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SNP data: Population genetic structure in bull sharks (Carcharhinus leucas)

Citation

Glaus, Kerstin (2020), SNP data: Population genetic structure in bull sharks (Carcharhinus leucas), Dryad, Dataset, https://doi.org/10.5061/dryad.0vt4b8gwf

Abstract

The bull shark (Carcharhinus leucas) is a large, mobile, circumglobally distributed high trophic level predator that inhabits a variety of remote islands and continental coastal habitats, including freshwater environments. Here, we hypothesise that the barriers to dispersal created by large oceanic expanses and deep-water trenches result in a heterogeneous distribution of the neutral genetic diversity between island bull shark populations compared to populations sampled in continental locations connected through continuous coastlines of continental shelves. We analysed 1,494 high-quality neutral Single Nucleotide Polymorphism (SNP) markers in 215 individual bull sharks from widespread locations across the Indian and Pacific Oceans (South Africa, Indonesia, Western Australia, Papua New Guinea, eastern Australia, New Caledonia and Fiji). Genomic analyses revealed partitioning between remote insular and continental populations, with the Fiji population being genetically different from all other locations sampled (FST 0.034-0.044, P < 0.001), and New Caledonia showing marginal isolation (FST 0.016-0.024, P < 0.001; albeit based on a small sample size) from most sampled sites. Discriminant Analysis of Principal Components (DAPC) identified samples from Fiji as a distinct cluster with all other sites as one large cluster. Genetic structure analyses (Admixture, STRUCTURE & AssignPOP) further supported the genetic isolation of bull sharks from Fiji, with the analyses in agreement. The observed differentiation in bull sharks from Fiji makes this site of special interest, as it indicates a lack of migration through dispersal across deep-water trenches and large ocean expanses.

Methods

Bull shark samples (white muscle and fin clips, 1 cm2) were obtained from fisheries independent surveys, observers on board commercial fleets, dive guides, and recreational and artisanal fishers from 2004 to 2017. Tissue samples were sent to Diversity Arrays Technology (DArT-Seq™) in Canberra Australia where genomic DNA was extracted from the tissues using standard robotic methods. DNA was processed for reduced representation library construction, sequenced and genotyped by DArT-Seq™ following previously developed and tested complexity reduction protocols for scalloped hammerhead sharks (Sphyrna lewini) (Marie, 2019).