Genetic structure and historical demography of Schizothorax nukiangensis (Cyprinidae) in continuous habitat

Geographic distance, different living habitats or Pleistocene climatic oscillations have frequently been found to shape population genetic structure in many species. The genetic structure of Schizothorax nukiangensis, a high altitude, valuable fish species, which is distributed throughout the Nujiang River, was investigated by mitochondrial DNA sequence analysis. The cytochrome c oxidase subunit I (COI), cytochrome b (cytb), and the mitochondrial control region (MCR) of S. nukiangensis were concatenated for examination of population structure and demographic history. The concatenated data set (2405 bp) implied a pronounced genetic population structure (overall F ST = 0.149) and defined two population units. Strong differentiation was detected between the Sanjiangkou (SJK) population and other populations due to environmental heterogeneity, dispersal ability, and/or glacial cycles. Additional DNA sequencing of the nuclear RAG2 gene also examined significant differentiation between two units and between SJK and the upstream populations (U-unit). Recent expansion events suggest that S. nukiangensis may have undergone a rapid increase during warm interglacial periods. Surprisingly, S. nukiangensis appears to have undergone an obvious expansion during the last glaciations (LG) for cold hardiness and a sharp contraction from 1.5 ka to the present. However, two population units exhibited different reflections during the LG, which might be closely related to their living habitats and cold hardiness. A clear pattern of isolation by distance was detected in S. nukiangensis due to feeding habits, limited dispersal ability, and/or philopatry. It is vitally important that more attention be given to S. nukiangensis due to low genetic diversity, lack of gene flow, and recent population contraction.