Development of Single Nucleotide Polymorphisms (SNPs) in Greater-White Fronted Geese (Anser albifrons) for Genetic Stock Identification on Wintering Grounds, 2019

Identification_Information:

Citation:

Citation_Information:

Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Ely, C.R. (ORCID: 0000-0003-4262-0892)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 20190422
Title:

Geospatial_Data_Presentation_Form: tabular digital data
Publication_Information:

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

Other_Citation_Details:

Suggested citation: Wilson, R.A., Pierson, B.J., Sonsthagen, S.A., Ely, C.R., and Talbot, S.L., 2019, Development of Single Nucleotide Polymorphisms (SNPs) in Greater-White Fronted Geese (Anser albifrons) for genetic stock identification on wintering grounds, 2019: U.S. Geological Survey data release, https://doi.org/10.5066/P9LYUFRH

Online_Linkage: https://doi.org/10.5066/P9LYUFRH
Larger_Work_Citation:

Citation_Information:

Originator: U.S. Geological Survey, Alaska Science Center
Publication_Date: 2000
Title:

Developing and Applying Molecular Tools to Natural Resource Problems in Alaska

Geospatial_Data_Presentation_Form: website
Series_Information:

Series_Name: Alaska Science Portal
Issue_Identification: 378

Publication_Information:

Publication_Place: Anchorage, AK
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=378

Description:

Abstract:

This data set contains a description of 3 mitochondrial DNA and 93 nuclear DNA Single Nucleotide Polymorphism (SNP) loci and sequence information developed through double digest restriction-site associated DNA sequencing (ddRADseq) techniques for Greater White-Fronted Goose (Anser albifrons) that winter in California.

Purpose:

The panel was developed as a tool to differentiate Tule White-Fronted Geese (Anser albifrons elgasi) from other Greater White-Fronted Geese that winter in California.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2016
Ending_Date: 2019

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: Unknown

Spatial_Domain:

Description_of_Geographic_Extent:

These data are from laboratory characterization of genetic sequences; geographic description does not pertain.

Bounding_Coordinates:

West_Bounding_Coordinate: -180.0
East_Bounding_Coordinate: 180.0
North_Bounding_Coordinate: 90.0
South_Bounding_Coordinate: -90.0

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC208

Theme:

Theme_Keyword_Thesaurus: NASA GCMD Earth Science Keywords Thesaurus
Theme_Keyword: Biological Classification
Theme_Keyword: Animals/Vertebrates
Theme_Keyword: Ducks/Geese/Swans

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Genetic Diversity
Theme_Keyword: Biodiversity
Theme_Keyword: Population Genetics
Theme_Keyword: Genetic Variance

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme_Keyword: environment

Theme:

Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: Animals
Theme_Keyword: Geese
Theme_Keyword: DNA
Theme_Keyword: DNA, Mitochondrial
Theme_Keyword: Polymorphism, Single Nucleotide

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Sciences
Theme_Keyword: Life Sciences
Theme_Keyword: Genetics
Theme_Keyword: Morphology (biological)
Theme_Keyword: Systematics and taxonomy
Theme_Keyword: Biological Population Management
Theme_Keyword: Game Species

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Anser albifrons
Taxonomic_Keywords: Anser albifrons elgasi
Taxonomic_Keywords: Anser albifrons frontalis
Taxonomic_Keywords: Anser albifrons flavirostris
Taxonomic_Keywords: Anser albifrons albifrons

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: Integrated Taxonomic Information System
Publication_Date: Unknown
Title: Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Publication_Information:

Publication_Place: Online
Publisher: ITIS-North America

Other_Citation_Details:

Retrieved March 8, 2019, from the Integrated Taxonomic Information System on-line database http://www.itis.gov

Online_Linkage: http://www.itis.gov/

Taxonomic_Procedures:

Data presented are not derived from unknown samples, rather data are presented for use in identifying samples to source species in future studies.

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Applicable_Common_Name: animals
Taxonomic_Classification:

Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:

Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:

Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Applicable_Common_Name: chordates
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Applicable_Common_Name: vertebrates
Taxonomic_Classification:

Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:

Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Aves
Applicable_Common_Name: Birds
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Anseriformes
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Anatidae
Applicable_Common_Name: Ducks
Applicable_Common_Name: Geese
Applicable_Common_Name: Swans
Taxonomic_Classification:

Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Anserinae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Anser
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Anser albifrons
Applicable_Common_Name: Greater White-fronted Goose
Applicable_Common_Name: TSN: 175020
Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Anser albifrons elgasi
Applicable_Common_Name: Tule Goose
Applicable_Common_Name: TSN: 714772

Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Anser albifrons frontalis
Applicable_Common_Name: Pacific White-Fronted Goose
Applicable_Common_Name: TSN: 175021

Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Anser albifrons flavirostris
Applicable_Common_Name: Greenland White-Fronted Goose
Applicable_Common_Name: TSN: 175023

Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Anser albifrons albifrons
Applicable_Common_Name: European White-Fronted Goose
Applicable_Common_Name: TSN: 714771

Access_Constraints: None
Use_Constraints:

If you use these data in a publication, presentation, or other product, it is requested that you credit USGS and the authors of this data for their contribution to your work.

