Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis

Abstract

The blue skate (Dipturus batis) has a patchy distribution across the North‐East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries‐induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by‐catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced‐representation sequencing approach. Genotypes were used to assess the species’ contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well‐annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already‐restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North‐East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.

First evidence of population genetic structure of the deep-water blackmouth catshark Galeus melastomus Rafinesque, 1810

“…Little information is available about blackmouth catshark genetic diversity and population structure (Ferrari et al, 2018;Ramıŕez-Amaro et al, 2018), being the molecular method previously applied for integrated taxonomy (Castilho et al, 2007) and food traceability (Clarke et al, 2006). With the refinement of genetic and genomic techniques, deepening the knowledge about species genetic diversity and structuring is becoming one of the pillars of elasmobranchs' conservation (Ovenden et al, 2019;Domingues et al, 2021;Delaval et al, 2022). Finding population structure across wide geographical or global scales failed in pelagic sharks (Hoelzel et al, 2006;Verıśsimo et al, 2017) although some exceptions are reported (Kraft et al, 2020), while the identification of isolated populations on smaller regional scales has been documented in multiple coastal species (Portnoy et al, 2015;Catalano et al, 2022).…”

Evaluating the suitability of close‐kin mark‐recapture as a demographic modelling tool for a critically endangered elasmobranch population

“…Due to cost considerations, we were unable to genotype all samples. Of those available, 683 were selected for genotyping, of which 387 had already been genotyped by Delaval et al ( 2022 ) using the same method. Samples primarily consisted of juveniles and young adults, but spanned as wide a size range as possible to maximize the number of cohorts included in the model.…”

“…In an effort to evaluate current management regimes, longitudinal fisheries‐dependent surveys have been initiated in collaboration with British (Bendall et al, 2018 ) and French (Barreau et al, 2016 ) fishing fleets in order to develop demographic models and identify biologically important sites for the species. Initial results from these surveys suggest the occurrence of juveniles and adults in the area, displaying a high degree of site fidelity, while population genomic analysis has identified the occurrence of siblings in the area and limited gene flow with offshore populations (Delaval et al, 2022 ). Altogether, these findings suggest that the Celtic Sea may host important reproductive and/or nursery sites for D. batis .…”

A decade of progress in marine evolutionary biology

“…Herein, these processes are addressed in diverse empirical model systems ranging from diatoms to mollusks and fish (Green et al, 2022 ; Le Moan et al, 2022 ; Sefbom et al, 2022 ; Zhang et al, 2022 ), as well as in silico in two theoretical modeling studies (Eriksson et al, 2022 ; Marshall & Connallon, 2022 ). The link between genotype and phenotype is also the focus of several empirical studies here (Gefaell et al, 2022 ; Stenger et al, 2022 ; Walker et al, 2022 ), as is the seascape genomics of a wide range of taxa (Delaval, Bendall, et al, 2022 ; Delaval, Frost, et al, 2022 ; Fitz et al, 2022 ; Lapègue et al, 2022 ; Matias et al, 2022 ; Palumbi et al, 2022 ; Pampoulie et al, 2022 ), which has important implications for management of marine resources. Finally, the breadth of phylogenetic diversity and evolutionary history in the oceans is the topic of several articles focusing on the larval development of gastropods (Korshunova et al, 2022 ; Sun et al, 2022 ) and the evolution of small RNAs in cnidarians (Li & Hui, 2022 ).…”