Hybrid zones are powerful natural settings for investigating how birds diversify into distinct species. Here we present the first genomic-scale exploration of the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) oriole hybrid zone, which is notable for its long history of study and for its prominence in debates about avian species concepts and species limits. We used a reduced-representation sequencing approach to generate a panel of 3,067 genetic markers for 297 orioles sampled along the Platte River, a natural west-to-east transect across the hybrid zone. We then explored patterns of hybridization and introgression by comparing variation in genomic and plumage traits. We found that hybridization remains prevalent in this area, with nearly all orioles within the hybrid zone showing some degree of genomic mixing, and 41% assigned as recent-generation (F1/F2) hybrids. The center and width of the genomic and plumage gradients are concordant and coincident, supporting our finding that classically scored plumage traits are an accurate predictor of pure versus hybrid genotypes. We find additional support for previous suggestions that the center of this hybrid zone has moved westward since it was first intensively sampled in the 1950s, but that this westward movement had slowed or ceased by the 1970s. Considered in concert, these results support previous inferences that some form of ongoing selection is counteracting the potential homogenization of these orioles via hybridization, thereby supporting their continued taxonomic separation as distinct species.

Filtered STACKS output for Baltimore and Bullock's Orioles sampled for this study. There are two files archived that were generated in populations using the following filtering options:

-r 0.8 -p 1 -t 15 --min_maf 0.05

One file ("FinalOrioles_AllSNPS_MAF_Filtered") contains all of the SNPs generated in STACKS and the other file ("FinalOrioles_SingleSNPS_MAF_Filtered) contains one SNP per locus. In both cases, individuals were removed if they had more than 50% missing data.

We have also included a spreadhseet containing plumage scores (see methods for details on plumage scoring).

Raw data may be made available upon request.