Genomic evidence of local adaptation in Scottish freshwater pearl mussels

Climate change is a global threat that is already impacting populations and species across diverse ecosystems. Local adaptation of populations, identified through genotype-environment association, can be used to guide conservation management. The critically endangered freshwater pearl mussel Margaritifera margaritifera has a widespread Holarctic distribution across a range of habitats. Here, we used 156 samples from 18 populations of M. margaritifera across Scotland to characterize neutral population structure and identify signals of environment-associated adaptation in this endangered mussel. This study revealed a complex pattern of population structure, indicated by high genetic diversity, high genetic clustering and high inbreeding, although neutral structure was not shaped by distances or environments. Controlling for host species, freshwater pearl mussels show significant patterns of local adaptation to abiotic habitat variables, including in response to elevational range of their sub-catchment, their specific altitude, and bioclimatic factors such as isothermality. Locally adapted and generalist populations were identified which could guide genetic rescue and restocking conservation efforts, while a subset of 302 genetic variants putatively under environmental selection were identified for further adaptation investigation.