Sonsthagen, Sarah A. (ORCID: 0000-0001-6215-5874)
Wilson, Robert E. (ORCID: 0000-0003-1800-0183)
20200728
Genomic Data from Ptarmigan and Grouse, Alaska
tabular digital data
Genomic Data from Ptarmigan and Grouse, Alaska
ver 2.0, December 2021
Anchorage, Alaska
U.S. Geological Survey, Alaska Science Center
Suggested Citation: Sonsthagen, S.A., Wilson, R.E., 2020, Genomic data from ptarmigan and grouse, Alaska (ver 2.0, December 2021): U.S. Geological Survey data release, https://doi.org/10.5066/P9DDB01R
https://doi.org/10.5066/P9DDB01R
U.S. Geological Survey, Alaska Science Center
2015
Genomics of Wildlife
website
Alaska Science Portal
416
Anchorage, Alaska
U.S. Geological Survey, Alaska Science Center
This is a link to the broader USGS Alaska Science Center research project supported by these data. Users will find a description of the research project and links to associated reports, publications, and data products.
https://alaska.usgs.gov/portal/project.php?project_id=416
This data set provides sample data and NCBI accession information for genomic sequencing of ptarmigan and grouse from Alaska.
To examine spatial genomic structure and functional genomic variation along a latitudinal gradient.
2015
2019
observed
None planned
Alaska, USA.
-176.6742
-136.0870
70.1754
51.8783
USGS Metadata Identifier
USGS:ASC284
ISO 19115 Topic Category
Biota
Environment
NASA GCMD Earth Science Thesaurus
Animals/Vertebrates
Birds
USGS CSA Biocomplexity Thesaurus
Herbivores
Population Genetics
USGS Thesaurus
Wildlife
Terrestrial ecosystems
Tundra ecosystems
Genetic diversity
DNA sequencing
MeSH-National Library of Medicine
Genomics
Transcriptome
None
Fowl
Galliformes
Upland game birds
Rock ptarmigan
Willow ptarmigan
White-tailed ptarmigan
Spruce grouse
Ruffed grouse
Sharp-tailed grouse
Sooty grouse
Lagopus muta
Lagopus lagopus
Lagopus leucura
Falcipennis canadensis
Bonasa umbellus
Tympanuchus phasianellus
Dendragapus fuliginosus
None
double digestion restriction associated DNA
ddrad
exon capture
whole transcriptome
whole methylome
whole mitogenome
whole genome
USGS Geographic Names Information System
Alaska
None
Animals
Birds
Game birds
ITIS Integrated Taxonomic Information System
Unknown
ITIS Integrated Taxonomic Information System
database
online
ITIS-North America
Taxonomic details for ptarmigan and grouse were retrieved December 27, 2021, from the Integrated Taxonomic Information System on-line database https://www.itis.gov
https://www.itis.gov
ITIS currently lists Sooty grouse as a subspecies of Blue grouse. However, the most current taxonomic designation by the American Ornithological Society's (AOU) Check-list of North American Birds ( http://checklist.aou.org/taxa ) considers Sooty grouse (Dendragapus fuliginosus) to be a distinct species.
Here, we follow the current AOU designation as described in: Chesser, R.T., Cicero, C., Dunn, J.L., Kratter, A.W., Rasmussen, P.C., Remsen, J.V. Jr., Rising, J.D., Stotz, D.F. 2006. Forty-seventh supplement to the American Ornithologists' Union Check-list of North American Birds. The Auk 123(3):926-936 https://doi.org/10.1093/auk/123.3.926
Species were identified by skilled observers in the field based on general appearance of feathers and plumage, behavior, and vocalization.
Kingdom
Animalia
Subkingdom
Bilateria
Infrakingdom
Deuterostomia
Phylum
Chordata
Subphylum
Vertebrata
Infraphylum
Gnathostomata
Superclass
Tetrapoda
Class
Aves
Order
Galliformes
Family
Phasianidae
Subfamily
Tetraoninae
Genus
Bonasa
Species
Bonasa umbellus
Ruffed grouse
TSN: 175790
Genus
Falcipennis
Species
Falcipennis canadensis
Spruce grouse
TSN: 553896
Genus
Lagopus
Species
Lagopus lagopus
Willow Ptarmigan
TSN: 175804
Species
Lagopus leucura
White-tailed ptarmigan
TSN: 677541
Species
Lagopus muta
Rock ptarmigan
TSN: 677542
Genus
Tympanuchus
Species
Tympanuchus phasianellus
Sharp-tailed grouse
TSN: 175841
Genus
Dendragapus
Species
Dendragapus obscurus
Sooty Grouse
None
It is requested that the authors and the USGS Alaska Science Center be cited for any subsequent publications that reference this dataset.
U.S. Geological Survey, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
Sweet, A.D.
Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Johnson, K.P.
2020
Lousy grouse: comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions
journal article
Ecology and Evolution
10(15):8379-8393
online
John Wiley and Sons, Inc
Sweet, A.D., Wilson, R.E., Sonsthagen, S.A., Johnson, K.P. 2020. Lousy grouse: comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions. Ecology and Evolution 10(15):8379-8393 doi:10.1002/ece3.6545
https://doi.org/10.1002/ece3.6545
Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Talbot, S.L.
