Genome sequencing of two cryptic Empidonax flycatchers

We performed whole-genome sequencing (WGS) and genotyping by sequencing (GBS) of alder flycatcher (Empidonax alnorum) and willow flycatcher (Empidonax traillii) from two separate contact zones in eastern and western North America. In eastern North America, the species overlap in a broad area of sympatry, whereas in western North America they overlap in a narrow contact zone. We sequenced individuals from sympatric and allopatric populations in each region, with the goal of characterizing levels of admixture and genome-wide patterns of genetic differentiation, and modelling the demographic history of populations from each region. This work provides insights into the comparative evolution of reproductive isolation in areas of broad sympatry vs. a narrow contact zone.