Rusty Blackbird (Euphagus carolinus) Genetic Data, North America

Identification_Information:

Citation:

Citation_Information:

Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Matsuoka, S.M. (ORCID: 0000-0001-6415-1885d)
Originator: Johnson, J.A. (ORCID: 0000-0002-2312-0633)
Originator: Demarest, D.W.
Originator: Stralberg, D. (ORCID: 0000-0003-4900-024X)
Originator: Powell, L.L. (ORCID: 0000-0002-2001-4982)
Publication_Date: 20210301
Title:

Geospatial_Data_Presentation_Form: tabular digital data
Publication_Information:

Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey, Alaska Science Center

Other_Citation_Details:

Suggested Citation: Sonsthagen, S.A., Wilson, R.E., Matsuoka, S.M., Johnson, J.A., Demarest, D.W., Stralberg, D., Powell, L.L., 2021, Rusty blackbird (Euphagus carolinus) genetic data, North America: U.S. Geological Survey data release, https://doi.org/10.5066/F7T43R9Q

Online_Linkage: https://doi.org/10.5066/F7T43R9Q
Larger_Work_Citation:

Citation_Information:

Originator: U.S. Geological Survey, Alaska Science Center
Publication_Date: 2015
Title: Genomics of Wildlife
Geospatial_Data_Presentation_Form: website
Series_Information:

Series_Name: Alaska Science Portal
Issue_Identification: 416

Publication_Information:

Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey, Alaska Science Center

Other_Citation_Details:

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.

Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=416

Description:

Abstract:

This data set provides NCBI accession numbers for nucleotide sequence data derived from a mitochondrial DNA locus (control region) and double digest restriction-site associated DNA (ddRAD).

Purpose: To examine genetic structure in rusty blackbird.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2005
Ending_Date: 2018

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

Alaska, USA, east to Newfoundland, Canada, and south to New Hampshire, USA.

Bounding_Coordinates:

West_Bounding_Coordinate: -161.7
East_Bounding_Coordinate: 57.3
North_Bounding_Coordinate: 66.3
South_Bounding_Coordinate: 44.7

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC356

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: Biota
Theme_Keyword: Environment

Theme:

Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keyword Thesaurus
Theme_Keyword: Animals/Vertebrates
Theme_Keyword: Birds

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Songbirds
Theme_Keyword: Migratory birds
Theme_Keyword: Gene flow
Theme_Keyword: Population genetics

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Wildlife
Theme_Keyword: Wetland ecosystems
Theme_Keyword: Migratory species
Theme_Keyword: Genetics
Theme_Keyword: Polymerase chain reaction

Theme:

Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: DNA
Theme_Keyword: DNA, Mitochondrial
Theme_Keyword: Genetic markers
Theme_Keyword: Polymorphism, SNP

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: Genetic structure
Theme_Keyword: Rusty blackbird
Theme_Keyword: Euphagus carolinus

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: Alaska
Place_Keyword: New Hampshire
Place_Keyword: Vermont

Place:

Place_Keyword_Thesaurus: NGA GEOnet Names Server
Place_Keyword: Alberta
Place_Keyword: Manitoba
Place_Keyword: Ontario
Place_Keyword: Yukon Territory
Place_Keyword: Newfoundland
Place_Keyword: Nova Scotia
Place_Keyword: New Brunswick

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals
Taxonomic_Keywords: Birds
Taxonomic_Keywords: Songbirds

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: ITIS Integrated Taxonomic Information System
Publication_Date: Unknown
Title: ITIS Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: online database
Series_Information:

Series_Name: Taxonomic Serial Number
Issue_Identification: TSN 179091

Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomic details for rusty blackbird were retrieved February 4, 2021, from the Integrated Taxonomic Information System on-line database https://www.itis.gov

Online_Linkage: https://www.itis.gov

Taxonomic_Procedures:

Species were identified by skilled observers in the field based on general appearance of feathers and plumage, behavior, and vocalization.

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:

Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertabrata
Taxonomic_Classification:

Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Aves
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Passeriformes
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Icteridae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Euphagus
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Euphagus carolinus
Applicable_Common_Name: Rusty Blackbird
Applicable_Common_Name: TSN 179091

Access_Constraints: None
Use_Constraints:

It is requested that the authors and the USGS Alaska Science Center be cited for any subsequent publications that reference this dataset.

