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  • Article
    Transgenerational marking of embryonic otoliths in marine fishes using barium stable isotopes
    (NRC Research Press, 2006-04-13) Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge ; Hare, Jonathan A.
    We describe a new technique for transgenerational marking of embryonic otoliths that promises significant advancements in the study of larval dispersal and population connectivity in marine fishes. The approach is based on maternal transmission of 137Ba from spawning females to egg material that is ultimately incorporated into the otoliths of embryos produced by an individual after exposure to the isotope. We injected females of a benthic-spawning clownfish (Amphiprion melanopus) and a pelagic-spawning serranid (Centropristis striata) with enriched 137BaCl2 and then reared the resulting progeny through to settlement. Barium isotope ratios in the cores of larval otoliths were quantified using laser ablation inductively coupled plasma mass spectrometry. Larval otoliths from both species contained unequivocal Ba isotope signatures over a wide range of doses (0.8–23 μg 137Ba·g female–1). Female A. melanopus continued to produce marked larvae over multiple clutches and for at least 90 days after a single injection. The ability to administer different combinations of stable Ba isotopes provides a new means of mass-marking larvae of benthic- and pelagic-spawning fishes from multiple populations over extended spawning periods.
  • Preprint
    Marine dispersal scales are congruent over evolutionary and ecological time
    ( 2016-10) Pinsky, Malin L. ; Saenz-Agudelo, Pablo ; Salles, Océane C. ; Almany, Glenn R. ; Bode, Michael ; Berumen, Michael L. ; Andrefouet, Serge ; Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge
    The degree to which offspring remain near their parents or disperse widely is critical for understanding population dynamics, evolution, and biogeography, and for designing conservation actions. In the ocean, most estimates suggesting short-distance dispersal are based on direct ecological observations of dispersing individuals, while indirect evolutionary estimates often suggest substantially greater homogeneity among populations. Reconciling these two approaches and their seemingly competing perspectives on dispersal has been a major challenge. However, here we show for the first time that evolutionary and ecological measures of larval dispersal can closely agree by using both to estimate the distribution of dispersal distances. In orange clownfish (Amphiprion percula) populations in Kimbe Bay, Papua New Guinea, we found that evolutionary dispersal kernels were 17 [95% CI: 12–24] km wide, while an exhaustive set of direct larval dispersal observations suggested kernel widths of 27 [19–36] km or 19 [15–27] km across two years. The similarity between these two approaches suggests that ecological and evolutionary dispersal kernels can be equivalent, and that the apparent disagreement between direct and indirect measurements can be overcome. Our results suggest that carefully applied evolutionary methods, which are often less expensive, can be broadly relevant for understanding ecological dispersal across the tree of life.
  • Preprint
    Connectivity dominates larval replenishment in a coastal reef fish metapopulation
    ( 2011-01-25) Saenz-Agudelo, Pablo ; Jones, Geoffrey P. ; Thorrold, Simon R. ; Planes, Serge
    Direct estimates of larval retention and connectivity are essential to understand the structure and dynamics of marine metapopulations, and optimize the size and spacing of reserves within networks of marine protected areas (MPAs). For coral reef fishes, while there are some empirical estimates of self-recruitment at isolated populations, exchange among sub-populations has been rarely quantified. Here we used microsatellite DNA markers and a likelihood-based parentage analysis to assess the relative magnitude of self-recruitment and exchange among 8 geographically distinct sub-populations of the panda clownfish Amphiprion polymnus along 30 km of coastline near Port Moresby, Papua New Guinea. In addition, we used an assignment/exclusion test to identify immigrants arriving from genetically distinct sources. Overall, 82% of the juveniles were immigrants while 18% were progeny of parents genotyped in our focal metapopulation. Of the immigrants, only 6% were likely to be genetically distinct from the focal metapopulation, suggesting most of the connectivity is among sub-populations from a rather homogeneous genetic pool. Of the 18% that were progeny of known adults, two thirds dispersed among the 8 sub-populations and only one third settled back into natal sub- populations. Comparison of our data with previous studies suggested that variation in dispersal distances is likely to be influenced by the geographic setting and spacing of sub-populations.
  • Article
    Seascape and life-history traits do not predict self-recruitment in a coral reef fish
    (The Royal Society, 2016-08-09) Herrera, Marcela ; Nanninga, Gerrit ; Planes, Serge ; Jones, Geoffrey P. ; Thorrold, Simon R. ; Saenz-Agudelo, Pablo ; Almany, Glenn R. ; Berumen, Michael L.
    The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4–0.5% at 0.15 km2) and the lagoon scale (0.6–0.8% at approx. 700 km2). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.
