A complex genomic architecture underlies reproductive isolation in a North American Oriole hybrid zone

Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species--the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) orioles--to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic ..., Sample Collection. Baltimore and Bullock’s orioles were sampled during the spring/summer (May 19 through June 27) of 2016-2018 from 12 localities along the Platte River in Colorado and Nebraska, USA. This intensive sampling effort resulted in the collection of 313 vouchered specimens of phenotypic Bullock’s Orioles, phenotypic Baltimore Orioles, and phenotypic hybrids from within the contact zone. From this collection, we sequenced the genomes of 60 male orioles from five genotypic classes, including allopatric Baltimore Orioles (n=10), allopatric Bullock’s Orioles (n=10), backcrossed Baltimore Orioles (n=10), backcrossed Bullock’s Orioles (n=10), and recent generation hybrids (n=20). 
Whole Genome Sequencing. Genomic DNA was extracted from all samples using the DNeasy blood and tissue kit (Qiagen, CA, USA). DNA concentrations were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies). For whole genome re-sequencing, individual libraries were prepared using the...,