Genetic Diversity and Population Genetic Structure of Endemic Schizothoracinae Fishes in the Upper Yellow River and Its Adjacent Waters

The endemic fishes in the upper Yellow River and its adjacent waters on the Qinghai-Tibet Plateau are very sensitive and vulnerable to human activities and climate changes. However, the status of populations, such as genetic diversity and population genetic structure, remains unclear, limiting further conservation and utilization of their natural resources. Here, genetic diversity and population genetic structure of the highly specialized Schizothoracinae fishes were analyzed by using concatenated mitochondrial COI and D-loop sequences of 517 samples from 21 geographic populations in Qinghai Lake (QHL), the canyon section and the river source section of the upper Yellow River (CUYR and RUYR), Qaidam River (DQDR), and Golmud River (GMR). The results showed that populations from CUYR, RUYR, and QHL showed higher genetic diversity than the DQDR populations, and the GMR population exhibited the lowest haplotype diversity but high nucleotide diversity. In the upper Yellow River, dam-affected populations with low resource supplementation showed reduced genetic diversity, while those with frequent stocking events exhibited comparable genetic diversity relative to undisturbed populations. All samples were divided into three distinct phylogenetic lineages, with QHL and DQDR samples belonging to only one single and distinct lineage each, and GMR samples included in both lineages, with CUYR and RUYR samples assigned to all lineages. Low genetic differentiation was detected between GMR and RUYR, QHL and CUYR, and CUYR and RUYR. These findings indicated that the population genetic structure of endemic Schizothoracinae fishes in the upper Yellow River and its adjacent waters was primarily shaped by hydrological connectivity and isolation caused by historical geological events, and the genetic diversity was influenced by dam construction and stocking activities.