the presence of \{DSP\} toxins above regulatory levels in harvesting areas.
    
},
keywords = {DSP events},
issn = {1568-9883},
doi = {http://dx.doi.org/10.1016/j.hal.2015.12.003},
url = {http://www.sciencedirect.com/science/article/pii/S1568988315001766},
author = {Manuel Ruiz-Villarreal and Luz M. Garc\'ia-Garc\'ia and Marcos Cobas and Patricio A. D\'iaz and Beatriz Reguera}
}
  • [DOI] N. j. Downey-Breedt, M. j. Roberts, W. h. h. Sauer, and N. Chang, “Modelling transport of inshore and deep-spawned chokka squid (loligo reynaudi) paralarvae off south africa: the potential contribution of deep spawning to recruitment,” Fisheries oceanography, vol. 25, p. 28{–}43, 2016.
    [Bibtex] 
    @article {235,
title = {Modelling transport of inshore and deep-spawned chokka squid (Loligo reynaudi) paralarvae off South Africa: the potential contribution of deep spawning to recruitment},
journal = {Fisheries Oceanography},
volume = {25},
year = {2016},
pages = {28{\textendash}43},
abstract = {
    The South African chokka squid, Loligo reynaudi, spawns both inshore (\≤70\ m) and on the mid-shelf (71\–130\ m) of the Eastern Agulhas Bank. The fate of these deep-spawned hatchlings and their potential contribution to recruitment is as yet unknown. Lagrangian ROMS-IBM (Regional Ocean Modelling System-Individual-Based Model) simulations confirm westward transport of inshore and deep-spawned hatchlings, but also indicate that the potential exists for paralarvae hatched on the Eastern Agulhas Bank deep spawning grounds to be removed from the shelf\ ecosystem. Using a ROMS-IBM, this study determined the transport and recruitment success of deep-spawned hatchlings relative to inshore-hatched paralarvae. A total of 12 release sites were incorporated into the model, six inshore and six deep-spawning sites. Paralarval survival was estimated based on timely transport to nursery grounds, adequate retention within the nursery grounds and retention on the Agulhas Bank shelf ({\textless}200\ m). Paralarval transport and survival were dependent on both spawning location and time of hatching. Results suggest the importance of the south coast as a nursery area for inshore-hatched paralarvae, and similarly the cold ridge nursery grounds for deep-hatched paralarvae. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off the Tsitsikamma coast, and the beneficial currents during this period (as indicated by the model results) it can be concluded that deep spawning may at times contribute significantly to recruitment.
    
},
keywords = {deep spawning, Loligo reynaudi, paralarval transport, Recruitment, Regional Ocean Modelling System-Individual-Based Model},
issn = {1365-2419},
doi = {10.1111/fog.12132},
url = {http://onlinelibrary.wiley.com/doi/10.1111/fog.12132/abstract},
author = {Downey-Breedt, N.j. and Roberts, M.j. and Sauer, W.h.h. and Chang, N.}
}
  • [DOI] C. S. Endres, N. F. Putman, D. A. Ernst, J. A. Kurth, C. M. F. Lohmann, and K. J. Lohmann, “Multi-modal homing in sea turtles: modeling dual use of geomagnetic and chemical cues in island-finding,” Frontiers in behavioral neuroscience, p. 19, 2016.
    [Bibtex] 
    @article {247,
title = {Multi-Modal Homing in Sea Turtles: Modeling Dual Use of Geomagnetic and Chemical Cues in Island-Finding},
journal = {Frontiers in Behavioral Neuroscience},
year = {2016},
pages = {19},
abstract = {
    Sea turtles are capable of navigating across large expanses of ocean to arrive at remote islands for nesting, but how they do so has remained enigmatic. An interesting example involves green turtles (Chelonia mydas) that nest on Ascension Island, a tiny land mass located approximately 2000 km from the turtles\’ foraging grounds along the coast of Brazil. Sensory cues that turtles are known to detect, and which might hypothetically be used to help locate Ascension Island, include the geomagnetic field, airborne odorants, and waterborne odorants. One possibility is that turtles use magnetic cues to arrive in the vicinity of the island, then use chemical cues to pinpoint its location. As a first step toward investigating this hypothesis, we used oceanic, atmospheric, and geomagnetic models to assess whether magnetic and chemical cues might plausibly be used by turtles to locate Ascension Island. Results suggest that waterborne and airborne odorants alone are insufficient to guide turtles from Brazil to Ascension, but might permit localization of the island once turtles arrive in its vicinity. By contrast, magnetic cues might lead turtles into the vicinity of the island, but would not typically permit its localization because the field shifts gradually over time. Simulations reveal, however, that the sequential use of magnetic and chemical cues can potentially provide a robust navigational strategy for locating Ascension Island. Specifically, one strategy that appears viable is following a magnetic isoline into the vicinity of Ascension Island until an odor plume emanating from the island is encountered, after which turtles might either: (1) initiate a search strategy; or (2) follow the plume to its island source. These findings are consistent with the hypothesis that sea turtles, and perhaps other marine animals, use a multi-modal navigational strategy for locating remote islands.
    
},
keywords = {Homing, magnetism, Navigation, olfaction, sea turtles},
doi = {10.3389/fnbeh.2016.00019},
url = {http://journal.frontiersin.org/article/10.3389/fnbeh.2016.00019/full},
author = {Endres, Courtney S. and Putman, Nathan F. and Ernst, David A. and Kurth, Jessica A. and Lohmann, Catherine M. F. and Lohmann, Kenneth J.}
}
  • [DOI] N. F. Putman, R. Lumpkin, A. E. Sacco, and K. L. Mansfield, “Passive drift or active swimming in marine organisms?,” Proc. r. soc. b, vol. 283, p. 20161689, 2016.
    [Bibtex] 
    @article {284,
title = {Passive drift or active swimming in marine organisms?},
journal = {Proc. R. Soc. B},
volume = {283},
year = {2016},
pages = {20161689},
abstract = {
    Predictions of organismal movements in a fluid require knowing the fluid\&$\#$39;s velocity and potential contributions of the organism\&$\#$39;s behaviour (e.g. swimming or flying). While theoretical aspects of this work are reasonably well-developed, field-based validation is challenging. A much-needed study recently published by Briscoe and colleagues in Proceedings of the Royal Society B compared movements and distribution of satellite-tracked juvenile sea turtles to virtual particles released in a data-assimilating hindcast ocean circulation model. Substantial differences observed between turtles and particles were considered evidence for an important role of active swimming by turtles. However, the experimental design implicitly assumed that transport predictions were insensitive to (i) start location, (ii) tracking duration, (iii) depth, and (iv) physical processes not depicted in the model. Here, we show that the magnitude of variation in physical parameters between turtles and virtual particles can profoundly alter transport predictions, potentially sufficient to explain the reported differences without evoking swimming behaviour. We present a more robust method to derive the environmental contributions to individual movements, but caution that resolving the ocean velocities experienced by individual organisms remains a problem for assessing the role of behaviour in organismal movements and population distributions.
    
},
issn = {0962-8452, 1471-2954},
doi = {10.1098/rspb.2016.1689},
url = {http://rspb.royalsocietypublishing.org/content/283/1844/20161689},
author = {Putman, Nathan F. and Lumpkin, Rick and Sacco, Alexander E. and Mansfield, Katherine L.}
}
  • [DOI] M. J. Silberberger, P. E. Renaud, B. Espinasse, and H. Reiss, “Spatial and temporal structure of the meroplankton community in a sub-arctic shelf system,” Marine ecology progress series, vol. 555, p. 79{–}93, 2016.
    [Bibtex] 
    @article {277,
title = {Spatial and temporal structure of the meroplankton community in a sub-Arctic shelf system},
journal = {Marine Ecology Progress Series},
volume = {555},
year = {2016},
pages = {79{\textendash}93},
abstract = {
    ABSTRACT: The early development of many benthic invertebrates involves planktonic larval stages enabling larvae to disperse over large distances and to utilize food from the productive upper water layers. Although many past studies have recognized the importance of this period in the benthic life cycle, knowledge of larval distribution in time and space remains limited, especially for high-latitude regions with pronounced seasonal variability in environmental conditions. Here, we present the first inventory of meroplankton over the continental shelf in the Lofoten-Vester\ålen region, northern Norway, over a full annual cycle. Six stations were sampled during 8 sampling events between September 2013 and August 2014. We recorded a total of 65 taxa, a considerably higher diversity than reported in studies from more northern regions. We observed a distinct seasonal pattern with characteristic meroplankton communities defining the seasons: spring, summer, and winter. Abundance and diversity during winter was low, with higher values in spring, and maximum abundances for most taxa in summer. Meroplankton community patterns did not reflect weak environmental spatial structure. Particle tracking was used to identify source and settlement locations of spring and summer communities. Spring and summer communities originated from shore and shelf areas, respectively. Larvae were generally transported toward Andfjord and adjacent shelf regions, irrespective of season. This spatially restricted dispersal and larval settlement highlights the importance of the local benthic communities for the resilience of the ecosystem.
    
},
doi = {10.3354/meps11818},
url = {http://www.int-res.com/abstracts/meps/v555/p79-93/},
author = {Silberberger, Marc J. and Renaud, Paul E. and Espinasse, Boris and Reiss, Henning}
}
  • [DOI] F. Christiansen, N. F. Putman, R. Farman, D. M. Parker, M. R. Rice, J. J. Polovina, G. H. Balazs, and G. C. Hays, “Spatial variation in directional swimming enables juvenile sea turtles to reach and remain in productive waters,” Marine ecology progress series, vol. 557, p. 247{–}259, 2016.
    [Bibtex] 
    @article {276,
title = {Spatial variation in directional swimming enables juvenile sea turtles to reach and remain in productive waters},
journal = {Marine Ecology Progress Series},
volume = {557},
year = {2016},
pages = {247{\textendash}259},
abstract = {
    ABSTRACT: Ocean currents play an important role in the movement and distribution of organisms and for small animals it is often assumed that their movements in the ocean are determined by passive drift. Here we challenge this assumption by conducting an experiment at the scale of an entire ocean basin to test whether small (\∼35 cm) juvenile loggerhead sea turtles Caretta caretta move independently of ocean currents. By comparing the trajectories of 46 satellite tracked turtles (11502 positions, 12850 tracking days) with Lagrangian drifters (3716303 positions, 927529 tracking days) and virtual particles tracked within the Hybrid Coordinate Ocean Model (HYCOM), we found that in certain areas turtles moved in a similar manner to ocean currents, but in other areas turtle movement was markedly different from ocean currents, with turtles moving to areas thousands of kilometres from where they would have drifted passively. We further found that turtles were distributed in more-productive areas than would be expected if their movement depended on passive transport only. These findings demonstrate that regional variation in directional swimming contributes to young sea turtles reaching more favourable developmental habitats and supports laboratory work suggesting that young turtles have a map sense to determine their location in a seemingly featureless ocean.
    
},
doi = {10.3354/meps11874},
url = {http://www.int-res.com/abstracts/meps/v557/p247-259/},
author = {Christiansen, F. and Putman, N. F. and Farman, R. and Parker, D. M. and Rice, M. R. and Polovina, J. J. and Balazs, G. H. and Hays, G. C.}
}

2015

  • [DOI] M. Andrello, D. Mouillot, S. Somot, W. Thuiller, and S. Manel, “Additive effects of climate change on connectivity between marine protected areas and larval supply to fished areas,” Diversity and distributions, vol. 21, p. 139{–}150, 2015.
    [Bibtex] 
    @article {193,
title = {Additive effects of climate change on connectivity between marine protected areas and larval supply to fished areas},
journal = {Diversity and Distributions},
volume = {21},
year = {2015},
pages = {139{\textendash}150},
keywords = {Biophysical model, conservation planning, Epinephelus marginatus, larval dispersal, larval growth rate, reproductive timing},
issn = {1472-4642},
doi = {10.1111/ddi.12250},
url = {http://dx.doi.org/10.1111/ddi.12250},
author = {Andrello, Marco and Mouillot, David and Somot, Samuel and Thuiller, Wilfried and Manel, St{\'e}phanie}
}
  • [DOI] C. Lett, C. van der Lingen, B. R. Loveday, and C. L. Moloney, “Biophysical models of larval dispersal in the benguela current ecosystem,” African journal of marine science, vol. 37, p. 457{–}465, 2015.
    [Bibtex] 
    @article {236,
title = {Biophysical models of larval dispersal in the Benguela Current ecosystem},
journal = {African Journal of Marine Science},
volume = {37},
year = {2015},
pages = {457{\textendash}465},
abstract = {
    We synthesise and update results from the suite of biophysical, larval-dispersal models developed in the Benguela Current ecosystem. Biophysical models of larval dispersal use outputs of physical hydrodynamic models as inputs to individual-based models in which biological processes acting during the larval life are included. In the Benguela, such models were first applied to simulate the dispersal of anchovy Engraulis encrasicolus and sardine Sardinops sagax ichthyoplankton, and more recently of the early life stages of chokka-squid Loligo reynaudii and Cape hakes Merluccius spp. We identify how the models have helped advance understanding of key processes for these species. We then discuss which aspects of the early life of marine species in the Benguela Current ecosystem are still not well understood and could benefit from new modelling studies.
    
},
issn = {1814-232X},
doi = {10.2989/1814232X.2015.1105295},
url = {http://dx.doi.org/10.2989/1814232X.2015.1105295},
author = {Lett, C. and Lingen, CD van der and Loveday, B. R. and Moloney, C. L.}
}
  • [DOI] A. D’Agostini, D. F. M. Gherardi, and L. P. Pezzi, “Connectivity of marine protected areas and its relation with total kinetic energy,” Plos one, vol. 10, p. e0139601, 2015.
    [Bibtex] 
    @article {229,
title = {Connectivity of Marine Protected Areas and Its Relation with Total Kinetic Energy},
journal = {PLoS ONE},
volume = {10},
year = {2015},
pages = {e0139601},
abstract = {
    The East Continental Shelf (ECS) of Brazil is a hotspot of endemism and biodiversity of reef biota in the South Atlantic, hosting a number of Marine Protected Areas (MPAs). Connectivity of MPAs through larval dispersal influences recruitment, population dynamics, genetic structure and biogeography in coral reef ecosystems. Connectivity of protected reef ecosystem in the ECS was investigated with a hydrodynamic model (ROMS) forcing an Individual Based Model (IBM\—Ichthyop), and used groupers (genus Mycteroperca) as functional group. The hydrodynamic output from ROMS was compared with satellite data and showed good agreement with observed surface fields. Eggs were released, in IBM experiments, from April to September along six years (2002\–2007) in five MPAs along the ECS. Intrannual variability in recruitment and self-recruitment of grouper larvae was observed, as well as a negative correlation of these population parameters with total Kinetic Energy (KE) used as a metric of the physical environment. Higher KE leads to increased offshore advection of larvae, reduced total recruitment and connectivity of MPAs. Our results indicate high and uni-directional connectivity between MPAs from north to south influenced by the Brazil Current flowing in the same direction. Results also showed that some MPAs act predominantly as \“sink\” while others are mainly \“source\” areas.
    
},
doi = {10.1371/journal.pone.0139601},
url = {http://dx.doi.org/10.1371/journal.pone.0139601},
author = {D'Agostini, Andressa and Gherardi, Douglas Francisco Marcolino and Pezzi, Luciano Ponzi}
}
  • [DOI] B. Koeck, O. Gérigny, E. D. H. Durieux, S. Coudray, L. Garsi, P. Bisgambiglia, F. Galgani, and S. Agostini, “Connectivity patterns of coastal fishes following different dispersal scenarios across a transboundary marine protected area (bonifacio strait, nw mediterranean),” Estuarine, coastal and shelf science, vol. 154, pp. 234-247, 2015.
    [Bibtex] 
    @article {195,
title = {Connectivity patterns of coastal fishes following different dispersal scenarios across a transboundary marine protected area (Bonifacio strait, NW Mediterranean)},
journal = {Estuarine, Coastal and Shelf Science},
volume = {154},
year = {2015},
pages = {234 - 247},
keywords = {Ichthyoplankton},
issn = {0272-7714},
doi = {http://dx.doi.org/10.1016/j.ecss.2015.01.010},
url = {http://www.sciencedirect.com/science/article/pii/S0272771415000232},
author = {Barbara Koeck and Olivia G{\'e}rigny and Eric Dominique Henri Durieux and Sylvain Coudray and Laure-H{\'e}l{\`e}ne Garsi and Paul-Antoine Bisgambiglia and Fran{\c c}ois Galgani and Sylvia Agostini}
}
  • [DOI] N. F. Putman, A. F. Abreu-Grobois, I. Iturbe-Darkistade, E. M. Putman, P. M. Richards, and P. Verley, “Deepwater horizon oil spill impacts on sea turtles could span the atlantic,” Biology letters, vol. 11, p. 20150596, 2015.
    [Bibtex] 
    @article {240,
title = {Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic},
journal = {Biology Letters},
volume = {11},
year = {2015},
pages = {20150596},
issn = {1744-9561, 1744-957X},
doi = {10.1098/rsbl.2015.0596},
url = {http://rsbl.royalsocietypublishing.org/content/11/12/20150596},
author = {Putman, Nathan F. and Abreu-Grobois, F. Alberto and Iturbe-Darkistade, I{\~n}aky and Putman, Emily M. and Richards, Paul M. and Verley, Philippe}
}
  • [DOI] G. Olivares, H. H. Sepúlveda, and B. Yannicelli, “Definition of sanitary boundaries to prevent \.Isav spread between salmon farms in southern chile based on numerical simulations of currents,” Estuarine, coastal and shelf science, vol. 158, pp. 31-39, 2015.
    [Bibtex] 
    @article {206,
title = {Definition of sanitary boundaries to prevent {\.I}SAv spread between salmon farms in southern Chile based on numerical simulations of currents},
journal = {Estuarine, Coastal and Shelf Science},
volume = {158},
year = {2015},
pages = {31 - 39},
keywords = {Chile},
issn = {0272-7714},
doi = {http://dx.doi.org/10.1016/j.ecss.2015.02.013},
url = {http://www.sciencedirect.com/science/article/pii/S0272771415000669},
author = {Gonzalo Olivares and H.H. Sep{\'u}lveda and B. Yannicelli}
}
  • [DOI] N. Putman and K. Mansfield, “Direct evidence of swimming demonstrates active dispersal in the sea turtle “lost years”,” Current biology, vol. 25, p. 1221{–}1227, 2015.
    [Bibtex] 
    @article {216,
title = {Direct Evidence of Swimming Demonstrates Active Dispersal in the Sea Turtle "Lost Years"},
journal = {Current Biology},
volume = {25},
year = {2015},
pages = {1221{\textendash}1227},
abstract = {
    Summary Although oceanic dispersal in larval and juvenile marine animals is widely studied, the relative contributions of swimming behavior and ocean currents to movements and distribution are poorly understood [1\–4]. The sea turtle \“lost years\” [5] (often referred to as the surface-pelagic [6] or oceanic [7] stage) are a\ classic example. Upon hatching, young turtles migrate offshore and are rarely observed until they return to coastal waters as larger juveniles [5]. Sightings of small turtles downcurrent of nesting beaches and in association with drifting organisms (e.g., Sargassum algae) led to this stage being described as a \“passive migration\” during which turtles\’ movements are dictated by ocean currents [5\–10]. However, laboratory and modeling studies suggest that dispersal trajectories might also be shaped by oriented swimming [11\–15]. Here, we use an experimental approach designed to directly test the passive-migration hypothesis by deploying pairs of surface drifters alongside small green (Chelonia mydas) and Kemp\’s ridley (Lepidochelys kempii) wild-caught turtles, tracking their movements via satellite telemetry. We conclusively demonstrate that these turtles do not behave as passive drifters. In nearly all cases, drifter trajectories were uncharacteristic of turtle trajectories. Species-specific and location-dependent oriented swimming behavior, inferred by subtracting track velocity from modeled ocean velocity, contributed substantially to individual movement and distribution. These findings highlight the importance of in\ situ observations for depicting the dispersal of weakly swimming animals. Such observations, paired with information on the mechanisms of orientation, will likely allow for more accurate predictions of the ecological and evolutionary processes shaped by animal movement.
    
