Mulhair Peter O, McCarthy Charley G P, Siu-Ting Karen, Creevey Christopher J, O'Connell Mary J
Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
Curr Biol. 2022 Dec 5;32(23):5180-5188.e3. doi: 10.1016/j.cub.2022.10.036. Epub 2022 Nov 9.
Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum or within Deuterostomia, sister to Ambulacraria. Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all. Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies. Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree. We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately..
相互矛盾的研究将一组包含异涡虫和无肠类的两侧对称无脊椎动物——异涡虫纲，要么置于最早出现的两侧对称动物门，要么置于后口动物中，为有 ambulacraria 的姐妹群。尽管它们作为所有两侧对称动物姐妹群的位置表明祖先两侧对称动物的形态相对简单，但它们在后口动物中的另一种位置表明祖先两侧对称动物形态复杂，同时异涡虫纲中主要表型特征大量丧失。最近的研究质疑后口动物是否应被视为单系类群。隐藏的旁系同源性和较差的系统发育信号对重建物种系统发育构成了重大挑战。在这里，我们评估这些问题是否导致了关于异涡虫纲位置的冲突。我们重新分析了已发表的数据集，富集了那些基因树在动物树其他地方支持解析良好的类群的直系同源群。我们发现，先前发表的数据集中的大多数基因违反了无可争议的类群，这表明隐藏的旁系同源性和低系统发育信号影响了重建动物树深层节点分支模式的能力。我们证明，去除那些无法概括无可争议关系的直系同源群会改变推断的最终拓扑结构，同时提高模型对数据的拟合度。我们在经过筛选的直系同源群集合中发现了对异无 ambulacraria 存在的支持增加，但最终并不确凿。在我们朝着对地球上所有生命进行测序迈进的时代，我们认为，生命之树中长期存在的有争议问题将通过使用数量更少但质量更高、能够得到充分建模的数据来解决。