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Alaska Science Center

Contact_Address:

Address_Type: Mailing and Physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA

Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov

Cross_Reference:

Citation_Information:

Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Matsuoka, S.M. (ORCID: 0000-0001-6415-1885d)
Originator: Powell, L.L. (ORCID: 0000-0002-2001-4982)
Originator: Johnson, J.A. (ORCID: 0000-0002-2312-0633)
Originator: Demarest, D.W.
Originator: Stralberg, D. (ORCID: 0000-0003-4900-024X)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Publication_Date: 2021
Title:

Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: the rusty blackbird

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Diversity
Issue_Identification: 13(3):103

Publication_Information:

Publication_Place: online
Publisher: MDPI journals

Other_Citation_Details:

Suggested citation: Wilson, R.E., Matsuoka, S.M., Powell, L.L., Johnson, J.A., Demarest, D.W., Stralberg, D., Sonsthagen, S.A. 2021. Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: the rusty blackbird. Diversity 13(3):103 doi:10.3390/d13030103

Online_Linkage: https://doi.org/10.3390/d13030103

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Identifying information about samples were cross-checked with original field data. Polymerase chain reaction (PCR) amplification and electrophoresis followed protocols described in Sonsthagen et al 2007. Quality control (QC) included a minimum of 20% re-extraction and PCR replication for each locus and all laboratory techniques were performed using sterile procedures. All duplicate characterizations of the same individual resulted in concordant data. NCBI BioSample and GenBank numbers were cross-referenced to the appropriate samples in attributes.

Logical_Consistency_Report: Attribute values fall within expected ranges.
Completeness_Report:

Data set is complete. No data were omitted and there are no missing data.

Lineage:

Methodology:

Methodology_Type: Field
Methodology_Description:

Blood samples were collected from the brachial vein and stored in preservation buffer.

Methodology:

Methodology_Type: Lab
Methodology_Description:

DNA was extracted using a Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Düsseldorf, Germany) following manufacturer’s protocol.

Methodology:

Methodology_Type: Lab
Methodology_Description:

Polymerase chain reaction (PCR) amplification and sequencing of mitochondrial DNA followed Sonsthagen et al 2007. For quality control purposes, we extracted, amplified, and genotyped, 20% of the samples in duplicate.

Methodology:

Methodology_Type: Lab
Methodology_Description:

Double digest restriction-site associated DNA (ddRAD) library preparation, sequencing, assembly of reads, and alignment of loci followed DaCosta and Sorenson 2014. DNA was digested with two restriction enzymes SfbI and EcoRI and ligated adapters included dual indices. Libraries were size-selected (size range 300–450 base pairs), amplified for 20 cycles, and single-end sequenced (150 base pairs) on an Illumina HiSeq 2500 at the Tufts University Core Genomics Facility. Raw data were uploaded to NCBI Short Read Archive.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Sonsthagen, S.A.
Originator: Talbot, S.L.
Originator: McCracken, K.G.
Publication_Date: 2007
Title:

Genetic characterization of common eiders (Somateria mollissima) breeding on the Yukon-Kuskokwim Delta, Alaska

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Condor
Issue_Identification: 109(4):879–894

Publication_Information:

Publication_Place: Oxford, UK
Publisher: Oxford University Press

Other_Citation_Details:

Sonsthagen, S.A., Talbot, S.L., McCracken, K.G. 2007. Genetic characterization of common eiders (Somateria mollissima) breeding on the Yukon-Kuskokwim Delta, Alaska. Condor 109(4):879–894

Online_Linkage: http://www.jstor.org/stable/40072332

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2007

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Sonsthagen et al 2007
Source_Contribution:

Laboratory Technique Citation: describes DNA extraction, polymerase chain reaction (PCR) amplification and electrophoresis and sequencing protocols.

Source_Information:

Source_Citation:

Citation_Information:

Originator: DaCosta, J.M.
Originator: Sorenson, M.D.
Publication_Date: 2014
Title:

Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: PLoS ONE
Issue_Identification: 9(9):e106713

Publication_Information:

Publication_Place: online
Publisher: Public Library of Science (PLoS)

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1371/journal.pone.0106713

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2014

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: DaCosta and Sorenson 2014
Source_Contribution:

Laboratory Technique Citation: describes double-digest restriction associated DNA sequence library preparation and read assembly protocol.

Source_Information:

Source_Citation:

Citation_Information:

Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: BioSample
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://www.ncbi.nlm.nih.gov/biosample/

Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2020

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI BioSample
Source_Contribution:

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).

Source_Information:

Source_Citation:

Citation_Information:

Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: GenBank
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://www.ncbi.nlm.nih.gov/genbank

Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2020

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI GenBank
Source_Contribution:

Sequence information are publicly accessible in the NCBI Genbank database (accession numbers provided in this data package).

