The impact of paralogy on phylogenomic studies - a case study on annelid relationships

Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebrat...

基于表达序列标签库（expressed sequence tags libraries）衍生的数百个基因开展的系统发育基因组学（Phylogenomics）研究，正日益用于揭示分类群的系统发育关系。此类研究的前提是将基因划分为直系同源序列簇（clusters of orthologous sequences）。尽管复杂的直系同源预测方法已应用于这类分析，但预测后极少评估是否有旁系同源序列被错误地归为直系同源序列，以及这是否会对采用超级矩阵法（super-matrix approach）的系统发育重建产生影响。本文中，我基于系统发育基因组数据集测试了旁系同源序列对环节动物（annelid）亲缘关系重建的影响。通过单分区分析、bootstrap支持率筛选、BLAST搜索以及超级矩阵中的序列修剪，研究发现8个分区存在错误归类的旁系同源序列，且5个分类群（环节动物Owenia、Scoloplos、Sthenelais、Eurythoe以及纽形动物Cerebrat...）的位置受到影响。