Harlequin Duck Genetic Data, North America, Greenland, and Iceland, 1945-2006

Identification_Information:

Citation:

Citation_Information:

Originator: Pierson, Barbara J. (ORCID: 0000-0001-8233-874X)
Originator: Scribner, Kim T. (ORCID: 0000-0003-3416-2828)
Originator: Esler, Daniel N. (ORCID: 0000-0001-5501-4555)
Originator: Talbot, Sandra L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 20231024
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: Pierson, B.J., Scribner, K.T., Esler, D.N., Talbot, S.L., 2023, Harlequin Duck genetic data, North America, Greenland, and Iceland, 1945-2006: U.S. Geological Survey data release, https://doi.org/10.5066/P9V2GYIU

Online_Linkage: https://doi.org/10.5066/P9V2GYIU
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, 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=378

Description:

Abstract:

This data package is comprised of three tables with data from wintering Harlequin Ducks (Histrionicus histrionicus) from Alaska, British Columbia, Washington, Maine, Greenland, and Iceland. The first table contains available allele sizes for 7 microsatellite loci (Sfiµ1, Sfiµ4, Sfiµ9, Sfiµ10, Bcaµ10, Hhiµ2, Hhiµ5) and mtDNA control region haplotypes. The second table contains the mtDNA control region sequences used to assign haplotypes. The third table provides the geographic locations of sampling sites.

Purpose:

The data were collected to assess geographic structuring in wintering Harlequin Duck (Histrionicus histrionicus) populations.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1945
Ending_Date: 2006

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

Eastern Russia in the west, Alaska, British Columbia, Washington, Maine, Greenland, and Iceland.

Bounding_Coordinates:

West_Bounding_Coordinate: 141.173
East_Bounding_Coordinate: -16.985
North_Bounding_Coordinate: 65.702
South_Bounding_Coordinate: 44.012

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC566

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_Keyword: Ducks/Geese/Swans

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Waterfowl
Theme_Keyword: Migratory birds
Theme_Keyword: Gene Flow
Theme_Keyword: Population Genetics
Theme_Keyword: Overwintering

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Wildlife
Theme_Keyword: Coastal ecosystems
Theme_Keyword: Wetland ecosystems
Theme_Keyword: Aquatic ecosystems
Theme_Keyword: Marine ecosystems
Theme_Keyword: Genetics
Theme_Keyword: Genetic diversity
Theme_Keyword: Polymerase chain reaction
Theme_Keyword: DNA sequencing

Theme:

Theme_Keyword_Thesaurus: NIH MeSH Thesaurus
Theme_Keyword: DNA
Theme_Keyword: DNA Primers
Theme_Keyword: Alleles
Theme_Keyword: DNA, Mitochondrial
Theme_Keyword: Genetic markers
Theme_Keyword: Microsatellite Repeats
Theme_Keyword: Genotype

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: Harlequin Duck
Theme_Keyword: Histrionicus histrionicus

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System (GNIS)
Place_Keyword: Alaska
Place_Keyword: Alaska Peninsula
Place_Keyword: Amalik Bay
Place_Keyword: Kodiak Island
Place_Keyword: Afognak Island
Place_Keyword: Bear Island
Place_Keyword: Foul Bay
Place_Keyword: Uyak Bay
Place_Keyword: Terror Bay
Place_Keyword: Maine
Place_Keyword: Isle au Haut
Place_Keyword: Merchants Point
Place_Keyword: York Island
Place_Keyword: Pribilof Islands
Place_Keyword: Bay of Isles
Place_Keyword: Channel Island
Place_Keyword: Green Island
Place_Keyword: Main Bay
Place_Keyword: Green Island
Place_Keyword: Port Chalmers
Place_Keyword: Stockdale Harbor
Place_Keyword: Crafton Island
Place_Keyword: Little Green Island
Place_Keyword: Shemya Island
Place_Keyword: Kongkok Bay
Place_Keyword: Powooiliak Bay
Place_Keyword: Siknik Cape
Place_Keyword: Washington
Place_Keyword: Duckabush River
Place_Keyword: Fort Flagler
Place_Keyword: Hamma Hamma River
Place_Keyword: Oak Harbor
Place_Keyword: Protection Island
Place_Keyword: Morse Creek
Place_Keyword: The Cow Pen
Place_Keyword: Little Spoon Island
Place_Keyword: Green Ledge
Place_Keyword: Brimstone Island
Place_Keyword: Uganik Passage
Place_Keyword: Uganik Island
Place_Keyword: Alf Island
Place_Keyword: Knight Island

