Population structure
The analysis of population structure was conducted using two different
clustering approaches, model-based maximum likelihood hierarchical
clustering via ADMIXTURE (Alexander and Lange 2011), individual based
principal component analysis (PCA) on genetic distances. Cross
validation as implemented in ADMIXTURE across 15 replicates identified K
= 4 as the optimal number of genetic clusters in the data (Figure S1).
Visualization of the coefficients of ancestry for each individual are
arrayed by geographic location from southwest to northeast in Figure 4A.
Figure 4B shows the admixture among populations as arranged by hosts. As
with genetic distance estimates, ADMIXTURE reveals evidence of
structuring among populations and hosts. In this case, patterns of
structuring among hosts is more evident than strictly along a geographic
gradient. For example, faba bean hosts have more similar patterns of
shared ancestry than that shared between faba bean and chickpea or
tomato, despite covering a broad range of geographical space. In
contrast, populations AT and BM are spatially and genetically isolated.
These data are consistent with the AMOVA results supporting a role for
an interaction between host and location partitioning genetic variance
among populations (Table 4).
The first 4 components from a PCA of genetic distance explained 66.16%
of the total variation in the data. To further examine the relationship
between samples within this PCA we conducted a Discriminant Analysis of
Principle Components (DAPC). DAPC identified 4 genetic clusters in the
data across 3 axes (Figure 5). Cluster assignments supported both the
model-based and AMOVA identified genetic differentiation by
host/population (Figure 6). Posterior assignment supports admixture
within chickpea, tomato, and faba bean hosts but not within carrot or
pea. Chickpea and tomato samples predominate cluster 1. Pea samples are
all placed in cluster 4 while carrot samples are all placed in cluster
2. Faba bean samples have significant overlap between cluster 3 (N=35)
and cluster 2 (N = 22) with two samples having shared membership.