Molecular Phylogeography and Evolutionary History of Poropuntius huangchuchieni (Cyprinidae) in Southwest China

et al. (2013) Molecular Phylogeography and Evolutionary History of Poropuntius huangchuchieni (Cyprinidae) in Southwest China. PLoS ONE 8(11): e79975. doi:10.1371/journal.pone.0079975 Molecular Phylogeography and Evolutionary History of Poropuntius huangchuchieni (Cyprinidae) in Southwest China Xiaoyun Wu 0 Jing Luo 0 Song Huang 0 Ziming Chen 0 Heng Xiao 0 Yaping Zhang 0 Senjie Lin, University of Connecticut, United States of America 0 1 Laboratory for Conservation and Utilization of Bio-resource, Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University , Kunming, Yunnan , China , 2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan , China , 3 Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan, China, 4 Kunming Zoo, Kunming, Yunnan , China Background: The evolution of the Yunnan Plateau's drainages network during the Pleistocene was dominated by the intense uplifts of the Qinghai-Tibetan Plateau. In the present study, we investigated the association between the evolutionary histories of three main drainage systems and the geographic patterns of genetic differentiation of Poropuntius huangchuchieni. Methodology/Principal Findings: We sequenced the complete sequences of mitochondrial control region for 304 specimens and the sequences of Cytochrome b gene for 15 specimens of the species P. huangchuchieni and 5 specimens of Poropuntius opisthoptera. Phylogenetic analysis identified five major lineages, of which lineages MK-A and MK-B constrained to the Mekong River System, lineages RL and LX to the Red River System, and lineage SW to the Salween River System. The genetic distance and network analysis detected significant divergences among these lineages. Mismatch distribution analysis implied that the population of P. huangchuchieni underwent demographic stability and the lineage MK-B, sublineages MK-A1 and LX-1 underwent a recent population expansion. The divergence of the 5 major lineages was dated back to 0.73-1.57 MYA. Conclusions/Significance: Our results suggest that P. opisthoptera was a paraphyletic group of P. huangchuchieni. The phylogenetic pattern of P. huangchuchieni was mostly associated with the drainage's structures and the geomorphological history of the Southwest Yunnan Plateau. Also the differentiation of the major lineages among the three drainages systems coincides with the Kunlun-Yellow River Movement (1.10-0.60 MYA). The genetic differentiation within river basins and recent demographical expansions that occurred in some lineages and sublineages are consistent with the palaeoclimatic oscillations during the Pleistocene. Additionally, our results also suggest that the populations of P. huangchuchieni had keep long term large effective population sizes and demographic stability in the recent evolutionary history, which may be responsible for the high genetic diversity and incomplete lineages sorting of Poropuntius huangchuchieni. - Past tectonic movements and climatic changes have greatly shaped the structure of hydrographic systems [1,2,3]. Likewise, since freshwater fish species are strictly confined to freshwater drainages, the historical connections, capture, reversal and separation of rivers are a driving force behind their diversification and speciation [1,4,5,6,7]. Consequently, the genetic structure and the dispersal of freshwater fish species is also strongly connected to historical and ecological changes to the aquatic environment [1,4,5,6,7], so by examining the historical biogeography of freshwater fishes could provide a natural link in understanding concurrent geographical and biotic evolution of a given region [8]. As the southeastern neighbor of QinghaiTibetan Plateau, the Yunnan Plateau has consistently responded to each period of the QinghaiTibetan Plateaus uplifting, which reached its present elevation some 3.4 MYA, during the Pliocene. The dramatic uplifting of Yunnan Plateau at the same time not only dramatically re-shaped the composition and configurations of geographic and aquatic environments, but also greatly changed the regions climate [9,10]. The three big rivers of the Yunnan Plateauthe Mekong, Salween, and Red Riversalso experienced remarkable changes to their drainage networks during these geologic movements [11]. These movements had a markedly different influence in shaping the geomorphologic configurations of each different region of the Yunnan Plateau. As such, the configuration of the modern rivers differs significantly from their earlier paleoconfiguration [9]. The resulting complex evolutionary patterns of the river drainages in Yunnan Plateau make it an especially interesting region for exploring the phylogeography of aquatic species. Chu [12] and Chu and Chen [13] illustrated the relationship of the six river systems in Yunnan Plateau, based on similarity of genera and suggested that the six river systems can be divided into two groups: Jinsha-Nanpan-Red and Mekong-Salween-Irrawaddy (Figure S1). In addition, Several molecular phylogenetic studies demonstrated that the evolutionary history of some fish species (e.g., glyptosternoid fishes, subfamily Schizothoracinae) are associated with the uplifts of the Tibetan plateau and the concomitant river rearrangements (mostly river capture) [14,15,16]. These studies also suggest that the Mekong River had a close relationship with the Salween River, while the Red River had closely related with Jinsa River, Nanpan River and Beipan River. However, because these studies were performed on the fish species that mainly inhabit the cold water of the upper river systems, it is difficult to know whether the evolutionary patterns are actually fitted to the basins of the Salween, Mekong and Red Rivers in the southwest of the Yunnan Plateau. A recent molecular study on the phylogeography of Yunnan spiny frog (Nanorana yunnanensis) suggested that the basins of the Salween, Mekong and Red Rivers in the southwest of the Yunnan Plateau have experienced little change since the early Pliocene, excepting in their upper portions near southeastern Tibet [17]. Previous geological studies on Quaternary sediments of these rivers, however, suggest that the mainstreams of the Salween, Mekong and Red Rivers roughly formed or joined up during the Kunlun-Yellow River Movement (KYM) (1.1 0.6 MYA) in the mid-Pleistocene [9,10,18]. On the surface, the results of the phylogeography of the Yunnan spiny frog seem inconsistent with the results of the geological studies of this region, suggesting the historical rearrangement of these rivers is still poorly understood. To date, studies examining the phylogeography at intraspecific level or between closely related fish species inhabiting these drainages tha (...truncated)