Fig. 1.

A trans-specific haplotype occurs at high frequency in both Drosophila simulans and D. sechellia. (A) The resequenced region of chromosome 3R with gene models and TFB sites projected onto the polymorphism table below. Arrows indicate the direction of transcription and thin lines above the gene models are annotated TFB sites. The triangle denotes the location of a class II insulator. The resequenced region corresponds to 3R: 16692096–16672738 of the D. melanogaster genome. (B) A polymorphism table with variable sites coded as ancestral (blue) and derived (yellow) states. The top matrix contains sequences from D. sechellia and the bottom matrix is from D. simulans. (C) Four maximum likelihood trees representing regions with distinct histories. Green circles represent the D. sechellia samples, red circles are the D. simulans samples, blue is D. mauritiana, and black is the D. melanogaster sequence.