Abstract
Identifying which populations within species to prioritize to maintain genetic diversity is challenging. Due to its direct connection to current patterns of adaptation and presumed connection to adaptive capacity, some researchers advocate prioritizing adaptive variation. Other researchers advocate prioritizing populations using genome‐wide variation, citing the many limitations in identifying adaptive genetic variation, an unknown future, and verbal theory that suggests patterns of easy‐to‐gather genome‐wide genetic variation and adaptive genetic variation may often be congruent. However, evidence for such congruence is mixed. We gathered genome‐wide and putatively adaptive genetic data (using single nucleotide polymorphisms; SNPs) across 34 published outlier and association studies of plants and animals to test congruence. We asked directly whether putatively adaptive subsets of genome‐wide SNPs identify similar sets of distinctive populations (measured using the Shapley value of distinctiveness) as do sets of genome‐wide SNPs. We find that genome‐wide and putatively adaptive SNPs generally agree on population prioritizations, with the level of agreement predicted by the proportion of putatively adaptive SNPs in the dataset. Unexpectedly, the prioritization agreement between putatively adaptive SNPs and genome‐wide SNPs is stronger than that between random sets of SNPs and genome‐wide SNPs. Overall, using genome‐wide genetic variation may be a generally sound and cost‐effective strategy for prioritizing populations in order to safeguard the species‐level genetic variation needed for ongoing adaptation.