Place:

Place_Keyword_Thesaurus: NGA GEOnet Names Server
Place_Keyword: Canada
Place_Keyword: British Columbia
Place_Keyword: Hornby Island
Place_Keyword: Quadra Island
Place_Keyword: Strait of Georgia
Place_Keyword: Haida Gwaii
Place_Keyword: Greenland
Place_Keyword: Iceland
Place_Keyword: Kjósarhreppur
Place_Keyword: Bugða
Place_Keyword: Skeiða- og Gnúpverjahreppur
Place_Keyword: Skútustaðahreppur
Place_Keyword: Dalsá
Place_Keyword: Laxá
Place_Keyword: Mývatn
Place_Keyword: Naajarluttuut
Place_Keyword: Ravneøer
Place_Keyword: Sermersooq
Place_Keyword: Russia
Place_Keyword: Sakha
Place_Keyword: Oymyakonskiy Rayon
Place_Keyword: Magadanskaya Oblast
Place_Keyword: Magadan
Place_Keyword: Norðurá
Place_Keyword: Þingeyjarsveit
Place_Keyword: Ljósavatn
Place_Keyword: Húnaþing Vestra
Place_Keyword: Kolbeinsá Stream
Place_Keyword: Hrauná
Place_Keyword: Vatnsdalsá
Place_Keyword: Húnabyggð

Place:

Place_Keyword_Thesaurus: None
Place_Keyword: Dunlop Point
Place_Keyword: Breton Islands
Place_Keyword: Mitlenatch Island
Place_Keyword: Francisco Point
Place_Keyword: Hnausakvísl River

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Histrionicus histrionicus

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
Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomic details retrieved October 22, 2023, from the Integrated Taxonomic Information System online database https://www.itis.gov

Online_Linkage: https://doi.org/10.5066/F7KH0KBK

Taxonomic_Procedures:

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

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
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
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
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
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Anseriformes
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Anatidae
Taxonomic_Classification:

Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Anatinae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Histrionicus
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Histrionicus histrionicus
Applicable_Common_Name: Harlequin Duck
Applicable_Common_Name: TSN: 175149

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

Data_Set_Credit:

Data collection: USGS Alaska Science Center - Molecular Ecology Lab; Department of Fisheries and Wildlife and Department of Integrative Biology, Michigan State University. Funding: Exxon Valdez Oil Spill Trustee Council (Restoration Project No. 98161); Region 5 U.S. Fish and Wildlife Service, Grant 96161; Danish Environmental Protection Agency; Environment and Climate Change Canada; Genome Canada. Many agency collaborators provided samples for this study: Iceland: Glen Howe, aviculturist from Ontario, Canada; Aevar Petersen, Icelandic Institute of Natural History, Reykjavik, Iceland; Arnor Sigfusson. Greenland: Greg Robertson, CWS Newfoundland. Maine: Glen Mittelhauser, Coastal Maine Biological Research Station, RR1, Box 750, Gouldsboro, ME 04607. Washington: Margeret Brown, Wildlife, Fish and Conservation Biology, UC-Davis; Greg Schirato, Washington Department of Fish and Wildlife. British Columbia: Ian Goudie and Ken Wright. Alaska: USGS Alaska Science Center. Katmai (Alaska): Buddy Goatcher, Katmai National Park and Preserve. Kodiak (Alaska): Denny Zwiefelhofer, Kodiak National Wildlife Refuge. Shemya (Alaska): Becky Howard, Alaska Maritime NWR. St. Lawrence Island (Alaska): Shawn W. Stephensen. St. George Island, Pribilofs (Alaska), Kent Sundseth. Museum samples (n=2) from birds wintering in Russia, were obtained from collections at the University of Washington Burke Museum (UWBM) (UWBM:Bird:51871; UWBM:Bird:44446).