2022
Species-specific responses to landscape features shaped genomic structure within Alaska galliformes.
journal article
Journal of Biogeography
49
online
Wiley
Sonsthagen, S.A., Wilson, R.E., Talbot, S.L. 2022. Species-specific responses to landscape features shaped genomic structure within Alaska galliformes. Journal of Biogeography doi:10.1111/jbi.14294
https://doi.org/10.1111/jbi.14294
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.
Field
Muscle or organ samples were collected and stored in preservation buffer.
Lab
DNA was extracted using a Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Düsseldorf, Germany) following manufacturer’s protocol.
Lab
Total RNA was extracted from individuals using a MasterPure™ RNA Purification Kit (Epicentre, Madison, WI, USA) following manufacturer’s protocol and quantified using a Quant-iT RNA Assay Kit (Invitrogen, Carlsbad, CA USA).
Lab
Double digest restriction-site associated DNA (ddRAD) library preparation, sequencing, assembly of reads, and alignment of loci followed DaCosta and Sorenson 2014.
Lab
Whole genome libraries were prepared using an Illumina TruSeq Nano library preparation kit (Illumina, California) following manufacturer's protocol.
Lab
Targeted exon capture of DNA libraries was completed using a MyBaits DNA sequence target capture kit (Arbor Biosciences, Michigan) following manufacturer’s protocol.
Lab
Whole transcriptome libraries were prepared using an Illumina TruSeq stranded mRNA library preparation kit (Illumina, California) following manufacturer’s protocol.
Lab
Whole methylome libraries were prepared using a Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Michigan) following manufacturer’s protocol.
DaCosta, J.M.
Sorenson, M.D.
2014
Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol
journal article
PLoS ONE
9(9):e106713
online
Public Library of Science (PLoS)
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 doi:10.1371/journal.pone.0106713
https://doi.org/10.1371/journal.pone.0106713
publication
2014
publication date
DaCosta and Sorenson 2014
Laboratory Technique Citation: describes double-digest restriction associated DNA sequence library preparation and read assembly protocol.
National Center for Biotechnology Information (NCBI)
Unknown
BioSample
database
https://www.ncbi.nlm.nih.gov/biosample/
digital database file
2020
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).
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.
Unknown
Raw read data generated in this study were submitted to the NCBI short read archive publicly available high throughput sequence data database.
Unknown
NCBI SRA
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
World Geodetic System of 1984
6378137
298.257223563
ptarmiganGrouse_genomicData_alaska_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
Field_ID
Unique field identification code used to mark individual samples collected in the field.
Author defined
Unique field identification.
Species_ID
Scientific name of bird species sampled. Details provided in the Taxonomy section of this metadata record.
Author Defined
Lagopus lagopus
Scientific name of Willow ptarmigan
Author defined
Lagopus muta
Scientific name of Rock ptarmigan
Author defined
Lagopus leucura
Scientific name of White-tailed ptarmigan
Author defined
Falcipennis canadensis
Scientific name of Spruce grouse
Author defined
Bonasa umbellus
Scientific name of Ruffed grouse
Author defined
Tympanuchus phasianellus
Scientific name of Sharp-tailed grouse
Author defined
Dendragapus fuliginosus
Scientific name of Blue grouse
Author defined
Collection_Region
Place names of sample collection site.
Author defined
Alaska: Interior
Samples collected in interior Alaska.
Geographic Names Information System (GNIS)
Alaska: Arctic Coastal Plain
Samples collected in the Arctic coastal plain Alaska.
Geographic Names Information System (GNIS)
Alaska: Southcentral
Samples collected in Southcentral Alaska.
Geographic Names Information System (GNIS)
Latitude
The latitude at which the individual was sampled from the field. Blank cells indicate hunter harvested birds and exact location not recorded.
Author defined
59.8660
70.1754
Decimal degrees (WGS84)
Longitude
The longitude at which the individual was sampled from the field. Blank cells indicate hunter harvested birds and exact location not recorded.
Author defined
-156.9280
-142.2227
Decimal degrees (WGS84)
Collection_date
Year and month that sample was collected in the field.
Author defined
2009-10
2018-03
Year Month (YYYY-MM)
Sex
Sex of bird sampled; identified in the field by morphological characteristics. Blank cells indicate hunter harvested birds and sex information was not collected for this sample.
Author defined
Female
Female
Author defined
Male
Male
Author defined
Version
The data package version that was current at the time each record was originally released by the USGS Alaska Science Center.
Author defined
v 1.0
Version 1.0, July 2020
Author defined
v 2.0
Version 2.0, December 2021
Author defined
NCBI_BioSample_ddRAD
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 ). 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, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
The USGS Alaska Science Center is the authoritative source and distributor of these data.
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
Data are distributed in a Zip package containing data in CSV format and FGDC metadata in XML and HTML formats.
Compression applied by the 7-Zip utility using default compression (5). The Zip package can be decompressed and unpacked by open source or commercially available unzip tools.
https://doi.org/10.5066/P9DDB01R
None
20220113
U.S. Geological Survey, Alaska Science Center
Mailing and Physical
4210 University Drive
Anchorage
Alaska
99508
USA
907-786-7000
ascweb@usgs.gov
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM)
FGDC-STD-001.1-1999