Transspecies beak color polymorphism in the Darwin’s finch radiation

Abstract Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles 1 , but little is known of how they affect fitness and are maintained as species multiply 2 . We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin’s finches. Beaks are pink or yellow, and yellow is recessive 3 . Here we show that the polymorphism arose in the Galápagos approximately half a million years ago through a regulatory mutation in the BCO2 gene, and is shared by 14 descendant species. The frequency of the yellow genotype is associated with cactus flower abundance in cactus finches, and is altered by introgressive hybridization. The polymorphism is most likely a balanced polymorphism, maintained by ecological selection pressures associated with diet, and augmented by occasional interspecific introgression. Polymorphisms that are hidden as adults, as here, may contribute to evolutionary diversification in underappreciated ways in other systems.