Genetic Variation of Schizothorax wangchiachii Populations Between the Jinsha and Yalong Rivers Using Simplified Genome Sequencing

<i>Schizothorax wangchiachii</i>, as a cold-water fish, is a predominant or common species in high-altitude areas with large population sizes. It is among the main edible economic fish species in the production area. We used genotype sequencing (GBS) technology to analyze the genetic diversity and population structure of 10 wild populations in the Jinsha River and Yalong River basins of the upper Yangtze River. A total of 724,858 single-nucleotide polymorphisms (SNPs) were detected in these 10 wild populations. The population genetic diversity was low; however, the degree of genetic differentiation was not significant. The populations from the Jinsha River and Yalong River could not be clustered separately on the basis of the SNPs. The Panzhihua (PZH) and Wudongde (WDD) populations from the Jinsha River exhibited gene flow with the Yajiang (YJ) population from the Yalong River, and a secondary pulse of gene flow subsequently connected the PZH and WDD populations to the upper-Jinsha population Suwalong (SWL). The demographic history of <i>S. wangchiachii</i>, reflected in its effective population size (<i>N_e</i>), has been influenced by the uplift of the Qinghai-Tibet Plateau (QTP). Furthermore, the identified SNPs are functionally associated with key cellular processes, environmental adaptation, and metabolism. These findings provide critical genomic insights that can inform conservation strategies and support the sustainable utilization of wild <i>S. wangchiachii</i> resources.