3.2 | Genetic structure and phylogenetic relationships
Principal components analysis (PCA) supported the clear separation amongParascaris spp. (Fig. 2a), with PC1 and PC2 separating the PEc and PEz&PEa populations (P <0.05). All PCs showed that PEz and PEa were located in the same cluster. Meanwhile, the phylogenetic relationship among the three populations inferred by ML tree highlighted a similar division as that of PCA (Fig. 2b). The tree showed two distinct clusters, the PEc population seems to be a separate clade, while the other two formed a distinct clade. Although the sampling sites of PEc and PEz partially overlapped, the divergence between them was still clear. Population structure analysis further confirmed the two distinct clusters presented by PCA and ML tree, where PEz and PEa had more ancestral components in common (Fig. 2c). We scanned the paired IBD regions at the genome-wide level of all individuals and found that PEz and PEa shared more IBD regions (98.5% of PEa shared with PEz), while PEc and the other two populations had almost no shared large fragments (Fig. S4, S5). In addition, lower inter-population Fst values were detected in PEz and PEa populations also indicating a closer relationship between them (Fig. S5).