Data from: 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. In the Alouette River
system (British Columbia, Canada), dam construction in 1928 impacted
passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last
records of migrants occurring in the 1930’s. Since that time, O. nerka
persisted as a resident population in Alouette Reservoir until
experimental water releases beginning in 2005 created conditions for
migration; two years later, returning migrants were observed for the first
time in ~70 years, raising important basic and applied questions regarding
life history variation and population structure in this system. Here, we
investigated the genetic distinctiveness and population history of
Alouette Reservoir O. nerka using genome-wide SNP data (n=7,709 loci)
collected for resident and migrant individuals, as well as for
neighbouring anadromous sockeye salmon and resident kokanee populations
within the Fraser River drainage (n=312 individuals). Bayesian clustering
and principal components analyses based on neutral loci revealed five
distinct clusters, largely associated with geography, and clearly
demonstrated that Alouette Reservoir resident and migrant individuals are
genetically distinct from other O. nerka populations in the Fraser River
drainage. At a finer-level, there was no clear evidence for
differentiation between Alouette Reservoir residents and migrants;
although we detected eight high-confidence outlier loci, they all mapped
to sex chromosomes suggesting that differences were likely due to uneven
sex ratios rather than life history. Taken together, these data suggest
that contemporary Alouette Reservoir O. nerka represents a landlocked
sockeye salmon population, constituting the first reported instance of
deep-water spawning behaviour associated with this life history form. This
finding punctuates the need for re-assessment of conservation status and
supports on-going fisheries management activities in Alouette
Reservoir.