The genomic basis of plumage polymorphism in the Eastern Screech-Owl (<i>Megascops asio</i>)

Understanding the genetic basis of polymorphic traits is useful for exploring the origin and maintenance of variable phenotypes. Previous work on color polymorphism in birds has evolved from targeting candidate genes to whole-genome scans, consequently revealing the often-complex genomic architecture underlying polymorphic coloration. The Eastern Screech-Owl (Megascops asio) is a small North American polymorphic forest owl in which both gray and rufous plumage morphs are common across much of its range. We used whole-genome resequencing to investigate the genomic basis of this polymorphic trait at a population level, revealing additive and epistatic sources of this color and pattern variation. Using three approaches, comparisons identified a genome-wide suite of loci known to be associated with coloration, several loci associated with noncoloration physiological pathways, and using a regression model-based approach identified substantial epistatic interactions between loci underlying variation in screech-owl coloration. In addition, we uncovered evidence of balancing selection at morph-associated loci, suggesting that differential selection on morph types maintains their relative frequency in this species. Many owls show similar patterns of color polymorphism, which is likely mediated through parallel and equally complex genomic architecture under similar selective pressures that may partly explain how this trait has been maintained over evolutionary time as this group radiated.