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.

Figure 1

Phylogenetic relationships of Aquifex genes according to the HOGENOM database. a: Informational genes. b: Non-informational genes.

Figure 2

Distribution of the site relative evolutionary rates. Rates were estimated using a 4 class discretized gamma distribution. The 4 peaks correspond to the rates associated to each class. The vertical red line corresponds to the threshold above which sites have been discarded due to their high evolutionary rate.

Figure 3

Unrooted phylogenetic tree of Bacteria. This tree was obtained after discarding all sites with evolutionary rate predicted to be above 2.2. Stars indicate branches with 100% bootstrap support (200 replicates). Bootstrap supports between 80% and 100% are shown, bootstraps below 80% have been removed for clarity. Aquificales are represented in bright red. Names of major groups are according to the NCBI taxonomy. Gracilicutes and Terrabacteria, two recently proposed superclades, are shown as dashed frames, and their names are between quotation marks to mark their unconsensual status.

Figure 4

Unrooted phylogenetic tree obtained from 56 genes of Bacteria based on the recoded alignment. Labels as in Fig. 3.

Figure 5

Comparison between site likelihoods when Aquificales are placed close to Epsilon-proteobacteria and when they are placed with Thermotogales. Upper panel: summed differences between site log-likelihoods obtained when Aquificales are placed with epsilon-Proteobacteria and when they are placed with Thermotogales. A descending trend means that a consecutive series of sites favours the Thermotogales position (T signal), whereas an ascending trend means that a series of sites favours the epsilon-proteobacterial position (E signal). Genes have been ordered according to their position along the Aquifex genome. Dashed blue lines represent gene boundaries. The red interval represents the genes which appear to contain most of the E signal. The green interval represents gene infB, in which the curve first decreases and then increases. Lower panel: result obtained by the Maximum Predictive Partitioning algorithm when asked to find the most likely partition of the sites in two segments. The a posteriori most likely model for the first segment is the tree in which Aquificales are sister group to Thermotogales, and the second segment is best fitted by the tree in which Aquificales are sister group to epsilon-Proteobacteria.

Figure 6

Unrooted tree obtained from the concatenation of rplL-rpoB-rpoC. Colors and symbols as in Fig. 3.

Figure 7

Unrooted trees corresponding to the infB gene. Left: tree corresponding to the first 301 sites. Right: tree corresponding to the remaining 246 sites. Colors as in Fig. 3.