Population Structure and Local Adaptation of Acrossocheilus yunnanensis in the Headwaters of the Chishui River

As a major tributary of the upper Yangtze River, the Chishui River possesses distinctive ecological frameworks and serves as a critical refuge for the aquatic germplasm resources of the Yangtze Basin. Acrossocheilus yunnanensis, a dominant native fish endemic to the river’s headwaters, contributes substantially to sustaining regional ecosystem functioning. Nevertheless, no population genetic research on this species has been documented in the headwater reaches of the Chishui River to date. Here, whole-genome resequencing was performed on 140 individuals from seven geographical populations of A. yunnanensis sampled from the headwaters of the Chishui River. A total of 242,504,293 high-quality single-nucleotide polymorphism (SNP) markers were identified, with an average sequencing depth of 10×. Population genetic analyses revealed observed heterozygosity (HO) ranging from 0.290 to 0.340, expected heterozygosity (He) from 0.303 to 0.333, and nucleotide diversity (π) spanning 8.063 × 10−4 to 1.086 × 10−3. Genome-wide FROH values were generally low across the seven populations, and only several individuals within Population A exhibited clear signs of inbreeding risk. Pairwise differentiation results indicated that the Banbanqiao (A) was highly genetically divergent from the other six populations. Further genome-wide selective sweep analyses verified that A has evolved unique local adaptive signatures in pathways related to mechanosensory perception, neuromotor integration, anaerobic metabolic remodeling and protein homeostasis regulation. This study systematically characterizes the population genetic architecture and local adaptation mechanisms of headwater A. yunnanensis, providing pivotal genetic evidence for wild germplasm conservation and scientific aquatic ecosystem management across the watershed.