},
issn = {0960-9822},
doi = {10.1016/j.cub.2015.03.014},
url = {http://www.sciencedirect.com/science/article/pii/S0960982215003280},
author = {Putman, Nathan~F. and Mansfield, Katherine~L.}
}
  • [DOI] B. C. Mbaye, T. Brochier, V. Echevin, A. Lazar, M. Lévy, E. Mason, A. T. Gaye, and E. Machu, “Do sardinella aurita spawning seasons match local retention patterns in the senegalese–mauritanian upwelling region?,” Fisheries oceanography, vol. 24, p. 69{–}89, 2015.
    [Bibtex] 
    @article {196,
title = {Do Sardinella aurita spawning seasons match local retention patterns in the Senegalese{\textendash}Mauritanian upwelling region?},
journal = {Fisheries Oceanography},
volume = {24},
year = {2015},
pages = {69{\textendash}89},
abstract = {
    Sardinella aurita is the most abundant small pelagic fish in the Senegalese\–Mauritanian region. The success of its reproduction crucially depends on the local circulation as this determines whether larvae reach coastal nursery areas favorable to their survival or are dispersed into the open ocean. As a first step towards evaluating sardinella vulnerability to climate-driven hydrodynamical changes, this study aims at underpinning how transport pathways drive optimal spatial and seasonal patterns for sardinella reproduction. We have used two estimates of the Senegalese\–Mauritanian coastal seasonal circulation simulated by two hydrodynamical model configurations that differ in their forcing and topography. Nursery areas are determined by evaluating coastal retention with a Lagrangian individual-based model that accounts for processes such as diel vertical migration and mortality as a result of lethal temperature exposure. Our results suggest that\ the shelf zones located at the Arguin Bank (19.5\°N\–21\°N) and south of Senegal (12\°N\–14.75\°N) are highly retentive. We find maximum retention rates in July\–August and November\–December over the Arguin Bank; from February\–July and November\–December over the southern Senegalese shelf; and lower retention rates over the central region (14.75\°N\–19.5\°N) that are locally maximum in June\–July when the upwelling weakens. These retention areas and their seasonality are in agreement with previously reported spawning patterns, suggesting that the Sardinella aurita spawning strategy may result from a trade-off between retention patterns associated with the seasonal circulation and food availability. Exposure to lethal temperatures, although not well studied, could be a further limiting factor for spawning. The Lagrangian analysis reveals important connectivity between sub-regions within and south of the system and hence underlines the importance for joint management of the Sardinella aurita stock.
    
},
keywords = {bio-physical model, canary current system, Connectivity, larval retention, Recruitment, Sardinella aurita, Senegalese{\textendash}Mauritanian upwelling, Spawning},
issn = {1365-2419},
doi = {10.1111/fog.12094},
url = {http://dx.doi.org/10.1111/fog.12094},
author = {Mbaye, Baye Cheikh and Brochier, Timoth{\'e}e and Echevin, Vincent and Lazar, Alban and L{\'e}vy, Marina and Mason, Evan and Gaye, Amadou Thierno and Machu, Eric}
}
  • [DOI] M. Andrello, M. N. Jacobi, S. Manel, W. Thuiller, and D. Mouillot, “Extending networks of protected areas to optimize connectivity and population growth rate,” Ecography, vol. 38, p. 273{–}282, 2015.
    [Bibtex] 
    @article {209,
title = {Extending networks of protected areas to optimize connectivity and population growth rate},
journal = {Ecography},
volume = {38},
year = {2015},
pages = {273{\textendash}282},
abstract = {
    Protected areas (PAs) are recognized as the flagship tool to offset biodiversity loss on Earth. Spatial conservation planning seeks optimal designs of PAs that meet multiple targets such as biodiversity representation and population persistence. Since connectivity between PAs is a fundamental requirement for population persistence, several methods have been developed to include connectivity into PA design algorithms. Among these, the eigenvalue decomposition of the connectivity matrix allows for identifying clusters of strongly connected sites and selecting the sites contributing the most to population persistence. So far, this method was only suited to optimize an entire network of PAs without considering existing PAs in the new design. However, a more cost-effective and realistic approach is to optimize the design of an extended network to improve its connectivity and thus population persistence. Here, we develop a flexible algorithm based on eigenvalue decomposition of connectivity matrices to extend existing networks of PAs while optimizing connectivity and population growth rate. We also include a splitting algorithm to improve cluster identification. The new algorithm accounts for the change in connectivity due to the increased biological productivity often observed in existing PAs. We illustrate the potential of our algorithm by proposing an extension of the network of \∼100 Mediterranean marine PAs to reach the targeted 10\% surface area protection from the current 1.8\%. We identify differences between the clean slate scenario, where all sites are available for protection, irrespective of their current protection status, and the scenario where existing PAs are forced to be included into the optimized solution. By integrating this algorithm to existing multi-objective and multi-specific algorithms of PA selection, the demographic effects of connectivity can be explicitly included into conservation planning.
    
},
issn = {1600-0587},
doi = {10.1111/ecog.00975},
url = {http://dx.doi.org/10.1111/ecog.00975},
author = {Andrello, Marco and Jacobi, Martin Nilsson and Manel, St{\'e}phanie and Thuiller, Wilfried and Mouillot, David}
}
  • [DOI] A. Ospina-Álvarez, I. A. Catalán, M. Bernal, D. Roos, and I. Palomera, “From egg production to recruits: connectivity and inter-annual variability in the recruitment patterns of european anchovy in the northwestern mediterranean,” Progress in oceanography, vol. 138, Part B, p. 431{–}447, 2015.
    [Bibtex] 
    @article {233,
title = {From egg production to recruits: Connectivity and inter-annual variability in the recruitment patterns of European anchovy in the northwestern Mediterranean},
journal = {Progress in Oceanography},
volume = {138, Part B},
year = {2015},
pages = {431{\textendash}447},
abstract = {
    We show the application of a Spatially-Explicit Individual-Based Model (SEIBM) to understand the recruitment process of European anchovy. The SEIBM is applied to simulate the effects of inter-annual variability in parental population spawning behavior and intensity, and ocean dynamics, on the dispersal of eggs and larvae from the spawning area in the Gulf of Lions (GoL) towards the coastal nursery areas in the GoL and Catalan Sea (northwestern Mediterranean Sea). For each of seven years (2003\–2009), we initialize the SEIBM with the real positions of anchovy eggs during the spawning peak, from an acoustics-derived eggs production model. We analyze the effect of spawners\’ distribution, timing of spawning, and oceanographic conditions on the connectivity patterns, growth, dispersal distance and late-larval recruitment (14 mm larva recruits, R14) patterns. The area of influence of the Rh\ône river plume was identified as having a high probability of larval recruitment success (64\%), but up to 36\% of R14 larvae end up in the Catalan Coast. We demonstrate that the spatial paths of larvae differ dramatically from year to year, and suggest potential offshore nursery grounds. We showed that our simulations are coherent with existing recruitment proxies and therefore open new possibilities for fisheries management.
    
},
issn = {0079-6611},
doi = {10.1016/j.pocean.2015.01.011},
url = {http://www.sciencedirect.com/science/article/pii/S0079661115000221},
author = {Ospina-{\'A}lvarez, Andr{\'e}s and Catal{\'a}n, Ignacio A. and Bernal, Miguel and Roos, David and Palomera, Isabel}
}
  • [DOI] N. F. Putman, P. Verley, C. S. Endres, and K. J. Lohmann, “Magnetic navigation behavior and the oceanic ecology of young loggerhead sea turtles,” The journal of experimental biology, vol. 218, p. 1044{–}1050, 2015.
    [Bibtex] 
    @article {202,
title = {Magnetic navigation behavior and the oceanic ecology of young loggerhead sea turtles},
journal = {The Journal of Experimental Biology},
volume = {218},
year = {2015},
pages = {1044{\textendash}1050},
abstract = {
    During long-distance migrations, animals navigate using a variety of sensory cues, mechanisms and strategies. Although guidance mechanisms are usually studied under controlled laboratory conditions, such methods seldom allow for navigation behavior to be examined in an environmental context. Similarly, although realistic environmental models are often used to investigate the ecological implications of animal movement, explicit consideration of navigation mechanisms in such models is rare. Here, we used an interdisciplinary approach in which we first conducted lab-based experiments to determine how hatchling loggerhead sea turtles (Caretta caretta) respond to magnetic fields that exist at five widely separated locations along their migratory route, and then studied the consequences of the observed behavior by simulating it within an ocean circulation model. Magnetic fields associated with two geographic regions that pose risks to young turtles (due to cold wintertime temperatures or potential displacement from the migratory route) elicited oriented swimming, whereas fields from three locations where surface currents and temperature pose no such risk did not. Additionally, at locations with fields that elicited oriented swimming, simulations indicate that the observed behavior greatly increases the likelihood of turtles advancing along the migratory pathway. Our findings suggest that the magnetic navigation behavior of sea turtles is intimately tied to their oceanic ecology and is shaped by a complex interplay between ocean circulation and geomagnetic dynamics.
    
},
keywords = {Caretta caretta, Magnetic orientation, Magnetoreception, Navigation, ocean circulation model},
issn = {0022-0949, 1477-9145},
doi = {10.1242/jeb.109975},
url = {http://jeb.biologists.org/content/218/7/1044},
author = {Putman, Nathan F. and Verley, Philippe and Endres, Courtney S. and Lohmann, Kenneth J.}
}
  • [DOI] L. Prieto, D. Macias, A. Peliz, and J. Ruiz, “Portuguese man-of-war (physalia physalis) in the mediterranean: a permanent invasion or a casual appearance?,” Scientific reports, vol. 5, 2015.
    [Bibtex] 
    @article {213,
title = {Portuguese Man-of-War (Physalia physalis) in the Mediterranean: A permanent invasion or a casual appearance?},
journal = {Scientific Reports},
volume = {5},
year = {2015},
abstract = {
    In 2010, the Mediterranean basin experienced Portuguese Man-of-War (Physalia physalis) swarms that had dramatic consequences, including the region\’s first recorded human fatality attributed to a jellyfish sting. Despite the impact of jellyfish on coastal economic activity and the importance of the tourism industry for the Mediterranean region (accounting for 15\% of global tourism), no scientific consensus has been achieved regarding the causes of this episode. Here, we analyse the meteorological and oceanographic conditions of the North-East Atlantic Ocean during the months previous to the appearance of P. physalis in the Mediterranean. We simulate the probable drift of Atlantic populations into the Mediterranean basin with a numerical model and compare model results with available observations. We conclude that the summer 2010 P. Physalis swarm was the result of an unusual combination of meteorological and oceanographic conditions during the previous winter and not a permanent invasion favoured by climatic changes.
    
},
keywords = {Climate sciences, ecology, Environmental sciences},
doi = {10.1038/srep11545},
url = {http://www.nature.com/srep/2015/150625/srep11545/full/srep11545.html$\#$ref23},
author = {Prieto, L. and Macias, D. and Peliz, A. and Ruiz, J.}
}
  • [DOI] C. David, S. Vaz, C. Loots, E. Antajan, J. van der Molen, and M. Travers-Trolet, “Understanding winter distribution and transport pathways of the invasive ctenophore mnemiopsis leidyi in the north sea: coupling habitat and dispersal modelling approaches,” Biological invasions, vol. 17, p. 2605{–}2619, 2015.
    [Bibtex] 
    @article {220,
title = {Understanding winter distribution and transport pathways of the invasive ctenophore Mnemiopsis leidyi in the North Sea: coupling habitat and dispersal modelling approaches},
journal = {Biological Invasions},
volume = {17},
year = {2015},
pages = {2605{\textendash}2619},
keywords = {Developmental Biology, ecology, Freshwater \& Marine Ecology, Habitat Modelling, Mnemiopsis leidyi, North Sea, Overwinter refuges, Particle tracking, Plant Sciences},
issn = {1387-3547, 1573-1464},
doi = {10.1007/s10530-015-0899-y},
url = {http://link.springer.com/article/10.1007/s10530-015-0899-y},
author = {David, Carmen and Vaz, Sandrine and Loots, Christophe and Antajan, Elvire and Molen, Johan van der and Travers-Trolet, Morgane}
}

2014

  • [DOI] M. C. Proietti, J. Reisser, L. F. Marins, M. A. Marcovaldi, L. S. Soares, D. S. Monteiro, S. Wijeratne, C. Pattiaratchi, and E. R. Secchi, “Hawksbill x loggerhead sea turtle hybrids at bahia, brazil: where do their offspring go?,” PeerJ, vol. 2, p. e255, 2014.
    [Bibtex] 
    @article {proietti_hawksbill_2014,
title = {Hawksbill x loggerhead sea turtle hybrids at Bahia, Brazil: where do their offspring go?},
journal = {{PeerJ}},
volume = {2},
year = {2014},
pages = {e255},
issn = {2167-8359},
doi = {10.7717/peerj.255},
url = {https://peerj.com/articles/255/},
author = {Proietti, Maira C. and Reisser, Julia and Marins, Luis F. and Marcovaldi, Maria A. and Soares, Luciano S. and Monteiro, Danielle S. and Wijeratne, Sarath and Pattiaratchi, Charitha and Secchi, Eduardo R.}
}
  • [DOI] S. Taebi and C. Pattiaratchi, “Hydrodynamic response of a fringing coral reef to a rise in mean sea level,” Ocean dynamics, vol. 64, pp. 975-987, 2014.
    [Bibtex] 
    @article {170,
title = {Hydrodynamic response of a fringing coral reef to a rise in mean sea level},
journal = {Ocean Dynamics},
volume = {64},
year = {2014},
pages = {975-987},
keywords = {Fringing coral reef, Hydrodynamic and transport modelling, Mean sea-level rise},
issn = {1616-7341},
doi = {10.1007/s10236-014-0734-5},
url = {http://dx.doi.org/10.1007/s10236-014-0734-5},
author = {Taebi, Soheila and Pattiaratchi, Charitha}
}
  • [DOI] L. Garavelli, D. M. Kaplan, F. Colas, W. Stotz, B. Yannicelli, and C. Lett, “Identifying appropriate spatial scales for marine conservation and management using a larval dispersal model: the case of concholepas concholepas (loco) in chile,” Progress in oceanography, vol. 124, pp. 42-53, 2014.
    [Bibtex] 
    @article {169,
title = {Identifying appropriate spatial scales for marine conservation and management using a larval dispersal model: The case of Concholepas concholepas (loco) in Chile},
journal = {Progress in Oceanography},
volume = {124},
year = {2014},
pages = {42 - 53},
abstract = {
    Abstract Along the coast of Chile, fisheries targeting the marine gastropod Concholepas concholepas, commonly named \“loco\”, were highly valuable until the end of the 80s when catches declined significantly. Since the late 90s, a management plan based on territorial-user-rights areas has been implemented, with limited effect on stock recovery. More effective loco conservation and management is impeded by lack of information regarding connectivity via larval dispersal between these individually-managed areas. To develop a regional view of loco connectivity, we integrate loco life history information into a biophysical, individual-based larval dispersal model. This model is used to evaluate scales of loco connectivity and seasonality in connectivity patterns, as well as to partition the coast into largely disconnected subpopulations using a recently developed connectivity-matrix clustering algorithm. We find mean dispersal distances ranging from 170 to 220\ km depending on release depth of larvae and planktonic larval duration. Settlement success levels depend quantitatively on the physical and biological processes included in the model, but connectivity patterns remain qualitatively similar. Model estimates of settlement success peak for larval release dates in late austral autumn, consistent with field results and with favorable conditions for larval coastal retention due to weak upwelling during austral autumn. Despite the relatively homogeneous Chilean coastline, distinct subpopulations with minimal connectivity between them are readily identifiable. Barriers to connectivity that are robust to changes in model configuration exist at 23\°S and 29\°S latitudes. These zones are all associated with important headlands and embayments of the Chilean coast.
    
