Population Genomics and Climate Change Vulnerability in Two Sympatric Desert Rodents

Climate change poses a severe threat to desert ecosystems; however, understanding how specialized desert species respond to changing climate remains limited. These species are confronting extreme changes, including intensified droughts, altered precipitation, and temperature patterns. Here, we integrate population and ecogenomic approaches to examine population genetic structure, demographic history, and climate adaptation in two distantly related, sympatric rodent species in arid and semi-arid regions in East Asia. We further combine genomic offset analysis, ecological niche modeling, and landscape connectivity assessments to evaluate their climate change risks. Our results reveal that the two species have diverged into five geographically distinct lineages, each associated with a different arid region. Lineage divergence times are estimated between 20 and 400 thousand years ago, with population size declines occurring around the Last Glacial Maximum. While the two species exhibited distinct climate adaptation, evidenced by different key climatic variables and associated genes identified for each species, they exhibited congruent vulnerability to future climate change. This was indicated by parallel patterns of genomic offset and niche suitability loss. Under future climate change scenarios, eastern lineages in high precipitation seasonality areas (e.g., DB lineages in Horqin Sandy Land) face a higher risk due to substantial genomic offset, habitat loss, and reduced connectivity. In contrast, lineages on the west ranges with low precipitation seasonality (e.g., QH lineages in the Qaidam Basin and HL lineage in the Changtang Plateau) appear less vulnerable, characterized by lower genomic offset and the expansion of desert habitats. Overall, this study provides a comprehensive framework for identifying vulnerable populations and predicting responses to climate changes in desert species, offering critical insights for the conservation of desert ecosystems.