Figure 4

Phylogenetic tree for complete genome haplotypes. A whole genome nucleotide phylogenetic tree was generated using the reconstructed haplotypes. The ML phylogenetic tree was made with PHYML using the GTR nucleotide substitution model, gamma distributed rate variation across sites and 9 substitution rate categories (see Methods for details). 100 bootstrap replicates were performed and support values of > = 90 are shown on the corresponding branch. Colors as in Figure 3.