},
issn = {0079-6611},
doi = {http://dx.doi.org/10.1016/j.pocean.2014.03.011},
url = {http://www.sciencedirect.com/science/article/pii/S0079661114000378},
author = {Lysel Garavelli and David Michael Kaplan and Fran{\c c}ois Colas and Wolfgang Stotz and Beatriz Yannicelli and Christophe Lett}
}
  • [DOI] D. F. Dias, L. P. Pezzi, D. F. M. Gherardi, and R. Camargo, “Modeling the spawning strategies and larval survival of the brazilian sardine (sardinella brasiliensis),” Progress in oceanography, vol. 123, p. 38{–}53, 2014.
    [Bibtex] 
    @article {dias_modeling_2014,
title = {Modeling the spawning strategies and larval survival of the Brazilian sardine (Sardinella brasiliensis)},
journal = {Progress in Oceanography},
volume = {123},
year = {2014},
pages = {38{\textendash}53},
abstract = {An Individual Based Model ({IBM}), coupled with a hydrodynamic model ({ROMS}), was used to investigate the spawning strategies and larval survival of the Brazilian Sardine in the South Brazil Bight ({SBB}). {ROMS} solutions were compared with satellite and field data to assess their representation of the physical environment. Two spawning experiments were performed for the summer along six years, coincident with ichthyoplankton survey cruises. In the first one, eggs were released in spawning habitats inferred from a spatial model. The second experiment simulated a random spawning to test the null hypothesis that there are no preferred spawning sites. Releasing eggs in the predefined spawning habitats increases larval survival, suggesting that the central-southern part of the {SBB} is more suitable for larvae development because of its thermodynamic characteristics. The Brazilian sardine is also capable of exploring suitable areas for spawning, according to the interannual variability of the {SBB}. The influence of water temperature, the presence of Cape Frio upwelling, and surface circulation on the spawning process was tested. The Cape Frio upwelling plays an important role in the modulation of Brazilian sardine spawning zones over {SBB} because of its lower than average water temperature. This has a direct influence on larval survival and on the interannual variability of the Brazilian sardine spawning process. The hydrodynamic condition is crucial in determining the central-southern part of {SBB} as the most suitable place for spawning because it enhances simulated coastal retention of larvae.},
issn = {0079-6611},
doi = {10.1016/j.pocean.2014.03.009},
url = {http://www.sciencedirect.com/science/article/pii/S0079661114000354},
author = {Dias, Daniela Faggiani and Pezzi, Luciano Ponzi and Gherardi, Douglas Francisco Marcolino and Camargo, Ricardo}
}
  • [DOI] R. S. Martins, M. J. Roberts, C. Lett, N. Chang, C. L. Moloney, M. G. Camargo, and E. A. G. Vidal, “Modelling transport of chokka squid (loligo reynaudii) paralarvae off south africa: reviewing, testing and extending the “westward transport hypothesis”,” Fisheries oceanography, vol. 23, iss. 2, p. 116{–}131, 2014.
    [Bibtex] 
    @article {martins_modelling_2014,
title = {Modelling transport of chokka squid (Loligo reynaudii) paralarvae off South Africa: reviewing, testing and extending the "Westward Transport Hypothesis"},
journal = {Fisheries Oceanography},
volume = {23},
number = {2},
year = {2014},
pages = {116{\textendash}131},
abstract = {Annual landings of chokka squid (Loligo reynaudii), an important fishing resource for South Africa, fluctuate greatly, and are believed to be related to recruitment success. The {\textquoteleft}Westward Transport Hypothesis{\textquoteright} ({WTH}) attributes recruitment strength to variability in transport of newly hatched paralarvae from spawning grounds to the {\textquoteleft}cold ridge{\textquoteright} nursery region some 100{\textendash}200 km to the west, where oceanographic conditions sustain high productivity. We used an individual-based model ({IBM}) coupled with a 3-D hydrodynamic model ({ROMS}) to test the {WTH} and assessed four factors that might influence successful transport {\textendash} Release Area, Month, Specific Gravity (body density) and Diel Vertical Migration ({DVM}) {\textendash} in numerical experiments that estimated successful transport of squid paralarvae to the cold ridge. A multifactor {ANOVA} was used to identify the primary determinants of transport success in the various experimental simulations. Among these, release area was found to be the most important, implying that adult spawning behaviour (i.e., birth site fidelity) may be more important than paralarval behaviour in determining paralarval transport variability. However, specific gravity and {DVM} were found to play a role by retaining paralarvae on the shelf and optimizing early transport, respectively. Upwelling events seem to facilitate transport by moving paralarvae higher in the water column and thus exposing them to faster surface currents.},
keywords = {Agulhas Bank, chokka squid, larval transport, paralarvae, Recruitment},
issn = {1365-2419},
doi = {10.1111/fog.12046},
url = {http://onlinelibrary.wiley.com/doi/10.1111/fog.12046/abstract},
author = {Martins, Rodrigo S. and Roberts, Michael J. and Lett, Christophe and Chang, Nicolette and Moloney, Coleen L. and Camargo, Maur\'icio G. and Vidal, Erica A. G.}
}
  • [DOI] N. F. Putman, A. F. Abreu-Grobois, A. C. Broderick, C. Ciofi, A. Formia, B. J. Godley, S. Stroud, T. Pelembe, P. Verley, and N. Williams, “Numerical dispersal simulations and genetics help explain the origin of hawksbill sea turtles in ascension island,” Journal of experimental marine biology and ecology, vol. 450, p. 98{–}108, 2014.
    [Bibtex] 
    @article {putman_numerical_2014,
title = {Numerical dispersal simulations and genetics help explain the origin of hawksbill sea turtles in Ascension Island},
journal = {Journal of Experimental Marine Biology and Ecology},
volume = {450},
year = {2014},
pages = {98{\textendash}108},
abstract = {Abstract Long-distance dispersal and ontogenetic shifts in habitat use are characteristic of numerous marine species and have important ecological, evolutionary, and management implications. These processes, however, are often challenging to study due to the vast areas involved. We used genetic markers and simulations of physical transport within an ocean circulation model to gain understanding into the origin of juvenile hawksbill sea turtles (Eretmochelys imbricata) found at Ascension Island, a foraging ground that is thousands of kilometers from known nesting beaches. Regional origin of genetic markers suggests that turtles are from Western Atlantic (86\%) and Eastern Atlantic (14\%) rookeries. In contrast, numerical simulations of transport by ocean currents suggest that passive dispersal from the western sources would be negligible and instead would primarily be from the East, involving rookeries along Western Africa (i.e., Principe Island) and, potentially, from as far as the Indian Ocean (e.g., Mayotte and the Seychelles). Given that genetic analysis identified the presence of a haplotype endemic to Brazilian hawksbill rookeries at Ascension, we examined the possible role of swimming behavior by juvenile hawksbills from {NE} Brazil on their current-borne transport to Ascension Island by performing numerical experiments in which swimming behavior was simulated for virtual particles (simulated turtles). We found that oriented swimming substantially influenced the distribution of particles, greatly altering the proportion of particles dispersing into the North Atlantic and South Atlantic. Assigning location-dependent orientation behavior to particles allowed them to reach Ascension Island, remain in favorable temperatures, encounter productive foraging areas, and return to the vicinity of their natal site. The age at first arrival to Ascension (4.5{\textendash}5.5 years) of these particles corresponded well to estimates of hawksbill age based on their size. Our findings suggest that ocean currents and swimming behavior play an important role in the oceanic ecology of sea turtles and other marine animals.},
keywords = {Dispersal, ocean circulation model, sea turtle, {mtDNA}},
issn = {0022-0981},
doi = {10.1016/j.jembe.2013.10.026},
url = {http://www.sciencedirect.com/science/article/pii/S0022098113003675},
author = {Putman, Nathan F. and Abreu-Grobois, F. Alberto and Broderick, Annette C. and Ciofi, Claudio and Formia, Angela and Godley, Brendan J. and Stroud, Stedson and Pelembe, Tara and Verley, Philippe and Williams, Natasha}
}
  • [DOI] F. Roullier, L. Berline, L. Guidi, X. Durrieu De Madron, M. Picheral, A. Sciandra, S. Pesant, and L. Stemmann, “Particle size distribution and estimated carbon flux across the arabian sea oxygen minimum zone,” Biogeosciences, vol. 11, p. 4541{–}4557, 2014.
    [Bibtex] 
    @article {173,
title = {Particle size distribution and estimated carbon flux across the Arabian Sea oxygen minimum zone},
journal = {Biogeosciences},
volume = {11},
year = {2014},
pages = {4541{\textendash}4557},
abstract = {
    The goal of the Arabian Sea section of the TARA oceans expedition was to study large particulate matter (LPM \> 100 \μm) distributions and possible impact of associated midwater biological processes on vertical carbon export through the oxygen minimum zone (OMZ) of this region. We propose that observed spatial patterns in LPM distribution resulted from the timing and location of surface phytoplankton bloom, lateral transport, microbial processes in the core of the OMZ, and enhanced biological processes mediated by bacteria and zooplankton at the lower oxycline. Indeed, satellite-derived net primary production maps showed that the northern stations of the transect were under the influence of a previous major bloom event while the most southern stations were in a more oligotrophic situation. Lagrangian simulations of particle transport showed that deep particles of the northern stations could originate from the surface bloom while the southern stations could be considered as driven by 1-D vertical processes. In the first 200 m of the OMZ core, minima in nitrate concentrations and the intermediate nepheloid layer (INL) coincided with high concentrations of 100 \μm \< LPM \< 200 \μm. These particles could correspond to colonies of bacteria or detritus produced by anaerobic microbial activity. However, the calculated carbon flux through this layer was not affected. Vertical profiles of carbon flux indicate low flux attenuation in the OMZ, with a Martin model b exponent value of 0.22. At three stations, the lower oxycline was associated to a deep nepheloid layer, an increase of calculated carbon flux and an increase in mesozooplankton abundance. Enhanced bacterial activity and zooplankton feeding in the deep OMZ is proposed as a mechanism for the observed deep particle aggregation. Estimated lower flux attenuation in the upper OMZ and re-aggregation at the lower oxycline suggest that OMZ may be regions of enhanced carbon flux to the deep sea relative to non OMZ regions.
    
},
doi = {10.5194/bg-11-4541-2014},
url = {http://www.biogeosciences.net/11/4541/2014/},
author = {Roullier, F. and Berline, L. and Guidi, L. and Durrieu De Madron, X. and Picheral, M. and Sciandra, A. and Pesant, S. and Stemmann, L.}
}
  • [DOI] B. Espinasse, M. Harmelin-Vivien, M. Tiano, L. Guilloux, and F. Carlotti, “Patterns of variations in c and n stable isotope ratios in size-fractionated zooplankton in the gulf of lion, nw mediterranean sea,” Journal of plankton research, vol. 36, pp. 1204-1215, 2014.
    [Bibtex] 
    @article {180,
title = {Patterns of variations in C and N stable isotope ratios in size-fractionated zooplankton in the Gulf of Lion, NW Mediterranean Sea},
journal = {Journal of Plankton Research},
volume = {36},
year = {2014},
pages = {1204-1215},
abstract = {
    Stable isotope ratios for six size fractions of zooplankton (80 to \>2000 \μm) were analyzed in the Gulf of Lion in spring 2010 and winter 2011. Environmental and plankton community variables were also recorded. The originality of this study is the use of a Lagrangian transport modeling system to determine the origin of the water masses and the assessment of the proportion of detritus in the plankton samples. The highest \δ15N values were observed in the 1000\–2000 \μm fraction in January and in the 500\–1000 \μm fraction in May. The largest size class (\>2000 \μm), dominated by salps, had lower \δ15N values owing to the low isotopic signatures of these organisms. The history of the water masses resulted in two main patterns with different isotopic signatures: the water masses which resided on the shelf and the waters masses carried onto the shelf from off-shelf region by the Northern Current. The \δ13C values varied strongly between January and May, mainly owing to changes in hydrographic conditions. The \δ15N values, plankton size structure and zooplankton feeding activity varied depending on the season, revealing differences in the seasonal trophic structure of the plankton communities. The trophic structure was characterized in January by a high chlorophyl a (Chl-a) concentration, a population dominated by small organisms and herbivores, and in May by patchy Chl-a distribution, higher particulate organic matter concentration, a population dominated by large size organisms and an increase in the number of omnivores.
    
},
doi = {10.1093/plankt/fbu043},
url = {http://plankt.oxfordjournals.org/content/36/5/1204.abstract},
author = {Espinasse, B. and Harmelin-Vivien, M. and Tiano, M. and Guilloux, L. and Carlotti, F.}
}
  • [DOI] S. A. Woodin, D. S. Wethey, and S. F. Dubois, “Population structure and spread of the polychaete diopatra biscayensis along the french atlantic coast: human-assisted transport by-passes larval dispersal,” Marine environmental research, vol. 102, pp. 110-121, 2014.
    [Bibtex] 
    @article {184,
title = {Population structure and spread of the polychaete Diopatra biscayensis along the French Atlantic coast: Human-assisted transport by-passes larval dispersal},
journal = {Marine Environmental Research},
volume = {102},
year = {2014},
pages = {110 - 121},
abstract = {
    Abstract Intertidal populations of the ecosystem engineering polychaete, Diopatra biscayensis, were analyzed on the French Atlantic coast for three years with individual size estimated from tube-cap aperture. All but the northernmost population along the Bay of Biscay have yearly recruitment. Individuals live 3\–5 years and are likely reproductive as one year olds. Simulations indicate dispersal distances are \<50\ km; yet, populations also exist within the Normano-Breton Gulf in the western English Channel, more than 450\ km from the northernmost Bay of Biscay population at La Trinit\é-sur-Mer. Three of the four populations in the Normano-Breton Gulf have no young of the year, but are near to active mussel culture where mussel seed is transported on ropes from dense D.\ biscayensis areas in the Vend\ée-Charente region in the Bay of Biscay. The majority of D.\ biscayensis were adjacent to the likely source, mussel seed ropes. Transport assisted by aquaculture is the likely explanation for the populations in the Normano-Breton Gulf.
    
},
keywords = {Connectivity},
issn = {0141-1136},
doi = {http://dx.doi.org/10.1016/j.marenvres.2014.05.006},
url = {http://www.sciencedirect.com/science/article/pii/S0141113614000993},
author = {Sarah Ann Woodin and David S. Wethey and Stanislas F. Dubois}
}
  • [DOI] E. Naro-Maciel, S. J. Gaughran, N. F. Putman, G. Amato, F. Arengo, P. H. Dutton, K. W. McFadden, E. C. Vintinner, and E. J. Sterling, “Predicting connectivity of green turtles at palmyra atoll, central pacific: a focus on mtDNA and dispersal modelling,” Journal of the royal society interface, vol. 11, iss. 93, p. 20130888, 2014.
    [Bibtex] 
    @article {naro-maciel_predicting_2014,
title = {Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on {mtDNA} and dispersal modelling},
journal = {Journal of The Royal Society Interface},
volume = {11},
number = {93},
year = {2014},
pages = {20130888},
abstract = {Population connectivity and spatial distribution are fundamentally related to ecology, evolution and behaviour. Here, we combined powerful genetic analysis with simulations of particle dispersal in a high-resolution ocean circulation model to investigate the distribution of green turtles foraging at the remote Palmyra Atoll National Wildlife Refuge, central Pacific. We analysed mitochondrial sequences from turtles (n = 349) collected there over 5 years (2008{\textendash}2012). Genetic analysis assigned natal origins almost exclusively (approx. 97\%) to the West Central and South Central Pacific combined Regional Management Units. Further, our modelling results indicated that turtles could potentially drift from rookeries to Palmyra Atoll via surface currents along a near-Equatorial swathe traversing the Pacific. Comparing findings from genetics and modelling highlighted the complex impacts of ocean currents and behaviour on natal origins. Although the Palmyra feeding ground was highly differentiated genetically from others in the Indo-Pacific, there was no significant differentiation among years, sexes or stage-classes at the Refuge. Understanding the distribution of this foraging population advances knowledge of green turtles and contributes to effective conservation planning for this threatened species.},
keywords = {Chelonia mydas, control region, feeding ground, marine turtle, mixed stock analysis, ocean currents},
issn = {1742-5689, 1742-5662},
doi = {10.1098/rsif.2013.0888},
url = {http://rsif.royalsocietypublishing.org/content/11/93/20130888},
author = {Naro-Maciel, Eugenia and Gaughran, Stephen J. and Putman, Nathan F. and Amato, George and Arengo, Felicity and Dutton, Peter H. and McFadden, Katherine W. and Vintinner, Erin C. and Sterling, Eleanor J.}
}
  • [DOI] R. S. Martins, R. de Camargo, and M. A. Gasalla, “The são paulo shelf (SE brazil) as a nursery ground for doryteuthis plei (blainville, 1823) (cephalopoda, loliginidae) paralarvae: a lagrangian particle-tracking individual-based model approach,” Hydrobiologia, vol. 725, iss. 1, p. 57{–}68, 2014.
    [Bibtex] 
    @article {martins_sao_2014,
title = {The S{\~a}o Paulo shelf ({SE} Brazil) as a nursery ground for Doryteuthis plei (Blainville, 1823) (Cephalopoda, Loliginidae) paralarvae: a Lagrangian particle-tracking Individual-Based Model approach},
journal = {Hydrobiologia},
volume = {725},
number = {1},
year = {2014},
month = {mar},
pages = {57{\textendash}68},
abstract = {The S{\~a}o Paulo shelf ranges from {\textasciitilde}23{\textdegree}S to 25{\textdegree}S, comprising nearly 622 km of shoreline. This region sustains historical landings of the tropical arrow squid Doryteuthis plei. As in other coleoid cephalopods, the broodstock dies following spawning and the continuance of the population relies exclusively upon the survival of the paralarvae, which are very sensitive to oceanographic conditions. As a first step towards the understanding of paralarval transport, the shelf area was evaluated in terms of retention/dispersion potential. A Lagrangian particle-tracking Individual-Based Model was set up using a 3D Princeton Ocean Model model forced with in situ data obtained from July 2009 to July 2011. Neutrally buoyant particles were released every first day of every month in the model, and tracked for 30 days. The retention potential was high for particles released from the bottom all over the study area from the coast to the shelf break (200 m isobath). Offshore losses showed a marked seasonality. Regarding inshore losses, the percentage of particles beached was constant year round and smaller than offshore losses, being higher south of 24{\textdegree}S. Simulation results seem to agree with present knowledge of the reproductive behaviour of the species in the region.},
keywords = {ecology, Freshwater \& Marine Ecology, Hydrodynamics, larval dispersal, Modelling, retention, Squid, Zoology, {SW} Atlantic},
issn = {0018-8158, 1573-5117},
doi = {10.1007/s10750-013-1519-4},
url = {http://link.springer.com/article/10.1007/s10750-013-1519-4},
author = {Martins, Rodrigo Silvestre and Camargo, Ricardo de and Gasalla, Maria A.}
}
  • [DOI] M. Cuif, D. M. Kaplan, J. Lefèvre, V. M. Faure, M. Caillaud, P. Verley, L. Vigliola, and C. Lett, “Wind-induced variability in larval retention in a coral reef system: a biophysical modelling study in the south-west lagoon of new caledonia,” Progress in oceanography, vol. 122, p. 105{–}115, 2014.
    [Bibtex] 
    @article {cuif_wind-induced_2014,
title = {Wind-induced variability in larval retention in a coral reef system: A biophysical modelling study in the South-West Lagoon of New Caledonia},
journal = {Progress in Oceanography},
volume = {122},
year = {2014},
pages = {105{\textendash}115},
abstract = {In the present work, a biophysical dispersal model is used to understand the role of the physical environment in determining reef fish larval dispersal patterns in the South-West Lagoon of New Caledonia. We focus on a reef fish species, the humbug damselfish Dascyllus aruanus, to investigate seasonal variability of simulated larval retention at the scale of a reef patch and at the scale of the lagoon, and to explore links between larval retention and wind variability. The model shows that retention exhibits considerable temporal variability and periodically reaches values much larger than anticipated. Non-zero larval settlement occurs over a large part of the lagoon. Nevertheless, settlement values decrease quickly away from the natal reef and mean dispersal distances are of order 25{\textendash}35 km. Cross-correlation analyses indicate that weather conditions characterized by strong south east trade winds lead to low retention rates at both local (reef) and regional (lagoon) scales. By contrast, subtropical weather conditions characterized by weak winds result in high retention rates. These results suggest that large-scale weather regimes can be used as proxies for larval retention of the humbug damselfish in the South-West Lagoon of New Caledonia. Nevertheless, relatively small mean dispersal distances suggest that metapopulation dynamics occur on relatively small spatial scales.},
issn = {0079-6611},
doi = {10.1016/j.pocean.2013.12.006},
url = {http://www.sciencedirect.com/science/article/pii/S0079661113002449},
author = {Cuif, Marion and Kaplan, David Michael and Lef{\`e}vre, J{\'e}r{\^o}me and Faure, Vincent Martin and Caillaud, Matthieu and Verley, Philippe and Vigliola, Laurent and Lett, Christophe}
}

