3.3 | Demographic history and divergence time
To examine the genome-wide divergence time among Parascaris spp. populations on the genome-wide, we constructed a molecular clock phylogenetic tree based on the calibrated mutation rate using all SNP sites. The tree topology showed that the divergence time of PEc and PEz&PEa was about 900-1500 years ago when the posterior probability was >95% (Fig. 3). The PSMC results showed similar effective population sizes (Ne ) of three populations (Fig. 4a). Besides, the MSMC2 inferred that the Ne of the three populations had almost a similar trend 1000 years before, without any differentiation, indicating the existence of possibly common ancestor (Fig. 4a, 4b). However, the Ne of the three populations began to diverge in the recent 1000 years (Fig 4b). The relative cross coalescence rates (RCCR) estimation between pairs of the three populations also showed that clear genetic separations occurred from 600 to 1500 years ago, with an earlier separation of PEc with PEz and PEa than that of PEz and PEa (Figure 4b). The change of Ne of each population and separation among the three population were further supported and validated by results inferred by SMC++ (Figure 4c). We carefully compared the relationship between the separation and the topological structure of the phylogenetic tree, and found high consistency. Both results showed that PEc vs PEz, PEc vs PEa had obvious divergence, but PEz vs PEa are not fully differentiated. Taken together, we considered that Parascarisspp. mainly produce two divergence clades, one from horse-derived (PEc) and the other from zebra & donkey-derived (PEz&PEa). The conservative divergence time was estimated to be about 200-1500 years ago. Finally, we used fastsimcoal2 to evaluate the population size after divergence based on the observed joint site frequency spectrum (SFS; Fig. S6), and found that the PEc population size after divergence event was significantly larger than PEz&PEa (Fig. 4d). The best coalescent simulation model inferred by fastsimcoal2 also indicates an early bidirectional gene flow between PEc and PEz&PEa.