ddRAD genotyping reveals hierarchical genetic population structure in anadromous Arctic char (Salvelinus alpinus) in the Lower Northwest Passage, Nunavut

Contemporary intraspecific patterns of genetic variation reflect the historical effects of population subdivision/expansion and forces like drift, gene flow and selection. We investigated the population structure of anadromous Arctic char in the Lower Northwest Passage (LNWP), Nunavut, using 3,074 genome-wide single nucleotide polymorphisms markers (SNPs). Overall, the genetic differentiation was weak to moderate among 18 sampling locales (global F_ST=0.037). Populations were structured hierarchically, with a deeper genetic division between King William Island (global F_ST=0.018) and mainland populations ~ 200 km away to the south (global F_ST=0.018), and some evidence of genetic subgroups within the former. These findings suggest a role for char migratory behaviour in shaping contemporary genetic population structure, with demographic modelling favouring an isolation with migration over a strict isolation scenario. Twenty-two SNPs were identified as potentially under divergent selection with putative functions including neurotransmission and bone development and growth during late embryogenesis. Our study is the first survey of Arctic char in the LNWP using genomics, and provides baseline data for the development of a sustainable fishery within this region.