—Phylogenetic trees and summary of nucleotide variation in the regions studied. Regions have been named in alphabetical order starting in the region most proximal to the centromere. The neighbor-joining trees were built using Jukes-Cantor corrected distances and rooted using D. melanogaster. Only bootstrap values >80% are shown. Sequences belonging to the homogeneous and heterogeneous subsets are depicted as squares and circles, respectively. The lines previously found to be homogeneous in the G region (Rozas et al. 2001) appear as solid, others appear as open. The D region includes two closely linked subregions that were pooled. The shaded values show the window identified by the sliding-window haplotype test. The bold values show the window identified by the single-locus haplotype tests. S, number of segregating sites; π, nucleotide diversity; K, average nucleotide divergence between D. simulans and D. melanogaster corrected by the Jukes-Cantor method; ns, not significant. Superscript a indicates parameter settings were modified to consider sequences differing in up to one nucleotide position.