DOI: 10.5061/dryad.n2z34tnbc
title: Black-capped and mountain chickadee hybridization and breeding ecology in Boulder County, CO

description: 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 urban forests may play a role. This dataset includes: reproductive
 information and genomic information for Colorado chickadees, as well as
 simulation data for assigning wild birds to genomic classes (i.e.,
 characterizing hybridization).
description: # 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.*, 2025). This study contains 119 males,
 110 females, and 340 individuals of unknown sex (i.e., all nestlings
 except the six first generation backcrosses + allopatric individuals). The
 data included in this project spans breeding data (location, timing,
 reproductive success for all individuals) as well as genomic data. Code
 used to analyse all data files is found
 in BoulderChickadeeStudy_Stats_DRYAD.Rmd. Given this data involves wild
 breeding birds, in some cases, data was not able to be collected for all
 adults & pairs (i.e., nest completion date). In this instance, NAs
 represent unknown data. Where possible, zeros have been entered for true
 zeros (i.e., a nest failed and did not fledge any chicks). ### Files and
 variables #### File: Nestling.HI.Location.csv **Description:** Hybrid
 index and breeding data for nestlings in the study ##### Variables *
 USGS.Number: federal band number (a unique identifier) * hi.POPID:
 population assignment based on simulations * Hybrid.Index: assessment of
 ancestry * Species.x: species based on phenotype * Date: date of banding *
 Year.x: year of banding * Location: site * Nest.ID: unique nest ID * Age:
 age at banding * Tarsus: ankle bone length at banding (mm) * Wing.Chord:
 wing length at banding (mm) * Mass: weight at banding (g) * Adult: parent
 at nest * Nest.Box.ID: unique box ID * Site: site of banding *
 Clutch.Initiation: date of first egg in nest * Hatch.Date: date of first
 egg hatching * Day12: date which chicks are 12 days old * Clutch.Size: how
 many eggs in the nest * Nestlings: how many nestlings at day 12 * Male.ID:
 social male at nest * Female.ID: social female at nest * Julian: date of
 hatching in julian date format * Julian.CI: date of egg laying in julian
 date format * Zone: UTM zone of nest  * Easting: UTM easting of nest *
 Northing: UTM northing of nest * Latitude: latitude of nest * Longitude:
 longitude of nest * Elevation: elevation of nest (m) * Prop.Nestlings:
 number of nestlings at day 12 over number of eggs laid #### File:
 ChickadeeNests_2019-2021.csv **Description:** Unique nests for the
 breeding season ##### Variables * Nest.ID: unique nest box ID + year *
 Nest.Box.ID: Unique nest box * Site: site of nest * Species: species of
 nest * Year: year of nest * Clutch.Initiation: date of first egg laid *
 Hatch.Date: date of first egg hatching * Day12: date when nestlings are 12
 days old * Clutch Size : how many eggs in nest * Nestlings: how many
 nestlings at day 12 in nest * Male ID: social male at nest * Female ID:
 social female at nest #### File: wgs_gghybrid_loci_1.csv
 **Description:** output from gghybrid used to calculate hybrid indexes for
 birds ##### Variables * hi.INDLABEL: unique bird identifier (here, federal
 band number) * hi.POPID: given population assignment *
 hi.h-posterior-mode: mode of hybrid index estimate * hi.h-cred-int-lower:
 lower interval of hybrid index estimate * hi.h-cred-int-upper: upper
 interval of hybrid index estimate * hi.beta-mean: mean of hybrid index
 estimate * hi.beta-var: * hi.beta-shape1: * hi.beta-shape2: *
 hi.npar-compare: #### File: ChickadeeNestBoxes.csv
 **Description:** location of all boulder chickadee study nest boxes
 (wooden boxes in field, not all have active chickadee nests) #####
 Variables * Nest.Box.ID: unique nest box ID * Zone: UTM zone of nest box *
 Easting: UTM easting of nest box * Northing: UTM northing of nest box *
 Elevation : elevation of nest box * Latitude: latitude of nest box *
 Longitude: longitude of nest box #### File:
 adults.hi.breeding.combined.csv **Description:** adult chickadees banded,
 along with calculated hybrid index from gghybrid  ##### Variables *
 USGS.Number: unique federal metal band identifier o * hi.POPID: *
 Hybrid.Index: hybrid index calculated using gghybrid * Species.x:
 phenotypic species * Band.Colors: unique color band combination * Year.x:
 year banded * Date: date banded * Site.x: site banded * Location: house
 banded * GPS.S: GPS location of banding * GPS.E: GPS location of banding *
 Elevation..m.: elevation of banding * Nest.ID: unique nest ID of adult *
 Nest.Stage: what nest stage (eggs, chicks) of adult * Captured.with: birds
 adult captured with * Nest.Box.ID: nest box adult captured at  *
 Species.y: species as identified by phenotype  *  Year.y: year banded *
 Clutch.Initiation: date of first egg laid * Hatch.Date: date of first egg
 hatching * Day12: date when nestlings are 12 days old * Clutch.Size: how
 many eggs  * Nestlings: how many nestlings * Male.ID: social male color
 combo * Female.ID: social female color combo * Julian: julian date of
 hatching * Julian.CI: julian date of egg laying * Zone: UTM zone of nest *
 Easting: UTM easting of nest  * Northing: UTM northing of nest * Latitude:
 Latitude of nest * Longitude: Longitude of nest * Elevation: elevation of
 nest * Prop.Nestlings: number of nestlings banded at Day 12 over number of
 eggs  #### File: chickadee_wgs_ADULTS.csv **Description:** List of adult
 chickadees ##### Variables * 
 
