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Appendix S1. Testing the effect of recombination on the fixation of a linked, neutral allele.

Appendix S2. Methods used for multilocus simulations.

Appendix S3. Derivations in mathematica (HartfieldOttoSM.nb file available for download).

Figure S1. The mean frequency of a linked neutral allele following a successful selective sweep, given as a function of the recombination rate Nr between different sites.

Figure S2. The mean number of deleterious alleles that fix genome-wide following the completion of a successful selection sweep, given as a function of the recombination rate NR (see Fig. 4 for data presented relative to Sa = 0). Sa = 0 (black dashed line), 20 (black solid line), 40 (dark gray), or 80 (light gray).

Figure S3. Fixation probability of the advantageous mutant in multilocus simulations, as a function of the recombination rate NR. Sa = 0 (black dashed line), 20 (black solid line), 40 (dark gray), or 80 (light gray).

Figure S4. Fixation probability of a recombinant carrying two beneficial mutations.

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