2013

  • [DOI] T. Brochier, V. Echevin, J. Tam, A. Chaigneau, K. Goubanova, and A. Bertrand, “Climate change scenarios experiments predict a future reduction in small pelagic fish recruitment in the humboldt current system,” Global change biology, vol. 19, iss. 6, p. 1841{–}1853, 2013.
    [Bibtex] 
    @article {brochier_climate_2013,
title = {Climate change scenarios experiments predict a future reduction in small pelagic fish recruitment in the Humboldt Current system},
journal = {Global Change Biology},
volume = {19},
number = {6},
year = {2013},
pages = {1841{\textendash}1853},
abstract = {The Humboldt Current System ({HCS}) sustains the world's largest small pelagic fishery. While a cooling of this system has been observed during recent decades, there is debate about the potential impacts of rising atmospheric {CO}2 concentrations on upwelling dynamics and productivity. Recent studies suggest that under increased atmospheric {CO}2 scenarios the oceanic stratification may strongly increase and upwelling-favorable winds may remain nearly constant off Peru and increase off Chile. Here we investigate the impact of such climatic conditions on egg and larval dispersal phases, a key stage of small pelagic fish reproduction. We used larval retention rate in a predefined nursery area to provide a proxy for the recruitment level. Numerical experiments are based on hydrodynamics downscaled to the {HCS} from global simulations forced by pre-industrial ({PI}), 2 {\texttimes} {CO}2 and 4 {\texttimes} {CO}2 scenarios. A biogeochemical model is applied to the {PI} and 4 {\texttimes} {CO}2 scenarios to define a time-variable nursery area where larval survival is optimum. We test two distinct values of the oxycline depth that limits larval vertical distribution: One corresponding to the present-day situation and the other corresponding to a shallower oxycline potentially produced by climate change. It appeared that larval retention over the continental shelf increases with enhanced stratification due to regional warming. However, this increase in retention is largely compensated for by a decrease of the nursery area and the shoaling of the oxycline. The underlying dynamics are explained by a combination of stratification effects and mesoscale activity changes. Our results therefore show that future climate change may significantly reduce fish capacity in the {HCS} with strong ecological, economic and social consequences.},
keywords = {climate change, Humboldt current system, Ichthyoplankton, Numerical model, nursery, oxygen minimum zone, retention, small pelagic fish, upwelling},
issn = {1365-2486},
doi = {10.1111/gcb.12184},
url = {http://onlinelibrary.wiley.com/doi/10.1111/gcb.12184/abstract},
author = {Brochier, Timoth{\'e}e and Echevin, Vincent and Tam, Jorge and Chaigneau, Alexis and Goubanova, Katerina and Bertrand, Arnaud}
}
  • [DOI] N. F. Putman and E. Naro-Maciel, “Finding the “lost years” in green turtles: insights from ocean circulation models and genetic analysis,” Proceedings of the royal society b: biological sciences, vol. 280, iss. 1768, p. 20131468, 2013.
    [Bibtex] 
    @article {putman_finding_2013,
title = {Finding the "lost years" in green turtles: insights from ocean circulation models and genetic analysis},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {280},
number = {1768},
year = {2013},
month = {jul},
pages = {20131468},
abstract = {Organismal movement is an essential component of ecological processes and connectivity among ecosystems. However, estimating connectivity and identifying corridors of movement are challenging in oceanic organisms such as young turtles that disperse into the open sea and remain largely unobserved during a period known as {\textquoteleft}the lost years{\textquoteright}. Using predictions of transport within an ocean circulation model and data from published genetic analysis, we present to our knowledge, the first basin-scale hypothesis of distribution and connectivity among major rookeries and foraging grounds ({FGs}) of green turtles (Chelonia mydas) during their {\textquoteleft}lost years{\textquoteright}. Simulations indicate that transatlantic dispersal is likely to be common and that recurrent connectivity between the southwestern Indian Ocean and the South Atlantic is possible. The predicted distribution of pelagic juvenile turtles suggests that many {\textquoteleft}lost years hotspots{\textquoteright} are presently unstudied and located outside protected areas. These models, therefore, provide new information on possible dispersal pathways that link nesting beaches with {FGs}. These pathways may be of exceptional conservation concern owing to their importance for sea turtles during a critical developmental period.},
keywords = {Chelonia mydas, Dispersal, distribution, marine turtles, ocean currents, population structure},
issn = {0962-8452, 1471-2954},
doi = {10.1098/rspb.2013.1468},
url = {http://rspb.royalsocietypublishing.org/content/280/1768/20131468},
author = {Putman, Nathan F. and Naro-Maciel, Eugenia}
}
  • [DOI] M. Andrello, D. Mouillot, J. Beuvier, C. Albouy, W. Thuiller, and S. Manel, “Low connectivity between mediterranean marine protected areas: a biophysical modeling approach for the dusky grouper epinephelus marginatus,” PLoS ONE, vol. 8, iss. 7, p. e68564, 2013.
    [Bibtex] 
    @article {andrello_low_2013,
title = {Low Connectivity between Mediterranean Marine Protected Areas: A Biophysical Modeling Approach for the Dusky Grouper Epinephelus marginatus},
journal = {{PLoS} {ONE}},
volume = {8},
number = {7},
year = {2013},
pages = {e68564},
abstract = {Marine protected areas ({MPAs}) are major tools to protect biodiversity and sustain fisheries. For species with a sedentary adult phase and a dispersive larval phase, the effectiveness of {MPA} networks for population persistence depends on connectivity through larval dispersal. However, connectivity patterns between {MPAs} remain largely unknown at large spatial scales. Here, we used a biophysical model to evaluate connectivity between {MPAs} in the Mediterranean Sea, a region of extremely rich biodiversity that is currently protected by a system of approximately a hundred {MPAs}. The model was parameterized according to the dispersal capacity of the dusky grouper Epinephelus marginatus, an archetypal conservation-dependent species, with high economic importance and emblematic in the Mediterranean. Using various connectivity metrics and graph theory, we showed that Mediterranean {MPAs} are far from constituting a true, well-connected network. On average, each {MPA} was directly connected to four others and {MPAs} were clustered into several groups. Two {MPAs} (one in the Balearic Islands and one in Sardinia) emerged as crucial nodes for ensuring multi-generational connectivity. The high heterogeneity of {MPA} distribution, with low density in the South-Eastern Mediterranean, coupled with a mean dispersal distance of 120 km, leaves about 20\% of the continental shelf without any larval supply. This low connectivity, here demonstrated for a major Mediterranean species, poses new challenges for the creation of a future Mediterranean network of well-connected {MPAs} providing recruitment to the whole continental shelf. This issue is even more critical given that the expected reduction of pelagic larval duration following sea temperature rise will likely decrease connectivity even more.},
doi = {10.1371/journal.pone.0068564},
url = {http://dx.doi.org/10.1371/journal.pone.0068564},
author = {Andrello, Marco and Mouillot, David and Beuvier, Jonathan and Albouy, Camille and Thuiller, Wilfried and Manel, St{\'e}phanie}
}
  • [DOI] A. Ospina-Álvarez, M. Bernal, I. A. Catalán, D. Roos, J. Bigot, and I. Palomera, “Modeling fish egg production and spatial distribution from acoustic data: a step forward into the analysis of recruitment,” PLoS ONE, vol. 8, iss. 9, p. e73687, 2013.
    [Bibtex] 
    @article {ospina-alvarez_modeling_2013,
title = {Modeling Fish Egg Production and Spatial Distribution from Acoustic Data: A Step Forward into the Analysis of Recruitment},
journal = {{PLoS} {ONE}},
volume = {8},
number = {9},
year = {2013},
pages = {e73687},
abstract = {To date, there are numerous transport simulation studies demonstrating the relevance of the hydrodynamics for the advection, dispersion and recruitment of early stages of marine organisms. However, the lack of data has conditioned the use of realistic locations for the model setup and configuration in transport studies. This work (I) demonstrates the key role played by the use of the realistic initial position of the eggs of small pelagic fishes in the analysis of late-larval recruitment in coastal nursery areas and ({II}) provides a general solution for deriving future egg positions and abundances from adult biomass obtained from acoustic surveys and available fecundity data. Using European anchovy in the {NW} Mediterranean as a case study, we first analyzed the impact of the initial location, timing, egg buoyancy and diel vertical migration of larvae on the potential late-larval recruitment to coastal areas. The results suggested that prior knowledge of the initial spawning grounds may substantially affect the estimates of potential recruitment. We then integrated biological and acoustics-derived data (the biomass and size structure, sex ratio, a weight-batch fecundity model, mean weight, number of fish and mean spawning) to build a predictive model for interannual egg production. This model was satisfactorily contrasted with field data for two years obtained with the Daily Egg Production Method ({DEPM}). We discuss our results in the context of the fluctuations of European anchovy egg abundance from 2003 through 2010 in the {NW} Mediterranean and in terms of the potential applicability of the acoustics-based spatial predictive egg production model.},
doi = {10.1371/journal.pone.0073687},
url = {http://dx.doi.org/10.1371/journal.pone.0073687},
author = {Ospina-{\'A}lvarez, Andr{\'e}s and Bernal, Miguel and Catal{\'a}n, Ignacio Alberto and Roos, David and Bigot, Jean-Louis and Palomera, Isabel}
}
  • [DOI] R. Fuchs, C. Pinazo, P. Douillet, M. Fraysse, C. Grenz, A. Mangin, and C. Dupouy, “Modelling ocean–lagoon interaction during upwelling processes in the south west of new caledonia,” Estuarine, coastal and shelf science, vol. 135, p. 5{–}17, 2013.
    [Bibtex] 
    @article {fuchs_modelling_2013,
title = {Modelling ocean{\textendash}lagoon interaction during upwelling processes in the South West of New Caledonia},
journal = {Estuarine, Coastal and Shelf Science},
volume = {135},
year = {2013},
pages = {5{\textendash}17},
abstract = {Since 2005, wind-driven {\textquoteleft}sporadic{\textquoteright} coastal upwelling events have been identified off the southwestern reef of New Caledonia. Several studies have described the main physical processes and induced surface patterns using 1D and 3D modelling, as well as in situ measurements. Previous models were applied at the mesoscale without taking into account the lagoon. Using a recently developed 3D coupled physical-biogeochemical model that considers the complex ocean-lagoon interface, we aim to understand better the impact of the upwelling on the lagoon. The model was found to be in good agreement with measured data reported in previous publications about two upwelling events. However, in general, levels of surface chlorophyll-a were overestimated by the model in the upwelling area when compared to ocean colour data and several hypotheses have been proposed to explain the discrepancy. We then tracked rich upwelled water using a forward Lagrangian transport analysis. Upwelled waters from the upper nutricline were found to be able to reach the South West lagoon. An anti-cyclonic eddy was detected near the upwelling area, potentially responsible, in part, for the rich water intrusions into the lagoon.},
keywords = {3D coupled physical-biogeochemical model, Lagrangian transport, New Caledonia, ocean-lagoon cross-shore processes, wind-driven coastal upwelling},
issn = {0272-7714},
doi = {10.1016/j.ecss.2013.03.009},
url = {http://www.sciencedirect.com/science/article/pii/S0272771413001352},
author = {Fuchs, R. and Pinazo, C. and Douillet, P. and Fraysse, M. and Grenz, C. and Mangin, A. and Dupouy, C.}
}
  • [DOI] V. Koné, C. Lett, and P. Fréon, “Modelling the effect of food availability on recruitment success of cape anchovy ichthyoplankton in the southern benguela upwelling system,” African journal of marine science, vol. 35, iss. 2, p. 151{–}161, 2013.
    [Bibtex] 
    @article {kone_modelling_2013,
title = {Modelling the effect of food availability on recruitment success of Cape anchovy ichthyoplankton in the southern Benguela upwelling system},
journal = {African Journal of Marine Science},
volume = {35},
number = {2},
year = {2013},
pages = {151{\textendash}161},
abstract = {Cape anchovy Engraulis encrasicolus adapted its reproductive strategies to the southern Benguela system by spawning over the Agulhas Bank, an area of low productivity that is located upstream of the predominant upwelling system. Frontal jet currents transport eggs and larvae toward the west coast of South Africa, where recruitment takes place. To characterise the recruitment dynamics of Cape anchovy ichthyoplankton, we used an individual-based model forced by a coupled hydrodynamic{\textendash}biogeochemical model. The results show the importance of food (especially diatoms and copepods) dynamics on the spatial and temporal patterns of recruitment success, and also confirm the importance of the spawning area, timing and water depth on the recruitment success of Cape anchovy larvae.},
issn = {1814-232X},
doi = {10.2989/1814232X.2013.796893},
url = {http://www.tandfonline.com/doi/abs/10.2989/1814232X.2013.796893},
author = {Kon{\'e}, V and Lett, C and Fr{\'e}on, P}
}
  • [DOI] R. F. T. Pires, M. Pan, M. A. P. Santos, lvaro Peliz, D. Boutov, and A. dos Santos, “Modelling the variation in larval dispersal of estuarine and coastal ghost shrimp: upogebia congeners in the gulf of cadiz,” Marine ecology progress series, vol. 492, p. 153{–}168, 2013.
    [Bibtex] 
    @article {pires_modelling_2013,
title = {Modelling the variation in larval dispersal of estuarine and coastal ghost shrimp: Upogebia congeners in the Gulf of Cadiz},
journal = {Marine Ecology Progress Series},
volume = {492},
year = {2013},
pages = {153{\textendash}168},
abstract = {{ABSTRACT}: Upogebia pusilla and U. deltaura are 2 common ghost shrimp species occurring in estuaries and over the shelves of European coasts, respectively. The adults have a great impact on benthic habitats and communities, as they depend on sandy and muddy substrates to construct long burrows that provide shelter and appropriate conditions for reproduction and feeding. Their planktonic larval phase lasts around 3 wk and consists of 4 zoeal stages and a decapodid that must settle in the benthos before recruiting to adult populations. In situ data were obtained from {CTD} casts and plankton hauls during an oceanographic survey that took place along the southern Portuguese coast in August 2010. All zoeal stages and decapodids of both species were found distributed over the shelf not exceeding 30 km from the coastline. A modelling approach was used to explain the differences in dispersal of these Upogebia congeners inhabiting different habitats of the same geographic area and exposed to similar oceanographic conditions. Their vertical distribution, oceanic circulation and the points of larval release were considered. A different dispersal strategy, influenced by natal origin and vertical behaviour, was evident for each species. The presence of decapodid stages close to substrates suitable for settlement where adult populations occur, especially for U. deltaura, suggests a good probability of successful settlement. Dispersal patterns observed for the 2 species and the agreement between field observations and model simulations indicate that these species are good models for other coastal invertebrates that reproduce in summer and have short larval development.},
doi = {10.3354/meps10488},
url = {http://www.int-res.com/abstracts/meps/v492/p153-168/},
author = {Pires, Rita F. T. and Pan, Maria and Santos, A. Miguel P. and Peliz, lvaro and Boutov, Dmitri and Santos, Antonina dos}
}
  • [DOI] N. Jouanneau, A. Sentchev, and F. Dumas, “Numerical modelling of circulation and dispersion processes in boulogne-sur-mer harbour (eastern english channel): sensitivity to physical forcing and harbour design,” Ocean dynamics, vol. 63, iss. 11-12, p. 1321{–}1340, 2013.
    [Bibtex] 
    @article {jouanneau_numerical_2013,
title = {Numerical modelling of circulation and dispersion processes in Boulogne-sur-Mer harbour (Eastern English Channel): sensitivity to physical forcing and harbour design},
journal = {Ocean Dynamics},
volume = {63},
number = {11-12},
year = {2013},
month = {dec},
pages = {1321{\textendash}1340},
abstract = {The {MARS}-3D model in conjunction with the particle tracking module Ichthyop is used to study circulation and tracer dynamics under a variety of forcing conditions in the eastern English Channel, and in the Boulogne-sur-Mer harbour (referred to hereafter as {BLH}). Results of hydrodynamic modelling are validated against the tidal gauge data, {VHF} radar surface velocities and {ADCP} measurements. Lagrangian tracking experiments are performed with passive particles to study tracer dispersal along the northern French coast, with special emphasis on the {BLH}. Simulations revealed an anticyclonic eddy generated in the harbour at rising tide. Tracers, released during flood tide at the Liane river mouth, move northward with powerful clockwise rotating current. After the high water, the current direction changes to westward, and tracers leave the harbour through the open boundary. During ebb tide, currents convergence along the western open boundary but no eddy is formed, surface currents inside the harbour are much weaker and the tracer excursion length is small. After the current reversal at low water, particles are advected shoreward resulting in a significant increase of the residence time of tracers released during ebb tide. The effect of wind on particle dispersion was found to be particularly strong. Under strong {SW} wind, the residence time of particles released during flood tide increases from 1.5 to 6 days. For release during ebb tide, {SW} wind weakens the southward tidally induced drift and thus the residence time decreases. Similar effects are observed when the freshwater inflow to the harbour is increased from 2 to 10 m3/s during the ebb tide flow. For flood tide conditions, the effect of freshwater inflow is less significant. We also demonstrate an example of innovative coastal management targeted at the reduction of the residence time of the pathogenic material accidentally released in the harbour.},
keywords = {Atmospheric Sciences, Environmental Monitoring/Analysis, Fluid- and Aerodynamics, Geophysics/Geodesy, Lagrangian tracking, Numerical modelling, Oceanography, Residence time, Tidal currents, Water quality},
issn = {1616-7341, 1616-7228},
doi = {10.1007/s10236-013-0659-4},
url = {http://link.springer.com/article/10.1007/s10236-013-0659-4},
author = {Jouanneau, Nicolas and Sentchev, Alexei and Dumas, Franck}
}
  • [DOI] N. F. Putman, K. L. Mansfield, R. He, D. J. Shaver, and P. Verley, “Predicting the distribution of oceanic-stage kemp’s ridley sea turtles,” Biology letters, vol. 9, iss. 5, p. 20130345, 2013.
    [Bibtex] 
    @article {putman_predicting_2013,
title = {Predicting the distribution of oceanic-stage Kemp's ridley sea turtles},
journal = {Biology Letters},
volume = {9},
number = {5},
year = {2013},
month = {oct},
pages = {20130345},
abstract = {The inaccessibility of open ocean habitat and the cryptic nature of small animals are fundamental problems when assessing the distribution of oceanic-stage sea turtles and other marine animals sharing similar life-history traits. Most methods that estimate patterns of abundance cannot be applied in situations that are extremely data limited. Here, we use a movement ecology framework to generate the first predicted distributions for the oceanic stage of the Kemp{\textquoteright}s ridley sea turtle (Lepidochelys kempii). Our simulations of particle dispersal within ocean circulation models reveal substantial annual variation in distribution and survival among simulated cohorts. Such techniques can help prioritize areas for conservation, and supply inputs for more realistic demographic models attempting to characterize population trends.},
keywords = {distribution, Gulf of Mexico, movement ecology, ocean circulation model, sea turtle},
issn = {1744-9561, 1744-957X},
doi = {10.1098/rsbl.2013.0345},
url = {http://rsbl.royalsocietypublishing.org/content/9/5/20130345},
author = {Putman, Nathan F. and Mansfield, Katherine L. and He, Ruoying and Shaver, Donna J. and Verley, Philippe}
}
  • [DOI] I. A. Catalán, D. Macias, J. Solé, A. Ospina-Álvarez, and J. Ruiz, “Stay off the motorway: resolving the pre-recruitment life history dynamics of the european anchovy in the SW mediterranean through a spatially-explicit individual-based model (SEIBM),” Progress in oceanography, vol. 111, p. 140{–}153, 2013.
    [Bibtex] 
    @article {catalan_stay_2013,
title = {Stay off the motorway: Resolving the pre-recruitment life history dynamics of the European anchovy in the {SW} Mediterranean through a spatially-explicit individual-based model ({SEIBM})},
journal = {Progress in Oceanography},
volume = {111},
year = {2013},
pages = {140{\textendash}153},
abstract = {We explore the underlying mechanisms of the early life history dynamics of the European anchovy, Engraulis encrasicolus, in the {SW} Mediterranean. By using a 3D {ROMS} hydrodynamic model coupled to an individual-based model ({IBM}) of the larval stages of the European anchovy, we tested the following hypotheses: (1) the plausible effective spawning zones (those generating late larvae to the known nursery grounds) are mainly found in the vicinity of Malaga Bay, as suggested by published empirical data; (2) the observed, back-calculated growth of larvae sampled in the nursery grounds can be reasonably simulated by a simple temperature-dependent growth model; and (3) the inclusion of biological behavior in the {IBM} significantly improves the match between the observed and modeled late-larval recruitment and/or growth patterns. We performed simulations for the peak spawning season in 2008, for which survey data were available, and an average climatological run. Hypothesis 1 was accepted, whereas hypothesis 2 resulted in a good imitation of anchovy growth only after 10 days post-hatch. The inclusion of an empirically derived equation for egg buoyancy in the model (hypothesis 3) resulted in a slight improvement of the model of late-larval recruitment patterns. Finally, our model was used to explore possible retention-based nursery areas in the whole Alboran Sea. Our simulations showed to agree well with the existing data both in the European and in the African coast and confer the physics a dominant role in shaping the spatial dynamics of early life stages of anchovy in the area.},
issn = {0079-6611},
doi = {10.1016/j.pocean.2013.02.001},
url = {http://www.sciencedirect.com/science/article/pii/S0079661113000189},
author = {Catal{\'a}n, Ignacio A. and Macias, Diego and Sol{\'e}, Jordi and Ospina-{\'A}lvarez, Andr{\'e}s and Ruiz, Javier}
}
  • [DOI] N. F. Putman and R. He, “Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution,” Journal of the royal society interface, vol. 10, iss. 81, p. 20120979, 2013.
    [Bibtex] 
    @article {putman_tracking_2013,
title = {Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution},
journal = {Journal of The Royal Society Interface},
volume = {10},
number = {81},
year = {2013},
pages = {20120979},
abstract = {Ocean circulation models are widely used to simulate organism transport in the open sea, where challenges of directly tracking organisms across vast spatial and temporal scales are daunting. Many recent studies tout the use of {\textquoteleft}high-resolution{\textquoteright} models, which are forced with atmospheric data on the scale of several hours and integrated with a time step of several minutes or seconds. However, in many cases, the model{\textquoteright}s outputs that are used to simulate organism movement have been averaged to considerably coarser resolutions (e.g. monthly mean velocity fields). To examine the sensitivity of tracking results to ocean circulation model output resolution, we took the native model output of one of the most sophisticated ocean circulation models available, the Global Hybrid Coordinate Ocean Model, and averaged it to commonly implemented spatial and temporal resolutions in studies of basin-scale dispersal. Comparisons between simulated particle trajectories and in situ near-surface drifter trajectories indicated that {\textquoteleft}over averaging{\textquoteright} model output yields predictions inconsistent with observations. Further analyses focused on the dispersal of juvenile sea turtles indicate that very different inferences regarding the pelagic ecology of these animals are obtained depending on the resolution of model output. We conclude that physical processes occurring at the scale of days and tens of kilometres should be preserved in ocean circulation model output to realistically depict the movement marine organisms and the resulting ecological and evolutionary processes.},
keywords = {Dispersal, North Atlantic, ocean circulation model, Particle tracking, pleuston, sea turtle},
issn = {1742-5689, 1742-5662},
doi = {10.1098/rsif.2012.0979},
url = {http://rsif.royalsocietypublishing.org/content/10/81/20120979},
author = {Putman, Nathan F. and He, Ruoying}
}