 #### File: Nestlings_to_Exclude.csv **Description:**  list of nestlings
 ##### Variables * 
 
 #### File: NestlingsBanded.csv **Description:**  list of banded nestlings
 ##### Variables * Band.Number: federal metal band of nestling * Species:
 species as identified by phenotype  * Date: date banded * Year: year
 banded * Location: where banded * Nest.ID: unique nest ID where sired *
 Age: age at banding * Tarsus : ankle length at banding (mm) * Wing.Chord:
 wing length at banding (mm) * Mass: weight at banding (g) * Adult : social
 parents at nest #### File: BirdsBanded.csv **Description:** list of banded
 adult chickadees  ##### Variables * Species: species as identified by
 phenotype * USGS.Number: federal metal band number * Band.Colors: unique
 color combo  * Year: year banded * Date: date banded * Time.Trapped: time
 caught * Time.Bled: time bled * Recap: has this bird been been caught
 before * Site: where caught * Location: house caught * GPS.S: GPS of net
 or nest * GPS.E: GPS of net or nest * Elevation.(m): elevation where bird
 caught * Bander: who banded bird * Sex: sex of bird  * How.Sex: how bird
 was sexed * Age: age of bird * How.Age: how bird was aged * Release: was
 this bird released * Bird+Bag.(g): what did the bird plus cloth bag weigh
 * bag.(g): what did the bag weigh * Bird.(g): by proxy, what did the bird
 weigh  * Wing.(mm): wing chord length * Tarsus.(mm): ankle bone length *
 Tail.(mm): tail length from center * Culmen.(mm): bill length * Culmen
 Depth.(mm): bill depth from nares * Culmen Width.(mm): bill width from
 nares * Bill+Head.(mm): bill plus head * Hemo: did we collect hemocrit *
 Plasma: did we collect plasma * Blood: did we collect blood * Fecal: did
 we collect fecal sample * Feather: did we collect feathers * Nest: nest ID
 * Nest.Stage: what stage is nest at * Captured.with: other birds captured
 with this bird #### File: adults.assortative.mating.csv
 **Description:** list of chickadee pairs  ##### Variables * Nest.Box.ID:
 unique nest ID * Male.ID: male color bands * Male.USGS: male federal metal
 band * Male.species: species of male by phenotype * Male.HI: hybrid index
 of male * Female.ID: female color bands * Female.USGS: female federal
 metal band * female.species: species of female by phenotype * Female.HI:
 hybrid index of  female * Diff.HIs: difference between social male hybrid
 index and social female hybrid index * Year.y: year of nest *
 Clutch.Initiation: date when first egg was laid * Hatch.Date: date first
 egg hatched * Day12: date when nestlings are 12 days old * Clutch.Size:
 how many eggs  * Nestlings: how many nestlings * Julian: julian date of
 egg hatching * Julian.CI: julian date of egg laying * Zone: UTM zone of
 nest * Easting: UTM easting of nest * Northing: UTM northing of nest *
 Latitude: latitude of nest * Longitude: longitude of nest * Elevation:
 elevation of nest (m) * Prop.Nestlings: number of nestlings banded at Day
 12 over eggs #### File: chickadee.wgs.admixture.2.Q
 **Description:** output from ADMIXTURE for 2 populations #### File:
 chickadee.wgs.admixture.3.Q **Description:** output from ADMIXTURE for 3
 populations #### File: chickadee.wgs.admixture.4.Q **Description:** output
 from ADMIXTURE for 4 populations #### File: wgs_filtered_missing_ind.txt
 **Description:** individuals included in ADMIXTURE analysis ##### ##
 Code/software All files were analysed in R. ## Access information Other
 publicly accessible locations of the data: All original code for
 processing genomic data and analyzing breeding data is deposited at github
 [[https://github.com/KathrynGrabenstein/Boulder-chickadee-hybridization](https://github.com/KathrynGrabenstein/Boulder-chickadee-hybridization)]. * This Whole Genome Shotgun project is deposited at DDBJ/ENA/GenBank under the accession JAAMOC020000000. The raw sequence data generated in this study from chickadees are deposited in the NCBI Sequence Read Archive (SRA) database under accession code PRJNA893818 [[https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893818](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893818)].