Population genomics of two deep sea sharks: Centroselachus crepidater and Deania calcea

Abstract

This study investigated two superficially similar species of deep sea sharks, Centroselachus crepidater and Deania calcea, with the purpose of better understanding the drivers of differentiation and subsequent biodiversity in the deep sea. To achieve this four sample sites were used to coarsely represent the Atlantic and Pacific distribution of each species, with the genomes of each individual being sampled using a ddRADseq protocol. From these genome samples thousands of single nucleotide polymorphisms (SNPs) were identified and bioinformatically separated into neutral and outlier (under possible selective forces) marker sets which were then investigated for patterns of population genetic structure and adaptive function.
Despite comparable life history traits and overlapping sample sites, the two species showed differing patterns of differentiation across their range. In the neutral loci, C. crepidater showed significant differentiation between the Pacific and Atlantic, and homogeneity in the Atlantic. D. calcea showed effective panmixia across all sample sites. In the outlier loci, C. crepidater again showed Atlantic-Pacific differentiation, but also a split between the Rockall Trough and the Mid Atlantic Ridge. D. calcea also showed outlier differentiation between the Atlantic and Pacific, as well as significant divergence between two spatially similar sample sites in the Rockall Trough. Two possible proteins were identified linked to adaptive function, which were not insightful in themselves, but provide a starting point for future study.
These data combined with previous work on this deep sea taxon suggest that there is variation in patterns of differentiation between closely related species. However, common to all species so far studied are apparent high levels of vagility and dispersive capacity across global ranges. This provides further evidence that geographical barriers to dispersal are of lesser importance in determining genetic structure in deep sea basins, whilst isolation by distance and diversification along environmental clines likely play a more predominant role.