Shared historical refugia and genetic diversity hotspots of co-distributed species on the Qinghai Tibet plateau

The Qinghai-Tibet Plateau (QTP) is a global biodiversity hotspot, yet the distribution of genetic diversity hotspots in co-distributed species remains poorly understood. Here, we integrate genomic data from three co-distributed endemic species (plateau pika and two snowfinches) on the QTP, with ecological niche models (ENMs) based on paleoclimate data to identify shared genetic diversity hotspots. Our results reveal a consistent northeast-to-southwest decline in genetic diversity, with a shared hotspot located in the northeastern QTP. ENMs further suggest that these species shared glacial refugia in this region during the last glacial maximum, followed by post-glacial expansions into the central plateau, resulting in similar spatial patterns of genetic diversity. Differences in genetic differentiation, demographic history, inbreeding depression, and genetic load suggest species-specific evolutionary responses to historical climate fluctuations. Overall, our study highlights the importance of protecting hotspots of shared genetic diversity across multiple species to preserve their evolutionary potential.