Genomic and Morphological Divergence Under Extreme Environments: Insights Into the Adaptation and Speciation of Lepus yarkandensis and Lepus tibetanus

ABSTRACT Environmental adaptation and speciation are key processes shaping biodiversity, especially in extreme environments. This study investigates the Yarkand hare ( Lepus yarkandensis ), inhabiting the arid Tarim Basin, and the Desert hare ( Lepus tibetanus ), residing in the cold and hypoxic Pamir Plateau. These species, facing distinct environmental pressures, provide an ideal model for understanding how organisms adapt to extreme conditions. Using whole‐genome resequencing, we identified genomic regions associated with environmental adaptation in both species, and employed selective sweep and functional enrichment analyses to pinpoint important candidate genes. Additionally, we examined morphological adaptations, measuring body size, nasal bone structure and tympanic bulla, to explore how these traits facilitate survival in their respective environments. The results reveal common adaptive strategies, such as selection for genes related to energy metabolism and immune function. However, due to their distinct environments, the species exhibit different evolutionary paths. The Yarkand hare has larger tympanic bullae but a smaller body size, aiding heat dissipation and predator avoidance. In contrast, the Desert hare has a larger body size and longer nasal bones, reducing heat loss and warming the cold air at high altitudes. These findings highlight the crucial role of divergent selection in shaping adaptive traits, contributing to ecological isolation and supporting speciation in response to environmental challenges. This research enhances our understanding of adaptive evolution and has implications for conservation strategies aimed at addressing climate change impacts.