Abstract A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits and its evolutionary relevance. Using whole-genome data of 3,958 Darwin’s finches on the Galápagos Island of Daphne Major we identify six loci of large effect that explain 46% of the variation in beak size of Geospiza fortis , a key ecological trait. Allele frequency changes across 30 years at these loci affected beak morphology in two ways. An abrupt change in beak size occurred in Geospiza fortis as a result of natural selection associated with a drought, and a more gradual change occurred in G. scandens as a result of introgressive hybridization. This study demonstrates how large effect loci are a major contributor to the genetic architecture of rapid diversification during adaptive radiations. One Sentence Summary Allele frequency change at six loci of large effect causes evolutionary change in key ecological traits.

Large effect loci have a prominent role in Darwin’s finch evolution