Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus
Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus
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DOI：
10.1093/biolinnean/blab139
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发表时间：
2021-11-23
影响因子：
1.9
通讯作者：
Klicka, John
中科院分区：
文献类型：
--
作者：
Blair, Christopher;Bryson, Robert W., Jr.;Klicka, John
基因组数据继续推进我们对物种限制和地理模式的理解。然而，仍然没有达成共识，适当的方法，使这些异质性数据集的最佳利用的基因组分析。在这项研究中，我们使用了成千上万的ultraconserved元素（UCE）的基因座从鳄鱼蜥蜴属Gerrhonotus比较和对比物种树推断使用多种当代方法，并提供了一个时间框架的生物多样性在墨西哥过渡区（MTZ）。串联最大似然（ML）和贝叶斯分析提供了高度一致的结果，差异仅限于支持较差的节点。从贝叶斯系统发生学、系统地理学和SVDquartets的结合分析中推断出类似的拓扑结构，尽管对某些节点的支持较低。所有的分歧时间落在中新世，连接到当地的新第三纪的vicariance和/或全球冷却趋势，中新世中期气候最佳。我们检测到一个形态上不同的物种限制在墨西哥东北部的干旱山区的基因组分化水平很高，并建立了一个新的属，以更好地反映进化历史。总之，我们的研究结果进一步倡导利用连接和合并方法的优点和缺点，为鳄鱼蜥蜴的旧分歧提供证据，并表明MTZ继续拥有大量未被识别的多样性。
Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.