Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized () Genes in the Polytypic Species .

Nodule bacteria (rhizobia) represent a suitable model to address a range of fundamental genetic problems, including the impacts of natural selection on the evolution of symbiotic microorganisms. Rhizobia possess multipartite genomes in which symbiotically specialized () genes differ from core genes in their natural histories. Diversification of genes is responsible for rhizobia microevolution, which depends on host-induced natural selection. By contrast, diversification of core genes is responsible for rhizobia speciation, which occurs under the impacts of still unknown selective factors. In this paper, we demonstrate that in goat's rue rhizobia () populations collected at North Caucasus, representing two host-specific biovars and (N-fixing symbionts of and ), the evolutionary mechanisms are different for core and genes. In both biovars, core genes are more polymorphic than genes. In bv. , the evolution of core genes occurs under the impacts of driving selection (dN/dS > 1), while the evolution of genes is close to neutral (dN/dS ≈ 1). In bv. , the evolution of core genes is neutral, while for genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and genes revealed using ANI analysis may be due to a low intensity of gene transfer within and between biovars. Polymorphism in both gene groups and the impacts of driving selection on core gene evolution are more pronounced in bv. than in bv. , reflecting the diversities of their respective host plant species. In bv. , a highly significant (P < 0.001) positive correlation is revealed between the p-distance and dN/dS values for core genes, while in bv. , this correlation is of low significance (0.05 < P < 0.10). For genes, the correlation between p-distance and dN/dS values is negative in bv. but is not revealed in bv. . These data, along with the functional annotation of core genes implemented using Gene Ontology tools, suggest that the evolution of bv. is based mostly on adaptation for in planta niches while in bv. , evolution presumably depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented, suggesting that gene nucleotide polymorphism may be extended by driving selection only in ecologically versatile organisms capable of supporting a broad spectrum of gene alleles in their gene pools.