Fig. 4
Influence of linkage disequilibrium on the genomic response of a polygenic trait. We simulated 50 generations of polygenic adaptation after a shift in trait optimum. One hundred replicates, each with 10 contributing loci in a 1 Mb region either with linkage equilibrium (blue) or strong LD (yellow) are shown in violin plots. A Mean r2 estimates displaying the degree of LD in the two scenarios. B Independent of linkage structure, the same mean phenotype was reached, but simulations with high LD were considerably more scattered. C Pronounced allele frequency changes were obtained for both, linkage equilibrium, and high LD. For linkage equilibrium, the genomic windows were all rather similar, indicating that no window showed a strong selection signature distinguishing it from the genomic background. Simulations with strong LD, however, resulted in highly heterogeneous selection responses, with some windows having a frequency change larger than 0.6, which is a strong selection signature distinguishing it from the remaining genomic windows. D The heterogeneity among five replicate populations is measured by the coefficient of variation. The selection response in simulations with linkage equilibrium was less parallel than in those with strong LD