Introgressed H. debilis haplotypes have increased linkage and larger-effect QTL than H. annuus haplotypes, which increase evolutionary repeatability. a) Lower recombination rates in simulations leads to a higher proportion of variation from selection. A simulation matching the experimental evolution population with two chromosomes, single DMI pair, and varied recombination rate tested. Bars represent 95% range of 100 simulations. Physical chromosome size was constant, while recombination rate variation changed cM size for chromosomes. b) The introgressed haplotype retains high LD. The average LD between haplotype-specific markers spaced at different distances at 1, 4, 8, and 12 generations. c) Stronger selection leads to higher proportion variance from selection in simulations. d) Effect sizes of interspecies QTL from introgression are larger than those of intraspecies QTL. The maximum effect size for each trait QTL for the F₁ cross (including the introgressed haplotype) compared with the maximum effect size for the BC₁ parent cross is plotted on the y axis.