Selection on cuticle color produces a genome-wide response that does not localize to known major genes in Drosophila

Complex traits are often deemed highly polygenic when a mapping study fails to localize the loci underlying them, but a result that fails to identify major genes can also reflect a lack of power. Cuticle color in Drosophila offers a natural test of this distinction, since genes of large effect segregate in natural populations. We selected for dark and light thoracic trident color for 16 generations in two populations of D. melanogaster and two of D. simulans, then used pooled sequencing to scan each genome for allele-frequency differentiation between selected and control lines. Selection produced a strong, genome-wide shift in allele frequencies in every population, exceeding the expectation under drift. Simulations demonstrate that our design has low power to detect major-effect genes, which may explain why we do not observe peaks localizing to known color genes. We further show that a highly significant peak in each genome, on chromosome 3L, is an artifact of chorion-gene amplification in the pooled adult females. A source of false signal in pool-seq studies that has not been reported before. Cosmopolitan inversions shifted in frequency under selection in the one population that carried them, but direct testing showed they did not inflate genome-wide noise, contradicting a common assumption in the field. Together, these results demonstrate that a diffuse, polygenic-type response can arise from a trait with known large-effect genes, and provide a quantitative account of why an evolve-and-resequence design can fail to localize even a well-characterized genetic architecture.