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• W3144821712 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 γ -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 β-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 γ -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. (Concatenate alignment; incongruence; microbial evolution; phylome; supermatrix alignment; supertree analysis.) The evolution of Bacteria is strongly influenced by the fluid nature of their genomes. Processes such as duplica- tion, gene gain and loss limit the inference of their evo- lutionary relationships. However, in the last decade the genomic revolution has represented not only a change in scale for the analysis of sequences but also for phylo- genetic inference. The phylogenomic approach, initially proposed as the application of phylogenetic analysis to help annotating complete genome sequences (Eisen, 1998), has transformed into the (possibly) most appropri- ate way to derive the phylogenetic history of organisms through genome-scale phylogenetic inference (O'Brien" @default.
• W3144821712 created "2021-04-13" @default.
• W3144821712 creator A5018762386 @default.
• W3144821712 creator A5086177695 @default.
• W3144821712 date "2007-01-01" @default.
• W3144821712 modified "2023-09-27" @default.
• W3144821712 title "From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-Proteobacteria as a Test Case" @default.
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