Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
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DOI：
10.1016/j.cub.2017.11.008
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发表时间：
2017-12-18
期刊：
影响因子：
9.2
通讯作者：
Pisani, Davide
中科院分区：
文献类型：
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作者：
Feuda, Roberto;Dohrmann, Martin;Pisani, Davide
在动物树的根的关系已被证明是难以解决的，与目前的争论集中在海绵（孔动物门）或梳水母（门Ctenophora）是否是所有其他动物的姐妹组[1 - 5]。进化模型的选择似乎是问题的核心，因为当对位点特异性氨基酸差异进行建模时（例如，[6，7]），而Ctenophora出现作为姐妹集团的所有其他动物（"Ctenophora-sister"）时，他们被忽视（例如，[8 - 11]）。我们发现，以前支持栉水母姐妹[10，12]的两个关键的cDNA基因组数据集在不同位点和类群的氨基酸组成中显示出很强的异质性，并且没有常规使用的进化模型可以充分描述这两种形式的异质性。我们表明，数据重新编码方法[13 - 15]减少了这些数据集的组成异质性，并且适应位点特异性氨基酸偏好的模型可以更好地描述重新编码的数据集。增加模型充分性与支持多孔菌属姐妹的显著拓扑变化相关。由于对生成数据的进化过程进行充分建模是恢复准确系统发育的基础[16 - 20]，我们的结果强烈支持海绵是所有其他动物的姐妹群，并提供了进一步的证据表明栉水母姐妹代表了树木重建文物。
The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1-5]. The choice of evolutionary models seems to be at the core of the problem because Porifera tends to emerge as the sister group of all other animals ("Porifera-sister'') when site-specific amino acid differences are modeled (e.g., [6, 7]), whereas Ctenophora emerges as the sister group of all other animals ("Ctenophora-sister'') when they are ignored (e.g., [8-11]). We show that two key phylogenomic datasets that previously supported Ctenophora-sister [10, 12] display strong heterogeneity in amino acid composition across sites and taxa and that no routinely used evolutionary model can adequately describe both forms of heterogeneity. We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets and that models accommodating site-specific amino acid preferences can better describe the recoded datasets. Increased model adequacy is associated with significant topological changes in support of Porifera-sister. Because adequate modeling of the evolutionary process that generated the data is fundamental to recovering an accurate phylogeny [16-20], our results strongly support sponges as the sister group of all other animals and provide further evidence that Ctenophora-sister represents a tree reconstruction artifact.