Data from: Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers

The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.

更新世冰期循环对生物当代遗传结构形成的作用，在中国已得到广泛研究，其中尤以青藏高原（Tibetan Plateau）为重点。然而，中国地形复杂、局地气候多样，冰期循环如何塑造该区域亚热带与热带生物区系的问题，迄今仍未得到充分解答。
为探究影响一种广布常绿森林鸟类系统地理学（phylogeography）与种群历史的因素，我们对白鹇（Silver Pheasant, Lophura nycthemera）的形态特征、线粒体DNA序列及核微卫星位点展开分析。
研究检测到局限于不同地理区域的高度分化线粒体谱系，这一模式大体与表型类群相符，但与命名亚种并不一致。溯祖模拟（coalescent simulations）结果显示，主要分化事件的发生时间对应更新世的主要冰期阶段，且仅部分种群间的水系屏障会降低基因交流水平。
研究揭示了种内核质不一致现象：海南岛与四川盆地的线粒体谱系存在该现象，且有证据表明四川盆地种群的核基因流来自邻近群体。令人意外的是，在盈江地区发现白鹇与黑鹇（Kalij Pheasant, Lophura leucomelanos）存在杂交现象，且二者在线粒体DNA与核基因层面均存在广泛的遗传渐渗（genetic introgression）。
本研究结果凸显了亚热带区域一种全新的系统地理模式，该模式由气候波动、部分水系屏障及种间杂交的共同作用所塑造。核质不一致现象结合形态分化表明，复杂的历史因素塑造了中国南部这一生物多样性热点区域（biodiversity hot spot）的物种分化进程。