Low coverage shotgun sequencing from 12 Arborophila species. Arborophila

The advent of the phylogenomic era has improved our understanding of the biogeographic patterns and evolutionary histories of the avian fauna of Southeast Asia. However, there remains many Southeast Asian bird taxa whose evolutionary histories remain poorly resolved, especially those that have experienced both ancient and recent geological and climatic events. In this study, we examined the evolutionary history of hill partridges (Galliformes: Phasianidae: Arborophila spp.), which is thought to be an early colonizer into Southeast Asia from Africa and currently the second most speciose galliform genus. We used low coverage shotgun sequencing to generate ultra-conserved elements, exon, and mitochondrial genomes from both fresh and old museum tissue samples of almost complete coverage of all Arborophila species. Our results suggest that although the ancestor of Arborophila arrived in Indochina during the early Miocene, the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification of Arborophila was affected by a number of tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling, and extensive dispersal and radiation of Sundaic Arborophila during Pleistocene sea level fluctuations. Taken together, these results suggest that the evolutionary history of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia. Furthermore, our study highlights that phylogenomic studies can provide unprecedented opportunities to explore biogeographic patterns and the evolutionary history in biologically complex parts of Asia that support high species diversity.

系统基因组学时代的到来，加深了我们对东南亚鸟类区系的生物地理格局与演化历史的认知。然而，仍有诸多东南亚鸟类类群的演化历史分辨率较低，尤其是那些同时经历过古、近地质与气候事件的类群。本研究聚焦于鸡形目（Galliformes）雉科（Phasianidae）Arborophila属（Arborophila）的山鹧鸪类群——该类群被认为是从非洲最早殖民东南亚的类群之一，同时也是当前物种丰富度排名第二的鸡形目属。我们通过低覆盖度鸟枪法测序，从几乎覆盖所有Arborophila属物种的新鲜及馆藏老组织样本中，获取了超保守元件（ultra-conserved elements）、外显子及线粒体基因组数据。研究结果显示，尽管Arborophila属的祖先于早中新世（early Miocene）抵达中南半岛，但该属的初始分化直至约10 Ma（百万年）前才随着全球降温加剧而发生。后续Arborophila属的扩散与多样化进程，受到了多起构造与气候事件的影响。具体而言，我们发现中南半岛的Arborophila属类群在上新世（Pliocene）全球降温期间发生了快速辐射演化，而巽他地区的Arborophila属类群则在更新世（Pleistocene）海平面波动中经历了广泛的扩散与辐射演化。综上，上述结果表明，Arborophila属的演化历史受到东南亚地区历史、地质与气候事件间复杂交互作用的影响。此外，本研究凸显了系统基因组学研究可为探索物种多样性极高的亚洲生物复杂区域的生物地理格局与演化历史提供前所未有的机遇。