Figure 4.

Test for complex speciation. (A) For the autosomes, the globally best-fitting model is a polytomy with a divergence time of T_A = 1.21 × 2N_sim,A generations before the present, while for the X chromosome it is also a polytomy with T_X = 1.72 × 2N_sim,X generations. This corresponds to ∼242,000 yr ago for the autosomal data set. (B) Divergence time between pairs of species is allowed to be <1.21 × 2N_sim,A generations in 1-kb windows across the autosomes. Windows that reject the globally best-fitting model in favor of a more recent divergence time are shown. A total of 379 of autosomal windows support a more recent divergence time between D. simulans and D. mauritiana (31 for the X chromosome), while 507 autosomal windows support a more recent divergence time between D. simulans and D. sechellia (27 for the X). Lastly, 294 autosomal windows support a more recent divergence time between D. mauritiana and D. sechellia (22 for the X). This set of results does not correct for multiple tests, and ∼30% of the windows shown are expected to be false positives.