Cross_Reference:

Citation_Information:

Originator: Lanctot, R. (ORCID: 0000-0001-9873-0199)
Originator: Goatcher, B.
Originator: Scribner, K.T. (ORCID: 0000-0003-3416-2828)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Esler, D.N. (ORCID: 0000-0001-5501-4555)
Originator: Zwiefelhofer, D.
Publication_Date: 1999
Title:

Harlequin Duck Recovery from the Exxon Valdez Oil Spill: A Population Genetics Perspective

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: The Auk
Issue_Identification: 116(3):781-791

Publication_Information:

Publication_Place: online
Publisher: Oxford Academic

Other_Citation_Details:

Lanctot, R., Goatcher, B., Scribner, K., Talbot, S., Pierson, B., Esler, D., Zwiefelhofer, D., 1999. Harlequin duck recovery from the Exxon Valdez Oil Spill: a population genetics perspective. The Auk 116(3):781–791 doi:10.2307/4089338

Online_Linkage: https://doi.org/10.2307/4089338

Cross_Reference:

Citation_Information:

Originator: Scribner, K.T. (ORCID: 0000-0003-3416-2828)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Robinson, J.D. (ORCID: 0000-0002-9782-1598)
Originator: Lanctot, R.B. (ORCID: 0000-0001-9873-0199)
Originator: Esler, D.N. (ORCID: 0000-0001-5501-4555)
Originator: Dickson, K.M.
Publication_Date: Unknown
Title:

A Phylogeographic Study of the Discontinuously Distributed Harlequin Duck Suggests Recent Expansions from Eastern and Western Refugia

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Ibis
Issue_Identification: .

Publication_Information:

Publication_Place: online
Publisher: British Ornithological Union

Other_Citation_Details:

Scribner, K.T., Talbot, S.L., Pierson, B.J., Robinson, J.D., Lanctot, R.B., Esler, D.N., Dickson, K.M. in prep. A phylogeographic study of the discontinuously distributed Harlequin Duck suggests recent expansions from eastern and western refugia.

Online_Linkage: .

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Individual sample ID's, collection dates, sampling locations, numbers, and reported sex of individual samples provided by collectors were cross-checked and verified to match the accompanying worksheet. Sampling locations were verified with collectors and formally labelled and cross-referenced to the Geographic Names Information Service (GNIS) and NGA Geonet Names Server (GNS) when possible and in reference to official place names otherwise. Genbank accession numbers were cross-referenced to the appropriate individual samples as recorded. We observed sterile techniques in the handling of all DNA, and all procedures were performed with positive and negative controls to provide evidence of replication without contamination. Per laboratory standard operating procedures, if discrepancies occurred, analyses were repeated until the laboratory manager was satisfied results were accurate. This included interlab calibration between USGS MEL and MSU.

Logical_Consistency_Report:

For microsatellite data, reported allele sizes were reviewed to confirm they conform to expected distributions (e.g. dinucleotide repeats with 1 base pair differences were reviewed on gel images with laboratory personnel, gaps in allele sizes were reviewed, z-linked loci were confirmed to have only one allele for females, and single occurrences of an allele size were scrutinized). Interlab calibrations were performed between data gathered at USGS MEL and MSU. Blank cells indicate that no data are available for a particular sample (see Attribute Definitions for details).

Completeness_Report:

Data omissions for particular entities are explained in the Entity and Attribute definitions. Blank data indicates no data were collected or not provided with the sample for a particular attribute. Specifically, collection dates indicated are the most precise dates available given original field sampling information; field sex was not provided with all samples, nor were all field sexes confirmed with a laboratory analysis for all individuals; samples from Iceland had differing scales of geographic sampling resolution when provided to the lab.

Lineage:

Methodology:

Methodology_Type: Field
Methodology_Description:

All samples were collected from non-breeding birds on wintering or molting sites and provided by collaborators. Sampling methods are described in Lanctot et al. (1999).

Methodology:

Methodology_Type: Lab
Methodology_Description:

DNA was extracted as described in Lanctot et al 1999 and Scribner et al 2003 using Puregene Nucleic Acid Extraction Kits (ThermoFisher) and standard proteinase-K phenol-chloroform methods (Sambrook et al. 1989). Extracts were quantified using fluorometry and diluted to 50 ng/uL concentrations prior to pcr amplification.

Methodology:

Methodology_Type: Lab
Methodology_Description:

