Fig. S1. ML tree from partial 16S rRNA sequences.

Fig. S2. ML tree from partial recA gene sequences.

Fig. S3. ML tree from partial atpD gene sequences.

Fig. S4. ML tree from partial gln II gene sequences.

Fig. S5. Split graph from neighbor-network analysis based on concatenated sequence of recA-atpD-glnII genes of Lentil symbionts plus previously described strains of R. leguminosarum. R. etli and other related species.

Fig. S6. Majority rule consensus tree (50%) inferred from concatenated partial sequence of recA-atpD-glnII genes using CLONALFRAME without allowing recombination.

Fig. S7. Un-rooted ML tree from partial nodD gene sequences.

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Table S1. Isolate numbers, soil pH and rhizobial density for different sample collection localities.

Table S2. Isolates under different lineages and sub-lineages in different analyses.

Table S3. List of primers and PCR conditions.

Table S4. GenBank accession numbers.

Table S5. Genetic distances among different sub-lineages (SL).

Table S6. Hierarchical amova of the genetic structure and gene flow of sub-lineages.

Table S7. Time to the most recent common ancestor (TMRCA) of all samples using CLONALFRAME.

Table S8. Phylogenetic incongruence using Shimodaira-Hasegawa (S-H) test.

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