RT Journal Article SR Electronic T1 An examination of the evolve-and-resequence method using Drosophila simulans JF bioRxiv FD Cold Spring Harbor Laboratory SP 337188 DO 10.1101/337188 A1 John K. Kelly A1 Kimberly A. Hughes YR 2018 UL http://biorxiv.org/content/early/2018/06/03/337188.abstract AB We develop a set of analytical and simulation tools for Evolve-and-Resequence (E&R) experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood based test statistics combined with permutation suggest parallel evolution of about 120 polymorphisms across the genome. Whole genome simulations calibrated from several Drosophila genetic datasets indicate this response could be generated by as few as 20 loci under strong directional selection, with a corresponding hitch-hiking effect. While this resolves the “excessive significance” paradox typical of E&R experiments, a rank-based correlation analysis of genomic windows that suggests that weaker selection might be acting at a much larger number of sites. Finally, the allele frequency spectrum at sites that experience strong selection in the novel laboratory environment suggests that loci responding to selection may be balanced polymorphisms in nature.