Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

Pierpaolo Maisano Delser 1 Shannon Corrigan 2 Matthew Hale 3 Chenhong Li 4 Michel Veuille 1 Serge Planes 5 Gavin Naylor 2 Stefano Mona 1
1 Biologie Intégrative des Populations
2 department of biology,College of Charleston
3 MUSC - Medical University of South Carolina [Charleston]
4 Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of Ministry of Education and College of Fisheries and Life Sciences
5 CRIOBE - Centre de recherches insulaires et observatoire de l'environnement
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.
Keywords : Evolutionary genetics Genetic variation
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Journal articles
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Pierpaolo Maisano Delser, Shannon Corrigan, Matthew Hale, Chenhong Li, Michel Veuille, et al.. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Scientific Reports, Nature Publishing Group, 2016, pp.33753. ⟨10.1038/srep33753⟩. ⟨hal-01380023⟩

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