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Abstract

Carotenoid-based color ornaments often distinguish closely related taxa. In vertebrates, red ornamentation is the result of endogenous conversion of yellow dietary carotenoids into red ketocarotenoids. Here we examine a naturally occurring avian hybrid system to characterize the genetics and evolutionary history underlying phenotypic variation in a carotenoid ornament. The long-tailed finch (Poephila acuticauda) is an Australian songbird with two hybridizing subspecies that differ prominently in bill coloration: yellow in western subspecies acuticauda and red in eastern subspecies hecki. Using linked-read genomic sequence data and reflectance spectrophotometry measurements of bill color collected from wild sampled and captive bred finches, we identify four loci that together explain most variation in this trait. Each of these regions show evidence of selective sweeps: the first occurred within yellow-billed subspecies acuticauda and the second is currently in process within subspecies hecki resulting from introgression following their hybridization. We showcase the power of population-scale linked-read sequence data (haplotagging) to accurately phase genetic variation and use an ancestral recombination graph (ARG) approach to characterize the evolutionary history and selective regimes underlying population divergence in this carotenoid-based color trait.