Proteins are listed using NCBI locus tags. Bootstrap values are shown for selected branches and correspond to confidence levels. A) Black: B. subtilis 168 FosB (outgroup), green: Bacillus subtilis 168 proteins, orange: Bacillus subtilis subsp. natto BEST195 proteins, magenta: Bacillus subtilis subsp. spizizenii TU-B-10 proteins, cyan: Bacillus subtilis subsp. spizizenii str. W23 proteins, red: Bacillus subtilis subsp. subtilis str. RO-NN-1 proteins See Table A in S1 File for additional information. B) Black: B. subtilis 168 FosB (outgroup), green: Bacillus subtilis 168 proteins, orange: Bacillus megaterium QM B1551 proteins, purple: Bacillus amyloliquefaciens subsp. plantarum str. FZB42 proteins, cyan: Bacillus halodurans C-125 proteins, red: Bacillus anthracis str. Ames, blue: Bacillus thuringiensis str. Al Hakam. See Table B in S1 File for additional information.