A simple approach to multiplexed PCR amplicon sequencing of plumage-associated loci in Vermivora warblers

The dynamics of hybridization between golden-winged ( Vermivora chrysoptera ) and blue-winged warblers ( V. cyanoptera ) has been of interest for over a century. Whole genome analysis found only a small number of genomic regions that differed between the species. We previously developed a restriction enzyme-based RFLP approach to genotype large numbers of individuals at each of these loci. Here we extend this approach to an amplicon sequencing method to genotype individuals at these six plumage-associated regions. We demonstrate the efficacy using preliminary data from 4 golden-winged and 4 blue-winged warblers as well as provide the data and scripts necessary to analyze these data for other interested in replicating this approach. Our hope is that these data are useful for other researchers interested in genotyping Vermivora warblers.