2012

  • [DOI] S. Fossette, N. F. Putman, K. J. Lohmann, R. Marsh, and G. C. Hays, “A biologist’s guide to assessing ocean currents: a review,” Marine ecology-progress series, vol. 457, p. 285{–}301, 2012.
    [Bibtex] 
    @article {fossette_biologists_2012,
title = {A biologist's guide to assessing ocean currents: a review},
journal = {Marine Ecology-Progress Series},
volume = {457},
year = {2012},
pages = {285{\textendash}301},
abstract = {We review how ocean currents are measured (in both Eulerian and Lagrangian frameworks), how they are inferred from satellite observations, and how they are simulated in ocean general circulation models ({OGCMs}). We then consider the value of these {\textquoteright}direct{\textquoteright} (in situ) and {\textquoteright}indirect{\textquoteright} (inferred, simulated) approaches to biologists investigating current-induced drift of strong-swimming vertebrates as well as dispersion of small organisms in the open ocean. We subsequently describe 2 case studies. In the first, {OGCM}-simulated currents were compared with satellite-derived currents; analyses suggest that the 2 methods yield similar results, but that each has its own limitations and associated uncertainty. In the second analysis, numerical methods were tested using Lagrangian drifter buoys. Results indicated that currents simulated in {OGCMs} do not capture all details of buoy trajectories, but do successfully resolve most general aspects of current flows. We thus recommend that the errors and uncertainties in ocean current measurements, as well as limitations in spatial and temporal resolution of the surface current data, need to be considered in tracking studies that incorporate oceanographic data. Whenever possible, cross-validation of the different methods (e. g. indirect estimates versus buoy trajectories) should be undertaken before a decision is reached about which technique is best for a specific application.},
keywords = {Argos, caretta-caretta, central north pacific, Dispersal, Ekman drift, Geostrophic, loggerhead sea-turtles, long-distance movement, Marine mammal, mesoscale eddies, Orientation, particle tracking model, Plankton, population genetic-structure, satellite telemetry, Satellite-tracking, southern elephant seal, surface currents, Turtle},
issn = {0171-8630},
doi = {10.3354/meps09581},
author = {Fossette, Sabrina and Putman, Nathan F. and Lohmann, Kenneth J. and Marsh, Robert and Hays, Graeme C.}
}
  • [DOI] A. Ospina-Álvarez, I. Palomera, and C. Parada, “Changes in egg buoyancy during development and its effects on the vertical distribution of anchovy eggs,” Fisheries research, vol. 117{–}118, p. 86{–}95, 2012.
    [Bibtex] 
    @article {ospina-alvarez_changes_2012,
title = {Changes in egg buoyancy during development and its effects on the vertical distribution of anchovy eggs},
journal = {Fisheries Research},
volume = {117{\textendash}118},
year = {2012},
month = {apr},
pages = {86{\textendash}95},
abstract = {Small pelagic fish populations exhibit reproductive strategies resulting from past natural selection pressure, by which certain traits become more or less common in a population, allowing them to adapt and become better suited to certain habitats. One such adaptation is the buoyancy of eggs, which is observed as density changes during development. This is an important issue in fisheries and modeling science, as it affects the vertical distribution of eggs and, therefore, egg transport. Recently, individual-based models for anchovies in the Mediterranean have focused on developing adequate biological algorithms to simulate realistic spatial variations of eggs and larvae. Some models that include movements of particles according to Stokes{\textquoteright} law also assume a constant value of egg density during egg development. However, field observations show differences in the vertical distribution of eggs when egg density during development is considered. We address the problem of egg density and its vertical distribution within a biological context. In Mediterranean waters, the incubation time for anchovy eggs during peak spawning is approximately 48{\textendash}70 h; during these first hours, egg density has an influence on the horizontal and vertical trajectories of eggs, as well as their routes and hatching zones. In this study, we introduce an algorithm describing the egg density of European anchovy eggs throughout development. Egg density measurements were carried out in a density gradient column ({DGC}). We fitted a polynomial model that estimated egg density, as a function of time from fertilization and that was dependent on temperature. Simulations to study the vertical transport of eggs in the Mediterranean were carried out using {ICHTHYOP}/{MARS}3D. The vertical distribution of pelagic eggs was determined by a set of interacting biological and physical parameters related to eggs (density, diameter) and ambient seawater (density, viscosity, turbulence), respectively. The egg buoyancy model introduced here was validated and will provide insight for the design of anchovy egg surveys, as the vertical position of the eggs in the water column during development can be inferred by the hydrographic structure of seawater.},
keywords = {Egg buoyancy, Egg density, European anchovy, Ichthyop, Individual based model, Vertical distribution, {CUFES}, {IBM}},
issn = {0165-7836},
doi = {10.1016/j.fishres.2011.01.030},
url = {http://www.sciencedirect.com/science/article/pii/S0165783611000506},
author = {Ospina-{\'A}lvarez, Andr{\'e}s and Palomera, Isabel and Parada, Carolina}
}
  • [DOI] B. Yannicelli, L. Castro, C. Parada, W. Schneider, F. Colas, and D. Donoso, “Distribution of pleuroncodes monodon larvae over the continental shelf of south-central chile: field and modeling evidence for partial local retention and transport,” Progress in oceanography, vol. 92{–}95, p. 206{–}227, 2012.
    [Bibtex] 
    @article {yannicelli_distribution_2012,
title = {Distribution of Pleuroncodes monodon larvae over the continental shelf of south-central Chile: Field and modeling evidence for partial local retention and transport},
journal = {Progress in Oceanography},
volume = {92{\textendash}95},
year = {2012},
month = {jan},
pages = {206{\textendash}227},
abstract = {In situ and modeled spatial distribution of squat lobster (Pleuroncodes monodon) larvae over the continental shelf off south central Chile (35{\textendash}37{\textdegree}S) was analyzed along with currents and hydrography. We aimed to identify the main larval transport/retention characteristics in the study area, which constitutes the southernmost P. monodon fishing grounds embedded in the Humboldt Current System. We hypothesized that the main contribution to population renewal originates in the two persistent adult aggregations close to the nursery ground that occurs over a continental shelf terrace limited by two submarine canyons. Two extensive bio-physical field campaigns were carried out during the main 2001{\textendash}2002 upwelling season field data indicated that larvae were released from late austral winter to spring from spots to the north and south of the nursery. Zoea I were found mainly below 50 m depth in southward-flowing waters, whereas older zoea dominated in northward flowing layers above 50 m. Larvae were circumscribed between the coast and the shelf break front and pelagic retention areas were identified over the widest shelf area. Megalopa and juveniles during March, were only found over the nursery area. Individual based simulations coupled to the output of a hydrodynamic model (climatological configuration) for the studied area, showed that the release sites close to the nursery made the largest contribution to recruitment. Sites further north could also contribute to recruitment if hatching occurred later in the upwelling season. The contribution of vertical behavior to larval success was also important, as was the former{\textquoteright}s interaction with the site and time of larval release. Our results support the relevance of coastal circulation (affected by topography) on the persistence of P. monodon populations off southern Chile, and the modulation of temporal variability. These results might apply to other abundant species in the area.},
keywords = {Ichthyop},
issn = {0079-6611},
doi = {10.1016/j.pocean.2011.07.005},
url = {http://www.sciencedirect.com/science/article/pii/S0079661111000590},
author = {Yannicelli, Beatriz and Castro, Leonardo and Parada, Carolina and Schneider, Wolfgang and Colas, Francois and Donoso, David}
}
  • [DOI] C. Parada, F. Colas, S. Soto-Mendoza, and L. Castro, “Effects of seasonal variability in across- and alongshore transport of anchoveta (engraulis ringens) larvae on model-based pre-recruitment indices off central chile,” Progress in oceanography, vol. 92{–}95, p. 192{–}205, 2012.
    [Bibtex] 
    @article {parada_effects_2012,
title = {Effects of seasonal variability in across- and alongshore transport of anchoveta (Engraulis ringens) larvae on model-based pre-recruitment indices off central Chile},
journal = {Progress in Oceanography},
volume = {92{\textendash}95},
year = {2012},
month = {jan},
pages = {192{\textendash}205},
abstract = {An individual-based model ({IBM}) of anchoveta (Engraulis ringens) larvae was coupled to a climatological hydrodynamic (Regional Oceanic Modeling System, {ROMS}) model for central-southern Chile to answer the question as to whether or not across- and alongshore transport off central-southern Chile enhances retention in the spawning areas during the winter and summer reproductive periods, using model-based pre-recruitment indices (simulated transport success to nursery areas). The hydrodynamic model validation showed that {ROMS} captures the mean Seas Surface Temperature and Eddie Kinetic Energy observed in satellite-based data over the entire region. The {IBM} was used to simulate the transport of eggs and larvae from spawning zones in central Chile (Constituci{\'o}n, Dichato, Gulf of Arauco and Lebu{\textendash}Corral) to historical nursery areas ({HRZ}, region between 35{\textdegree}S and 37{\textdegree}S). Model results corroborated {HRZ} as the most successful pre-recruitment zone (particles originated in the Dichato and Gulf of Arauco spawning areas), as well as identifying Lebu{\textendash}Corral as a zone of high retention with a high associated pre-recruitment index (particles originated in the Lebu{\textendash}Corral spawning zone). The highest pre-recruitment values were mainly found in winter. The Constituci{\'o}n and Dichato spawning zones displayed a typical summer upwelling velocity pattern, while the Gulf of Arauco in summertime showed strong offshore and alongshore velocity components. The Lebu{\textendash}Corral region in winter presented important near-surface cross-shore transport towards the coast (associated with downwelling events), this might be one of the major mechanisms leading to high retention levels and a high pre-recruitment index for Lebu{\textendash}Corral spawning zone. The limitations of the modeling approach are discussed and put into perspective for future work.},
keywords = {Ichthyop},
issn = {0079-6611},
doi = {10.1016/j.pocean.2011.07.015},
url = {http://www.sciencedirect.com/science/article/pii/S0079661111000693},
author = {Parada, Carolina and Colas, Francois and Soto-Mendoza, Samuel and Castro, Leonardo}
}
  • [DOI] K. J. Lohmann, N. F. Putman, and C. M. Lohmann, “The magnetic map of hatchling loggerhead sea turtles,” Current opinion in neurobiology, vol. 22, iss. 2, p. 336{–}342, 2012.
    [Bibtex] 
    @article {lohmann_magnetic_2012,
title = {The magnetic map of hatchling loggerhead sea turtles},
journal = {Current Opinion in Neurobiology},
volume = {22},
number = {2},
year = {2012},
pages = {336{\textendash}342},
abstract = {Young loggerhead sea turtles (Caretta caretta) from eastern Florida, U.S.A., undertake a transoceanic migration in which they gradually circle the North Atlantic Ocean before returning to the North American coast. Hatchlings in the open sea are guided at least partly by a {\textquoteleft}magnetic map{\textquoteright} in which regional magnetic fields function as navigational markers and elicit changes in swimming direction at crucial locations along the migratory route. The magnetic map exists in turtles that have never migrated and thus appears to be inherited. Turtles derive both longitudinal and latitudinal information from the Earth{\textquoteright}s field, most likely by exploiting unique combinations of field inclination and intensity that occur in different geographic areas. Similar mechanisms may function in the migrations of diverse animals.},
keywords = {Ichthyop},
issn = {0959-4388},
doi = {10.1016/j.conb.2011.11.005},
url = {http://www.sciencedirect.com/science/article/pii/S0959438811001954},
author = {Lohmann, Kenneth J and Putman, Nathan F and Lohmann, Catherine MF}
}
  • [DOI] L. Garavelli, A. Grüss, B. Grote, N. Chang, M. Smith, P. Verley, E. K. Stenevik, D. M. Kaplan, and C. Lett, “Modeling the dispersal of cape hake ichthyoplankton,” Journal of plankton research, vol. 34, iss. 8, p. 655{–}669, 2012.
    [Bibtex] 
    @article {garavelli_modeling_2012,
title = {Modeling the dispersal of Cape hake ichthyoplankton},
journal = {Journal of Plankton Research},
volume = {34},
number = {8},
year = {2012},
pages = {655{\textendash}669},
abstract = {The two Cape hake species of the southern Benguela ecosystem, the shallow-water and deep-water hakes Merluccius capensis and M. paradoxus, are economically the most important marine resources in South Africa. Recruitment is a key process in the dynamics of marine organisms, yet very little is known about the early life history of Cape hakes, especially the location of spawning grounds and transport of eggs and larvae. For each species, ichthyoplankton dispersal off South Africa is simulated by coupling oceanographic simulations to an individual-based model in order to track virtual individuals. Results indicate that the most favorable spawning areas for transport to nursery areas are located off the south-western coast and the eastern Agulhas Bank, and highlight partly different drift routes followed by the two ichthyoplankton species off Cape Columbine. Transport from spawning to nursery areas is the highest in austral winter for a spawning depth ranging between 0 and 100 m. These modeling results are in broad agreement with available knowledge on the ecology of Cape hakes. The present work on Cape hakes complements previous modeling studies on anchovy and sardine in the same area. Taken together, these studies underline the correspondence between cross-shore (for hakes) or alongshore (for anchovy and sardine) transport mechanisms and the spawning strategies used by these key species of the southern Benguela ecosystem.},
