Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs

Genetic introgression is pervasive in nature and may lead to large-scale phenotypic assimilation and/or admixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, biometric and spectrophotometric data from a flycatcher (Tyrannidae) system in the Neotropical genus Zimmerius, we document a mosaic pattern of phenotypic admixture in which a population of Z. viridiflavus in northern Peru (henceforth ‘mosaic’) is vocally and biometrically similar to conspecifics to the south but shares plumage characteristics with a different species (Z. chrysops) to the north. To clarify the origins of the mosaic population, we used the RAD-seq approach to generate a dataset of 37,361 genome-wide SNPs. A range of population-genetic diagnostics shows that the genome of the mosaic population is largely indistinguishable from southern Z. viridiflavus and distinct from northern Z....