Genome-wide SNPs reveal the population structure and evolutionary history of the endemic toad-headed agama Phrynocephalus przewalskii in the Gobi Desert

The Northern Arid Belt of China serves as a geographic barrier that plays an important role in shaping the biodiversity in East Asia. However, the phylogeographic pattern for desert species that live within the belt remains unclear. As an indicator species of the Gobi Desert, Phrynocephalus przewalskii provides an excellent model to investigate how species have evolved inside the Northern Arid Belt. Here, by using 109 samples from 39 sites, we obtained a total of 22,682 genome-wide markers and inferred the population structure and evolutionary history of P. przewalskii in the Gobi Desert. Our results revealed three genetic groups of this species, separated by the Yabulai and Yin Mountains, with admixed populations around their geographic borders. Furthermore, phylogeographic analyses suggested that the extant P. przewalskii may have originated in the west and undergone an eastward diversification and dispersal process around 2.51 million years ago, influenced by intensified aridification in inland Asia. During this process, their current distribution pattern was likely shaped by both geographical and environmental factors. These findings elucidated the evolutionary trajectory of a key desert species in the Northern Arid Belt, providing new insights into the mechanisms underlying biodiversity formation in East Asia.