Analysis of molecular variance and isolation by distance
A hierarchical AMOVA, as implemented in poppr with method = ‘ade4’, was carried out using population within host (Table 4). Consistent with previous studies in O. crenata (Romàn et al. 2001) the majority of variation is found within individuals, suggesting very little population differentiation. However, there is some evidence for separation by host (phi = 0.031, p = 0.004) and population within host (phi = 0.028, p=0.001). The observed increased individual variation among O. crenata populations results from a significant excess of heterozygosity (FIS = -0.22, Bartlett’s K-squared = 1969, df = 1, p-value < 2.2e-16).
To test the role of isolation by distance (IBD), a Mantel test was conducted using Edward’s genetic distance and a geographic distance matrix (latitude, longitude). Overall, we find no support for IBD (R = 0.55, p = 0.10) across populations. We do find however, two distinct patches in the kernel density estimates for IBD (Figure 3). This patchiness appears to be driven by the outlying population, AT, which exhibits moderate genetic differentiation, with mean FST= 0.075 (Table 2) and geographic distance, mean = 1.94. This outlying patch drives a significant linear relationship between genetic distance and geographic distance (dashed line Figure 3, R2 = 0.283, p = 0.0001)