Fischer William M, Palmer Jeffrey D
Biology Department, Indiana University, Jordan Hall 142, Bloomington, IN 47405-3700, USA.
Mol Phylogenet Evol. 2005 Sep;36(3):606-22. doi: 10.1016/j.ympev.2005.03.031.
The phylum Microsporidia comprises a species-rich group of minute, single-celled, and intra-cellular parasites. Lacking normal mitochondria and with unique cytology, microsporidians have sometimes been thought to be a lineage of ancient eukaryotes. Although phylogenetic analyses using small-subunit ribosomal RNA (SSU-rRNA) genes almost invariably place the Microsporidia among the earliest branches on the eukaryotic tree, many other molecules suggest instead a relationship with fungi. Using maximum likelihood methods and a diverse SSU-rRNA data set, we have re-evaluated the phylogenetic affiliations of Microsporidia. We demonstrate that tree topologies used to estimate likelihood model parameters can materially affect phylogenetic searches. We present a procedure for reducing this bias: "tree-based site partitioning," in which a comprehensive set of alternative topologies is used to estimate sequence data partitions based on inferred evolutionary rates. This hypothesis-driven approach appears to be capable of utilizing phylogenetic information that is not available to standard likelihood implementations (e.g., approximation to a gamma distribution); we have employed it in maximum likelihood and Bayesian analysis. Applying our method to a phylogenetically diverse SSU-rRNA data set revealed that the early diverging ("deep") placement of Microsporidia typically found in SSU-rRNA trees is no better than a fungal placement, and that the likeliest placement of Microsporidia among non-long-branch eukaryotic taxa is actually within fungi. These results illustrate the importance of hypothesis testing in parameter estimation, provide a way to address certain problems in difficult data sets, and support a fungal origin for the Microsporidia.
微孢子虫门包含一组种类丰富的微小单细胞细胞内寄生虫。微孢子虫缺乏正常的线粒体且具有独特的细胞学特征,有时被认为是古代真核生物的一个谱系。尽管使用小亚基核糖体RNA(SSU - rRNA)基因进行的系统发育分析几乎总是将微孢子虫置于真核生物树的最早分支之中,但许多其他分子却表明它们与真菌存在亲缘关系。我们使用最大似然法和多样的SSU - rRNA数据集,重新评估了微孢子虫的系统发育归属。我们证明,用于估计似然模型参数的树拓扑结构会对系统发育搜索产生重大影响。我们提出了一种减少这种偏差的方法:“基于树的位点划分”,即使用一组全面的替代拓扑结构,根据推断的进化速率来估计序列数据分区。这种由假设驱动的方法似乎能够利用标准似然法实现中无法获取的系统发育信息(例如,近似伽马分布);我们已将其应用于最大似然分析和贝叶斯分析。将我们的方法应用于一个系统发育多样的SSU - rRNA数据集,结果显示,在SSU - rRNA树中通常发现的微孢子虫的早期分化(“深度”)位置并不比真菌位置更好,而且在非长分支真核生物类群中,微孢子虫最可能的位置实际上是在真菌内部。这些结果说明了假设检验在参数估计中的重要性,提供了一种解决困难数据集中某些问题的方法,并支持微孢子虫起源于真菌的观点。