Additional molecular support for the new chordate phylogeny

Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. Despite the inclusion of 25 taxa representing all major lineages, the monophyly of deuterostomes remained poorly supp...

最近的系统发生基因组学分析表明，尾索动物（tunicates）而非头索动物（cephalochordates）是脊椎动物现存的最近亲缘类群。这一关于脊索动物演化的新系统发育假说与长期公认的真脊索动物（Euchordates）观点直接相悖，因此受到了一定程度的质疑。我们整合了一个针对后口动物（deuterostomes）的扩展系统发生基因组数据集。采用标准模型的最大似然法，以及使用氨基酸替换的CAT位点异质性混合模型的贝叶斯系统发育分析，均为尾索动物与脊椎动物（嗅球类群，Olfactores）之间的姐妹群关系提供了明确支持。脊索动物被恢复为单系群，其中头索动物是最基部的类群。这些结果在基因抽样和缺失数据方面均表现出稳健性。当成分偏倚被缓解时，核糖体rRNA的新分析也恢复了嗅球类群（Olfactores）。尽管纳入了代表所有主要类群的25个分类单元，但后口动物的单系性仍然缺乏充分支持……