Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

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 ...生命之树（Tree of Life）的重建几乎完全依赖串联法（concatenation methods），这类方法无法适配基因树异质性——模拟研究与演化理论均已证实，该特性可能是导致系统发育树不一致的诱因。但目前尚未有实证研究证实这类系统发育不一致现象。真哺乳亚纲（Eutherian）哺乳动物间的若干关键演化关系仍存在争议，且不同既往研究结果相互冲突，其中包括真哺乳亚纲系统发育树的根部节点，以及灵长总目（Euarchontoglires）与劳亚兽总目（Laurasiatheria）内部的演化关系。针对37个物种的447个核基因全基因组数据开展的贝叶斯（Bayesian）分析与最大似然（maximum-likelihood）分析结果显示：串联法确实会在真哺乳亚纲哺乳动物的系统发育分析中产生显著的不一致性，该结论通过基因座与类群的亚抽样分析得到验证——该分析得到了高度冲突的拓扑结构。与之形成鲜明对比的是，可适配基因树异质性的溯祖法（coalescent methods）所构建的系统发育树，对可变基因取样与类群取样均具有稳健性，且……