Phylogenetic analysis of RPW8 gene family. A maximum-likelihood tree constructed from 369 alignable coding nucleotides of the RPW8 gene family, with bootstrap support values (100 replicates). Maximum-parsimony analysis arrived at exactly the same topology and comparable branch lengths (bootstrap values shown in brackets). In the absence of an outgroup sequence, the root position of the tree was defined from the mid-point root of a neighbor-joining analysis of synonymous distances. This method removes the problem of substitution rate differences among branches caused by differing selective pressures for amino acid change that could lead to incorrect rooting. Branches and nodes are color-coded to represent genetic divergences arising from speciation events. Red lines and red node denote the divergence between Brassica and Arabidopsis, blue lines and nodes denote speciation between B. rapa and B. oleracea, and green lines and nodes denote speciation between A. thaliana and A. lyrata. Letters at nodes correspond to the divergence time estimates (see Materials and Methods) in the table beside the tree. Numbers under branches are Ka/Ks ratios found to be significantly above 1