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

Abstract Glacial history is an important contributor to contemporary biogeographical patterns because it has resulted in population fragmentation and consequently diversification. The Arctic charr (Salvelinus alpinus) is a highly diverse, non-anadromous salmonid fish species in Britain and Ireland, which was probably anadromous when it colonized around the end of the last ice age. The colonization history of the species remains largely unexplored and so the potential impact on contemporary patterns of genetic diversity and differentiation remains unclear. To address this, we conducted a national-scale genetic study of Arctic charr using a genome-wide dataset of single nucleotide polymorphisms (SNPs) (24,878 SNPs and 410 individuals) and mitochondrial ND1 sequences (238 sequences). We found that several mitochondrial haplotypes were shared across Britain, Ireland, and the wider Holarctic, which suggests that colonization occurred by multiple sub-lineages of the species’ Atlantic lineage. Genetic differentiation was not correlated with geographical 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 colonization and subsequently contemporary patterns of genetic differentiation in this widespread species.