Figure 5 Phylogenetic tree and distance matrix of Chloroflexi including
all 16S rRNA copies. (A) Phylogenetic tree of the eubacterial phylum Chloroflexi including all 16S rRNA copies, reconstructed using Bayesian analysis. On the nodes posterior probabilities >0.90 are displayed. Colored taxa mark species Selleckchem LY2157299 where 16S rRNA copy numbers evolved rather via divergent evolution, than being homogenized within a strain via concerted evolution. The letter “R” denote gene copies that are positioned on the reverse DNA strand. (B) Distance matrix of Chloroflexi. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species. 16S rRNA sequences are conserved within Trametinib species, but exhibit more variation than found for cyanobacteria. Evolution of 16S rRNA gene copies in cyanobacteria Two mechanisms
may conserve sequences of gene copies: purifying selection and concerted evolution. These two can be distinguished by examining variation patterns in non-coding regions [1, 50]. In the case of purifying selection, non-coding regions are thought to evolve neutrally, accumulating mutations over time due to genetic drift. If concerted evolution shapes gene copies, the entire gene sequence including non-coding regions and synonymous sites are homogenized. During this process, genes evolve in ‘concert’, which is commonly observed in plants and fungi [51, 52] (Figure 6). Subsequently, paralogs show stronger similarities than orthologs, as a result of intragenomic homologous recombination . Figure 6 Divergent and concerted
evolution. (A) The phylogenetic pattern Tacrolimus (FK506) of divergent and concerted evolution evolution. Paralogs and orthologs diverge at similar degrees in the first scenario, while they get frequently homogenized during concerted evolution. A cyanobacterial cell during cell division without homologous recombination. All daughter cells will exhibit the same chromosome as the mother cell. (B) Replication pattern during cell division under divergent and concerted evolution. If during cell devision homologous recombination takes place in half of the recombinants the daughter cells will exhibit the same chromosome as the mother. For the other half of recombinants, each gene copy has a chance of replacing the other. Once gene copies are identical homologous recombination cannot reverse the process. Hence if this process is repeated recursively at a population level, one gene copy will eventually get fixed. The strong conservation of 16S rRNA sequence copies in cyanobacteria and Eubacteria examined here suggests that 16S rRNA in these species is shaped by strong purifying selection and/or concerted evolution. Generally, it is assumed that ribosomal genes in Archaea and Eubacteria are shaped by concerted evolution . 16S rRNA genes can be subdivided in strongly conserved and more variable regions.