Comparative and population genomics approaches reveal basis of adaptation to desert conditions in a small rodent

Life in extreme environments offers the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for animals and plants living there. The Cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in Cactus mice, we built a chromosome-level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrate comparative, population, and functional genomic approaches. We identify 16 gene families exhibiting significant contractions or expansions in the Cactus mouse compared to17 other Myodontine rodent genomes and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, and a growth factor involved in lipid metabolism, suggesting a dietary shift associated with desert life, potentially increasing palatability of chemically defended desert plants and insects. Understanding how species adapt to the recent emergence of deserts in North America will provide important foundation for predicting future evolutionary responses to increasing desertification.