FIG. 2.

MP and ML trees among P, N1, N2, and reference sequences (RT). (a) Strict consensus of the MP trees under no weighting of substitution types. BV under exclusion and inclusion of group O sequences are indicated above and below the branches, respectively. Including the group O sequences collapsed the branch indicated as dashed and rooted the tree (with a BV value of 53) as indicated by the arrow. N1 and P are separated by three branches (thick line) supported by BV > 95. Sequence labels correspond to reference strain names from the LANL website (see text). (b) Strict consensus of the 3 ML trees (−ln L = 2062.54867). Estimation of Ti/Tv ratio, proportion of invariable sites, and gamma shape parameter for variable sites are 4.09, 0.32, and 0.64, respectively. When group O sequences are included, the branching pattern is unchanged but the tree is rooted as indicated by the arrow.