Figure 9

An expanded tree of four protein pairs. These maximum likelihood trees include genes from all four R. sphaeroides species (2.4.1, ATCC 17025, ATCC 17029, and KD131) along with two related genes from species outside of R. sphaeroides (orthologs). These genes in the other R. sphaeroides strains were also only present in only two copies. The relationships again depict two types of topology - Type A or Type B, where the left two trees are Type A trees while the right two trees are Type B trees. For the top Type-A tree, the two R. sphaeroides 2.4.1 genes are phaD (RSP_0994) and a hypothetical protein (RSP_3713) while for the bottom Type-A tree the two R. sphaeroides 2.4.1 genes are prfA (RSP_2907) and prfB (RSP_2977). For the top Type-B tree, the two R. sphaeroides 2.4.1 genes are cbbF1 (RSP_1285) and fbpB (RSP_3266) while for the bottom Type-B tree, both genes encode for hypothetical proteins (RSP_3325 and RSP_3719). The trees were rooted to provide a better sense of the tree topology. The numbers on the branches represent the substitutions per site while the numbers that point to branching points represent the bootstrap support values for those nodes. The NCBI reference number for the corresponding gene is given to the right of the organism description for all nodes except those labeled R. sphaeroides 2.4.1, where an RSP number is given for consistency with the rest of the information provided in the paper. Notice on the Type A trees how the duplicated genes in all R. sphaeroides branch from the orthologs while on the Type B trees the duplications branch from R. sphaeroides genes and the orthologs form their own branch.