Process_Step:

Process_Description:

Raw Illumina reads were de-multiplexed and processed using DaCosta and Sorenson (2014) pipelines.

Process_Date: Unknown

Process_Step:

Process_Description:

Raw read data generated in this study were submitted to the NCBI short read archive publicly available high throughput sequence data database.

Process_Date: Unknown
Source_Produced_Citation_Abbreviation: NCBI SRA

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

States and providences are listed to describe generalized field sampling locations.

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: rustyBlackbird_geneticData_sonsthagen
Entity_Type_Definition:

Table with sample identifying information, sample location data, NCBI BioSample accession numbers, and NCBI GenBank accession numbers. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: Sample_ID
Attribute_Definition: Unique laboratory label for each individual characterized.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique alphanumeric label assigned by the laboratory for materials originating from a single individual.

Attribute:

Attribute_Label: Sample_Location
Attribute_Definition:

Place names of sample collection site. Latitudes and longitudes are provided for general geographic location and are not necessarily specific sampling locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Bethel, Alaska
Enumerated_Domain_Value_Definition: Samples collected in Bethel, Alaska, USA (approx 60.8N, 161.8W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Anchorage, Alaska
Enumerated_Domain_Value_Definition:

Samples collected in Anchorage, Alaska, USA (approx 61.2N, 149.9W)

Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Cordova, Alaska
Enumerated_Domain_Value_Definition:

Samples collected in Cordova, Alaska, USA (approx 60.5N, 145.7W)

Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Tetlin, Alaska
Enumerated_Domain_Value_Definition: Samples collected in Tetlin, Alaska, USA (approx 63.1N, 142.5W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Tanana, Alaska
Enumerated_Domain_Value_Definition: Samples collected in Tanana, Alaska, USA (approx 64.7N, 147.9W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Yukon Flats, Alaska
Enumerated_Domain_Value_Definition:

Samples collected in Yukon Flats, Alaska, USA (approx 66.3N, 145.8W)

Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Yukon Territory
Enumerated_Domain_Value_Definition:

Samples collected in Yukon Territory, Canada (approx 60.7N, 135.2W)

Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Alberta
Enumerated_Domain_Value_Definition: Samples collected in Alberta, Canada (approx 53.5N, 113.5W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Manitoba
Enumerated_Domain_Value_Definition: Samples collected in Manitoba, Canada (approx 58.7N, 94.2W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Ontario
Enumerated_Domain_Value_Definition: Samples collected in Ontario, Canada (approx 46.3N, 79.1W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Nova Scotia
Enumerated_Domain_Value_Definition: Samples collected in Nova Scotia, Canada (approx 44.5N, 65.3W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: New Brunswick
Enumerated_Domain_Value_Definition:

Samples collected in New Brunswick, Canada (approx 46.1N, 67.1W)

Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: New Hampshire
Enumerated_Domain_Value_Definition: Samples collected in New Hampshire, USA (approx 45.0N, 71.3W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Vermont
Enumerated_Domain_Value_Definition: Samples collected in Vermont, USA (approx 44.7N, 71.7W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Newfoundland
Enumerated_Domain_Value_Definition: Samples collected in Newfoundland, Canada (approx 49.8N, 57.3W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute:

Attribute_Label: NCBI_BioSample
Attribute_Definition:

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.

Attribute_Definition_Source: NCBI BioSample
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier: an alphanumeric accession number available in the NCBI BioSample database.

Attribute:

Attribute_Label: GenBank_Accession
Attribute_Definition:

GenBank Accession Number. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) of the mitochondrial DNA control region nucleotide sequence. This number may be used to retrieve detailed sample and sequence information from the NCBI GenBank database https://www.ncbi.nlm.nih.gov/genbank Blank cells indicate that sequence data from this locus were not collected for this sample.

Attribute_Definition_Source: NCBI GenBank accession
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier: an alphanumeric accession number available in the NCBI GenBank database.

Distribution_Information:

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Alaska Science Center

Contact_Address:

Address_Type: Mailing and Physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA

Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov

Resource_Description:

The U.S. Geological Survey, Alaska Science Center is the authoritative source and distributor of these data.

Distribution_Liability:

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.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name: CSV
Format_Information_Content:

Data are distributed in a Zip package containing data in CSV format and FGDC metadata in XML and HTML formats.

File_Decompression_Technique:

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.

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name: https://doi.org/10.5066/F7T43R9Q

Fees: None

Rusty Blackbird (Euphagus carolinus) Genetic Data, North America

Metadata: