Population structure and local adaptation in elasmobranchs: insights from the small-spotted catshark (Scyliorhinus canicula)

Abstract

One quarter of elasmobranchs, which includes sharks and rays, are now threatened with extinction. Their unique life history traits make them particularly susceptible to anthropogenic pressures such as overfishing, habitat loss and global warming. To understand how these pressures are affecting natural shark populations we must understand their genetic diversity and how they become adapted to their local environment. Key to this is identifying discrete populations (or units for management), understanding the neutral and adaptive processes shaping population structure and identifying key genes responsible for local adaptation. In chapter one of this thesis, the importance and use of genetics and genomics in elasmobranch conservation and managements is reviewed. In chapter two, mitochondrial DNA control region sequencing of Scyliorhinus canicula edge populations was performed to resolve range wide population structuring. Samples from across the northeast Atlantic (NEA) were genetically homogenous. More complex structuring was seen in the Mediterranean with evidence of an isolated, genetically distinct cluster in the eastern Mediterranean, highlighting the importance of neutral processes in promoting genetic differentiation in this species. In chapter 3, double-digest restriction associated DNA (ddRAD) and seascape genomics was utilised to identify putative genomic regions under selection and to investigate the genomic basis of regional adaptation. Using a panel of 9,052 single nucleotide polymorphisms (SNPs) fine-scale structuring was revealed in both the NEA and the Mediterranean, with temperature, salinity, oxygen and depth all appearing to drive local adaptation in this small-coastal shark species. This thesis highlights the importance of studying genetic diversity and its drivers for successful future conservative of elasmobranchs.