Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa
Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa
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DOI：
10.1093/molbev/msp148
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发表时间：
2009-10-01
影响因子：
10.7
通讯作者：
Pisani, Davide
中科院分区：
文献类型：
--
作者：
Sperling, Erik A.;Peterson, Kevin J.;Pisani, Davide
后生动物树根部的关系很难得到可靠的解决，关于海绵、刺胞动物、栉水母动物、长生动物和两侧对称动物之间的相互关系有几种不同的假设，每种假设对动物最后共同祖先的身体结构和前寒武纪晚期的古生态学都有不同的影响。我们对来自 17 种新海绵的 7 个核管家基因进行了测序，使分析的物种总数达到 29 个，包括海绵海绵动物门、海绵动物门、六角海绵动物门和同硬形动物的多个代表，并使用各种系统发育方法和进化模型分析了还包括 6 个非后生动物外群和 36 个真后生动物的数据集。我们利用叶子稳定性来识别流氓类群，并研究它们对树木节点支持的影响，并通过比较使用不同方法（和模型）衍生的树木和通过位点剥离分析，识别出最有可能代表系统发育工件的分支。此外，我们研究了成分异质性并测试了氨基酸成分偏差是否影响我们的结果。最后，我们使用贝叶斯因子将我们的结果与之前发表的系统发育进行比较。我们所有的最大似然 (ML) 和贝叶斯分析都发现海绵是并系的，所有分析都发现了三个现存的并系海绵谱系：Demospongiae 加 Hexactinellida、Calcarea 和 Homoscleromorpha。除了一项ML和贝叶斯分析外，我们的所有分析都支持Eumetazoa（此处为Cnidaria + Bilateria）的单系性以及Placozoa（此处为Trichoplax adhaerens）和Eumetazoa之间的姐妹群关系。当与多孔动物门和刺胞动物之间的姐妹群关系或与单系多孔动物门相对于单系真后生动物的姐妹群关系进行比较时，贝叶斯因子总是提供有利于多孔动物并系的决定性支持。尽管我们能够使用我们的数据集恢复海绵单系，但这只有在不切实际的进化模型下，如果使用性能不佳的系统发育方法，或者在人为加剧生成树重建伪影的可能性的情况下才有可能。综合考虑，我们的数据集没有为单系双叶纲（此处为板动物 + 刺胞动物 + 多孔动物门）提供任何支持，并表明单系多孔动物门可能更好地被视为系统发育人工制品。
The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood (ML) and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea, and Homoscleromorpha. All but one of our ML and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria + Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria or with a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly using our data set, this was only possible under unrealistic evolutionary models, if poorly performing phylogenetic methods were used, or in situations where the potential for the generation of tree reconstruction artifacts was artificially exacerbated. Everything considered, our data set does not provide any support for a monophyletic Diploblastica (here Placozoa + Cnidaria + Porifera) and suggests that a monophyletic Porifera may be better seen as a phylogenetic artifact.