keywords = {larval dispersal, Merluccius spp., modeling, Southern Benguela},
issn = {0142-7873, 1464-3774},
doi = {10.1093/plankt/fbs039},
url = {http://plankt.oxfordjournals.org/content/34/8/655},
author = {Garavelli, L. and Gr{\"u}ss, A. and Grote, B. and Chang, N. and Smith, M. and Verley, P. and Stenevik, E. K. and Kaplan, D. M. and Lett, C.}
}
  • [DOI] S. Soto-Mendoza, C. Parada, L. Castro, F. Colas, and W. Schneider, “Modeling transport and survival of anchoveta eggs and yolk–sac larvae in the coastal zone off central-southern chile: assessing spatial and temporal spawning parameters,” Progress in oceanography, vol. 92{–}95, p. 178{–}191, 2012.
    [Bibtex] 
    @article {soto-mendoza_modeling_2012,
title = {Modeling transport and survival of anchoveta eggs and yolk{\textendash}sac larvae in the coastal zone off central-southern Chile: Assessing spatial and temporal spawning parameters},
journal = {Progress in Oceanography},
volume = {92{\textendash}95},
year = {2012},
month = {jan},
pages = {178{\textendash}191},
abstract = {A hydrodynamic model was coupled to an individual-based model ({IBM}) initialized with conditions observed during 2004 to examine the influence of spatial and temporal spawning parameters on transport and survival of Engraulis ringens in central-southern Chile. Processes modeled were transport, growth, and mortality of the early stages. The results showed that spatial and temporal variations in spawning modulated the survival of anchoveta eggs and yolk{\textendash}sac larvae. The resultant transport of the early stages had an important south{\textendash}north direction. In terms of connectivity, the greatest transfer of eggs and larvae to the pre-recruitment zone came from four spawning zones. Retention occurred in all spawning zones and was strongest in the Gulf of Arauco and at Lebu{\textendash}Corral. Mortality due to temperature and advective losses was more intense at higher latitudes (Lebu{\textendash}Corral). Observed and simulated distributions of eggs and larvae were compared, and the differences are discussed herein. A conceptual model is proposed, and we discuss the relevance of {IBMs} as useful tools with which to assess spawning zones for purposes of management.},
keywords = {Ichthyop},
issn = {0079-6611},
doi = {10.1016/j.pocean.2011.07.001},
url = {http://www.sciencedirect.com/science/article/pii/S0079661111000553},
author = {Soto-Mendoza, Samuel and Parada, Carolina and Castro, Leonardo and Colas, Francois and Schneider, Wolfgang}
}
  • [DOI] N. F. Putman, R. Scott, P. Verley, R. Marsh, and G. C. Hays, “Natal site and offshore swimming influence fitness and long-distance ocean transport in young sea turtles,” Marine biology, vol. 159, iss. 10, p. 2117{–}2126, 2012.
    [Bibtex] 
    @article {putman_natal_2012,
title = {Natal site and offshore swimming influence fitness and long-distance ocean transport in young sea turtles},
journal = {Marine Biology},
volume = {159},
number = {10},
year = {2012},
pages = {2117{\textendash}2126},
abstract = {Although long-distance transport of marine organisms is constrained by numerous oceanic and biological factors, some species have evolved life-histories reliant on such movements. We examine the factors that promote long-distance transport in a transoceanic migrant, young loggerhead sea turtles (Caretta caretta), from the southeastern U.S. Empirical data from near-surface buoys and simulations in two ocean circulation models indicated that passive drifters are often retained for long periods shoreward of oceanic fronts that delineate coastal and offshore waters. Further simulations revealed that offshore swimming aided newly hatched turtles in moving past fronts and increased turtles{\textquoteright} probability of survival, reaching distant foraging grounds, and encountering favorable temperatures. Swimming was most beneficial in regions that were more favorable under scenarios assuming passive drift. These results have broad implications for understanding the movement processes of many marine species, highlighting likely retention of more planktonic species and potential for dispersal in more nektonic species.},
keywords = {Freshwater \& Marine Ecology, Ichthyop, Marine \& Freshwater Sciences, Microbiology, Oceanography, Zoology},
issn = {0025-3162, 1432-1793},
doi = {10.1007/s00227-012-1995-5},
url = {http://link.springer.com/article/10.1007/s00227-012-1995-5},
author = {Putman, Nathan F. and Scott, Rebecca and Verley, Philippe and Marsh, Robert and Hays, Graeme C.}
}
  • [DOI] N. F. Putman, P. Verley, T. J. Shay, and K. J. Lohmann, “Simulating transoceanic migrations of young loggerhead sea turtles: merging magnetic navigation behavior with an ocean circulation model,” The journal of experimental biology, vol. 215, iss. 11, p. 1863{–}1870, 2012.
    [Bibtex] 
    @article {putman_simulating_2012,
title = {Simulating transoceanic migrations of young loggerhead sea turtles: merging magnetic navigation behavior with an ocean circulation model},
journal = {The Journal of Experimental Biology},
volume = {215},
number = {11},
year = {2012},
month = {jan},
pages = {1863{\textendash}1870},
keywords = {Dispersal, distribution, Ichthyop, loggerhead sea turtle, magnetic map, magnetorecpetion, ocean circulation model},
issn = {0022-0949, 1477-9145},
doi = {10.1242/jeb.067587},
url = {http://jeb.biologists.org/content/215/11/1863},
author = {Putman, Nathan F. and Verley, Philippe and Shay, Thomas J. and Lohmann, Kenneth J.}
}
  • N. F. Putman, P. Verley, T. J. Shay, and K. J. Lohmann, “Transoceanic migratory dispersal in young sea turtles: the role of currents and geomagnetic navigation,” Integrative and comparative biology, vol. 52, p. E142{–}E142, 2012.
    [Bibtex] 
    @article {putman_transoceanic_2012,
title = {Transoceanic migratory dispersal in young sea turtles: the role of currents and geomagnetic navigation},
journal = {Integrative and Comparative Biology},
volume = {52},
year = {2012},
note = {{WOS}:000303165001034},
month = {apr},
pages = {E142{\textendash}E142},
issn = {1540-7063},
author = {Putman, N. F. and Verley, P. and Shay, T. J. and Lohmann, K. J.}
}
  • [DOI] A. Ospina-Álvarez, C. Parada, and I. Palomera, “Vertical migration effects on the dispersion and recruitment of european anchovy larvae: from spawning to nursery areas,” Ecological modelling, vol. 231, p. 65{–}79, 2012.
    [Bibtex] 
    @article {ospina-alvarez_vertical_2012,
title = {Vertical migration effects on the dispersion and recruitment of European anchovy larvae: From spawning to nursery areas},
journal = {Ecological Modelling},
volume = {231},
year = {2012},
month = {apr},
pages = {65{\textendash}79},
abstract = {Recruitment of European anchovy has been traditionally thought to largely depend on the passive transport and dispersion of eggs and larvae from spawning to nursery areas. Knowledge of the factors influencing the vertical distribution of fish early stages, and consequently influencing the transport, is a crucial issue in fisheries science. The aim of this study is to assess the relevance of diel vertical migration ({DVM}) as a mechanism involved in the transport of European anchovy larvae toward nursery areas taking into account age/stage-dependent vertical migration (i.e., the maximum migration). We developed a simplified vertical migration sub-model for anchovy larvae included in an Individual-based ({IBM}) hydrodynamic coupled model. Two types of simulation experiments were conducted: (1) {\textquoteleft}Pure{\textquoteright} Lagrangian (passive) transport experiments and (2) biological behavior transport experiments with a realistic scheme for egg-buoyancy, larval growth, and {DVM} scheme. We detected high variability in the trajectory and final position of larvae with 14 mm length between the passive and biological behavior experiments. The particles were less clustered in the passive transport experiment. In the biological experiment the particles were aggregated depending on the mesoscale oceanographic structures, evidencing a transport associated to filaments and meanders. The formation of schools was facilitated by the transport in filaments and larvae transported within filaments generally avoided the nucleus of the eddies and the central part of the North Current. Moreover, our results suggest that there is interconnectivity between all the anchovy sub-populations in the {NW} Mediterranean and that the Gulf of Lions and the shelf waters surrounding the Ebro River Delta are the most important areas for anchovy reproduction in this region. Additionally, we detected that the pre-recruitment is higher in those years when the larvae retention is favored. We underline that bottlenecks in larval transport modeling are related to the scarcity of knowledge in developmental biology and behavior of anchovy larvae and emergent mechanistic processes.},
keywords = {anchovy, Connectivity, Dispersion, Ebro Delta, Gulf of Lions, Ichthyop, Mediterranean, Recruitment, Schooling, Vertical migration, {DVM}, {IBM}},
issn = {0304-3800},
doi = {10.1016/j.ecolmodel.2012.02.001},
url = {http://www.sciencedirect.com/science/article/pii/S0304380012000567},
author = {Ospina-{\'A}lvarez, Andr{\'e}s and Parada, Carolina and Palomera, Isabel}
}

2011

  • [DOI] T. Brochier, E. Mason, M. Moyano, A. Berraho, F. Colas, P. Sangrà, S. Hernández-León, O. Ettahiri, and C. Lett, “Ichthyoplankton transport from the african coast to the canary islands,” Journal of marine systems, vol. 87, iss. 2, p. 109{–}122, 2011.
    [Bibtex] 
    @article {brochier_ichthyoplankton_2011,
title = {Ichthyoplankton transport from the African coast to the Canary Islands},
journal = {Journal of Marine Systems},
volume = {87},
number = {2},
year = {2011},
pages = {109{\textendash}122},
abstract = {The Canary Upwelling System ({CUS}), a major eastern boundary upwelling system, sustains large cross-border fisheries of small pelagic fish, which poses the question of stock connectivity. Studies suggest that ichthyoplankton transport from the northwest African coast to the Canary Islands ({CI}) is facilitated by coastal-upwelling associated filaments. Here we analyze connections between larval supply to the {CI} and sardine and anchovy populations that spawn over the continental shelf. For both species, ichthyoplankton observations (1) at the shelf and (2) near the island of Gran Canaria ({GC}) are used. Predictions of ichthyoplankton transport to {GC} are obtained from the Ichthyop Lagrangian transport model, which is forced by a high-resolution hydrodynamic model ({ROMS}) that reproduces the regional circulation. Results show that upwelling filaments play an important role in the transport of larvae to {GC}. However, (1) filaments are not the only mechanism, and (2) filament presence does not necessarily imply larval transport. Anchovy and sardine larval presence at {GC} appears to be independent of the respective adult spawning seasonality. Combining of observed and modeled data does not succeed in reproducing the observed larval patterns at {GC}. Various hypotheses are proposed to explain this discrepancy in larval transport to {GC}.},
keywords = {Canary Current, Gran Canaria, Hydrodynamic model, Ichthyop, Ichthyoplankton, Lagrangian model, Pelagic fish, Transport, Upwelling filaments},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2011.02.025},
url = {http://www.sciencedirect.com/science/article/pii/S0924796311000698},
author = {Brochier, Timoth{\'e}e and Mason, Evan and Moyano, Marta and Berraho, Amina and Colas, Francois and Sangr{\`a}, Pablo and Hern{\'a}ndez-Le{\'o}n, Santiago and Ettahiri, Omar and Lett, Christophe}
}
  • [DOI] T. Brochier, C. Lett, and P. Fréon, “Investigating the “northern humboldt paradox” from model comparisons of small pelagic fish reproductive strategies in eastern boundary upwelling ecosystems,” Fish and fisheries, vol. 12, iss. 1, p. 94{–}109, 2011.
    [Bibtex] 
    @article {brochier_investigating_2011,
title = {Investigating the "northern Humboldt paradox" from model comparisons of small pelagic fish reproductive strategies in eastern boundary upwelling ecosystems},
journal = {Fish and Fisheries},
volume = {12},
number = {1},
year = {2011},
pages = {94{\textendash}109},
abstract = {Eastern boundary upwelling ecosystems are highly productive and sustain the world{\textquoteright}s largest fisheries, usually dominated by sardine and anchovy species. Stock size is highly variable from year to year due to the impact of the unstable physical environment on fish early stages. Biophysical models of early life-stage dispersal of marine organisms have been built by coupling (i) hydrodynamic models and (ii) life history models (i.e. egg and larva stages), and are therefore useful tools to investigate physical{\textendash}biological interactions. Here, we review biophysical models of anchovy and sardine ichthyoplankton dispersals developed in the Benguela, Humboldt and Canary Current upwelling ecosystems. We also include a similar study conducted in the California Current upwelling on zooplankton. We then integrate this information into a comparative analysis of sardine and anchovy reproductive strategies in the different systems. We found that the main spawning periods match the season of (i) maximal simulated ichthyoplankton retention over the continental shelf in the northern Benguela, southern Humboldt and Canary (for sardine); (ii) maximal food concentration in the southern Benguela, California and Canary (for anchovy); and (iii) maximal shelf retention of ichthyoplankton and food concentration in the northern Humboldt (for both anchovy and sardine). This specificity of the northern Humboldt ecosystem could explain why it sustains the largest small pelagic fish stock. Finally, the possible effects of climate change on these patterns are discussed.},
keywords = {Comparative approach, Ichthyop, Ichthyoplankton, reproductive strategy, retention, small pelagic fish, upwelling systems},
issn = {1467-2979},
doi = {10.1111/j.1467-2979.2010.00385.x},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-2979.2010.00385.x/abstract},
author = {Brochier, Timoth{\'e}e and Lett, Christophe and Fr{\'e}on, Pierre}
}

