Population Diversity of Grape Phylloxera in California and Evidence for Sexual Reproduction

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Figure 1
Neighbor-joining tree of the California grape phylloxera samples in Batch B. The four populations identified by the admixture-model clustering method employed in STRUCTURE are presented on the right. Two samples, marked by a circle and a triangle, were not placed by either STRUCTURE or the neighbor-joining tree method. The five control samples are named and indicated with an arrow.
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Figure 2
Principal coordinate analysis of phylloxera in the Napa1 and Napa2 populations to identify possible sexual offspring between the two populations. The samples marked by squares received q values between 0.4 and 0.6 for both populations in STRUCTURE. All remaining samples received a q value above 0.7 in STRUCTURE for one of the two populations. The x-axis accounts for 23.26% of the diversity, while the y-axis accounts for 10.41%.

Table 1
Host-plant and collection location information of five reference phylloxera samples used in both study batches. WEO4802 was collected from a foliar gall; the other four were collected from root galls.
Table 2
Sampling locations, code names, and number of phylloxera samples collected for SSR genotyping and analysis. Samples were separated by host tissue (root versus leaf) and collection batch (A and B).
Table 3
Distribution of phylloxera samples into the four populations determined in this study based on association with collection location or host plant.
Table 4
Nei’s genetic distance (below diagonal) and pairwise F_ST (above diagonal) for the four phylloxera populations identified in Batch A.
Table 5
Sample size, number of multilocus genotypes (MLGs), clonal diversity (R), mean number of alleles (na), mean observed heterozygosity (Ho), mean expected heterozygosity (He), and F_IS values for the four phylloxera populations identified in this study.
Table 6
Allele-frequency comparison of the Napa1 and Napa2 populations and five samples identified as being possible sexual offspring between the two populations.

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Supplemental Data -

Supplemental Table 1 Primer name, size range, fluorescent label, source, and sample batches used in this study of phylloxera diversity.

Supplemental Table 2 Multilocus genotypes (MLGs), number of samples, site location, and years of collection for phylloxera samples in Batch B.

Supplemental Figure 1 (A) Unweighted neighbor-joining tree results for foliar phylloxera samples in Batch A. Two root samples, MLG12 and MLG13, grouped closer to four strains (blue color) collected from roots in California. One hundred fifty-four foliar samples matched with the reference foliar sample (red color) collected from the St. George rootstock. (B) The differences among the 11 foliar multilocus genotypes (MLGs) were due to loss of allele with one or more markers.

Supplemental Figure 2 Principal coordinate analysis of all samples in the northern California Diversity Batch B. Clusters are color-coded with the STRUCTURE results for four populations. One sample, marked by a diamond, was not assigned to a cluster by STRUCTURE, and a second sample, marked by a triangle, was not assigned consistently by STRUCTURE and the neighbor-joining tree method. The x-axis accounts for 21.07% of the variation, while the y-axis accounts for 15.19%.