Genetic recovery in an alpine climate-sensitive pika species during upward treeline shift

Climate change endangers global biodiversity at an unprecedented pace, necessitating urgent understanding of rapid adaptive mechanisms. Notably, the alpine treeline ecotone has experienced marked environmental changes, characterized by an average upward elevation shift of 0.4 m/year. This trend raises critical questions about the evolutionary trajectory and genetic resilience of endemic species, and whether treeline upward migration benefits or harms treeline-endemic animals remains unclear. This study investigates the genomic basis of temporal adaptation and genetic response in the climate-sensitive Gansu pika (Ochotona cansus Lyon, 1907), an alpine treeline endemic species in the Hengduan Mountains in China. We integrated whole-genome sequencing (WGS) and DNA methylation data from the same 200-square-meter plot population (2015: WGS n = 3, methylation n = 1; 2016: both n = 6; 2022: both n = 7). Kinship analyses demonstrate that all sequenced individuals pertain to a single population and exclude direct kinship among these individuals. Principal component analysis demonstrated significant overlap among individuals collected between two periods, coupled with stable levels of heterozygosity and nucleotide diversity. However, a significant reduction in Tajima’s D was observed within the 2022 sample cohort when compared with that of 2015 and 2016. Concurrently, runs of homozygosity (ROH) analysis showed a decrease in inbreeding in the 2022 samples. Furthermore, the overall effective population size of this species increased over approximately 15 generations, collectively indicating enhanced genetic health. DNA methylation analysis detected localized hypomethylation within gene bodies against a globally stable background, suggesting epigenetic remodeling. Integrative cross-omics analysis revealed key genes (GLIS3 and FZD4) that are subject to both positive selection and significantly altered epigenetic regulation. These genes are functionally implicated in energy metabolism and tissue homeostasis, respectively, and may underpin the species’ adaptive response. This study demonstrates rapid adaptive evolution coinciding with a period of marked treeline upward shift in the Gansu pika, providing insights into potential persistence mechanisms of alpine endemics during environmental change.