Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)

Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. Here, we investigated the genetic distinctiveness and demographic history of sockeye salmon (Oncorhynchus nerka) in Alouette Lake in British Columbia, Canada using genome-wide SNP data collected for resident and migrant individuals, as well as for neighboring populations within the Fraser River drainage. We found clear evidence that Alouette Lake resident and migrant individuals are genetically distinct from other O. nerka populations in the Fraser River drainage, but are not differentiated from each other, likely constituting the first reported instance of deep-spawning behaviour associated with this life history form and suggesting the need for reassessment of conservation status.