Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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使用系统发育组学和多物种合并模型解决真兽哺乳动物系统发育中的冲突
DOI：
10.1073/pnas.1211733109
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发表时间：
2012-09-11
影响因子：
11.1
通讯作者：
Wu, Shaoyuan
中科院分区：
文献类型：
--
作者：
Song, Sen;Liu, Liang;Wu, Shaoyuan
生命之树的重建几乎完全依赖于串联方法，这种方法不适应基因树的异质性，模拟和理论已经确定这种特性是不一致遗传的可能原因。然而，这种不一致性尚未在实证研究中得到证明。真兽目哺乳动物之间的几个关键关系在以往的研究中仍然存在争议和冲突，包括真兽目树的根以及真巨齿兽目和劳亚兽目之间的关系。贝叶斯和最大似然分析的全基因组数据的447个核基因，从37个物种表明，串联方法确实产生强烈的不一致性，在真兽目哺乳动物的生殖发育，所揭示的亚抽样分析的基因座和类群，产生强烈冲突的拓扑结构。相比之下，合并的方法，它适应基因树的异质性，产生一个系统发育，是强大的可变基因和分类单元采样，是一致的地理数据。数据还表明，不完整的谱系排序，基因树异质性的主要来源，是相关的深层次的遗传，如真兽目哺乳动物。我们的研究结果坚定地把真兽根之间的arctogenata和Boreoeutheria和支持有蹄类多系和姐妹群之间的关系Scandentia和灵长类动物。这项研究表明，由串联方法引入的不一致性是长期存在的不确定性的真兽目哺乳动物的生殖发育的一个主要原因，这同样可能适用于其他分支。我们的分析表明，这种不一致性可以解决使用的基因组数据和合并的方法，明确处理基因树的异质性。
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.