Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.

在构建脊椎动物生命之树的研究中，仍存在两个核心未解问题：其一，龟类在羊膜动物（amniotes）中的系统发育位置；其二，滑体两栖类（lissamphibian，即现生两栖类）三大主要类群间的演化关系。长期以来，此类演化关系的厘清颇具难度：针对龟类的系统发育位置，学界已提出五种不同假说；而滑体两栖类内部则存在四种已被提出的分支模式。为解答上述悬而未决的问题，我们构建了一套大型脊椎动物互补DNA/表达序列标签（cDNA/EST）数据集，涵盖129个分类单元的75个基因。单基因系统发育分析显示，各基因的最优拓扑结构存在显著差异，使得合并数据集得到的结论存在拓扑结构歧义。由于不同基因对相同的分歧拓扑结构存在一致的偏好性，我们推测部分演化差异源于系统性系统发育误差。据此，我们开发并验证了一种全新的统计方法，该方法可识别出对特定系统发育关系携带偏倚信号概率较高的位点。移除推定带有偏倚的位点后，分析结果支持龟类与鳄形类（crocodilians）或初龙类（archosaurs）构成姐妹群支系；同时也支持滑体两栖类内部蚓螈（caecilian）与蝾螈（salamander）形成姐妹群，且滑体两栖类可能为并系群（paraphyletic）。