Black-capped and mountain chickadee hybridization and breeding ecology in Boulder County, CO

Here, we combine three years of population monitoring with 569 whole genomes to characterize the reproductive ecology of, and hybridization between, two common songbirds, black-capped (Poecile atricapillus) and mountain (P. gambeli) chickadees, for which hybridization is correlated with human habitat disturbance across North America. Working within a geographic region that we previously identified as a hotspot of contemporary chickadee hybridization, we find that, despite geographic and temporal breeding overlap, few early generation hybrids are produced, indicating that reproductive barriers typically prevent contemporary hybridization. Yet, every chickadee we sampled in sympatry possessed heterospecific ancestry, indicating that both contemporary and historical hybridization have occurred during the evolutionary history of chickadees in Colorado. Why contemporary hybridization continues to occur despite evidence for character displacement of chickadee song remains less clear, but urba..., , # Black-capped and mountain chickadee hybridization and breeding ecology in Boulder County, CO

Dataset DOI: [10.5061/dryad.n2z34tnbc](https://doi.org/10.5061/dryad.n2z34tnbc)

## Description of the data and file structure

We installed 373 wooden nest boxes throughout Boulder County, CO, USA, along an elevation gradient spanning both species' breeding distributions (1475m to 3383m) to attract nesting black-capped and mountain chickadees and then monitored breeding chickadees for three years (2019-2021). This study contains sequence data from 222 adult chickadees and their 274 associated nestlings from Boulder County, plus 73 allopatric chickadees (total: 569 individuals). Allopatric mountain chickadee samples came from Sagehen Experimental Forest (north of Truckee, California, USA; Semenov *et al.*, 2024), and allopatric black-capped chickadees came from Poague and Peabody Conservation Areas in western Missouri, USA, as well as New York, USA and Pennsylvania, USA (Semenov *et al.*, 202..., , **Changes after Nov 20, 2025:** Removed bird (2018-47, line 4) with erroneous Hybrid Index

**Changes after Dec 2, 2025:** Added VCF file for medium coverage (10x) sequencing