Fig. 2.
The rooted coalescent-based gene genealogy showing the distribution of mutations for South American (SA: Peru, Ecuador, Bolivia, Brazil) and non-South American (NSA: Costa Rica, Mexico, U.S., Ireland) populations for the IRRAS locus of Phytophthora infestans generated using GENETREE (32). Time scale is in coalescent units of effective population size. The direction of divergence is from the top (past–oldest) to the bottom (present–youngest). The numbers below the tree from top to bottom designate each distinct haplotype and its count (i.e., the number of occurrences of the haplotype in the sample), the count of each haplotype in each population, the mating type of the isolates, and the mtDNA haplotype (33). Maximum likelihood estimates of the tree with the highest root probability, standard deviation (SD) and Watterson's theta (55) were as follows: Likelihood = 3.5320 × 10−23, SD = 4.8689 × 10−20, theta = 2.0. Estimates were based on 10 million coalescent simulations and five independent runs to ensure convergence. Simulations were performed assuming constant population size.