Geographic structuring of genetic variation differs across two contact zones in the Diglossa carbonaria superspecies

Rapid radiations, where species quickly diversify with little to no change in the genetic composition of the taxa, provide unique opportunities to understand the processes underlying lineage divergence, especially when the newly formed species come into contact. This study examines three parapatrically distributed taxa of the Andean Diglossa carbonaria superspecies that differ strikingly in plumage and have been classified as an example of rapid lineage divergence. Using RADSeq data, we characterized the geographic structuring of genetic variation and investigated the possibility of introgressive hybridization at the contact zones between D. humeralis atterima and D. b. brunneiventris in northern Peru and between D. b. brunneiventris and D. carbonaria in Bolivia. We found weak genetic differentiation between D. humeralis atterima and D. b. brunneiventris and low, but diagnosable, differentiation between D. b. brunneiventris and D. carbonaria. At the contact zone between D. humeralis atterima and D. b. brunneiventris, the lack of genetic differentiation did not allow us to determine if hybridization was occurring between the taxa. In contrast, clustering analyses, diagnostic allele identification, and PCA analyses showed geographic patterns consistent with introgressive hybridization at the contact zone between D. b. brunneiventris and D. carbonaria, a geographic region where birds that are intermediate in plumage have been observed. Finally, we found a genetic break within the distribution of D. b. brunneiventris. The genetic divergence across this [~]450 km wide break is greater than that found between D. humeralis atterima and D. b. brunneiventris. Our results add to previous work documenting weak genetic differentiation between taxa that have striking plumage differences, and in showing that plumage color may be a poor phylogenetic marker. Lay SummaryO_LIWe studied three closely related avian taxa in Peru and Bolivia which have different plumages and adjacent ranges to examine how genetically distinct they are. C_LIO_LITo do this, we used RADseq data from 72 flowerpiercers sampled across their ranges to examine their population structure and to test whether the three taxa hybridize where their ranges meet. C_LIO_LIDespite their striking differences in plumage color, the three species showed few genetic differences. In one area where the ranges are adjacent, the groups were so similar that interbreeding could not be confirmed. In another, there was evidence of admixture, supported by observations of birds with intermediate plumage. C_LIO_LIFor these taxa, feather color may not reflect evolutionary relationships, and more extensive genetic sampling is needed to understand how these plumage differences evolved. C_LI