A mosaic of modular variation at a single gene underpins convergent plumage coloration.

The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture. Editor's summary: Even when controlled by single genes, traits can still show great variability when multiple regulatory elements affect their expression. Lutgen et al. extensively characterized four species of wheatears, birds that are notable for their varied black or white mantles, throats, and necks. They found that although a single locus containing the known pigmentation gene ASIP segregates with these traits, each body part is affected by different regulatory variation in addition to a coding variant responsible for white feathers. The story is complicated further by the extensive hybridization of these species, leading to an old white haplotype spreading more broadly from one species, Oenanthe melanoleuca, and more recent mutations causing similar phenotypes in others. —Corinne Simonti INTRODUCTION: Phenotypic diversification abundantly reuses existing variation that is available within species or introgressed from other species. Still, insights into how such variation is integrated with new mutations to form new phenotypes and how this process may be limited by genetic architectures remain scarce. RATIONALE: In this work, we investigated the genetic architecture and evolutionary history of plumage coloration in a group of songbirds. Wheatears (genus Oenanthe) show a high incidence of convergent plumage color evolution and frequent hybridization in the Oenanthe hispanica complex, within which three species (O. hispanica, O. melanoleuca, and O. pleschanka) exhibit a black or white throat color polymorphism, and the mantle coloration that is divergent black or white between species is abundantly recombined by hybridization. We leveraged the throat color polymorphism and the recombined mantle coloration to infer the genetic architecture underpinning plumage coloration. On the basis of population genetic patterns observed for the color-related genomic variation, we reconstructed plumage colorations' evolutionary histories. RESULTS: Genome-wide association studies associate throat and mantle coloration with variation at a single gene, the agouti signaling protein (ASIP) locus. Throat coloration is underpinned by the interaction of a new transposable element (TE) insertion 5′ of ASIP with nonsynonymous variation within the ASIP coding sequence. Mantle coloration is governed by additive effects at multiple sites up to 50 kbp 5′ of ASIP. Expression patterns and isoform structures of ASIP in regrowing feathers confirm this role of ASIP in the regulation of the melanin-based plumage coloration. Population genetic analyses based on the ancestral recombination graph place the evolution of white throat and mantle coloration in O. melanoleuca, from where both introgressed into O. hispanica, and white throat coloration introgressed into O. pleschanka. In O. melanoleuca and O. hispanica, throat phenotypes are associated with different nitrogen stable isotope signatures that suggest an association of throat coloration with alternative foraging niches. At the genus level, the convergent evolution of throat and mantle coloration involved variation different from that recovered in the O. hispanica complex; that is, new variation. CONCLUSION: The convergent plumage coloration in wheatears evolved from a combination of new and introgressed variation at a single gene. Whereas the convergent pattern of coloration predominantly roots in past introgression within the O. hispanica complex, it involved new mutations at genus scale. Introgression further contributed to the formation of recombined phenotypes in extant hybrid zones that may constitute a source for future phenotypic evolution. The complex patterns of color evolution in wheatears demonstrate how phenotypes can be decoupled between body parts within the constraints of a monogenic architecture. Despite the strong linkage within a single gene, fine-scale recombination can integrate linked regulatory modules from divergent origins into new, recombined haplotypes. This appears to imperatively involve long-term recombination; be it within species, in their ancestors, or in hybrid zones that ever increasingly come into focus as notable melting pots that enable evolutionary tinkering. Plumage color evolution in wheatears.: White mantle and throat coloration evolved in O. melanoleuca through regulatory mutations (mantle) and coding mutations and TE insertion (throat) at the ASIP gene. Introgression of ASIP variation led to white mantle coloration in O. hispanica and a throat polymorphism in O.hispanica and O. pleschanka. Fine-scale ASIP recombination in hybrid zones underpins the expression of intermediate plumage phenotypes. SNP, single-nucleotide polymorphism. [ABSTRACT FROM AUTHOR]