Hybridization and genome‐wide introgression in sympatric populations of North American wood‐pewees (<i>Contopus sordidulus</i> and <i>Contopus virens</i>)

The Great Plains contains many contact zones between eastern and western North American bird species. In these contact zones, closely related lineages or species vary widely in both the geographical and the genomic extent of their hybridization. Two phenotypically similar sister species of flycatchers – the Eastern Wood‐Pewee Contopus virens and the Western Wood‐Pewee Contopus sordidulus – have sparse geographical overlap in the Great Plains, including a few isolated planted forest stands and along forested riparian corridors of the Niobrara and Platte rivers in central Nebraska, USA. Our previous genetic work found low levels of genetic differentiation between these two flycatcher species, along with several putatively admixed individuals in this zone of sympatry in Nebraska. Here, we used whole‐genome sequencing to confirm the presence of admixed individuals and quantify nonrandom gene flow, both in direction between taxa and location in the genome. We confirm the presence of both early‐generation hybrids and highly backcrossed individuals in this contact zone. We found moderate levels of genetic differentiation between the two species, with the highest differentiation on the Z chromosome. In addition, all individuals in sympatry contained at least some minor parental genomic ancestry, suggestive of bidirectional introgression. There was evidence of introgression in sympatric individuals across the entire genome, except for approximately half the Z chromosome, suggesting that there is some selection and resistance to admixture in this genomic region.