Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

<p>Abstract</p> <p>Background</p> <p>The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.</p> <p>Results</p> <p>We sequenced the complete flagellin gene <it>(flaA</it>) in 18 different species and subspecies of <it>Aeromonas</it>. Sequences ranged in size from 870 (<it>A. allosaccharophila</it>) to 921 nucleotides (<it>A. popoffii</it>). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze <it>flaA </it>sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an ω ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.</p> <p>Conclusion</p> <p>The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the <it>flaA </it>gene in <it>Aeromonas</it>, suggesting that this gene have probably been evolving independently in the two groups of <it>Aeromonas </it>species since the divergence of a distant common ancestor after one or several episodes of positive selection.</p> <p>Reviewers</p> <p>This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).</p

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process

Contour plots of the likelihood surfaces.

<p>Contour plots of the likelihood surface were inferred from the relation between the net diversification rate (λ – μ) and extinction fraction (μ/λ) for the Bayes (left) and MLA (right) chronograms. Likelihoods were calculated using the R package LASER. The maximum likelihood estimates (i.e., the peak of the surface) are marked with an arrow.</p

Testing departure of the empirical chronograms of <i>Aeromonas</i> from a constant rate diversification model.

<p>Dark lines represent the LTT plots obtained for empirical Bayesian (left) and MLA (right) <i>Aeromonas</i> phylogenies, while grey lines correspond to the LTT plots of 5,000 simulated phylogenies. In both cases, the root was rescaled to the time to the most recent common ancestor.</p

Regression plot between the number of animal genera and the number of <i>Aeromonas</i> species.

<p>The plot shows the number of animal genera obtained from Sepkoski’s data and the number of <i>Aeromonas</i> species in the last 250 Ma, applying both the Bayesian and the MLA approaches.</p

Fit of alternative diversity models to LTT plots derived from Bayes and MLA chronograms.

a<p>Akaike Information Criterium.</p>b<p>ΔAIC_RC test. See text for details.</p>c<p>breakpoint at 13 Ma ago.</p>d<p>breakpoint at 1.3 Ma ago.</p>e<p><i>P</i> value obtained by simulation (5,000 iterations). See text for additional explanation of simulations.</p>f<p>standard error.</p

<i>Aeromonas</i> species maximum likelihood phylogenetic tree.

<p><i>E.coli</i> and <i>S. enterica</i> were used as the outgroup. Nodes supported by bootstrap values ≥70% are indicated. The scale bar represents 20% sequence divergence.</p

LTT plots for the genus <i>Aeromonas</i>.

<p>Log-lineage-through-time (LTT) plot for the genus <i>Aeromonas</i> based on Bayes (dark line) and MLA (grey line) approaches.</p

Diversification rates and model of speciation for the major clades of <i>Aeromonas.</i>

a<p>clade numbers appear in the MLA chronogram in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088805#pone-0088805-g002" target="_blank">Figure 2</a>.</p><p>Clades 7 and 8 were not analysed due to their low number of species (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088805#pone-0088805-g002" target="_blank">Fig. 2</a>).</p><p>Abbreviations: N, clade size; se, standard error.</p