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Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.

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Figure S1. We created custom Agilent high-density–CGH array (8 × 15K) e-array including 6975 pairs of probes (Agilent part number G4427A, Amadid #022089) Drosophila sechellia genomic regions are shaded, Drosophila simulans regions are clear.

Figure S2. Plot of interactions between loci.

Figure S3. Interactions between QTL-II and sex, and QTL-II and QTL-X for the Drosophila sechellia back-cross (A,C), and the Drosophila simulans back-cross (B,D).

Figure S4. Whole genome effect plots for (A) the Drosophila sechellia backcross, (B) the Drosophila simulans backcross, and (C) the F2 intercross.

Appendix S1. The sequence of 384 bar-coded adapters.

Appendix S2. The identity, stock number, and collection site of fly strains used in this study.

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