Figure 2

Phylogenetic trees. a, phylogenetic tree based on 16S rRNA sequences by maximum likelihood; b, phylogenetic tree based on average distance from 480 single copy protein families; c, third possible tree topology for the acidophilus complex. Bootstrap support values for internal branches are indicated. Evolutionary distance scales for trees a and b are presented (expected number of substitutions per site). 16S rRNA tree reconstruction is based on a HKY model (expected transition/transversion ratio 1.68 and expected pyrimidine transition/purine transition ratio 0.62) with rate heterogeneity between sites modeled using a gamma distribution with coefficient of variation 2.64. Pairwise evolutionary distances for proteins are estimated with a JTT model and include separate gamma-corrections for each protein family (average coefficient of variation is 1.14).