Sonsthagen, Sarah A. (ORCID: 0000-0001-6215-5874) Wilson, Robert E. (ORCID: 0000-0003-1800-0183) Armstrong, Matthew R. (ORCID: 0009-0004-6875-4631) Johnson, James A. (ORCID: 0000-0002-2312-0633) Booms, Travis L. (ORCID: 0000-0002-6053-355X) Gesmundo, Callie F. (ORCID: 0009-0008-9188-5540) Pohlen, Zachary M. (ORCID: 0009-0001-8043-142X) Leonard, Paul B. (ORCID: 0000-0001-8032-7449) 20250513 tabular digital data Anchorage, Alaska U.S. Geological Survey, Alaska Science Center Suggested Citation: Sonsthagen, S.A., Wilson, R.E., Armstrong, M.R., Johnson, J.A., Booms, T.L., Gesmundo, C.F., Pohlen, Z.M., Leonard, P.B., 2025, Genomic data from Gray-headed Chickadee and Boreal Chickadee: U.S. Geological Survey data release, https://doi.org/10.5066/P14VRAFK https://doi.org/10.5066/P14VRAFK This dataset provides sample data and NCBI accession information for genomic sequencing of Gray-headed Chickadee and Boreal Chickadee from North America and Russia To estimate levels of introgression between chickadee species and provide within species estimates of genetic structure. 2020 2025 observed Complete None planned North America and eastern Russia 163.5213 -54.4197 68.3781 43.2849 USGS Metadata Identifier USGS:6823d734d4be025fcef5a7ce ISO 19115 Topic Category Biota Environment NASA GCMD Earth Science Keyword Thesaurus Animals/Vertebrates Birds USGS CSA Biocomplexity Thesaurus Songbirds Population Genetics USGS Thesaurus Wildlife Terrestrial ecosystems Genetic diversity DNA sequencing MeSH-National Library of Medicine Genomics DNA, Mitochondrial None Passerines Gray-headed Chickadee Boreal Chickadee Poecile cinctus Poecile hudsonicus None double digestion restriction associated DNA ddRAD Mitochondrial DNA USGS Geographic Names Information System (GNIS) Alaska None Animals Birds Passerines ITIS Integrated Taxonomic Information System Unknown online database online ITIS-North America Taxonomic details retrieved May 10, 2025 from the Integrated Taxonomic Information System online database https://www.itis.gov https://doi.org/10.5066/F7KH0KBK Species were identified by skilled observers in the field based on general appearance, plumage, behavior, and vocalization. Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Passeriformes Family Paridae Genus Poecile Species Poecile hudsonicus Boreal Chickadee TSN: 554386 Species Poecile cinctus Gray-headed Chickadee TSN: 554384 No access constraints. No use constraints. These data are marked with a Creative Common CC0 1.0 Universal License and are in the public domain. It is requested that this USGS data release be cited for any subsequent publications that reference or utilize these data. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov Armstrong, M.R. Wilson, R.E. Johnson, J.A. Booms, T.L. Gesmundo, C.F. Pohlen, Z.M. Leonard, P.B. Sonsthagen, S.A. Unknown journal article . . online . Armstrong, M.R., Wilson, R.E., Johnson, J.A.,Booms, T.L., Gesmundo, C.F., Pohlen, Z.M., Leonard, P.B., Sonsthagen, S.A., (in prep), Hybridization and asymmetrical introgression between the vulnerable Gray-headed Chickadee and a more abundant congener, the Boreal Chickadee: implications for conservation, Ecology and Evolution. . Identifying information about samples were cross-checked with original field data. Preparation of DNA fragments for sequencing on a next generation sequencing platform follow protocols described in DaCosta and Sorenson (2014). All laboratory techniques were performed using sterile procedures. Attribute values fall within expected ranges and data were proofed for the presence of duplication and omission. Blank cells are described for each attribute. National Center for Biotechnology Information (NCBI) Unknown database https://www.ncbi.nlm.nih.gov/biosample/ digital database file 2025 observed NCBI BioSample Information regarding sampling and the biological source material used in this study are publicly accessible in the NCBI BioSample database (accession numbers provided in this data package). METHODS - FIELD: Muscle or organ samples were collected and stored in preservation buffer. Unknown METHODS - LAB: DNA was extracted using a Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Düsseldorf, Germany) following manufacturer's protocol. Double digest restriction-site associated DNA (ddRAD) library preparation, sequencing, assembly of reads, and alignment of loci followed DaCosta and Sorenson 2014. Mitochondrial DNA polymerase change reaction, sequencing, and reconciling of raw sequence data followed Lait and Burg 2013. Low quality reads were filtered and identical reads collapsed for each sample. Assembled reads were clustered into putative loci if sequences were >85% similar. Genotypes were scored as homozygous if > 93% of sequence reads were consistent with a single haplotype, whereas heterozygotes were scored if a second haplotype was represented by at least 29% of reads. We used Geneious (Biomatters Inc.) to manually check and edit loci. Raw read data generated in this study were submitted to the NCBI short read archive publicly available high throughput sequence data database. Unknown LITERATURE CITED: DaCosta, J.M., Sorenson, M.D., 2014. Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS ONE 9(9):e106713, https://doi.org/10.1371/journal.pone.0106713 Lait, L.A., Burg, T.M., 2013. When east meets west: population structure of a high-latitude resident species, the Boreal Chickadee (Poecile hudsonicus). Heredity 111:321–329. https://doi.org/10.1038/hdy.2013.54 Unknown General sampling locations have been described by corresponding entries in the USGS Geographic Names Information System (GNIS) when possible. Point 0.0001 0.0001 Decimal degrees World Geodetic System of 1984 (WGS84) World Geodetic System of 1984 (WGS84) 6378137 298.257223563 chickadee_genomic_sonsthagen.csv Table with sample identifying information, collection data, and NCBI biosample accession numbers for high throughput sequence data. Presented in a Comma Separated Value (CSV) formatted table. Author defined Sample_ID Unique laboratory identification code used to mark individual samples processed in the laboratory. Author defined Unique laboratory identification. specimen_voucher Museum specimen voucher identification code. The prefix letter code indicates the museum collection: MVZ = Museum of Vertebrate Zoology (University of California, Berkley), NYSM = New York State Museum (Albany New York), UAM = Museum of the North (University of Alaska - Fairbanks), USNM = Smithsonian National Museum of Natural History (Washington, D.C.), UWBM = Burke Museum of Natural History and Culture (University of Washington, Seattle). Blank cells indicate samples that are not archived in a museum collection. Museum defined Unique museum identification. Species Scientific name of bird species sampled. Author Defined Poecile hudsonicus Scientific name of Boreal Chickadee Author defined Poecile cinctus Scientific name of Gray-headed Chickadee Author defined Collection_Location Place names of sample collection site. Blank cells indicate that source data are owned by museum. Author defined United States: Kelly River, Alaska Samples collected along Kelly River, Noatak National Preserve, Alaska. Geographic Names Information System (GNIS) United States: Sheenjek and Coleen River, Alaska Samples collected along the Sheenjek and Coleen River, Arctic National Wildlife Refuge, Alaska. Geographic Names Information System (GNIS) United States: Chicken, Alaska Samples collected near Chicken, Alaska (approximately 64.1 N, 141.9 W) Geographic Names Information System (GNIS) United States: Anchorage, Alaska Samples collected near Anchorage, Alaska. (approximately 61.2 N, 149.7 W) Geographic Names Information System (GNIS) Collection_Date Year, month, and day that sample was collected in the field. Blank cells indicate that source data are owned by museum. Author defined 2021 08/18/2023 Year Month Day (YYYY-MM-DD) NCBI_BioSample BioSample Accession Number. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) of the biological source material used in this study. This number may be used to retrieve detailed sample and experiment information from the NCBI BioSample database https://www.ncbi.nlm.nih.gov/biosample NCBI BioSample Unique identifier: an alphanumeric accession number available in the NCBI BioSample database. NCBI_Accession Accession Number for NCBI mitochondrial DNA sequence. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) of the biological source material used in this study. This number may be used to retrieve detailed sample and experiment information from the NCBI nucleotide database https://www.ncbi.nlm.nih.gov . Blank cells indicate that source data were not provided for this sample. NCBI BioSample Unique identifier: an alphanumeric accession number available in the NCBI BioSample database. U.S. Geological Survey USGS ScienceBase Team Mailing and Physical

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Denver Colorado 80225 USA 1-888-275-8747 sciencebase@usgs.gov The U.S. Geological Survey, Alaska Science Center is the authoritative source of these data, distributed by ScienceBase (a USGS Trusted Digital Repository). Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. CSV Tabular data in CSV format; FGDC metadata in XML and HTML formats. https://doi.org/10.5066/P14VRAFK None 20250513 U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM) FGDC-STD-001.1-1999