Is the deuterostome clade an artefact?

There is a long-standing consensus that the animal phyla closest to our own phylum of Chordata are the Echinodermata and Hemichordata. These three phyla constitute the major clade of Deuterostomia. Recent analyses have questioned the support for the monophyly of Deuterostomia, however, showing that the branch leading to deuterostomes is very short and may be influenced by systematic error. Here we use a site-by-site approach to explore possible sources of error. Under conditions that promote long-branch attraction (LBA) – especially branch-length heterogeneity and sites constrained in their amino acid composition – we find that deuterostome monophyly is strongly supported. When we make efforts to mitigate these sources of error, support for Deuterostomia markedly decreases or even disappears. Our results call into question one of the longest established major branches of the animal kingdom. A very short, or non-existent, deuterostome branch has implications for interpretating putative d..., , , # Is the deuterostome clade an artefact? ## Directory list: `dataProvenance.xlsx`: contains the accession numbers and sources for the proteomic and transcriptomic data used in this study `rawData.zip`: contains the pre-processed input data * OrthoFinder_input contains the raw genomes/proteomes/transcriptomes listed in dataProvenance.xlsx * orthoGroups_raw.zip contains the raw [OrthoFinder output](https://github.com/davidemms/OrthoFinder), excluding the WorkingDirectory and the empty Single_Copy_Orthologue_Sequences * orthoGroups_paraFilter contains the 183 paralogue filtered orthogroups, see main text for methodology `scripts.zip`: contains any additional script needed to run/modify analyses or their output that are not already available from GitHub repositories (cited in main text). The scripts are roughly organised by task: * dataProcessing * IQTreeOutputProcessing * IQTreeSearches * plotting * renamingScripts * simulations From here all subfolders follow these naming conventio...,学界长期以来存在共识：与我们所在的脊索动物门（Chordata）亲缘关系最近的动物门类为棘皮动物门（Echinodermata）与半索动物门（Hemichordata）。上述三个门类共同构成后口动物总门（Deuterostomia）的核心类群。然而近期的分析对后口动物总门的单系群（monophyly）支持度提出了质疑，研究显示后口动物的演化分支极短，且可能受到系统误差的影响。本研究采用逐位点分析方法，对潜在的误差来源进行探究。在促进长枝吸引（long-branch attraction, LBA）效应显现的条件下——尤其是枝长异质性与氨基酸组成受限的位点——我们发现后口动物单系群的支持度极高。当我们采取措施缓解上述误差来源时，后口动物总门的支持度显著下降，甚至完全消失。本研究结果对动物界中确立时间最久的核心分支之一提出了质疑。极短甚至不存在的后口动物演化分支，对解读推定的d……具有重要意义。 # 后口动物类群是否为人工假象？ `dataProvenance.xlsx`：收录本研究使用的蛋白质组学与转录组学数据的登录号及来源信息。 `rawData.zip`：包含经预处理的输入数据。 * `OrthoFinder_input`：收录`dataProvenance.xlsx`中列出的原始基因组、蛋白质组及转录组数据。 * `orthoGroups_raw.zip`：包含原始[OrthoFinder分析结果](https://github.com/davidemms/OrthoFinder)，已剔除WorkingDirectory目录与空的Single_Copy_Orthologue_Sequences文件夹。 * `orthoGroups_paraFilter`：包含经183个旁系同源基因过滤后的直系同源基因簇，具体分析方法详见正文。 `scripts.zip`：包含本研究所需的额外脚本（正文已引用的GitHub公开仓库脚本除外），用于运行、修改分析流程或其输出结果。脚本按功能大致分类如下： * 数据处理脚本 * IQTree结果处理脚本 * IQTree搜索脚本 * 绘图脚本 * 重命名脚本 * 模拟分析脚本 自此处起，所有子文件夹均遵循以下命名规范……