Introgression facilitates rapid evolution of Galápagos tree finches

Adaptive radiations provide powerful models to study the origins of phenotypic novelty and species diversity. Darwin’s finches constitute a classic example in which beak morphology is a key trait related to fitness. Here, we focused on <i>Camarhynchus</i> tree finches, one of the most recent clades of the radiation, whose diversification remains poorly understood. We analysed whole genomes in combination with morphological data to revisit long-standing questions regarding their origins raised before genetic evidence became available. <i>Camarhynchus</i> diversified at least 100,000 kya, yielding striking morphological differences despite shallow genetic divergence. We identified seven highly differentiated loci, including <i>G03</i>, a supergene affecting beak and body size. We reveal an unusual example of genomic mosaicism, in which autosomal differentiation between a large tree finch lineage and the small tree finch is restricted primarily to a single locus -(<i>G03</i>)- that approaches fixation. Contextualized in a broader phylogenetic context, we show that the small and large <i>G03</i> alleles diverged early in the radiation, suggesting a key genetic innovation enabling ecological expansion among species of Darwin’s finches. Our results establish <i>Camarhynchus</i> as a model example of speciation with gene flow, underscoring the broader role of hybridization in generating biodiversity.