  • Article
    Expanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)
    (Frontiers Media, 2019-12-11) Gorsky, Gabriel ; Bourdin, Guillaume ; Lombard, Fabien ; Pedrotti, Maria Luiza ; Audrain, Samuel ; Bin, Nicolas ; Boss, Emmanuel S. ; Bowler, Chris ; Cassar, Nicolas ; Caudan, Loic ; Chabot, Genevieve ; Cohen, Natalie R. ; Cron, Daniel ; De Vargas, Colomban ; Dolan, John R. ; Douville, Eric ; Elineau, Amanda ; Flores, J. Michel ; Ghiglione, Jean-Francois ; Haëntjens, Nils ; Hertau, Martin ; John, Seth G. ; Kelly, Rachel L. ; Koren, Ilan ; Lin, Yajuan ; Marie, Dominique ; Moulin, Clémentine ; Moucherie, Yohann ; Pesant, Stephane ; Picheral, Marc ; Poulain, Julie ; Pujo-Pay, Mireille ; Reverdin, Gilles ; Romac, Sarah ; Sullivan, Mathew B. ; Trainic, Miri ; Tressol, Marc ; Troublé, Romain ; Vardi, Assaf ; Voolstra, Christian R. ; Wincker, Patrick ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Gilson, Eric ; Reynaud, Stephanie ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Vega Thurber, Rebecca ; Zoccola, Didier ; Planes, Serge ; Allemand, Denis ; Karsenti, Eric
    Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.
  • Preprint
    Otolith geochemistry does not reflect dispersal history of clownfish larvae
    ( 2010-06) Berumen, Michael L. ; Walsh, Harvey J. ; Raventos, N. ; Planes, Serge ; Jones, Geoffrey P. ; Starczak, Victoria R. ; Thorrold, Simon R.
    Natural geochemical signatures in calcified structures are commonly employed to retrospectively estimate dispersal pathways of larval fish and invertebrates. However, the accuracy of the approach is generally untested due to the absence of individuals with known dispersal histories. We used genetic parentage analysis (genotyping) to divide 110 new recruits of the orange clownfish, Amphiprion percula, from Kimbe Island, Papua New Guinea, into two groups: “self-recruiters” spawned by parents on Kimbe Island and “immigrants” that had dispersed from distant reefs (>10km away). Analysis of daily increments in sagittal otoliths found no significant difference in PLDs or otolith growth rates between self-recruiting and immigrant larvae. We also quantified otolith Sr/Ca and Ba/Ca ratios during the larval phase using laser ablation inductively coupled plasma mass spectrometry. Again, we found no significant differences in larval profiles of either element between self-recruits and immigrants. Our results highlight the need for caution when interpreting otolith dispersal histories based on natural geochemical tags in the absence of water chemistry data or known-origin larvae with which to test the discriminatory ability of natural tags.
  • Article
    Rank change and growth within social hierarchies of the orange clownfish, Amphiprion percula
    (Springer, 2022-10-05) Fitzgerald, Lucy M. ; Harrison, Hugo B. ; Coker, Darren J. ; Sáenz-Agudelo, Pablo ; Srinivasan, Maya ; Majoris, John E. ; Boström Einarsson, Lisa ; Pujol, Benoit ; Bennett-Smith, Morgan ; Thorrold, Simon R. ; Planes, Serge ; Jones, Geoffrey P. ; Berumen, Michale L.
    Social hierarchies within groups define the distribution of resources and provide benefits that support the collective group or favor dominant members. The progression of individuals through social hierarchies is a valuable characteristic for quantifying population dynamics. On coral reefs, some clownfish maintain size-based hierarchical communities where individuals queue through social ranks. The cost of waiting in a lower-ranked position is outweighed by the reduced risk of eviction and mortality. The orange clownfish,Amphiprion percula, maintains stable social groups with subordinate individuals queuing to be part of the dominant breeding pair. Strong association with their host anemone, complex social interactions, and relatively low predation rates make them ideal model organisms to assess changes in group dynamics through time in their natural environment. Here, we investigate the rank changes and isometric growth rates ofA. percula from 247 naturally occurring social groups in Kimbe Island, Papua New Guinea (5° 12′ 13.54″ S, 150° 22′ 32.69″ E). We used DNA profiling to assign and track individuals over eight years between 2011 and 2019. Over half of the individuals survived alongside two or three members of their original social group, with twelve breeding pairs persisting over the study period. Half of the surviving individuals increased in rank and experienced double the growth rate of those that maintained their rank. Examining rank change in a wild fish population provides new insights into the complex social hierarchies of reef fishes and their role in social evolution.
