Data for: Genomic insights into inbreeding and adaptive divergence of trout populations to inform genetic rescue

Genetic rescue, specifically translocation to facilitate gene flow among
populations and reduce the effects of inbreeding, is an increasingly used
approach in conservation. However, this approach comes with tradeoffs,
wherein gene flow may reduce fitness when populations have adaptive
differentiation (i.e., outbreeding depression). A better understanding of
the interaction between isolation, inbreeding, and adaptive divergence in
key traits, such as life history traits, will help to inform genetic
rescue efforts. Stream dwelling salmonids, such as the westslope cutthroat
trout (Oncorhynchus lewisi;WCT), are well-suited for examining these
tradeoffs because they are increasingly isolated by habitat degradation,
exhibit substantial variation in life history traits among populations,
and include many species of conservation concern. However, few genomic
studies have examined the potential tradeoffs in inbreeding versus
outbreeding depression in salmonids. We used >150,000 SNPs to
examine genomic variation and inbreeding coefficients in 565 individuals
across 25 WCT populations that differed in their isolation status and
demographic histories. Analyses of runs of homozygosity revealed that
several isolated WCT populations had ‘flatlined’, having extremely low
genetic variation and high inbreeding coefficients. Additionally, we
conducted genome scans to identify potential outlier loci that could
explain life-history differences among ten isolated populations. Genome
scans identified one candidate genomic region that influenced maximum
length and age-1 to age-2 growth. However, the limited number of candidate
loci suggests that the life history traits examined may be driven by many
genes of small effect or phenotypic plasticity. Although adaptive
differentiation should be considered, the high inbreeding coefficients in
several populations suggest that genetic rescue may benefit the most
genetically depauperate WCT populations.