Disentangling evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences

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（phylogenomic era）的到来，深化了我们对东南亚鸟类区系（avian fauna）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（taxa）的演化历史尚未得到清晰解析，尤其是那些既经历过古老地质气候事件、又受近期地质气候事件扰动的类群。本研究以山鹧鸪属（鸡形目Galliformes：雉科Phasianidae：Arborophila spp.）为研究对象，解析其演化历史：该类群被认为是从非洲早期迁入东南亚的类群，亦是当前物种丰富度位列第二的鸡形目属级类群。我们采用低覆盖度鸟枪测序（low coverage shotgun sequencing）技术，对几乎涵盖所有山鹧鸪属物种的新鲜样本与老旧博物馆组织样本进行测序，成功获取了超保守元件（ultra-conserved elements）、外显子（exon）及线粒体基因组（mitochondrial genomes）数据。研究结果表明，尽管山鹧鸪属的祖先类群于中新世早期（early Miocene）抵达印度支那（Indochina）地区，但该属内的初始分化直至约10 Ma（百万年前）全球变冷加剧时才得以发生。后续山鹧鸪属的扩散与多样化过程，受到多次构造与气候事件的共同调控。具体而言，我们发现上新世（Pliocene）全球变冷期间，印度支那地区的山鹧鸪属类群发生了快速辐射演化；而更新世（Pleistocene）海平面波动时期，巽他地区（Sundaic）的山鹧鸪属类群则经历了广泛的扩散与辐射演化。综合来看，上述结果表明，山鹧鸪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相互作用的影响。此外，本研究亦凸显出，系统基因组学研究可为探究物种多样性极高的亚洲复杂生物区系的生物地理格局与演化历史提供前所未有的契机。