Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.Bacterial species typically contain large amounts of genetic variation in the form of single nucleotide polymorphisms (SNPs), which originate by mutation and have dynamics that depend on the balance between natural selection and genetic drift [1,2]. There is some debate on whether or not most of these polymorphisms are selectively neutral at the molecular level [3]. Species have been genetically defined through the analysis of DNA variation using comparative techniques such as hybridization, the sequencing of gene markers, and (more recently) complete genome sequences [4,5]. It has been proposed that similarity values greater than 70% obtained in DNA-DNA hybridization experiments are sufficient to define a coherent group of organisms as belonging to the same species [6]. These estimates are very rough, subject to experimental variation, and they only indirectly measure similarity (i.e. via hybridization efficiency) [7]. A comparative analysis of complete genomes minimizes most of these limitations. Several measures of genomic