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Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white‐browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species' nuclear genomes using ddRAD‐seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and AXIN1. Both are involved in the Wnt/β‐catenin signalling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole‐genome homogenization and reveals new candidate genes potentially involved in plumage divergence. [ABSTRACT FROM AUTHOR]

Hybrid zones provide a window into the evolutionary processes governing species divergence. Yet, the contribution of mate choice to the temporal and spatial stability of hybrid zones remains poorly explored. Here, we investigate the effects of assortative mating on hybrid‐zone dynamics by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all‐black carrion and gray‐coated hooded crows. In the best‐fit model, narrow clines of the two mating‐trait loci were maintained by a moderate degree of assortative mating inducing pre‐ and postzygotic isolation via positive frequency‐dependent selection. Epistasis between the two loci induced hybrid‐zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favoring gray‐coated phenotypes ∼1200 generations after secondary contact. Unlinked neutral loci diffused near‐unimpeded across the zone. These results were generally robust to the choice of matching rule (self‐referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating‐trait loci without generalizing to genome‐wide reproductive isolation. It further emphasizes the importance of the genetic mating‐trait architecture for spatio‐temporal hybrid‐zone dynamics. [ABSTRACT FROM AUTHOR]