Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

Abstract

BackgroundThe bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. The main reasons have been the absence of sufficient data, the highly derived nature of the symbiont genomes and lack of appropriate phylogenetic methods. Due to the extremely aberrant nature of their DNA, the symbiotic lineages within Enterobacteriaceae form long branches and tend to cluster as a monophyletic group. This state of phylogenetic uncertainty is now improving with an increasing number of complete bacterial genomes and development of new methods. In this study, we address the monophyly versus polyphyly of enterobacterial symbionts by exploring a multigene matrix within a complex phylogenetic framework.ResultsWe assembled the richest taxon sampling of Enterobacteriaceae to date (50 taxa, 69 orthologous genes with no missing data) and analyzed both nucleic and amino acid data sets using several probabilistic methods. We particularly focused on the long-branch attraction-reducing methods, such as a nucleotide and amino acid data recoding and exclusion (including our new approach and slow-fast analysis), taxa exclusion and usage of complex evolutionary models, such as nonhomogeneous model and models accounting for site-specific features of protein evolution (CAT and CAT+GTR). Our data strongly suggest independent origins of four symbiotic clusters; the first is formed by Hamiltonella and Regiella (S-symbionts) placed as a sister clade to Yersinia, the second comprises Arsenophonus and Riesia (S- and P-symbionts) as a sister clade to Proteus, the third Sodalis, Baumannia, Blochmannia and Wigglesworthia (S- and P-symbionts) as a sister or paraphyletic clade to the Pectobacterium and Dickeya clade and, finally, Buchnera species and Ishikawaella (P-symbionts) clustering with the Erwinia and Pantoea clade.ConclusionsThe results of this study confirm the efficiency of several artifact-reducing methods and strongly point towards the polyphyly of P-symbionts within Enterobacteriaceae. Interestingly, the model species of symbiotic bacteria research, Buchnera and Wigglesworthia, originated from closely related, but different, ancestors. The possible origins of intracellular symbiotic bacteria from gut-associated or pathogenic bacteria are suggested, as well as the role of facultative secondary symbionts as a source of bacteria that can gradually become obligate maternally transferred symbionts.

A novel intracellular mutualistic bacterium in the invasive antCardiocondyla obscurior

“…Nevertheless, its phylogenetic placement has to be considered with caution, because of long-branch attraction. As already observed by Husník et al (2011), the monophyly of the cluster formed by Sodalis, Baumannia, Blochmannia and Wigglesworthia, in which Westeberhardia appears, needs to be further tested.…”

“…Besides Wolbachia, we identified six scaffolds of an unknown Enterobacteriaceae. Following de novo genome assembly and annotation (see below), we used translated CDS sequences for phylogenetic placement following Husník et al (2011). Briefly, we performed Dayhoff6 recoding followed by a phylogenomic reconstruction with PhyloBayes v.3.3f (Lartillot et al, 2009), based on 64 single-copy protein clusters (Supplementary Information).…”

Evidence of Environmental and Vertical Transmission of Burkholderia Symbionts in the Oriental Chinch Bug, Cavelerius saccharivorus (Heteroptera: Blissidae)

“…occasionally acquired from surrounding environments (or bacteria that contaminated insects) and that provided benefits to the host (53,54). In this context, the symbiotic association found in C. saccharivorus may represent an intermediate stage from the evolutionarily primitive gut symbiosis from environmental transmission to the sophisticated association maintained by vertical transmission.…”

Pitfalls in supermatrix phylogenomics

“…Interestingly, the progressive removal of these positions violating the assumption of homogeneity PHILIPPE H. et al, Pitfalls in supermatrix phylogenomics 17 of the CAT mixture model (Lartillot & Philippe 2004) led to a single topological change: the recovery of the more classical sister-group relationship between cnidarians and bilaterians. Similarly, the gammaproteobacterial endosymbionts of insects have an AT-rich genome and tend to be artificially clustered in trees based on nucleotide sequences Husník et al (2011). By progressively removing the positions that were the most compositionally biased (i.e., a position only containing A and T, or G and C, is unbiased), Husník et al (2011) were able to overcome this composition-based artefact and to recover a tree identical to the one obtained from amino-acid sequences.…”

“…Similarly, the gammaproteobacterial endosymbionts of insects have an AT-rich genome and tend to be artificially clustered in trees based on nucleotide sequences Husník et al (2011). By progressively removing the positions that were the most compositionally biased (i.e., a position only containing A and T, or G and C, is unbiased), Husník et al (2011) were able to overcome this composition-based artefact and to recover a tree identical to the one obtained from amino-acid sequences. Finally, recent studies of genome datasets in mammals (Romiguier et al 2013) and birds (Jarvis et al 2014) have revealed that AT-rich genes hold a much clearer phylogenetic signal than GC-rich genes, which are subjects to GC-biased geneconversion (Eyre-Walker 1993) episodes possibly leading to an increased heterogeneity in both base composition and evolutionary rate among taxa.…”