The historical patterns that have shaped contemporary genetic differentiation across populations of Arctic charr in Scotland

Glacial history is an important contributor to contemporary biogeographic patterns because it caused population fragmentation and consequently diversification. The Arctic charr (Salvelinus alpinus) is a highly diverse non-anadromous salmonid fish species in Britain and Ireland, which likely was anadromous when it colonised around the end of the last ice age. Colonisation history of the species remains largely unexplored and so the potential impact on contemporary patterns of genetic differentiation remains unclear. To address this, we conducted a national-scale genetic study of Arctic charr using a genome-wide dataset of SNPs (24,878 SNPs and 410 individuals) and mitochondrial ND1 sequences (238 sequences). We found several mitochondrial haplotypes were shared across Britain, Ireland, and the wider Holarctic suggesting colonisation by multiple sub-lineages of the Atlantic lineage of the species. Genetic differentiation was not correlated with geographic distance among river catchments, highlighting the effect of spatial isolation and genetic drift. Several populations across different river catchments showed atypical ancestries and evidence for genetic mixing, which we speculate are due to asynchronous ice coverage and the presence of ice-dammed lakes. Our results highlight how glacial history can impact colonisation history and subsequently contemporary patterns of genetic differentiation in this widespread species.