HExT, a software supporting tree-based screens for hybrid taxa in multilocus datasets, and an evaluation of the homoplasy excess test

The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).
We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written ...

同质性过剩检验（homoplasy excess test, HET）是一种基于系统发育树的筛选方法，用于多位点核基因系统发育树中的杂交类群检测。当某一杂交类群与其亲本类群所在演化支之间存在同质性时，会降低系统发育树的自展支持率（bootstrap support）。HET的核心假设为：将该杂交类群从数据集中移除后，其亲本演化支的自展支持率会得到提升；而移除非杂交类群则对节点的统计支持率几乎无影响。执行HET分析时，需基于类群剔除法数据集（taxon-jackknife data sets）计算自展树，即每次仅移除一个类群（物种或种群）。若移除某一特定类群后，特定节点的自展支持率出现过度提升，则表明该被移除类群为杂交类群，且其亲本类群对应支持率上升的演化支。
本研究引入一款全新的软件工具hext，该工具可生成类群剔除法数据集、运行自展树计算流程，并通过箱线图（boxplot graphs）中的异常值识别自展支持率的过度提升现象。hext的代码编写为……