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From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-Proteobacteria as a Test Case (2007)
| Venue: | SYST. BIOL |
| Citations: | 11 - 0 self |
BibTeX
@ARTICLE{Comas07fromphylogenetics,
author = {Inaki Comas and Andres Moya and Fernando Gonzalez-candelas},
title = {From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-Proteobacteria as a Test Case},
journal = {SYST. BIOL},
year = {2007},
volume = {56},
number = {1},
pages = {1--16}
}
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Abstract
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 y-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 /3-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 y-Proteobacteria insect endosymbionts by a combination of phylogenetic and phylogenomic methods. In our analysis, the
Keyphrases
insect endosymbiotic gamma proteobacteria evolutionary relationship monophyletic origin insect endosymbionts presumed specie test case individual gene phylogenomic method phylogenetic tree complete genome sequence blochmannia floridanus different approach additional proteobacteria genome phylogenetic reconstruction strong evidence different gene y-proteobacteria insect endosymbionts phylogenetic inference protein-coding gene reference phylogeny evolutionary tree functional category assignment operational gene information-processing category new phylogenomic method primary endosymbiont carpenter ant presumed orthologs
