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

Abstract

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.

Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species

“…This is expected, as different molecular markers and metrics vary in characteristics such as sample size and mutation rate (Morin et al, 2004). However, it is interesting to note that the two marker types displayed highly similar spatial arrays of diversity for C. punctatus and P. angulosus, corroborating other studies that suggest that although different markers may display varying degrees of genetic diversity, the spatial arrangement of diversity is the same (Beatty & Provan, 2011b;Kraft et al, 2020).…”

Interdisciplinary analysis of larval dispersal for a coral reef fish: opening the black box

“…Genetic parent age analyses compare DNA between adults and new recruits, thereby connecting parent− offspring pairs (Christie et al 2017, Coleman 2019. While single-nucleotide polymorphism (SNP)-based parentage analyses have become more accessible and cost-effective in recent years (Kraft et al 2020), these analyses are still constrained by the need to collect tissue specimens from large numbers of individuals. This can make interannual variation hard to quantify, in part because of the extensive effort required to collect a large number of tissue samples, and in part because destructive sampling methods remove possible future adults from the population (however, see Catalano et al 2021 for a 7 yr parentage study of an ane mone fish).…”

Indo‐Pacific origins of silky shark fins in major shark fin markets highlights supply chains and management bodies key for conservation

“…Existing population genetic analysis suggests that there may be population structure within the Indo-Pacific, but it is unclear how population boundaries align with RMFO jurisdictions (Clarke et al, 2015). Genomic studies may clear this up and help build a clearer baseline for finer scale genetic tracing of silky shark fins in the future (Kraft et al, 2020).…”