Data from: Squamate phylogenetics, molecular branch lengths, and molecular apomorphies: a response to McMahan et al. (2015)

Morphology-based studies of squamate phylogenetics recover very different topologies from studies that use molecular or combined molecular and morphological data. This has led to some stimulating dialogue regarding the respective merits of the alternative hypotheses, with the primary point of disagreement being the placement of Iguania. Molecular phylogenetic studies place Iguania in a highly nested position as a member of the clade Toxicofera, additionally containing Anguimorpha and Serpentes, whereas morphology-only studies have traditionally placed Iguania as sister to all remaining squamates. McMahan and colleagues recently posited that the molecular phylogenetic hypothesis of the placement of Iguania is a result of incorrect root placement. These authors mapped molecular data (i.e., DNA sequence data) onto phylogenetic hypotheses and identified more molecular apomorphies on the basal branches of the morphology-based phylogeny. They concluded from this result that the molecular data support the morphological phylogenetic hypothesis of Iguania being sister to all remaining squamates. Here, we map molecular data onto additional phylogenetic hypotheses and show that the conclusions of McMahan and colleagues are flawed for three key reasons: 1) they misinterpreted a measure of branch length as a measure of branch support; 2) they considered only two phylogenetic hypotheses; and 3) their counts of molecular apomorphies are severely biased by their decision to collapse clades into large polytomies. We demonstrate that counting the molecular apomorphies along a given branch is a poor measure of support for a clade and that the molecular data do not provide support for the morphology-based squamate phylogeny as the optimal topology.

基于形态学的有鳞目（squamate）系统发育学研究，其得到的拓扑结构与基于分子数据或分子结合形态学数据的研究存在显著差异。这一现象引发了关于两种假说各自优势的富有启发性的讨论，其中核心争议点在于鬣蜥下目（Iguania）的系统位置。分子系统发育学研究将鬣蜥下目置于毒蜥类分支（Toxicofera）的高度嵌套位置，该分支同时包含蛇蜥下目（Anguimorpha）与蛇类（Serpentes）；而传统仅基于形态学的研究则将鬣蜥下目定位为其余所有有鳞类的姐妹群。麦克马汉（McMahan）及其团队近期提出，鬣蜥下目系统位置的分子系统发育假说源于错误的根节点定位。该团队将分子数据（即DNA序列数据）映射至系统发育假说中，并在基于形态学的系统发育树的基部分支上识别出更多分子衍征（apomorphies），由此得出结论称分子数据支持鬣蜥下目作为其余所有有鳞类姐妹群的形态学系统发育假说。本研究将分子数据映射至更多系统发育假说中，证明麦克马汉及其团队的结论存在三处关键缺陷：1. 他们将分支长度指标误判为分支支持度指标；2. 他们仅考量了两种系统发育假说；3. 他们将分支合并为大型多歧支的操作，严重偏倚了分子衍征的统计结果。本研究证实，沿指定分支统计分子衍征并非衡量分支支持度的合理指标，且分子数据并不支持基于形态学的有鳞目系统发育树为最优拓扑结构。