Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous‐throated parrotbill (Paradoxornis webbianus)
Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous‐throated parrotbill (Paradoxornis webbianus)
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DOI：
10.1111/mec.12080
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发表时间：
2012-12
影响因子：
4.9
通讯作者：
Yanhua Qu;Ruiying Zhang;Qing Quan;G. Song;Shou-Hsien Li;F. Lei
中科院分区：
文献类型：
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作者：
Yanhua Qu;Ruiying Zhang;Qing Quan;G. Song;Shou-Hsien Li;F. Lei
尽管更新世冰期对北美和欧洲许多物种的种群遗传模式产生了重大影响，但尚不清楚这些气候波动如何促进东亚物种多样化。其中一个原因是很难区分二次接触后的遗传混合和不完整的谱系分类，两者都可以产生类似的遗传变异模式。利用多位点分析和聚结模拟相结合的方法，我们探讨了这两个过程是如何在一种广泛分布的东亚鸟类——Vinous - throsed parrotbill， Paradoxornis webbianus的更新世进化史中发生的。最大似然树确定了两个主要的线粒体谱系，它们在地理上是分开的，但在一些采样点是共域的。对微卫星数据集的NJ树和结构分析表明，两个分离的类群之间存在广泛的混合，种群结构较少。然而，来自核DNA数据集的网络并没有显示任何地理上孤立的群体，而是一个泛群，因此支持不完整的谱系分类。通过使用聚结模拟方法，我们表明这两个过程确实发生了，尽管在不同的时间尺度上。在更新世冰期，大约在0.1-0.5 Ma（海洋同位素阶段6，MIS6）， webbianus压缩成两个独立的避难所，随后积累了遗传分化。在间冰期MIS5期间，物种扩展到先前的冰川地区，使曾经分离的群体接触并混合在一起。综上所述，我们的研究结果表明，目前webbianus的遗传变异是一种组合模式，即在更新世前广泛分布，然后在冰期推进期间收缩和破碎成分离的栖息地，然后是最近的冰期后扩张和混合。
Although Pleistocene glaciations had a major impact on the population genetic patterns of many species in North America and Europe, it remains unclear how these climatic fluctuations contributed to species diversification in East Asia. One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the Pleistocene evolutionary history of a widespread East Asian bird, the Vinous‐throated parrotbill, Paradoxornis webbianus. Maximum likelihood (ML) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. NJ tree and Structure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear DNA data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the Pleistocene glaciations, probably around 0.1–0.5 Ma (the Marine Isotope Stage 6, MIS6), P. webbianus contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial MIS5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within P. webbianus is a combination pattern of widespread distribution in pre‐Pleistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.