Discussion
The maintenance and evolution of colour polymorphism remains one of the most appealing yet elusive evolutionary questions. Since diversity in life history strategies and complex traits have shown to segregate with colour-defined phenotypes, it is plausible to expect evidence of those associations also at molecular level. Here we report the first assemblies of the tawny owl genome and a comprehensive genome-wide-association study leading to the discovery of structural variation associated with colour polymorphism – though not on the traditional M1CR gene. Given the pleiotropic effect of the POMCgene, our results sheds light on the genetic basis of so-called melanin-phenotypes and pave the way to explore evolutionary mechanisms underlying the maintenance of colour polymorphism in melanin-pigmented avian taxa.