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LD between shared SNPs generated by balancing selection or by recurrent mutations. Fifty chromosomes were sampled from each species in both scenarios. We assumed an allele frequency of 0.5 for the scenario of balancing selection and sampled an equal number of chromosomes from each allelic class (see Supporting Information for details of the simulations). Panels (A) and (B) show the distribution of r2 in the two species, respectively.
