Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
复制标题
DOI：
10.1093/molbev/msr185
复制
发表时间：
2012-02-01
影响因子：
10.7
通讯作者：
Ruiz-Trillo, Inaki
中科院分区：
文献类型：
--
作者：
Torruella, Guifre;Derelle, Romain;Ruiz-Trillo, Inaki
迄今为止，许多真核生物的基因组分析都是基于数百到数千个基因的比对。在这类分析中，经常使用目前最现实的进化模型，以尽量减少系统误差的影响。然而，关于特异质基因家族动力学（即，基因重复和丢失）和不正确的同源性分配总是被适当地考虑。在本文中，我们提出了一个创新的策略，克服正交分配问题。而不是识别和消除基因的旁系问题，我们已经构建了一个数据集，完全由保守的单拷贝蛋白质结构域，不像大多数常用的基因组数据集，应该是混淆的直系错误分配。为了评估这种方法的功效，我们进行了最大似然和贝叶斯分析，以推断后突动物（包括后生动物，真菌和相关的单细胞谱系）内的进化关系。我们使用这种方法来测试1）Filasterea和Ichthyosporea是否形成一个分支，2）早期分支后生动物的相互关系，以及3）早期分支真菌之间的关系。我们还评估了一些已知的方法，以尽量减少系统误差的影响，包括减少外群和内群类群之间的距离或使用CAT进化模型。总的来说，我们的分析支持丝状动物假说，其中鱼孢子虫是第一个出现的全动物谱系，其次是丝状动物，Choanoflagellata和后生动物。芽枝菌门似乎是一个独立于壶菌门的谱系，尽管这一结果没有得到有力的支持。这些结果代表了以前的系统发育假说的独立测试，突出了复杂的方法在基因组分析中的同源性分配的重要性。
Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses.