Skip to Main content Skip to Navigation
Journal articles

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Abstract : Background Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. Results To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found. Conclusion Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.
Document type :
Journal articles
Complete list of metadata

https://hal.archives-ouvertes.fr/hal-00428101
Contributor : Stéphane Delmotte Connect in order to contact the contributor
Submitted on : Wednesday, October 28, 2009 - 5:23:31 PM
Last modification on : Monday, October 4, 2021 - 2:52:05 PM

Links full text

Identifiers

Collections

Citation

Bastien Boussau, Laurent Guéguen, Manolo Gouy. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evolutionary Biology, BioMed Central, 2008, 8, pp.272-272. ⟨10.1186/1471-2148-8-272⟩. ⟨hal-00428101⟩

Share

Metrics

Record views

474