Abstract
Neosalanx taihuensis is a fish species endemic to China, primarily distributed in the middle and lower reaches of the Yangtze and Huaihe rivers and their affiliated lakes. To assess its resource status and facilitate targeted conservation of genetic diversity, we analyzed genetic differences among populations in the lower Yangtze River. Samples were collected from four natural river populations (JJ, AQ, NJ, and TZ) and one lacustrine population (THL). Whole genome resequencing was performed to characterize genetic diversity, population structure, and selection signatures across the five populations. The results showed no obvious genetic divergence among the natural river populations, whereas all natural river populations were distinctly separated from the THL population. The natural river populations harbored higher genetic diversity than the THL population. Gene flow analysis suggested that historical gene exchange might have occurred between TZ and THL, as well as between TZ and NJ. Selective sweep analysis identified Chr01, Chr04, Chr09, and Chr15 as candidate genomic regions potentially carrying adaptive selection signatures. In summary, conservation efforts should prioritize the genetic diversity of both natural river populations and the THL population, facilitate gene flow among populations, and adopt differentiated management strategies for each group.