Genomic insights into fossorial transition, hibernation, and hypoxia adaptation in ground squirrels

The evolutionary shift from arboreal to fossorial lifestyles, coupled with deep hibernation and high-altitude hypoxia tolerance, represents a suite of extreme physiological adaptations unique to ground squirrels. To investigate the molecular basis of these interconnected traits, we generated a chromosome-level genome of the Himalayan marmot (Marmota himalayana) and conducted comparative analyses across 11 squirrel species. Evolutionary breakpoint regions distinguishing arboreal from fossorial taxa were enriched in bone morphogenesis and motor nervous system genes, providing testable hypotheses for the fossorial transition. Positively selected genes in hibernating ground squirrels included circadian regulators, and a hibernator-specific TIMELESS Leu173Phe mutation enhanced PER2 binding in co-immunoprecipitation assays, offering a candidate mechanism for circadian dampening during torpor. In M. himalayana, a fixed EPAS1 Thr478Met variant reduced protein expression under hypoxia while upregulating LDHA and VEGF, revealing a fine-tuned strategy for high-altitude adaptation. Together, these findings provide molecular insights into three key evolutionary innovations with TIMELESS and EPAS1 variants are supported by functional validations and the fossorial transition representing comparative genomic hypotheses awaiting further testing. The authors sequence the Himalayan marmot genome and compare 11 squirrel species, revealing candidate genes underlying fossorial transition, a hibernator-specific TIMELESS mutation enhancing PER2 binding, and an EPAS1 variant tuning hypoxia adaptation.