3.4 | Genetic changes and migration events
We used the δaδi to further explore the demographic history prior to the
separation of the three populations. Following the method of Portik
(Portik et al., 2017), We employed a four-round optimization technique
to ensure that all final optimizations resulted in a similar
log-likelihood score (Table S4). In order to better validate the
possible divergence patterns between populations, we first constructed
ten 3D models for three independent populations (Fig. S7). Models with
the lowest scoring log-likelihoods was “Adjacent ancient migration,
shorter isolation” (Fig. 5a, Table S5). This ancient migration model
involving early gene flow with symmetric migration was supported as the
best fit for the three populations. Next, in our eight 2D simulations
(Fig. S8), the ancient migration or secondary contact plus instantaneous
size change model involving divergence with ancient continuous
symmetrical migration, isolation with instantaneous size change provided
the best fit regarding the PEc and PEz&PEa lineages (Fig. 5b, Table
S5). By comparing the best 2D and 3D models, it was found that the best
2D models have larger log values and lower residuals, which coincided
with the results of our phylogenetic tree. Furthermore, the best model
revealed a possible divergence of roundworm populations, that is, there
was bidirectional gene flow in the early ancient periods, but in the
middle and current stages, the gene flow between the populations almost
ceased.