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

Data_Set_Credit:

U.S. Geological Survey, Alaska Science Center, Anchorage, AK

Core Genomics Facility, Tufts University, Boston, MA

Fluidigm Corporation, South San Francisco, CA

Cross_Reference:

Citation_Information:

Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: DaCosta, J.M.
Originator: Ely, C.R. (ORCID: 0000-0003-4262-0892)
Originator: Sorenson, M.D.
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 2019
Title:

Identification of Single Nucleotide Polymorphisms for Use in a Genetic Stock Identification System for Greater White-Fronted Goose (Anser albifrons) Subspecies Wintering in California

Geospatial_Data_Presentation_Form: document
Series_Information:

Series_Name: U.S. Geological Survey Open-File Report
Issue_Identification: 2019-1040

Publication_Information:

Publication_Place: online
Publisher: U.S. Geological Survey

Other_Citation_Details:

Wilson, R.E., Sonsthagen, S.A., DaCosta, J.M., Ely, C.R., Sorenson, M.D., Talbot, S.L. 2019. Identification of Single Nucleotide Polymorphisms for Use in a Genetic Stock Identification System for Greater White-Fronted Goose (Anser albifrons) Subspecies Wintering in California: U.S. Geological Survey Open-File Report 2019-1040, https://doi.org/10.3133/ofr20191040

Online_Linkage: https://doi.org/10.3133/ofr20191040

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Attributes are an exact copy of documentation minus uninformative columns provided by Fluidigm Corporation, South San Franciso, accompanying the final SNP panel. The addition of an attribute listing the target genome (GENOME) was cross-checked with double digest restriction site associated DNA sequencing (ddRADseq) data and verified to match the target genome on the accompanying worksheet.

Logical_Consistency_Report:

All data presented fall within expected norms as descriptors of a SNP panel.

Completeness_Report:

Data for all 96 SNPs are present and complete for all attributes.

Lineage:

Methodology:

Methodology_Type: Lab
Methodology_Description:

ddRADseq library preparation followed Wilson et al 2019 with a portion of the samples documented in Wilson 2018.

Methodology:

Methodology_Type: Lab
Methodology_Description:

Multiplexed libraries were sequenced with a single-end 150-base pair run on an Illumina HiSeq 2500 at the Tufts University, Core Genomics Facility, Boston, MA.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Wilson, R.E.
Originator: Sonsthagen, S.A.
Originator: DaCosta, J.M.
Originator: Ely, C.R.
Originator: Sorenson, M.D.
Originator: Talbot, S.L.
Publication_Date: 2019
Title:

Identification of Single Nucleotide Polymorphisms for Use in a Genetic Stock Identification System for Greater White-Fronted Goose (Anser albifrons) Subspecies Wintering in California

Geospatial_Data_Presentation_Form: document
Series_Information:

Series_Name: U.S. Geological Survey Open-File Report
Issue_Identification: 2019-1040

Publication_Information:

Publication_Place: online
Publisher: U.S. Geological Survey

Other_Citation_Details:

Online_Linkage: https://doi.org/10.3133/ofr20191040

Type_of_Source_Media: online
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2019

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Wilson et al 2019
Source_Contribution: Detailed methodology can be found within this report.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Wilson, R.E.
Publication_Date: 2018
Title:

Greater White-Fronted Goose genetic data, circumpolar, 1988-2009 (ver. 2.0, July 2018)

Geospatial_Data_Presentation_Form: tabular digital data
Series_Information:

Series_Name: U.S. Geological Survey data release
Issue_Identification: ver. 2.0, July 2018

Publication_Information:

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

Other_Citation_Details:

Wilson, R.E., 2018, Greater White-Fronted Goose genetic data, circumpolar, 1988-2009 (ver. 2.0, July 2018): U.S. Geological Survey data release, https://doi.org/10.5066/F71G0JGN

Online_Linkage: https://doi.org/10.5066/F71G0JGN

Type_of_Source_Media: online
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2018

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Wilson 2018
Source_Contribution:

Sample documentation for samples used in double digest restriction-site associated DNA sequencing (ddRADseq) portion of the lab work.

