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      Genetic Network and Breeding Patterns of a Sicklefin Lemon Shark ( Negaprion acutidens) Population in the Society Islands, French Polynesia

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          Abstract

          Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population’s mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.

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          Most cited references25

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          Statistical confidence for likelihood-based paternity inference in natural populations.

          Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.
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            COLONY: a program for parentage and sibship inference from multilocus genotype data.

            Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface. © 2009 Blackwell Publishing Ltd.
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              Cascading effects of the loss of apex predatory sharks from a coastal ocean.

              Impacts of chronic overfishing are evident in population depletions worldwide, yet indirect ecosystem effects induced by predator removal from oceanic food webs remain unpredictable. As abundances of all 11 great sharks that consume other elasmobranchs (rays, skates, and small sharks) fell over the past 35 years, 12 of 14 of these prey species increased in coastal northwest Atlantic ecosystems. Effects of this community restructuring have cascaded downward from the cownose ray, whose enhanced predation on its bay scallop prey was sufficient to terminate a century-long scallop fishery. Analogous top-down effects may be a predictable consequence of eliminating entire functional groups of predators.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                13 August 2013
                : 8
                : 8
                : e73899
                Affiliations
                [1 ]LabEx «CORAIL» - USR 3278 CNRS-EPHE, Centre de Recherche Insulaire et Observatoire de l’Environnement (CRIOBE), Papetoai, Moorea, French Polynesia
                [2 ]National Marine Fisheries Service, Silver Spring, Maryland, United States of America
                [3 ]Délégation Régionale à la Recherche et Technologie, Haut-commissariat de la République française, Papeete, Tahiti, Polynésie Française
                [4 ]Ministère de l’Agriculture et de la Pêche, Paris, France
                CNRS, Université de Bourgogne, France
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: JM NB EC SP. Performed the experiments: JM NB JKS EC SP. Analyzed the data: JM SP. Contributed reagents/materials/analysis tools: JM SP. Wrote the manuscript: JM NB JKS EC SP.

                Article
                PONE-D-13-14386
                10.1371/journal.pone.0073899
                3742621
                23967354
                4d7ee556-df51-49c0-bf76-37a8bd57e5c3
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 10 April 2013
                : 23 July 2013
                Funding
                This study benefited from the financial support of the Direction à l’Environnement (DIREN) of French Polynesia and the scientific support of Coordination Unit of the Coral Reef Initiatives for the Pacific (CRISP Programme), based in New Caledonia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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