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Background   Rhynchocypris oxycephalus  is a cold water fish with a wide geographic distribution including the relatively warm temperate regions of southern China. It also occurs in second- and third-step geomorphic areas in China. Previous studies have postulated that high-altitude populations of  R. oxycephalus  in southern China are Quaternary glacial relics. In this study, we used the mitochondrial gene  Cytb  and the nuclear gene  RAG2  to investigate the species phylogeographical patterns and to test two biogeographic hypotheses: (1) that divergence between lineages supports the three-step model and (2) climatic fluctuations during the Quaternary resulted in the present distribution in southern China.    Results  Phylogenetic analysis detected three major matrilines (A, B, and C); with matrilines B and C being further subdivided into two submatrilines. Based on genetic distances and morphological differences, matriline A potentially represents a cryptic subspecies. The geographic division between matrilines B and C coincided with the division of the second and third geomorphic steps in China, suggesting a historical vicariance event. Pliocene climatic fluctuations might have facilitated the southwards dispersal of  R. oxycephalus  in matriline C, with the subsequent warming resulting in its split into submatrilines C1 and C2, leaving submatriline C2 as a relic in southern China.    Conclusions  Our study demonstrates that geological events (three steps orogenesis) and climate fluctuations during the Pliocene were important factors in shaping phylogeographical patterns in  R. oxycephalus . Notably, no genetic diversity was detected in several populations, all of which possessed unique genotypes. This indicates the uniqueness of local populations and calls for a special conservation plan for the whole species at the population level.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-014-0225-9) contains supplementary material, which is available to authorized users.

bmc evolutionary biology

Geological events and Pliocene climate fluctuations explain the phylogeographical pattern of the cold water fish Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) in China