Figure 3.

Bayesian phylogeny of Alphaproteobacteria using the P4 software. (a) Tree employing a composition-heterogeneous model that is adequate to the data. (b) Tree employing a composition-homogeneous model that significantly violates the data. Both trees are based on a Dayhoff-recoded sequence with a concatenation of 52 proteins, in which 28 are composition-homogeneous while the remaining 24 are composition-heterogeneous. The value near each internal branch is the posterior probability for that branch. Trees are rooted using species from Betaproteobacteria and Gammaproteobacteria.