  • Preprint
    First genealogy for a wild marine fish population reveals multi-generational philopatry
    ( 2016-10) Salles, Océane C. ; Pujol, Benoit ; Maynard, Jeffrey A. ; Almany, Glenn R. ; Berumen, Michael L. ; Jones, Geoffrey P. ; Saenz-Agudelo, Pablo ; Srinivasan, Maya ; Thorrold, Simon R. ; Planes, Serge
    Natal philopatry — the return of individuals to their natal area for reproduction — has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation but may also increase the probability of inbreeding that can compromise persistence. While natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multi-generational pedigrees that are currently lacking for marine fishes. Here we present the first multi-generational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) over a 10-year period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multi-generational pedigrees over a relatively short time period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
  • Article
    Reef-fidelity and migration of tiger sharks, Galeocerdo cuvier, across the Coral Sea
    (Public Library of Science, 2014-01-08) Werry, Jonathan M. ; Planes, Serge ; Berumen, Michael L. ; Lee, Kate A. ; Braun, Camrin D. ; Clua, Eric
    Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark–human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km3. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.
  • Preprint
    Estimating connectivity in marine populations : an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios
    ( 2008-11-21) Saenz-Agudelo, Pablo ; Jones, Geoffrey P. ; Thorrold, Simon R. ; Planes, Serge
    The application of spatially explicit models of population dynamics to fisheries management and the design marine reserves network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among 5 spatially discrete locations separated by 2-6km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (Fst = 0.1) located at Schumann Island, New Britain, 1,500km to the north-east. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.
  • Article
    Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region
    (Nature Research, 2019-11-01) Boissin, Emilie ; Thorrold, Simon R. ; Braun, Camrin D. ; Zhou, Yuxiang ; Clua, Eric ; Planes, Serge
    Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (FST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.
  • Preprint
    Coral reef fish populations can persist without immigration
    ( 2015-10) Salles, Océane C. ; Maynard, Jeffrey A. ; Joannides, Marc ; Barbu, Corentin M. ; Saenz-Agudelo, Pablo ; Almany, Glenn R. ; Berumen, Michael L. ; Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge
    Determining the conditions under which populations may persist requires accurate estimates of demographic parameters, including immigration, local reproductive success, and mortality rates. In marine populations, empirical estimates of these parameters are rare, due at least in part to the pelagic dispersal stage common to most marine organisms. Here, we evaluate population persistence and turnover for a population of orange clownfish, Amphiprion percula, at Kimbe Island in Papua New Guinea. All fish in the population were sampled and genotyped on five occasions at 2-year intervals spanning eight years. The genetic data enabled estimates of reproductive success retained in the same population (reproductive success to self-recruitment), reproductive success exported to other subpopulations (reproductive success to local connectivity), and immigration and mortality rates of sub-adults and adults. Approximately 50% of the recruits were assigned to parents from the Kimbe Island population and this was stable through the sampling period. Stability in the proportion of local and immigrant settlers is likely due to: low annual mortality rates and stable egg production rates, and the short larval stages and sensory capacities of reef fish larvae. Biannual mortality rates ranged from 0.09 to 0.55 and varied significantly spatially. We used these data to parameterize a model that estimated the probability of the Kimbe Island population persisting in the absence of immigration. The Kimbe Island population was found to persist without significant immigration. Model results suggest the island population persists because the largest of the subpopulations are maintained due to having low mortality and high self-recruitment rates. Our results enable managers to appropriately target and scale actions to maximize persistence likelihood as disturbance frequencies increase.
  • Article
    The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean
    (Public Library of Science, 2019-09-23) Planes, Serge ; Allemand, Denis ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Boss, Emmanuel S. ; Bourdin, Guillaume ; Bowler, Chris ; Douville, Eric ; Flores, J. Michel ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Ghiglione, Jean-Francois ; Gilson, Eric ; Lombard, Fabien ; Moulin, Clémentine ; Pesant, Stephane ; Poulain, Julie ; Reynaud, Stephanie ; Romac, Sarah ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Troublé, Romain ; de Vargas, Colomban ; Vega Thurber, Rebecca ; Voolstra, Christian R. ; Wincker, Patrick ; Tara Pacific Consortium
    Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
  • Article
    Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea
    (Nature Research, 2020-12-10) Boissin, Emilie ; Neglia, Valentina ; Baksay, Sandra ; Micu, Dragos ; Bat, Levent ; Topaloglu, Bulent ; Todorova, Valentina ; Panayotova, Marina ; Kruschel, Claudia ; Milchakova, Nataliya ; Voutsinas, Emanuela ; Beqiraj, Sajmir ; Nasto, Ina ; Aglieri, Giorgio ; Taviani, Marco ; Zane, Lorenzo ; Planes, Serge
    To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
  • Preprint
    On minimising assignment errors and the trade‐off between false positives and negatives in parentage analysis
    ( 2013-05) Harrison, Hugo B. ; Saenz-Agudelo, Pablo ; Planes, Serge ; Jones, Geoffrey P. ; Berumen, Michael L.
    Genetic parentage analyses provide a practical means with which to identify parent–offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses.
