Studying species interactions at hybrid zones allows biologists to understand the forces that promote speciation. Hybridization among Sphyrapicus nuchalis, S. varius, and S. ruber has long been acknowledged, and hybrid zones between S. nuchalis/S. ruber and S. varius/S. ruber have been characterized with both genetic and genomic data. Using a combination of next-generation Restriction Site-Associated DNA sequencing (RAD-Seq) and traditional genetic methods, we examined patterns of introgression in the poorly characterized S. nuchalis/S. varius contact zone; the two most similar species in the complex, though they are not each other’s closest relatives. We found high introgression rates, with several early and many advanced generation hybrids along a 275 km stretch of Rocky Mountain foothill, pointing to a well-established hybrid zone with hybrid individuals backcrossing with individuals from the parental species and each other. Plumage colouration in the hybrid zone was a relatively poor indicator of parental or hybrid status, which could be attributed to the possible involvement of few large effect genes.

Genetic data were taken from sapsucker blood and tissue samples. These were sequenced using GBS or ddRAD sequencing methods and/or screened at three polymorphic SNP loci. GBS data were processed in Stacks, ddRAD in Tassel, then statistical analyses were performed in R. PCAs were made using scripts (named genomics_r_functions.R) from Irwin, D.E., Alcaide, M., Delmore, K.E., Irwin, J.H., & Owens, G. (2016). Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Molecular Ecology, 25(18), 4488–4507.