Historical and contemporary genomes of an endangered rodent reveal shifts in environmentally associated genes

Global climate change poses a substantial challenge for many species, particularly when habitat loss and fragmentation prevent a species from shifting its range to track suitable climate conditions. Instead, these species must adapt in situ to a different climate environment, making their capacity for adaptation critical to persistence. Yet endangered species often face the added challenge of low standing genetic variation needed for an evolutionary response. Here, we assess adaptive potential in the endangered Pacific pocket mouse ( Perognathus longimembris pacificus ). Using whole-genome sequences spanning nearly a century, we identify 14 candidate genes associated with temperature and moisture, including many with vascular and circulatory functions. Using a reintroduced population, we find more alleles than expected by chance shifted toward the frequencies predicted for the climate of the reintroduction locality. Despite extreme population declines over the past century, these findings indicate that conservation breeding and reintroduction have retained genetic variation relevant to adaptive potential in the Pacific pocket mouse.