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Table S1. Location of housekeeping and symbiotic genes used in this study on the chromosomes of Bradyrhizobium japonicum USDA6T (GenBank, NC017249) and USDA110 (GenBank, NC004463).

Table S2. GenBank accession numbers of housekeeping (atpD, glnII, recA, gyrB, rpoB, dnaK) and symbiotic (nodC) partial gene sequences representing 220 Bradyrhizobium isolates from soybean field sites A and B.

Table S3. GenBank nucleotide sequence accession numbers for Bradyrhizobium reference strains.

Table S4. Nucleotide accession numbers of 148 partial recA gene sequences representing soybean-nodulating bacteria from Amphicarpaea bracteata and Desmodium canadense.

Table S5. GenBank nucleotide accession numbers for (a) selected soybean-nodulating bacteria from Amphicarpaea bracteata and Desmodium canadense (dnaK, nodC, and nifH partial gene sequences) and (b) reference strains and selected isolates from soybean field sites A and B (nifH partial gene sequences).

Table S6. Primers and DNA amplification conditions.

Table S7. Example of R scripts based on the phangorn phylogenetic package to test the extent of congruence between maximum-likelihood trees reconstructed for each of six housekeeping genes.

Table S8. Statistics for five separate runs of STRUCTURE using the admixture model (independent allele frequencies) for values of K between 2 and 7.

Table S9. Genetic diversity statistics for Bradyrhizobium isolates from soybean cultivars M and O.

Table S10. Genetic differentiation and gene flow statistics for selected core gene lineages based on six concatenated gene sequences.

Figure S1. Maximum-likelihood tree of concatenated atpD-glnII-recA-gyrB-rpoB-dnaK partial gene sequences (3210 bp) for Bradyrhizobium reference strains and 35 unique STs representing soybean-nodulating bacteria from field sites A and B.

Figure S2. Randomization test to assess congruence between maximum-likelihood (ML) trees of six housekeeping genes and 100 random trees.

Figure S3. Distribution of external to internal branch length ratios of a tree of lineage II (= 120) inferred by ClonalFrame relative to that expected under coalescent simulation.

Figure S4. Maximum-likelihood tree of unique gyrB partial gene sequences (618 bp) of Bradyrhizobium isolates from soybean field sites A and B and reference taxa showing putative xenologous sequences.

Figure S5. Maximum-likelihood phylogenetic trees of (a) recA (462 bp) and (b) concatenated recA-dnaK (831 bp) partial gene sequences representing soybean-nodulating bacteria from Amphicarpaea bracteata and Desmodium canadense, from soybean field sites A and B, and, reference taxa.

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