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.