BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: The 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.

• MeSH
• Bayesova věta MeSH
• Buchnera genetika   fyziologie   MeSH
• DNA bakterií genetika   MeSH
• Enterobacteriaceae genetika   fyziologie   MeSH
• fylogeneze * MeSH
• genom bakteriální MeSH
• molekulární evoluce MeSH
• symbióza * MeSH
• Wigglesworthia genetika   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA bakterií MeSH

BACKGROUND: Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attraction (LBA) artifacts. In several steps of increasing stringency, the slow-fast analysis omits the fastest substituting alignment positions from the analysed dataset and thus increases its signal/noise ratio. RESULTS: Our program SlowFaster automates the process of assessing the substitution rate of the alignment positions and the process of producing new alignments by deleting the saturated positions. Its use is very simple. It goes through the whole process in several steps: data input - necessary choices - production of new alignments. CONCLUSION: SlowFaster is a user-friendly tool providing new alignments prepared with slow-fast analysis. These data can be used for further phylogenetic analyses with lower risk of long branch attraction artifacts.

• MeSH
• Blastocystis genetika   MeSH
• časové faktory MeSH
• fylogeneze * MeSH
• protozoální DNA MeSH
• sekvenční seřazení MeSH
• uživatelské rozhraní počítače * MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• protozoální DNA MeSH