2010

  • [DOI] L. Velo-Suárez, B. Reguera, S. González-Gil, M. Lunven, P. Lazure, E. Nézan, and P. Gentien, “Application of a 3d lagrangian model to explain the decline of a dinophysis acuminata bloom in the bay of biscay,” Journal of marine systems, vol. 83, iss. 3{–}4, p. 242{–}252, 2010.
    [Bibtex] 
    @article {velo-suarez_application_2010,
title = {Application of a 3D Lagrangian model to explain the decline of a Dinophysis acuminata bloom in the Bay of Biscay},
journal = {Journal of Marine Systems},
volume = {83},
number = {3{\textendash}4},
year = {2010},
pages = {242{\textendash}252},
abstract = {During July 2006, a cruise was carried out in the Northern Bay of Biscay (off Brittany, France) to study meso- and microscale patterns of phytoplankton distribution. Moderate concentrations (102{\textendash}103 cells L-1) of Dinophysis acuminata were constrained to specific depths (upper layers above the pycnocline) at stations with lower surface salinity (34.5) and steep temperature gradients (18{\textendash}13.5 {\textdegree}C between 4 and 7 m depth) within the Loire and Vilaine river plumes. On board incubations revealed a healthy D. acuminata population at the biomass maxima with 89\% of viable ({FDA}-treated) cells and moderate division rates (up to 0.10 d-1). Despite its good physiological condition, the population of D. acuminata declined rapidly to undetectable levels during the second leg of the cruise. A 3D Lagrangian Particle-Tracking Model (3D {LPTM}) was used to simulate the transport of D. acuminata cells in the Loire and Vilaine river plumes from 15 June to 30 July. This 3D {LPTM} model was coupled to a {MARS}3D (Model for Applications at Regional Scale) model previously calibrated and validated for the region. Model results suggest that physical processes alone could explain the dispersion of the D. acuminata population within the area. The application of a 3D-{LPTM} model shows how individual based model approaches are valuable to identify Dinophysis spp. transport pathways and reproduce retention/dispersion patterns observed in the field.},
keywords = {Bay of Biscay, Dinophysis acuminata, Harmful algal blooms, Ichthyop, Lagrangian individual particle-tracking models, Physical{\textendash}biological interactions},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2010.05.011},
url = {http://www.sciencedirect.com/science/article/pii/S0924796310001004},
author = {Velo-Su{\'a}rez, L. and Reguera, B. and Gonz{\'a}lez-Gil, S. and Lunven, M. and Lazure, P. and N{\'e}zan, E. and Gentien, P.}
}
  • [DOI] R. S. Martins, M. J. Roberts, N. Chang, P. Verley, C. L. Moloney, and E. A. G. Vidal, “Effect of yolk utilization on the specific gravity of chokka squid (loligo reynaudii) paralarvae: implications for dispersal on the agulhas bank, south africa,” ICES journal of marine science: journal du conseil, vol. 67, iss. 7, p. 1323{–}1335, 2010.
    [Bibtex] 
    @article {martins_effect_2010,
title = {Effect of yolk utilization on the specific gravity of chokka squid (Loligo reynaudii) paralarvae: implications for dispersal on the Agulhas Bank, South Africa},
journal = {{ICES} Journal of Marine Science: Journal du Conseil},
volume = {67},
number = {7},
year = {2010},
month = {jan},
pages = {1323{\textendash}1335},
abstract = {Martins, R. S., Roberts, M. J., Chang, N., Verley, P., Moloney, C. L., and Vidal, E. A. G. 2010. Effect of yolk utilization on the specific gravity of chokka squid (Loligo reynaudii) paralarvae: implications for dispersal on the Agulhas Bank, South Africa. {\textendash} {ICES} Journal of Marine Science, 67: 1323{\textendash}1335. Specific gravity is an important parameter in the dispersal of marine zooplankton, because the velocity of currents, and therefore the speed of transport, is usually greatest near the surface. For the South African chokka squid (Loligo reynaudii), recruitment is thought to be influenced by the successful transport of paralarvae from the spawning grounds to a food-rich feature known as the cold ridge some 100{\textendash}200 km away. The role of paralarval specific gravity on such transport is investigated. Specific gravity ranged from 1.0373 to 1.0734 g cm-3 during the yolk-utilization phase, implying that paralarvae are always negatively buoyant, regardless of yolk content. The data were incorporated into a coupled individual-based model ({IBM}){\textemdash}Regional Ocean Modelling System model. The output showed that dispersal was dominantly westward towards the cold ridge. Also, modelled paralarval vertical distribution suggested that hydrodynamic turbulence was an important factor in dispersal. The negative buoyancy of early chokka squid paralarvae may reduce the risk of paralarvae being advected off the eastern Agulhas Bank and into the open ocean, where food is less abundant, so specific gravity may be important in enhancing the survival and recruitment of chokka squid.},
keywords = {Agulhas Bank, chokka squid, Dispersal, Ichthyop, paralarvae, specific gravity},
issn = {1054-3139, 1095-9289},
doi = {10.1093/icesjms/fsq098},
url = {http://icesjms.oxfordjournals.org/content/67/7/1323},
author = {Martins, Rodrigo S. and Roberts, Michael J. and Chang, Nicolette and Verley, Philippe and Moloney, Coleen L. and Vidal, Erica A. G.}
}
  • [DOI] M. J. Roberts and C. Mullon, “First lagrangian ROMS–IBM simulations indicate large losses of chokka squid loligo reynaudii paralarvae from south africa’s agulhas bank,” African journal of marine science, vol. 32, iss. 1, p. 71{–}84, 2010.
    [Bibtex] 
    @article {roberts_first_2010,
title = {First Lagrangian {ROMS}{\textendash}{IBM} simulations indicate large losses of chokka squid Loligo reynaudii paralarvae from South Africa's Agulhas Bank},
journal = {African Journal of Marine Science},
volume = {32},
number = {1},
year = {2010},
pages = {71{\textendash}84},
abstract = {Present knowledge of ocean currents based on in situ observation and models suggests that passive biological material such as eggs and larvae can be advected offshore away from the Agulhas Bank, South Africa, and hence removed from the ecosystem on which their survival and recruitment depends. Such losses have been cited as the root cause of the sudden drop in annual squid catches experienced in 2001. In this study, a Lagrangian {IBM} (individual-based model) coupled to a {ROMS} (regional ocean model system) model was used to investigate this hypothesis. Three simulations were performed for 12 model months using neutrally buoyant particles released from the seabed (120 m) every second day on the mid-shelf of the eastern, central and western regions of the Agulhas Bank. Boundary effects and resolution precluded the release of virtual particles on the inshore spawning grounds. Particles were given lifespans of 40 days. Results demonstrated large particle losses from the eastern Agulhas Bank (76\%) and the western Agulhas Bank (64\%). In contrast, few particles were lost from the central Agulhas Bank (2\%), making this, in terms of the model, the most suitable place on the Agulhas Bank for spawning. Visualisation of the {ROMS} outputs revealed that leakage on the eastern Agulhas Bank was caused by a cyclonic eddy resident in the Agulhas Bight. Similarly, leakage from the western Agulhas Bank was caused by deep-water cyclonic eddies in the adjacent Atlantic Ocean.},
keywords = {Ichthyop},
issn = {1814-232X},
doi = {10.2989/18142321003714518},
url = {http://www.tandfonline.com/doi/abs/10.2989/18142321003714518},
author = {Roberts, M J and Mullon, C}
}
  • [DOI] N. F. Putman, T. J. Shay, and K. J. Lohmann, “Is the geographic distribution of nesting in the kemp’s ridley turtle shaped by the migratory needs of offspring?,” Integrative and comparative biology, vol. 50, iss. 3, p. 305{–}314, 2010.
    [Bibtex] 
    @article {putman_is_2010,
title = {Is the Geographic Distribution of Nesting in the Kemp's Ridley Turtle Shaped by the Migratory Needs of Offspring?},
journal = {Integrative and Comparative Biology},
volume = {50},
number = {3},
year = {2010},
month = {jan},
pages = {305{\textendash}314},
abstract = {Across the geographic area that a species uses for reproduction, the density of breeding individuals is typically highest in locations where ecological factors promote reproductive success. For migratory animals, fitness depends, in part, on producing offspring that migrate successfully to habitats suitable for the next life-history stage. Thus, natural selection might favor reproduction in locations with conditions that facilitate the migration of offspring. To investigate this concept, we studied the Kemp{\textquoteright}s ridley sea turtle (Lepidochelys kempii) to determine whether coastal areas with the highest levels of nesting have particularly favorable conditions for hatchling migration. We modeled the passive drift of young Kemp{\textquoteright}s ridley turtles from seven nesting regions within the Gulf of Mexico to foraging grounds using the particle-tracking program {ICHTHYOP} and surface-current output from {HYCOM} ({HYbrid} Coordinate Ocean Model). Results revealed that geographic regions with conditions that facilitate successful migration to foraging grounds typically have higher abundance of nests than do regions where oceanographic conditions are less favorable and successful migration is difficult for hatchlings. Thus, our findings are consistent with the hypothesis that, for the Kemp{\textquoteright}s ridley turtle and perhaps for other migrants, patterns of abundance across the breeding range are shaped in part by conditions that promote or impede the successful migration of offspring.},
keywords = {Ichthyop},
issn = {1540-7063, 1557-7023},
doi = {10.1093/icb/icq041},
url = {http://icb.oxfordjournals.org/content/50/3/305},
author = {Putman, Nathan F. and Shay, Thomas J. and Lohmann, Kenneth J.}
}

2009

  • [DOI] A. Nicolle, P. Garreau, and B. Liorzou, “Modelling for anchovy recruitment studies in the gulf of lions (western mediterranean sea),” Ocean dynamics, vol. 59, iss. 6, p. 953{–}968, 2009.
    [Bibtex] 
    @article {nicolle_modelling_2009,
title = {Modelling for anchovy recruitment studies in the Gulf of Lions (Western Mediterranean Sea)},
journal = {Ocean Dynamics},
volume = {59},
number = {6},
year = {2009},
month = {dec},
pages = {953{\textendash}968},
abstract = {Anchovy (Engraulis encrasicolus) is an important commercial species and one of the most abundant pelagic fish in the Gulf of Lions and the Catalan Sea. The factors influencing its recruitment are crucial to fisheries and ecological research. Among those factors transport of larvae by hydrodynamics (currents) is important because it determines whether the organisms can reach areas favourable to recruitment or are dispersed. Therefore, the first step in anchovy recruitment modelling is to simulate North-western Mediterranean Sea circulation. Several years (2001{\textendash}2008) of hydrodynamics were simulated with the {MARS}-3D code. The resulting simulated currents and salinity are used by Lagrangian tool, Ichthyop, to transport anchovy eggs and larvae to the Western Mediterranean Sea. The aim of this study is to understand the main hydrodynamic processes that control anchovy transport and the effects of diel vertical migration on the transport and final distribution of anchovy.},
keywords = {anchovy, Diel vertical migration, Environmental Monitoring/Analysis, Fluid- and Aerodynamics, Geophysics/Geodesy, Gulf of Lions, Ichthyop, Lagrangian transport, Mediterranean Sea, Meteorology/Climatology, Numerical model, Oceanography},
issn = {1616-7341, 1616-7228},
doi = {10.1007/s10236-009-0221-6},
url = {http://link.springer.com/article/10.1007/s10236-009-0221-6},
author = {Nicolle, Amandine and Garreau, Pierre and Liorzou, Bernard}
}
  • [DOI] T. Brochier, F. Colas, C. Lett, V. Echevin, L. A. Cubillos, J. Tam, M. Chlaida, C. Mullon, and P. Fréon, “Small pelagic fish reproductive strategies in upwelling systems: a natal homing evolutionary model to study environmental constraints,” Progress in oceanography, vol. 83, iss. 1{–}4, p. 261{–}269, 2009.
    [Bibtex] 
    @article {brochier_small_2009,
title = {Small pelagic fish reproductive strategies in upwelling systems: A natal homing evolutionary model to study environmental constraints},
journal = {Progress in Oceanography},
volume = {83},
number = {1{\textendash}4},
year = {2009},
pages = {261{\textendash}269},
abstract = {Although little is known about the individual-level mechanisms that influence small pelagic fish species{\textquoteright} reproductive strategy, Mullon et al. [Mullon, C., Cury, P., Penven, P., 2002. Evolutionary individual-based model for the recruitment of anchovy (Engraulis capensis) in the southern Benguela. Canadian Journal of Fisheries and Aquatic Sciences 59, 910{\textendash}922] showed that the observed anchovy spawning patterns in the southern Benguela Current system off South Africa could be accurately reproduced by simulating a natal homing reproductive strategy, i.e. individuals spawning at their natal date and place. Here we used a similar method, i.e., an individual-based model of the natal homing reproductive strategy, and applied it to other upwelling systems: the northern Humboldt Current system off Peru, the southern Humboldt Current system off Chile and the central Canary Current system off Morocco. We investigated the spatial (horizontal and vertical) and seasonal spawning patterns that emerged after applying different environmental constraints in the model, and compared these to observed spawning patterns of sardine and anchovy in their respective systems. The selective environmental constraints tested were: (1) lethal temperature; (2) retention over the continental shelf; and (3) avoidance of dispersive structures. Simulated horizontal spatial patterns and seasonal patterns compared reasonably well with field data, but vertical patterns in most cases did not. Similarly to what was found for the southern Benguela, temperature was a determinant constraint in the southern Humboldt. The shelf retention constraint led to selection of a particular spawning season during the period of minimum upwelling in all three of the upwelling regions considered, and to spatial patterns that matched observed anchovy spawning off Chile and sardine spawning off Morocco. The third constraint, avoidance of dispersive structures, led to the emergence of a spawning season during the period of maximum upwelling off Chile and Morocco, but not in Peru. The most accurate representation of observed spatio-temporal spawning patterns off Peru was achieved through a combination of shelf retention and non-dispersion constraints.},
keywords = {Ichthyop},
issn = {0079-6611},
doi = {10.1016/j.pocean.2009.07.044},
url = {http://www.sciencedirect.com/science/article/pii/S0079661109000901},
author = {Brochier, T. and Colas, F. and Lett, C. and Echevin, V. and Cubillos, L.A. and Tam, J. and Chlaida, M. and Mullon, C. and Fr{\'e}on, P.}
}

2008

  • [DOI] C. Parada, C. Mullon, C. Roy, P. Fréon, L. Hutchings, and C. van der Lingen, “Does vertical migratory behaviour retain fish larvae onshore in upwelling ecosystems? a modelling study of anchovy in the southern benguela,” African journal of marine science, vol. 30, iss. 3, p. 437{–}452, 2008.
    [Bibtex] 
    @article {parada_does_2008,
title = {Does vertical migratory behaviour retain fish larvae onshore in upwelling ecosystems? A modelling study of anchovy in the southern Benguela},
journal = {African Journal of Marine Science},
volume = {30},
number = {3},
year = {2008},
pages = {437{\textendash}452},
abstract = {A spatially explicit individual-based model ({IBM}) forced by 3D temperature and current fields simulated by a hydrodynamic model of the southern Benguela upwelling region was used to test two hypotheses concerning the role of diel vertical migration ({DVM}) by Cape anchovy Engraulis encrasicolus larvae and pre-recruits. These hypotheses were that: (1) {DVM} enhances alongshore transport of anchovy eggs and larvae from the spawning grounds to the nursery area while avoiding the lethal effect of low water temperatures in the upwelling system, and/or (2) {DVM} enhances the transport of larvae and pre-recruits from the offshore to the onshore domain of the nursery area, and then counteracts offshore advection by favouring retention. We tracked the trajectories of virtual particles in the model and calculated a pre-recruitment index as a proxy for transport success to the nursery area (onshore and offshore) and found that the index increased from 10\% to 20\% after the incorporation of larval vertical migration into the {IBM}, with virtual individuals held at depths of around 60 m showing maximal pre-recruitment index values. Hence, {DVM} does appear to enhance transport to the nursery area (offshore) for early and late larvae. Model outputs showed coarse-scale horizontal distribution patterns of larvae by age/size class that are similar to field observations for early, small larvae but not for large larvae and pre-recruits. Observations show that early/small larvae are located offshore whereas older/larger larvae and pre-recruits are found closer to the continental shelf and the inner nursery grounds. This disparity between model results and field observations does not support the hypothesis that {DVM} is one of the mechanisms involved in the onshore movement of early life-history stages, especially for large larvae.},
keywords = {Ichthyop},
issn = {1814-232X},
doi = {10.2989/AJMS.2008.30.3.1.635},
url = {http://www.tandfonline.com/doi/abs/10.2989/AJMS.2008.30.3.1.635},
author = {Parada, C and Mullon, C and Roy, C and Fr{\'e}on, P and Hutchings, L and van der Lingen, CD}
}
  • [DOI] T. Brochier, C. Lett, J. Tam, P. Fréon, F. Colas, and P. Ayón, “An individual-based model study of anchovy early life history in the northern humboldt current system,” Progress in oceanography, vol. 79, iss. 2{–}4, p. 313{–}325, 2008.
    [Bibtex] 
    @article {brochier_individual-based_2008,
title = {An individual-based model study of anchovy early life history in the northern Humboldt Current system},
journal = {Progress in Oceanography},
volume = {79},
number = {2{\textendash}4},
year = {2008},
pages = {313{\textendash}325},
abstract = {We used an individual-based model of anchovy (Engraulis ringens) early life history coupled with hydrodynamic outputs from the regional oceanic modeling system ({ROMS}) to investigate the factors driving variability in egg and larval survival rates in the northern Humboldt upwelling region off Peru. Individuals were released within a coastal area and followed for a period of 30 days. Those that were still in the coastal area at that time were considered as retained. We investigated the spatial and temporal variability in the release locations of the individuals retained, and compared these to observed egg concentration patterns reconstructed from a 40-year period of monitoring. A first set of simulations using passive particles to represent anchovy eggs and larvae revealed a large sensitivity of the results to the initial vertical distribution of particles. We then conducted two additional sets of simulations that included the effect of egg buoyancy, larval vertical swimming behavior and lethal temperature. We obtained (1) maximal coastal retention close to the surface in winter and in deeper layers in summer, (2) a large influence of egg buoyancy and of larval vertical behavior on coastal retention in all seasons, (3) a partial match between dates and locations of enhanced retention and observed egg concentration patterns and (4) a low effect of lethal temperature on survival except when associated with high egg density. The model suggests that an optimal temporal spawning pattern for maximizing coastal retention would have two maximums, the most significant in austral winter and the second in summer. This pattern agrees roughly with observed spawning seasonality, but with temporal discrepancy of about two months in the peaks of both series. Spatially, we obtained higher retention from 10 S to 20 S, whereas the observed maximum egg concentration was located between 6{\textdegree}S and 14{\textdegree}S. Among the three sets of simulations, the one taking into account larval vertical swimming behavior lead to the best match with the data.},
keywords = {Biophysical model, Egg buoyancy, Engraulis ringens, Hydrodynamic model, Ichthyop, Ichthyoplankton, Larval survival, Peru, {DVM}, {IBM}},
issn = {0079-6611},
doi = {10.1016/j.pocean.2008.10.004},
url = {http://www.sciencedirect.com/science/article/pii/S0079661108001845},
author = {Brochier, Timoth{\'e}e and Lett, Christophe and Tam, Jorge and Fr{\'e}on, Pierre and Colas, Francois and Ay{\'o}n, Patricia}
}
  • [DOI] C. Lett, P. Verley, C. Mullon, C. Parada, T. Brochier, P. Penven, and B. Blanke, “A lagrangian tool for modelling ichthyoplankton dynamics,” Environmental modelling & software, vol. 23, iss. 9, p. 1210{–}1214, 2008.
    [Bibtex] 
    @article {lett_lagrangian_2008,
title = {A Lagrangian tool for modelling ichthyoplankton dynamics},
journal = {Environmental Modelling \& Software},
volume = {23},
number = {9},
year = {2008},
pages = {1210{\textendash}1214},
abstract = {Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics. It incorporates the most important processes involved in fish early life: spawning, movement, growth, mortality and recruitment. The tool uses as input time series of velocity, temperature and salinity fields archived from {ROMS} or {MARS} oceanic models. It runs with a user-friendly graphic interface and generates output files that can be post-processed easily using graphic and statistical software.},
keywords = {Biophysical model, Fish early life, Fish eggs and larvae, Ichthyop, Individual-based model, Lagrangian model, Particle tracking, Transport},
issn = {1364-8152},
doi = {10.1016/j.envsoft.2008.02.005},
url = {http://www.sciencedirect.com/science/article/pii/S136481520800025X},
author = {Lett, Christophe and Verley, Philippe and Mullon, Christian and Parada, Carolina and Brochier, Timoth{\'e}e and Penven, Pierrick and Blanke, Bruno}
}
  • [DOI] T. Brochier, A. Ramzi, C. Lett, E. Machu, A. Berraho, P. Fréon, and S. Hernández-León, “Modelling sardine and anchovy ichthyoplankton transport in the canary current system,” Journal of plankton research, vol. 30, iss. 10, p. 1133{–}1146, 2008.
    [Bibtex] 
    @article {brochier_modelling_2008,
title = {Modelling sardine and anchovy ichthyoplankton transport in the Canary Current System},
journal = {Journal of Plankton Research},
volume = {30},
number = {10},
year = {2008},
month = {jan},
pages = {1133{\textendash}1146},
abstract = {The Canary Current System, centred along the north-western coast of Africa, is one of the four major eastern boundary currents of the world ocean. It sustains a large amount of small pelagic fish, mainly sardine (Sardina pilchardus; Sardinella spp.) and anchovy (Engraulis encrasicolus). One of the particularities of this system is the presence of the Canary archipelago, which is close enough to the continental coast to allow exchange of biological material between the two areas. We used intermediate-resolution (7 km) hydrodynamic simulations as inputs for an individual-based model to assess the transport of ichthyoplankton (i) along the African coast and (ii) from the African coast to the Canary archipelago. We explored different scenarios of passive versus active vertically swimming larvae to assess the possible impact of vertical migration on transport and retention. Transport along the coast was essentially southward. The zone located between Cape Dr{\^a}a (\~{}28{\textdegree}45'N) and Cape Juby (\~{}27{\textdegree}56 N) had relatively high levels of retention in autumn and winter. The zone extending from Cape Boujdor (\~{}26{\textdegree}12'N) up to Cape Blanc (\~{}21{\textdegree}N) had high retention levels during the entire year. Larvae transported from the coast to the archipelago came mainly from the area located between Cape Ghir (\~{}30{\textdegree}38'N) and Cape Juby, whereas larvae retained in the eddy field downstream of the islands originated mainly from the area between Cape Juby to Dakhla (\~{}24{\textdegree}N). The results are discussed in relation to available field data of anchovy and sardine egg distributions over the continental shelf, and compared with oceanic surveys of larval presence near the Canary archipelago.},
keywords = {Ichthyop},
issn = {0142-7873, 1464-3774},
doi = {10.1093/plankt/fbn066},
url = {http://plankt.oxfordjournals.org/content/30/10/1133},
author = {Brochier, Timoth{\'e}e and Ramzi, Azeddine and Lett, Christophe and Machu, Eric and Berraho, Amina and Fr{\'e}on, Pierre and Hern{\'a}ndez-Le{\'o}n, Santiago}
}

