Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)

Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.