Phylogenomic analysis reveals the demographic history and cryptic barriers of three desert fishes

Abstract East Asia's largest inland arid ecological region—the Tarim Basin and Hexi Corridor—serves as an independent evolutionary center for highland ichthyofauna. However, systematic studies on the evolutionary patterns of fishes in this region remain limited. In this study, we integrated mitochondrial cytochrome b (Cyt b ) and nuclear SNP data to investigate the demographic structure and historical dynamics of three desert fish species: Triplophysa tenuis , Triplophysa bombifrons , and Hedinichthys yarkandensis . Our results indicate that populations in the Hexi Corridor and Tarim Basin diverged approximately 0.8 million years ago (Ma), coinciding with a period of increasing aridity, followed by alternating phases of population contraction and secondary contact. Demographic fluctuations were likely driven by westerly atmospheric circulation interacting with regional geological activity. Furthermore, this study provides evidence for the existence of an ancient South Tarim River and suggests the need for taxonomic re‐evaluation of T. bombifrons . These findings offer critical insights into the evolutionary processes shaping fish diversity in arid regions of China and inform strategies for their conservation.