2007

  • C. Lett, J. Veitch, C. D. Van der Lingen, and L. Hutchings, “Assessment of an environmental barrier to transport of ichthyoplankton from the southern to the northern benguela ecosystems,” Marine ecology progress series, vol. 347, p. 247{–}259, 2007.
    [Bibtex] 
    @article {lett_assessment_2007,
title = {Assessment of an environmental barrier to transport of ichthyoplankton from the southern to the northern Benguela ecosystems},
journal = {Marine Ecology Progress Series},
volume = {347},
year = {2007},
pages = {247{\textendash}259},
keywords = {Ichthyop},
url = {http://www.int-res.com/articles/theme/m347p247.pdf},
author = {Lett, C. and Veitch, J. and Van der Lingen, C. D. and Hutchings, L.}
}
  • [DOI] C. Lett, P. Penven, P. Ayón, and P. Fréon, “Enrichment, concentration and retention processes in relation to anchovy (engraulis ringens) eggs and larvae distributions in the northern humboldt upwelling ecosystem,” Journal of marine systems, vol. 64, iss. 1{–}4, p. 189{–}200, 2007.
    [Bibtex] 
    @article {lett_enrichment_2007,
title = {Enrichment, concentration and retention processes in relation to anchovy (Engraulis ringens) eggs and larvae distributions in the northern Humboldt upwelling ecosystem},
journal = {Journal of Marine Systems},
volume = {64},
number = {1{\textendash}4},
year = {2007},
pages = {189{\textendash}200},
abstract = {A Lagrangian model is used to simulate and quantify in the northern Humboldt upwelling ecosystem the processes of enrichment, concentration and retention, identified by Bakun [Bakun, A., 1996. Patterns in the ocean. Ocean processes and marine population dynamics. University of California Sea Grant, California, {USA}, in cooperation with Centro de Investigaciones Biologicas de Noroeste, La Paz, Baja California Sur, Mexico, 323 pp.] as being important for the survival and recruitment of early life stages of pelagic fish. The method relies on tracking the positions of particles within water velocity fields generated by a three-dimensional hydrodynamic model. Simple criteria for considering particles as participating to enrichment, concentration or retention are used to derive indices of the three processes. We analyse the spatial distribution of and seasonal variability in these indices. The results are discussed in relation to anchovy (Engraulis ringens) eggs and larvae distributions off Peru, and to a comparable study conducted in the southern Benguela upwelling ecosystem.},
keywords = {concentration, enrichment, Hydrodynamic model, Ichthyop, Ichthyoplankton, Lagrangian model, mesoscale, ocean triad, Pelagic fish, Peru, Recruitment, retention},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2006.03.012},
url = {http://www.sciencedirect.com/science/article/pii/S0924796306001114},
author = {Lett, Christophe and Penven, Pierrick and Ay{\'o}n, Patricia and Fr{\'e}on, Pierre}
}

2006

  • [DOI] D. C. M. Miller, C. L. Moloney, C. D. Van Der Lingen, C. Lett, C. Mullon, and J. G. Field, “Modelling the effects of physical–biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine sardinops sagax eggs and larvae in the southern benguela ecosystem,” Journal of marine systems, vol. 61, iss. 3{–}4, p. 212{–}229, 2006.
    [Bibtex] 
    @article {miller_modelling_2006,
title = {Modelling the effects of physical{\textendash}biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine Sardinops sagax eggs and larvae in the southern Benguela ecosystem},
journal = {Journal of Marine Systems},
volume = {61},
number = {3{\textendash}4},
year = {2006},
pages = {212{\textendash}229},
abstract = {A particle-tracking individual-based model ({IBM}) coupled with a 3-D hydrodynamic model was used to investigate how spatial variability in spawning and nursery grounds may influence transport and retention of sardine (Sardinops sagax) eggs and larvae in the southern Benguela ecosystem. A temperature-dependent B{\v e}lehr{\'a}dek development model based on laboratory growth data was used to determine the duration of one egg and two larval stages. Successful transport/retention depended on each particle{\textquoteright}s stage of development rather than its age. Results show that recruitment could occur in two distinct nursery areas on the west and south coasts of South Africa. Three viable recruitment {\textquoteleft}systems{\textquoteright} were identified: two are retention-based (spawned and retained on the west coast ({WC}{\textendash}{WC}) or the south coast ({SC}{\textendash}{SC})) and one is transport-based (spawned on the south coast and transported to the west coast ({SC}{\textendash}{WC})). In the {WC}{\textendash}{WC} system, the vertical distribution of eggs influenced retention; at intermediate depths of spawning (25{\textendash}50 m) eggs avoided both offshore Ekman drift and deep cold water. In the {SC}{\textendash}{SC} system, the area of spawning was important; \> 50\% of eggs from the eastern Agulhas Bank ({EAB}) were retained in the south coast nursery grounds, whereas very few eggs were transported there from west of Cape Agulhas. In the {SC}{\textendash}{WC} system, area of spawning was also important; 40\% of the eggs spawned on the western Agulhas Bank ({WAB}) were transported to the west coast nursery ground. Sardine life history strategy could be divided between two main systems: the west coast system (spawning on the {WAB} and {WC}, and recruiting to the {WC}) and the Agulhas Bank system (spawning on the central and eastern Agulhas Bank, and recruiting to the {SC}).},
keywords = {Agulhas Bank, Hydrodynamic model, Ichthyop, Individual-based model, Recruitment, retention, sardine, Sardinops sagax, Southern Benguela, Spawning, Transport},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2005.03.007},
url = {http://www.sciencedirect.com/science/article/pii/S092479630600025X},
author = {Miller, David C.M. and Moloney, Coleen L. and Van Der Lingen, Carl D. and Lett, Christophe and Mullon, Christian and Field, John G.}
}
  • [DOI] C. Lett, C. Roy, A. Levasseur, C. D. Van Der Lingen, and C. Mullon, “Simulation and quantification of enrichment and retention processes in the southern benguela upwelling ecosystem,” Fisheries oceanography, vol. 15, iss. 5, p. 363{–}372, 2006.
    [Bibtex] 
    @article {lett_simulation_2006,
title = {Simulation and quantification of enrichment and retention processes in the southern Benguela upwelling ecosystem},
journal = {Fisheries Oceanography},
volume = {15},
number = {5},
year = {2006},
pages = {363{\textendash}372},
abstract = {Important environmental processes for the survival and recruitment of early life stages of pelagic fishes have been synthesized through Bakun{\textquoteright}s fundamental triad as enrichment, concentration and retention processes (A. Bakun, 1996, Patterns in the Ocean. Ocean Processes and Marine Population Dynamics. San Diego, {CA}, {USA}: University of California Sea Grant). This conceptual framework states that from favourable spawning habitats, eggs and larvae would be transported to and/or retained in places where food originating from enrichment areas would be concentrated. We propose a method for quantifying two of the triad processes, enrichment and retention, based on the Lagrangian tracking of particles transported within water velocity fields generated by a three-dimensional hydrodynamic model. We apply this method to the southern Benguela upwelling ecosystem, constructing putative maps of enrichment and retention. We comment on these maps regarding main features of the circulation in the region, and investigate seasonal variability of the processes. We finally discuss the results in relation to available knowledge on the reproductive strategies of two pelagic clupeoid species abundant in the southern Benguela, anchovy (Engraulis encrasicolus) and sardine (Sardinops sagax). Our approach is intended to be sufficiently generic so as to allow its application to other upwelling systems.},
keywords = {anchovy, Benguela, concentration, Engraulis encrasicolus, enrichment, Hydrodynamic model, Ichthyop, Ichthyoplankton, Lagrangian, mesoscale, ocean triad, reproductive strategy, retention, sardine, Sardinops sagax, simulation, Transport, upwelling},
issn = {1365-2419},
doi = {10.1111/j.1365-2419.2005.00392.x},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2419.2005.00392.x/abstract},
author = {Lett, Christophe and Roy, Claude and Levasseur, Anne and Van Der Lingen, Carl D. and Mullon, Christian}
}

2003

  • [DOI] C. Mullon, P. Fréon, C. Parada, C. Van Der Lingen, and J. Huggett, “From particles to individuals: modelling the early stages of anchovy (engraulis capensis/encrasicolus) in the southern benguela,” Fisheries oceanography, vol. 12, iss. 4-5, p. 396{–}406, 2003.
    [Bibtex] 
    @article {mullon_particles_2003,
title = {From particles to individuals: modelling the early stages of anchovy (Engraulis capensis/encrasicolus) in the southern Benguela},
journal = {Fisheries Oceanography},
volume = {12},
number = {4-5},
year = {2003},
pages = {396{\textendash}406},
abstract = {Several individual-based models ({IBMs}) have recently been developed to improve understanding of factors impacting on recruitment variability of anchovy (Engraulis capensis/encrasicolus) in the southern Benguela. These {IBMs} have focused on early life history stages (eggs through to post-larvae) as it is thought that variations in anchovy recruitment strength are primarily driven by biological and/or physical factors impacting on these stages. The pelagic zone of the Benguela system constitutes an ideal system for studying the coupling between biological and physical processes; in the {IBMs} this coupling is obtained by releasing particles endowed with biological properties in the virtual currents resulting from the output of a hydrodynamic model of the southwestern coast of South Africa. The particles are tracked through virtual time and space and their final locations are assessed in terms of previously defined criteria deemed to promote successful recruitment. The aim of this paper is to provide a synthesis of the results of {IBMs} of the early stages of anchovy in the southern Benguela constructed to date. Emphasis is placed on the methodological aspects of these studies and on the sequential link of several simulation experiments of increasing complexity. In addition to improving understanding, such an approach allows for effective interplay between modelling experiments and surveys or laboratory experiments. Details of individual {IBM} experiments and their results have been published elsewhere.},
keywords = {anchovy, Ichthyop, individual based modelling, Particle tracking, simulation, Southern Benguela},
issn = {1365-2419},
doi = {10.1046/j.1365-2419.2003.00240.x},
url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2419.2003.00240.x/abstract},
author = {Mullon, C. and Fr{\'e}on, P. and Parada, C. and Van Der Lingen, C. and Huggett, J.}
}
  • [DOI] C. Parada, C. d. Van Der Lingen, C. Mullon, and P. Penven, “Modelling the effect of buoyancy on the transport of anchovy (engraulis capensis) eggs from spawning to nursery grounds in the southern benguela: an IBM approach,” Fisheries oceanography, vol. 12, iss. 3, p. 170{–}184, 2003.
    [Bibtex] 
    @article {parada_modelling_2003,
title = {Modelling the effect of buoyancy on the transport of anchovy (Engraulis capensis) eggs from spawning to nursery grounds in the southern Benguela: an {IBM} approach},
journal = {Fisheries Oceanography},
volume = {12},
number = {3},
year = {2003},
pages = {170{\textendash}184},
abstract = {An individual-based model ({IBM}) was used to investigate the effects of physical and biological variables on the transport via a jet current of anchovy (Engraulis capensis) eggs from spawning to the nursery grounds in the southern Benguela ecosystem. As transport of eggs and early larvae is considered to be one of the major factors impacting on anchovy recruitment success, this approach may be useful to understand further the recruitment variability in this economically and ecologically important species. By coupling the {IBM} to a 3D hydrodynamic model of the region called Plume, and by varying parameters such as the spatial and temporal location of spawning, particle buoyancy, and the depth range over which particles were released, we could assess the influences of these parameters on transport success. A sensitivity analysis using a General Linear Model identified the primary determinants of transport success in the various experimental simulations, and model outputs were examined and compared with patterns observed in field studies. Model outputs compared well with observed patterns of vertical and horizontal egg distribution. Particle buoyancy and area of particle release were the major single determinants of transport success, with an egg density of 1.025 g cm-3 maximizing average particle transport success and the western Agulhas Bank being the most successful spawning area. This {IBM} may be useful as a generic prototype for other upwelling ecosystems.},
keywords = {anchovy, eggs, Ichthyop, Individual-based model, larvae, Southern Benguela, Transport},
issn = {1365-2419},
doi = {10.1046/j.1365-2419.2003.00235.x},
url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2419.2003.00235.x/abstract},
author = {Parada, C. and Van Der Lingen, C.d. and Mullon, C. and Penven, P.}
}
  • J. Huggett, P. Fréon, C. Mullon, and P. Penven, “Modelling the transport success of anchovy engraulis encrasicolus eggs and larvae in the southern benguela: the effect of spatio-temporal spawning patterns,” Marine ecology progress series, vol. 250, p. 247{–}262, 2003.
    [Bibtex] 
    @article {huggett_modelling_2003,
title = {Modelling the transport success of anchovy Engraulis encrasicolus eggs and larvae in the southern Benguela: the effect of spatio-temporal spawning patterns},
journal = {Marine Ecology Progress Series},
volume = {250},
year = {2003},
pages = {247{\textendash}262},
keywords = {Ichthyop},
url = {http://www.brest.ird.fr/personnel/ppenven/publications/hugget_meps2003.pdf},
author = {Huggett, J. and Fr{\'e}on, P. and Mullon, C. and Penven, P.}
}

2002

  • [DOI] C. Mullon, P. Cury, and P. Penven, “Evolutionary individual-based model for the recruitment of anchovy ( engraulis capensis ) in the southern benguela,” Canadian journal of fisheries and aquatic sciences, vol. 59, iss. 5, p. 910{–}922, 2002.
    [Bibtex] 
    @article {mullon_evolutionary_2002,
title = {Evolutionary individual-based model for the recruitment of anchovy ( Engraulis capensis ) in the southern Benguela},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
volume = {59},
number = {5},
year = {2002},
pages = {910{\textendash}922},
keywords = {Ichthyop},
issn = {0706-652X, 1205-7533},
doi = {10.1139/f02-064},
url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f02-064},
author = {Mullon, Christian and Cury, Philippe and Penven, Pierrick}
}