Pleistocene climatic oscillations have greatly influenced the evolutionary histories and distribution patterns of most extant species. In this study, the phylogeographic patterns and evolutionary history of Triplophysa stenura were investigated. A total of 359 individuals from 19 locations covering the species' distribution range were collected, and two mitochondrial genes (COI and Cyt b) and the recombination activating protein 1 gene (Rag1) were analyzed. Two deeply divergent lineages, corresponding geographically to the northern and southern Tanggula Mountain, were observed, and shallow divergences were found within the southern and central Qinghai-Tibetan plateau (QTP). The estimated divergence time between the northern and southern Tanggula lineages was around 1.07 Mya. Within the southern Tanggula Mountain lineages, the Nu and Subansiri rivers populations were split about 0.74 Mya, and the southwestern and central QTP populations were divided with the southeastern QTP ones approximately 0.67 Mya. The divergence times of the lineages were matched with two major glaciations in QTP (the Xixiabangma Glaciation, 1.17-0.80 Mya and Kunlun Glaciation, 0.72-0.62 Mya). Together with demographic history analyses, our results highlighted that major glacial cycles during the mid-Pleistocene played a major role in sculpting the distribution pattern of T. stenura, and led to the gene homogenization crossing the drainage populations in the southwestern and central QTP.
Keywords: Climate oscillation; Phylogeography; Pleistocene glacial cycles; The Qinghai-Tibetan plateau; Triplophysa stenura.