title: Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives.
abstract: Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.
authors.affiliation: Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France.|EPHE, PSL Research University, Paris, France.
authors.forename: Pierpaolo
authors.initials: P
authors.lastname: Maisano Delser
authors.affiliation: Department of Biology, College of Charleston, Charleston 29412, SC, USA.
authors.forename: Shannon
authors.initials: S
authors.lastname: Corrigan
authors.affiliation: Medical University of South Carolina, College of Graduate Studies, Charleston 29403, SC, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hale
authors.affiliation: Department of Biology, College of Charleston, Charleston 29412, SC, USA.|Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
authors.forename: Chenhong
authors.initials: C
authors.lastname: Li
authors.affiliation: Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France.|EPHE, PSL Research University, Paris, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Veuille
authors.affiliation: CRIOBE-USR 3278, CNRS-EPHE-UPVD, Laboratoire d'Excellence 'CORAIL', 58 Avenue Paul Alduy, 66860 Perpignan, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Planes
authors.affiliation: Department of Biology, College of Charleston, Charleston 29412, SC, USA.
authors.forename: Gavin
authors.initials: G
authors.lastname: Naylor
authors.affiliation: Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France.|EPHE, PSL Research University, Paris, France.
authors.forename: Stefano
authors.initials: S
authors.lastname: Mona
mesh_terms: D000818:Animals; D001315:Australia; D005828:Genetics, Population; D023281:Genomics; D019156:Indian Ocean; D011157:Population Dynamics; D012754:Sharks / Q000235:genetics*