Opulation genetic approach by analysing the polymorphisms present in all seven-gene
Opulation genetic approach by analysing the polymorphisms present in all seven-gene fragments (Fig. 2c) with STRUCTURE, which employs a Bayesian method to discern groupings among Anlotinib web recombining organisms. The linkage model of STRUCTURE assigns probabilities of derivation from ancestral source groups for each polymorphic nucleotide. The ancestry of each strain is then estimated as the summed probability of derivation from each group over all polymorphic nucleotides. STRUCTURE recognized three ancestral sources of polymorphisms within the MAB (K = 3 populations shows a clear inflection in the likelihood values) and separated most M. abscessus, M. bolletii and M. massiliense isolates into those groups (Fig. 2b). Those results highlight that the separation into three groups is the most valuable, and thus we willAfter having attributed each sequence type (ST) to a given subspecies, we determined the percentage of exogenous SNPs for each ST (Fig. 2d). Subspecies belonging to M. massiliense and M. abscessus strains display the highest proportion of foreign SNPs, whereas M. bolletii strains are far more homogenous. Moreover, allelic flux going from M. massiliense to M. bolletii was significantly lower than other allelic exchanges (Fisher test P < 0.01. Fig. 2d). Consistently, mosaic strains proportion is significantly higher for M. massiliense STs than for M. bolletii (Fisher test P < 0.05. Fig. 2e). Although they should be confirmed by whole genomic survey, these results suggest that allelic fluxes between the three subspecies are not homogenous. They indicate asymmetrical gene flow between subspecies, especially between M. massiliense and M. bollettii. We also sought to quantify the frequency of homologous recombination within groups by implementing the composite likelihood of r/ (the probability that a nucleotide will change by recombination divided by the probability that the same nucleotide will change by mutation) [49]. The test confirmed that significant levels of recombination had occurred within each subspecies (Table 1). Interestingly, if we consider results from the concatenated housekeeping genes (that allow to integrate large-scale inter-locus recombination), recombination estimates raise dramatically for M. abscessus and M. massiliense. Taken together, these data suggest that the main driving evolutionary force is recombination and not mutation in M. abscessus and M. massiliense, and that these recombination events occur at genomic scale involving large inter-locus PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 fragments.rpoB typingA side effect of the allelic flux within MAB concerns the suitability of rpoB for subspecies identification. Indeed, there is no reason that this gene will escape interlineage homologous recombination and consequently using it as a diagnostic marker for species determination within the MAB might be misleading (Additional file 4: Figure S4A). According to STRUCTURE assignments, and consistent with our previous result emphasizing PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26740125 M. massiliense highSapriel et al. BMC Genomics (2016) 17:Page 4 ofFig. 1 (See legend on next page.)Sapriel et al. BMC Genomics (2016) 17:Page 5 of(See figure on previous page.) Fig. 1 Densitree of 130 STs belonging to the MAB. The phylogenetic reconstruction is based on the concatenated housekeeping genes (3576 bp) and the GTR + I + G evolutionary model was implemented in BEAST 1.7.5. The best 8000 trees generated during the Markov chain are drawn transparently (in green). As a result, areas where the vast majority of the trees.