Process_Step:

Process_Description:

Pairwise phi-st and nucleotide diversity of each ddRAD-seq locus were calculated and used along with a Principle Components Analysis (PCA) to identify loci for a 96-locus SNP Fluidigm Corporation EP1 (trademarked) Genotyping System Panel. Loci with elevated phi-st and high contribution PCA results were further evaluated per Fluidigm guidelines and reduced to 93 nuclear and three mtDNA SNPs to be included in the panel. Allele frequencies for Tule only, Pacific Flyway minus Tule Geese and Mid-Continent Flyway were derived from double digest restriction-site associated DNA sequencing (ddRADseq) results to aid selection of SNPs to be included. Detailed methodology can be found in Wilson et al (2019).

Source_Used_Citation_Abbreviation: Wilson et al 2019
Process_Date: Unknown

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: whiteFrontedGoose_SNPS_Wilson_2019
Entity_Type_Definition:

This entity is a CSV worksheet with label, target, polymorphism, SNP sequence, primer sequences, and GC content for 96 SNPs found in Greater-White Fronted Geese.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: SNP_NAME
Attribute_Definition: Name of the target SNP locus.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain: This is an alphanumeric unique identifier for each SNP.

Attribute:

Attribute_Label: GENOME
Attribute_Definition: Genome (mitochondrial or nuclear) containing the target SNP
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: mitochondrial
Enumerated_Domain_Value_Definition: Indicates SNP is located within the mitochondrial genome.
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: nuclear
Enumerated_Domain_Value_Definition: Indicates SNP is located within the nuclear genome.
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: ALLELE_1
Attribute_Definition:

The single-nucleotide base difference (G, A, T, or C) found in variant 1 of a particular SNP locus.

Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: G
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 1 of a particular SNP locus is guanine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: A
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 1 of a particular SNP locus is adenine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: T
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 1 of a particular SNP locus is thymine.

Enumerated_Domain_Value_Definition_Source: Author defined.

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: C
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 1 of a particular SNP locus is cytosine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: -
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 1 of a particular SNP locus is a gap.

Enumerated_Domain_Value_Definition_Source: Author defined.

Attribute:

Attribute_Label: ALLELE_2
Attribute_Definition:

The single-nucleotide base difference (G, A, T, or C) found in variant 2 of a particular SNP locus.

Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: G
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 2 of a particular SNP locus is guanine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: A
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 2 of a particular SNP locus is adenine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: T
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 2 of a particular SNP locus is thymine.

Enumerated_Domain_Value_Definition_Source: Author defined.

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: C
Enumerated_Domain_Value_Definition:

The single-nucleotide base difference found in variant 2 of a particular SNP locus is cytosine.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: SNP_SEQ
Attribute_Definition: Nucleotide sequences containing a particular target SNP.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain:

Nucleotide sequences containing a particular target SNP located within brackets ([ ]) with allele 1 separated from allele 2 by a slash (/).

Attribute:

Attribute_Label: ASP1_SEQ
Attribute_Definition: Allele-specific primer 1 sequence.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain:

The nucleotide sequences for the allele-specific primer that amplifies Allele 1 in a particular SNP locus.

Attribute:

Attribute_Label: ASP2_SEQ
Attribute_Definition: Allele-specific primer 2 sequence.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain:

The nucleotide sequences for the allele-specific primer that amplifies Allele 2 in a particular SNP locus.

Attribute:

Attribute_Label: LSP_SEQ
Attribute_Definition: Locus specific primer sequence.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain:

The nucleotide sequences for the locus-specific primer that, along with the two allele-specific primers (ASP1_SEQ and ASP2_SEQ) for a standard allele-specific assay, or with a STA_SEQ primer for specific target amplification assay, to amplify a specific SNP locus in a Fluidigm SNP Type genotyping assay.

Attribute:

Attribute_Label: STA_SEQ
Attribute_Definition: Specific target amplification sequences.
Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Unrepresentable_Domain:

Primer sequence for use along with LSP (locus specific primers) in Fluidigm STA assays. STA is an assay used in a Fluidigm SNP Type assay that amplifies a subset of a target SNP from low-quality DNA samples to increase the likelihood that more DNA will be amplified in downstream PCR reactions that use allele-specific primers.

Attribute:

Attribute_Label: GC_CONTENT
Attribute_Definition:

The guanine-cytosine content of the SNP_SEQ; that is, the proportion of nitrogenous bases in the SNP_SEQ that are either a guanine or cytosine.

Attribute_Definition_Source: Fluidigm Corporation, South San Francisco, CA
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0.27
Range_Domain_Maximum: 0.76

Development of Single Nucleotide Polymorphisms (SNPs) in Greater-White Fronted Geese (Anser albifrons) for Genetic Stock Identification on Wintering Grounds, 2019

Metadata: