Figure 3

The flaA gene maximum likelihood tree from 18 Aeromonas species. Bootstrap values (1,000 replicates) are indicated in the nodes. Estimates of ω ratios, obtained under the "free-ratios" model, which assumes an independent ω ratio (d_N/d_S) for each branch in the tree, are shown in bold along branches. Ancestral sequences were reconstructed from Bayes Empirical Bayes analysis under a model that assumed a background ω ratio for branches of Group 1 and 2 (background branches) and another ω ratio for the branch connecting the two groups (foreground branch). Changes in the ancestral amino acids are indicated in the table (lower right position in the figure). Shadowed amino acid changes identify positions under positive selection, inferred from the M8 model (Table 6).