From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-Proteobacteria as a Test Case

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 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.

Reconstructing genome trees of prokaryotes using overlapping genes

“…This dataset was previously used by Comas et al . [21] for their phylogenomic study on the monophyletic origin of insect endosymbionts from the γ -Proteobacteria, a debated issue with several conflicting reports. In addition, we used the phylogenetic tree constructed by Comas et al .…”

“…[21] based on concatenated sequences of 60 homologous proteins as a reference tree (Figure 1) and compared the genome tree obtained by our OGtree2 (Figure 2) to those phylogenetic trees predicted by BPhyOG (Figure 3) [8] and our previous OGtree (Figure 4) [15]. As was argued in [21], the phylogenetic tree in Figure 1 can be considered as a good reference tree because it coincides with the taxonomy accepted by biologists for these Proteobacteria. In particular, the three Buchnera species in this reference tree form a monophyletic group with the other insect endosymbionts of B. floridanus and W. glossinidia .…”

A Consistent Phylogenetic Backbone for the Fungi

“…However, they provide no information on how closely the reconstructed tree resembles the true evolutionary relationships of the analyzed species. Currently, the only way to reenforce phylogenetic hypotheses is the analysis of complementary data (e.g., Comas et al 2007). If the phylogenetic placement of a taxon remains stable over different data sets and different tree reconstruction methods, it is likely to reflect the true evolutionary relationships of this taxon.…”

“…Phylogenomic analyses (Delsuc et al 2005; Telford 2007) use the phylogenetic signal integrated over many genes as a proxy for the species phylogeny (Gatesy and Baker 2005; Comas et al 2007). It is hoped that this approach reduces the influence of gene-specific signals (noise) and accentuates the phylogenetic signal generated by the evolutionary relationships of the species.…”

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…The family (and order) itself has a complicated evolutionary history; while it is nominally within the gamma-proteobacteria, its relationship to that group is not straightforward. Phylogenies generally depict the lineage as splitting from the rest of the gamma-proteobacteria, and a gene-bygene analysis has revealed that many genes are more similar to genes of the alpha or beta proteobacteria, implying that much of the genome was acquired from these other lineages and the placement within gamma-proteobacteria may not be reliable (Comas et al 2007). …”