Data from: Application of genomic offsets to inform freshwater fisheries management under climate change

Genomic tools are becoming increasingly necessary for mitigating
biodiversity loss and guiding management decisions in the context of
climate change. Freshwater fish species are particularly susceptible to
the impacts of changing environments, including kokanee, the resident form
of sockeye salmon (Oncorhynchus nerka), which has already been negatively
impacted by increases in extreme temperature throughout its distribution.
A previous study using whole genome resequencing of wild kokanee stocks
identified 1412 environmentally-associated SNPs and demonstrated genomic
offset, a measure of climate vulnerability, to be significantly correlated
with higher increases in extreme warm temperatures across much of the
species’ range in western Canada. Here, we aimed to operationalize this
information for fisheries management by first developing a
Genotyping-in-Thousands by sequencing (GT-seq) panel populated exclusively
with environment-associated SNPs. We then evaluated the robustness of the
GT-seq panel relative to the signal in the whole genome resequencing
baseline, and demonstrated a novel application of donor and recipient
importance (DI/RI) analysis to inform recreational fisheries stocking
decisions. We found that a reduced GT-seq panel of 616 SNPs exhibited a
significant positive correlation with those calculated from the full set
of 1412 SNPs across the climate change scenarios tested; similar results
were obtained when adding new reference populations not included in the
original whole genome resequencing baseline. The DI/RI analysis revealed
clear spatial trends, with populations situated in the warmest regions of
southern interior British Columbia (Canada) having the highest probability
for successful translocations to different recipient locations to the
north. Similarly, candidate recipient lakes for stocking at the centre of
the distribution had higher recipient importance values than those located
towards the eastern and western range peripheries. Although further
refinement is required, pairing targeted genotyping with genomic offset
and DI/RI predictions holds great promise for informing freshwater
fisheries management moving forward.