Figure 1.
Population clustering of Phytophthora plurivora.
Genetic clustering (K = 4) of the 16 populations (N = 221 isolates) using 11 microsatellite markers. Each bar represents an individual isolate and colors code the proportion of membership to each cluster. The assignment probability is indicated on the left hand side. Populations are abbreviated as follows (left to right in the bar plot): Italy (I), Finland (FIN), United Kingdom (UK), US East Coast (EC), Austria (A), Switzerland (CH), US West Coast (WC), France (F), Belgium and Netherlands (BNL), Serbia (SRB), Slovenia (SLO), Czech Republic (CZ), Hungary (H), Poland (PL), Germany (D, D nurs), Turkey (TR). D nurs indicates isolates derived from German nurseries only, D all other isolates. Pie charts depict the genetic membership (q-mean) per population, in parentheses the number of isolates = multilocus genotypes per population.
Table 1.
Population diversity measures for 12 European and US Phytophthora plurivora populations.
Table 2.
Bayesian assessment of migration within and among sampling localities of Phytophthora plurivora implemented in BAYESASS [51].
Figure 2.
Haplotype networks for Phytophthora plurivora.
(a) Haplotype networks for the 6 nuclear genes: transcriptomal gene fusion protein (TigA, 33 isolates), heat shock protein 90 (HSP90, 36 isolates), enolase (36 isolates), tryptophan biosynthesis gene 1 (trp, 28 isolates), internal transcribed spacer (ITS, 37 isolates) and the beta tubulin gene (btub, 32 isolates). (b) Haplotype network of the mitochondrial gene cytochrome C oxidase subunit I (cox I, 33 isolates). Each circle represents a different haplotype, small grey circles represent unsampled, intermediate, haplotypes and colors represent the affiliation to a certain population. Color code: light green – Belgium, white – Czech Republic, purple – Finland, grey – France, green – Germany, turquois – Hungary, dark blue – Italy, orange – Netherlands, mauve – Slovenia, light blue – Serbia, red – Switzerland, pink – Turkey, and yellow – USA.
Table 3.
Genetic diversity observed per locus in Phytophthora plurivora isolates from Europe and the US.
Figure 3.
Phenogram of the four Phytophthora plurivora clusters detected with STRUCTURE.
The phenogram was constructed using the unweighted pair-group method of averages (UPGMA) algorithm based on Nei’s unbiased genetic distance [56] of clusters. Statistical support for branches was obtained using 1000 bootstrapped samples of the data set. Clusters match the color code in Fig. 1.
Figure 4.
Maximum clade credibility tree for European and US Phytophthora plurivora isolates.
The tree was depicted for six nuclear genes (ITS, btub, enolase, TigA, trp1 and HSP90) and the mitochondrial gene cox I. Extended Bayesian skyline plot (EBSP) for the six nuclear genes (ITS, btub, enolase, TigA, trp1 and HSP90). Posterior probabilities are indicated in red (>0.7), black (0.5 – 0.7) and blue (<0.5). Time is shown in coalescent units on the x-axis. The highest posterior density (hpd) median is depicted as a black dashed line and the hpd upper/ lower 95 limits as grey solid line. The scale bar on y-axis indicates the effective population size (Ne).