Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany.
Mol Biol Evol. 2012 Mar;29(3):1031-45. doi: 10.1093/molbev/msr270. Epub 2011 Nov 1.
Remipedes are a small and enigmatic group of crustaceans, first described only 30 years ago. Analyses of both morphological and molecular data have recently suggested a close relationship between Remipedia and Hexapoda. If true, the remipedes occupy an important position in pancrustacean evolution and may be pivotal for understanding the evolutionary history of crustaceans and hexapods. However, it is important to test this hypothesis using new data and new types of analytical approaches. Here, we assembled a phylogenomic data set of 131 taxa, incorporating newly generated 454 expressed sequence tag (EST) data from six species of crustaceans, representing five lineages (Remipedia, Laevicaudata, Spinicaudata, Ostracoda, and Malacostraca). This data set includes all crustacean species for which EST data are available (46 species), and our largest alignment encompasses 866,479 amino acid positions and 1,886 genes. A series of phylogenomic analyses was performed to evaluate pancrustacean relationships. We significantly improved the quality of our data for predicting putative orthologous genes and for generating data subsets by matrix reduction procedures, thereby improving the signal to noise ratio in the data. Eight different data sets were constructed, representing various combinations of orthologous genes, data subsets, and taxa. Our results demonstrate that the different ways to compile an initial data set of core orthologs and the selection of data subsets by matrix reduction can have marked effects on the reconstructed phylogenetic trees. Nonetheless, all eight data sets strongly support Pancrustacea with Remipedia as the sister group to Hexapoda. This is the first time that a sister group relationship of Remipedia and Hexapoda has been inferred using a comprehensive phylogenomic data set that is based on EST data. We also show that selecting data subsets with increased overall signal can help to identify and prevent artifacts in phylogenetic analyses.
动吻类是甲壳动物中的一个小而神秘的群体，仅在 30 年前首次被描述。最近，对形态和分子数据的分析表明动吻类与六足动物之间存在密切关系。如果这是真的，那么动吻类在泛甲壳动物的进化中占据着重要的地位，并且可能对理解甲壳动物和六足动物的进化历史至关重要。然而，使用新的数据和新的分析方法来检验这一假说非常重要。在这里，我们组装了一个包含 131 个分类群的系统基因组数据集，其中包括从六种甲壳动物中生成的新的 454 个表达序列标签（EST）数据，代表五个谱系（动吻类、软甲亚纲、有爪动物、介形亚纲和软甲亚纲）。这个数据集包括所有有 EST 数据的甲壳动物物种（46 种），我们最大的排列包含 866479 个氨基酸位置和 1886 个基因。进行了一系列系统基因组分析来评估泛甲壳动物的关系。我们通过矩阵缩减程序显著提高了预测假定的直系同源基因和生成数据子集的质量，从而提高了数据中的信噪比。构建了八个不同的数据集，代表了各种组合的直系同源基因、数据子集和分类群。我们的结果表明，以不同的方式编译核心直系同源基因的初始数据集，以及通过矩阵缩减选择数据子集，可以对重建的系统发育树产生显著影响。尽管如此，所有八个数据集都强烈支持泛甲壳动物，动吻类是六足动物的姐妹群。这是首次使用基于 EST 数据的综合系统基因组数据集推断动吻类和六足动物的姐妹群关系。我们还表明，选择具有更高整体信号的数据子集可以帮助识别和防止系统发育分析中的假象。
