The African indigobirds (Vidua spp.) are exceptional in that learning and mimicry of host vocalizations leads to adult behaviors that result in assortative mating and host fidelity. These behaviors provide a mechanism for rapid sympatric speciation via host shifts. Host shifts imply a non-zero rate of host infidelity, however, and the same behavioral mechanisms may lead to hybridization if eggs are laid in the nest of a host species already associated with another indigobird species. Thus, it is not clear if the morphological and genetic similarity of indigobird species is due to their recent common ancestry or ongoing hybridization. We addressed this question using "double-digest" restriction site-associated DNA sequencing (ddRAD-seq) to collect genomic data for three indigobird species (one of which has two host races) in Cameroon. Samples from all species were collected at two sampling localities, and we conducted population genetic analyses to determine if local gene flow or interspecific divergence best explains patterns of genomic variation. Results indicate that there is considerable divergence among species and species cohesion between sampling localities. Conspecific host races, however, are genetically similar and analyses of rare, derived alleles suggest that they continue to hybridize locally. Whether these incipient populations will eventually diverge into diagnosable species despite ongoing gene flow remains an open question.