  • Article
    Connectivity and resilience of coral reef metapopulations in marine protected areas : matching empirical efforts to predictive needs
    (Springer, 2009-02-11) Botsford, L. W. ; White, J. Wilson ; Coffroth, M.- A. ; Paris, Claire B. ; Planes, Serge ; Shearer, T. L. ; Thorrold, Simon R. ; Jones, Geoffrey P.
    Design and decision-making for marine protected areas (MPAs) on coral reefs require prediction of MPA effects with population models. Modeling of MPAs has shown how the persistence of metapopulations in systems of MPAs depends on the size and spacing of MPAs, and levels of fishing outside the MPAs. However, the pattern of demographic connectivity produced by larval dispersal is a key uncertainty in those modeling studies. The information required to assess population persistence is a dispersal matrix containing the fraction of larvae traveling to each location from each location, not just the current number of larvae exchanged among locations. Recent metapopulation modeling research with hypothetical dispersal matrices has shown how the spatial scale of dispersal, degree of advection versus diffusion, total larval output, and temporal and spatial variability in dispersal influence population persistence. Recent empirical studies using population genetics, parentage analysis, and geochemical and artificial marks in calcified structures have improved the understanding of dispersal. However, many such studies report current self-recruitment (locally produced settlement/settlement from elsewhere), which is not as directly useful as local retention (locally produced settlement/total locally released), which is a component of the dispersal matrix. Modeling of biophysical circulation with larval particle tracking can provide the required elements of dispersal matrices and assess their sensitivity to flows and larval behavior, but it requires more assumptions than direct empirical methods. To make rapid progress in understanding the scales and patterns of connectivity, greater communication between empiricists and population modelers will be needed. Empiricists need to focus more on identifying the characteristics of the dispersal matrix, while population modelers need to track and assimilate evolving empirical results.
  • Article
    Interspecific hybridization in pilot whales and asymmetric genetic introgression in northern Globicephala melas under the scenario of global warming
    (Public Library of Science, 2016-08-10) Miralles, Laura ; Oremus, Marc ; Silva, Monica A. ; Planes, Serge ; Garcia-Vazquez, Eva
    Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.
  • Article
    Like a rolling stone: colonization and migration dynamics of the gray reef shark (Carcharhinus amblyrhynchos)
    (Wiley Open Access, 2023-01-10) Lesturgie, Pierre ; Braun, Camrin D. ; Clua, Eric ; Mourier, Johann ; Thorrold, Simon R. ; Vignaud, Thomas ; Planes, Serge ; Mona, Stefano
    Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here, we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RADseq loci in 173 individuals in the Indo‐Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo‐Australian Archipelago (IAA) where two stepping‐stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm ~ 10 per generation) throughout the range, and isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long‐distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (FST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range‐wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon‐associated Carcharhinus melanopterus, known for its restricted dispersal ability. Carcharhinus melanopterus exhibits a similar RE dynamic but is characterized by a stronger genetic structure and a nonhomogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life‐history traits in shaping the extent of genetic structure and diversity.Carcharhinus amblyrhynchos is an endangered Indo‐Pacific reef shark, which shows reef fidelity but long‐distance movements, raising questions about connectivity patterns and the extent of conservation units. Using genomic data, we show that it has undergone a range expansion from the Indo‐Australian Archipelago (IAA) and is organized as a meta‐population characterized by homogeneous connectivity throughout its range. We highlight the low dependence of C. amblyrhynchos on reef availability and its ability to cross open sea expanses, which do not represent barriers to gene flow, contrasting with the sympatric Carcharhinus melanopterus, whose dispersal is strictly dependent on local reef distribution. Conversely, both species share similar range expansion dynamics, suggesting a major importance of the IAA as a source of biodiversity for reef sharks.
  • Article
    Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium
    (BioMed Central, 2016-03-17) Davies, Neil ; Field, Dawn ; Gavaghan, David ; Holbrook, Sally J. ; Planes, Serge ; Troyer, Matthias ; Bonsall, Michael ; Claudet, Joachim ; Roderick, George ; Schmitt, Russell J. ; Amaral-Zettler, Linda A. ; Berteaux, Veronique ; Bossin, Hervé C. ; Cabasse, Charlotte ; Collin, Antoine ; Deck, John ; Dell, Tony ; Dunne, Jennifer A. ; Gates, Ruth D. ; Harfoot, Mike ; Hench, James L. ; Hopuare, Marania ; Kirch, Patrick ; Kotoulas, Georgios ; Kosenkov, Alex ; Kusenko, Alex ; Leichter, James J. ; Lenihan, Hunter ; Magoulas, Antonios ; Martinez, Neo ; Meyer, Chris ; Stoll, Benoit ; Swalla, Billie ; Tartakovsky, Daniel M. ; Teavai Murphy, Hinano ; Turyshev, Slava ; Valdvinos, Fernanda ; Williams, Rich ; Wood, Spencer ; IDEA Consortium
    Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.