The Hengduan Mountains region is known for its river capture and drainage reversal events during the tectonic upheaval of the Qinghai-Tibetan Plateau. However, little is known of the geomorphological processes at fine scales such as in the upper and middle Yalong River. Here, we investigated whether the phylogeography of Schizopygopsis malacanthus reflected the palaeodrainage changes using the mitochondrial DNA control region and 12 microsatellite markers. A wide-range sampling of fish (439 individuals) was collected across the upper and middle Yalong River (14 populations: 5 in mainstream and 9 in seven major tributaries). Phylogenetic trees, hierarchical AMOVA, STRUCTURE and gene flow confirmed a river capture event in the upper mainstream of Yalong River and Xianshui River during the middle and late Pleistocene, provided evidence for historical drainage connection between the Jiulong and Liqiu rivers before the Gonghe Movement, and revealed a potential secondary contact event in upper reaches of the Litang and Huoqu rivers during the last interglacial period. Our results indicated that the current phylogeographic structure of S. malacanthus was impacted by the geological events and climatic fluctuations during the middle and late Pleistocene. The study provides insights into the historical drainage evolution across the upper and middle Yalong River in the Hengduan Mountains region. © 2022 The Authors
