Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai–Tibetan Plateau

1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai–Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi. 2. Nucleotide diversities (π) were moderate (0.0024–0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018–0.0021) in populations from Qiadam Basin. It is probable that the low intra‐population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history. 3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise F_ST tests were significant, with non‐significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north‐west of the Qinghai–Tibetan Plateau. Analysis of molecular variance (amova ) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems. 4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai–Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations. 5. The significantly large negative F_s‐value (−24.91, P < 0.01) of Fu's F_s‐test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement. 6. The results of this study indicate that each population from the Qinghai–Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.