Fig. 2.

Trees ii and xi with posterior estimates of population sizes (θs, numbers on the branches) and species divergence times (τs, the bottom horizontal axis; bars represent 95% HPD intervals) from bpp. Parameters for tree ii were estimated from all loci in chromosome 2L excluding 2La region, while those for tree xi were estimated from all loci in the Xag region of chromosome X. Divergence times were calculated assuming the mutation rate $2.8\times {10}^{-9}$ per site per generation for autosomal noncoding loci (A), with 11 generations per year, and 0.524 and 0.323 times (supplementary fig. S4, Supplementary Material online) as large for the coding autosomes (C) and coding Xag loci (D), respectively. Ma, million years ago.