Comas Iñaki, Moya Andrés, González-Candelas Fernando
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
Syst Biol. 2007 Feb;56(1):1-16. doi: 10.1080/10635150601109759.
The increasing availability of complete genome sequences and the development of new, faster methods for phylogenetic reconstruction allow the exploration of the set of evolutionary trees for each gene in the genome of any species. This has led to the development of new phylogenomic methods. Here, we have compared different phylogenetic and phylogenomic methods in the analysis of the monophyletic origin of insect endosymbionts from the gamma-Proteobacteria, a hotly debated issue with several recent, conflicting reports. We have obtained the phylogenetic tree for each of the 579 identified protein-coding genes in the genome of the primary endosymbiont of carpenter ants, Blochmannia floridanus, after determining their presumed orthologs in 20 additional Proteobacteria genomes. A reference phylogeny reflecting the monophyletic origin of insect endosymbionts was further confirmed with different approaches, which led us to consider it as the presumed species tree. Remarkably, only 43 individual genes produced exactly the same topology as this presumed species tree. Most discrepancies between this tree and those obtained from individual genes or by concatenation of different genes were due to the grouping of Xanthomonadales with beta-Proteobacteria and not to uncertainties over the monophyly of insect endosymbionts. As previously noted, operational genes were more prone to reject the presumed species tree than those included in information-processing categories, but caution should be exerted when selecting genes for phylogenetic inference on the basis of their functional category assignment. We have obtained strong evidence in support of the monophyletic origin of gamma-Proteobacteria insect endosymbionts by a combination of phylogenetic and phylogenomic methods. In our analysis, the use of concatenated genes has shown to be a valuable tool for analyzing primary phylogenetic signals coded in the genomes. Nevertheless, other phylogenomic methods such as supertree approaches were useful in revealing alternative phylogenetic signals and should be included in comprehensive phylogenomic studies.
全基因组序列的日益普及以及用于系统发育重建的更新、更快方法的发展，使得探索任何物种基因组中每个基因的进化树集成为可能。这推动了新的系统发育基因组学方法的发展。在此，我们比较了不同的系统发育和系统发育基因组学方法，以分析来自γ-变形菌门的昆虫内共生菌的单系起源，这是一个近期有诸多相互矛盾报道且备受争议的问题。在确定了木匠蚁主要内共生菌弗罗里达布洛赫曼氏菌基因组中579个已鉴定的蛋白质编码基因在另外20个变形菌门基因组中的假定直系同源基因后，我们获得了每个基因的系统发育树。通过不同方法进一步证实了反映昆虫内共生菌单系起源的参考系统发育关系，这使我们将其视为假定的物种树。值得注意的是，只有43个单个基因产生的拓扑结构与这个假定的物种树完全相同。该树与从单个基因或不同基因串联获得的树之间的大多数差异，是由于黄单胞菌目与β-变形菌门的分组，而非昆虫内共生菌单系性的不确定性。如前所述，与信息处理类别中的基因相比，操作基因更倾向于拒绝假定的物种树，但在基于功能类别分配选择用于系统发育推断的基因时应谨慎。通过系统发育和系统发育基因组学方法的结合，我们获得了强有力的证据支持γ-变形菌门昆虫内共生菌的单系起源。在我们的分析中，串联基因的使用已证明是分析基因组中编码的主要系统发育信号的有价值工具。然而，其他系统发育基因组学方法，如超树方法，在揭示替代系统发育信号方面很有用，应纳入全面的系统发育基因组学研究中。
