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Table S1 List of bacterial isolates used in this study. Strains isolated in this study with their host plant, host endemicity group, gene sequence groups, geographic information, result of nodulation tests, and sequence accession numbers. NT: Not tested, +: nodulation, -: no nodulation

Fig. S1 16S rRNA gene phylogeny of strains isolated in this study and reference strains. Tree based on maximum likelihood (ML), and bootstrap percentages over 70% from ML and NJ analyses are listed above and below the branches, respectively. The different strain clusters are shown with numbered boxes. Strains isolated in this study are identified by their JPY number. B: Burkholderia, C: Cupriavidus, R: Ralstonia.

Fig. S2recA gene phylogeny of strains isolated in this study and reference strains. Tree based on maximum likelihood (ML), and bootstrap percentages over 70% from ML and NJ analyses are listed above and below the branches, respectively. The different strain clusters are showed with numbered boxes. Strains isolated in this study are identified by their JPY number. B: Burkholderia, C: Cupriavidus, R: Ralstonia.

Fig. S3nifH gene phylogeny of strains isolated in this study and reference strains. Tree based on maximum likelihood (ML), and bootstrap percentages over 70% from ML and NJ analyses are listed above and below the branches, respectively. The different strain clusters are showed with numbered boxes. Strains isolated in this study are identified by their JPY number. B: Burkholderia, C: Cupriavidus, R: Ralstonia.

Fig. S4nodC gene phylogeny of strains isolated in this study and reference strains. Tree based on maximum likelihood (ML), and bootstrap percentages over 70% from ML and NJ analyses are listed above and below the branches, respectively. The different strain clusters are showed with numbered boxes. Strains isolated in this study are identified by their JPY number. B: Burkholderia, C: Cupriavidus, R: Ralstonia.

Fig. S5 Altitudinal differences between species complexes. Sample sites of the two most frequent taxa SC5 (blue) and SC6 (red), and all other species combined (white), ranked by altitude for each species complex separately, within each of the sampled subregions within Goiás and Distrito Federal.

Fig. S6 Phylogeny of partial NodC peptide sequences from representative rhizobia in the alpha- and betaproteobacteria, illustrating the relative divergence of their symbiosis genes. Filled triangles – Burkholderia; open triangle – Cupriavidus; open diamonds – Methylobacterium; filled diamonds – Bradyrhizobium; filled circles – Rhizobium; open circles – Sinorhizobium; filled squares – Mesorhizobium; open square – Azorhizobium. Maximum Likelihood method with JTT matrix and gamma rate distribution with invariable sites. Percentage bootstrap support (100 replicates) shown if >70%. This is a detailed version of the phylogeny in Fig. 3. Full accession numbers and strain names are included.

File S1 Sampling locations in compressed KML format for visualization in Google Earth.

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Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.