Figure 1.
UPGMA dendrogram of genetic distance among all observed multilocus genotypes.
Multilocus genotypes (MGs) are labeled as in Table S2 for NA1 isolates. Only two NA2 and EU1 multilocus genotypes were found. NA1 genotypes with null alleles are marked with asterisks. Support values greater than 70% using 1,000 bootstrap samples are shown.
Table 1.
Summary of the genetic diversity of P. ramorum nursery isolates by state and year collected.
Figure 2.
Minimum spanning networks for West Coast NA1 populations.
A. California, B. Oregon, and C. Washington. For constructing the networks multilocus genotypes were collapsed to multilocus haplotypes, which are represented by circles, squares, or diamonds containing the number of associated isolates and sized in proportion to haplotype frequency. Blue circles and red squares represent the two different groups identified by Structure. Purple diamonds are haplotypes that could not be assigned to one group or the other with high confidence (>75% probability). Bolded haplotypes are those that were found in only that state (some haplotypes found only in Washington were seen in multiple years). Branches are proportional to Bruvo et al.'s [56] genetic distance and are labeled with distance if different than 0.10. Broken lines connect haplotypes that only differ by null alleles at one locus. Loops in the networks indicate multiple tied minimum spanning trees.
Figure 3.
Minimum spanning networks for four 2004 NA1 populations.
A. Georgia, B. Virginia, C. Texas, and D. Connecticut. Multilocus genotypes were collapsed to multilocus haplotypes, which are represented by circles, squares, or diamonds containing the number of associated isolates and sized in proportion to haplotype frequency. Blue circles and red squares represent the two different groups identified by Structure. Purple diamonds are haplotypes that could not be assigned to one group or the other with high confidence (>75% probability). Bolded haplotypes are those that were found in only that state. Branches are proportional to Bruvo et al.'s [56] genetic distance and are labeled with distance if different than 0.10. Loops in the networks indicate multiple tied minimum spanning trees. For GA, TX, and VA the most common haplotype corresponds to MG 1 in Table S2. The most common haplotype for CT is MG 2.
Table 2.
Analysis of molecular variance (AMOVA) among California, Oregon, and Washington samples.
Figure 4.
Clustering of isolates by Structure 2.2 into two underlying groups.
For each state isolates are ordered by their probability of membership in the group common among Connecticut, Oregon, and Washington isolates. The order of the “other states”, from left to right, is AL, AR, CO, FL, LA, MD, NC, NM, PA, SC, and TN. See Table 1 for state abbreviations.
Figure 5.
Comparison of the genetic groups identified by three clustering algorithms.
The UPGMA dendrogram was produced for the 18 clusters identified by BAPS 5.2. The membership of each cluster is indicated to the far right by state, with the number of isolates if greater than one in parentheses. Pie charts show the group assignment of the isolates in each BAPS cluster by Structure 2.2 (left) and k-means clustering (right). See Table 1 for state abbreviations.
Figure 6.
Pie charts show the distribution of the two groups of NA1 isolates, as identified by Structure, among sampled states. Arrows indicate confirmed P. ramorum-positive nursery trace forwards. Blue arrows are 2004 trace forwards and red arrows are 2006 trace forwards. There were no confirmed trace forwards in 2005 or 2007.
Table 3.
Influential loci and alleles in Structure 2.2 analysis.
Figure 7.
Estimates of relative rates of immigration to mutation (m/µ).
The ratio of immigration rate to mutation rate was estimated for each of four populations. Isolates were combined across years for CA, OR, and WA, and combined across both years and states for a population of all non-West Coast isolates. The migration model allowed the three West Coast populations to both send and receive migrants, but the fourth population to only receive immigrants. Bars show the maximum likelihood estimate of the parameter for four independent runs of the program Migrate (indicated by different colors). Error bars indicate 95% confidence intervals.