Diversifying selection and adaptive introgression of carotenoid-processing genes underlie the evolution of bill color in the long-tailed finch

Abstract

AbstractCarotenoid pigmentation produces the yellow and red coloration of birds and other vertebrates, but our understanding of the genetic architecture of carotenoid ornamentation is largely limited to studies of novel color variants observed in captively bred populations. The complexity of carotenoid-based color evolution in nature remains poorly characterized. Here, we examine the long-tailed finchPoephila acuticauda, an Australian songbird with two hybridizing subspecies that differ in bill coloration: yellow in western subspeciesacuticaudaand red in eastern subspecieshecki. We characterize the carotenoid composition of each subspecies and find that yellow bills can be explained by the loss of C(4)-oxidation, thus blocking yellow dietary pigments from being metabolized to red. Combining linked-read genomic sequencing and reflectance spectrophotometry measurements of bill color collected from wild-sampled finches and laboratory crosses, we identify four loci that together explain 53% of variance in this trait. The two loci of largest effect contain the genesCYP2J19, an essential enzyme for the ketolation via C(4)-oxidation of dietary carotenoids, andTTC39B, an enhancer of ketocarotenoid production. Evolutionary genealogy reconstruction indicates that the red-billed phenotype is ancestral and yellow alleles at bothCYP2J19andTTC39Barose and fixed inacuticaudaapproximately 100 kya. Yellow alleles then introgressed intoheckiless than 5 kya. Across all four loci,acuticaudaderived variants show evidence of selective sweeps, implying that yellow bill coloration has been favored by natural selection. Our study suggests that the frequent adaptive evolutionary transitions between red and yellow ornamentation in nature can have a simple genetic basis.SignificanceWe studied variation in carotenoid ornamentation of an Australian songbird with two hybridizing subspecies that differ in bill color: one yellow and the other red. We identified a single metabolic process, C(4)-oxidation, underlying the distinct carotenoid composition of these two bill colors. Genetic association mapping revealed four major effect loci that explained most of the observed variation the trait, including the oxidative ketolation enzymeCYP2J19and the carotenoid ketolation enhancer geneTTC39B. Evolutionary reconstruction indicates that yellow alleles are derived, ancient (~100 kya), and under positive selection. This has driven their recent (<5 kya) adaptive introgression across the hybrid zone. These findings have important implications for understanding the role of natural selection in phenotypic evolution in natural systems.