Six bi-parentally-inherited loci (Bcaμ10, Hhiμ2, Hhiμ5: Buchholz et al. 1998; Sfiμ4: Fields and Scribner 1997; and Sfiμ9 and Sfiμ10: Libants et al.unpubl., GenBank accession number AF180500, AF180499) and one Z-linked locus (Sfiμ1: Fields and Scribner 1997) were pcr amplified and labelled radioactively (see Lanctot et al. 1999) or after 2000, fluorescently labelled (see Scribner et al. 2003). To combine datasets generated at USGS Alaska Science Center MEL and Michigan State University (MSU), samples were exchanged, and sizes calibrated between labs. An approximate 327 base-pair (bp) fragment at the 5' end of the mtDNA control region was amplified following protocols in Lanctot et al. (1999). Amplification, visualization, purification and sequencing of PCR products were performed as described in Lanctot et al. (1999; ASC), or using Epicentre Technologies SequiTherm EXCEL II DNA sequencing kits (Madison, Wisconsin) (MSU/ASC) whereby sequencing products were analyzed on a 3.7% polyacrylamide gel on a LiCor DNA 4200 system and aligned using the LiCor AlignIR program (MSU/ASC). We analyzed 163 bp portion to assign haplotypes.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Lanctot, R.
Originator: Goatcher, B.
Originator: Scribner, K.
Originator: Talbot, S.
Originator: Pierson, B.
Originator: Esler, D.
Originator: Zwiefelhofer, D.
Publication_Date: 1999
Title:

Harlequin Duck Recovery from the Exxon Valdez Oil Spill: A Population Genetics Perspective

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: The Auk
Issue_Identification: 116(3):781–791

Publication_Information:

Publication_Place: online
Publisher: Oxford Academic

Other_Citation_Details:

Online_Linkage: https://doi.org/10.2307/4089338

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1999

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Lanctot et al. 1999
Source_Contribution:

Lab Technique: describes the process for lab techniques, including DNA extraction and microsatellite and mtDNA amplification prior to 1999 (using radioactive labels for both sequence and microsatellite data).

Source_Information:

Source_Citation:

Citation_Information:

Originator: Scribner, K.T.
Originator: Malecki, R.A.
Originator: Batt, B.D.J.
Originator: Inman, R.L.
Originator: Libants, S.
Originator: Prince, H.H.
Publication_Date: 2003
Title:

Identification of Source Population for Greenland Canada Geese: Genetic Assessment of a Recent Colonization

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Condor
Issue_Identification: 105(4):771-782

Publication_Information:

Publication_Place: online
Publisher: Oxford Academic

Other_Citation_Details:

Scribner, K.T., Malecki, R.A., Batt, B.D.J., Inman, R.L., Libants, S., Prince, H.H., 2003. Identification of source population for Greenland Canada Geese: genetic assessment of a recent colonization. Condor 105(4):771-782 doi:10.1093/condor/105.4.771

Online_Linkage: https://doi.org/10.1093/condor/105.4.771

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2003

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Scribner et al. 2003
Source_Contribution:

Lab Technique: describes the process for MSU lab techniques after 1999 (using fluorescent labels for both sequence and microsatellite data).

Source_Information:

Source_Citation:

Citation_Information:

Originator: Scribner, K.T.
Originator: Talbot, S.L.
Originator: Pierson, B.J.
Originator: Robinson, J.D.
Originator: Lanctot, R.B.
Originator: Esler, D.
Originator: Dickson, K.M.
Publication_Date: Unknown
Title:

A Phylogeographic Study of the Discontinuously Distributed Harlequin Duck Suggests Recent Expansions from Eastern and Western Refugia

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Ibis
Issue_Identification: .

Publication_Information:

Publication_Place: online
Publisher: British Ornithological Union

Other_Citation_Details:

Online_Linkage: .

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: Unknown

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Scribner et al. in prep
Source_Contribution: Additional methods details

Source_Information:

Source_Citation:

Citation_Information:

Originator: University of Washington Burke Museum
Publication_Date: Unknown
Title: University of Washington Burke Museum
Geospatial_Data_Presentation_Form: tabular digital data
Other_Citation_Details:

Burke Museum, Genetic Resources, University of Washington, Box 353010 Seattle, WA 98195

Online_Linkage:

https://www.burkemuseum.org/collections-and-research/biology/genetic-resources

Type_of_Source_Media: Digital and/or Hardcopy
Source_Time_Period_of_Content:

Time_Period_Information:

Multiple_Dates/Times:

Single_Date/Time:

Calendar_Date: 19940724

Single_Date/Time:

Calendar_Date: 19920630

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: UWBM
Source_Contribution: Russian samples: UWBM:Bird:51871; UWBM:Bird:44446

Source_Information:

Source_Citation:

Citation_Information:

Originator: Sambrook, J.
Originator: Fritsch, E.R.
Originator: Maniatis, T.
Publication_Date: 1989
Title: Molecular Cloning: A Laboratory Manual
Edition: 2nd
Geospatial_Data_Presentation_Form: publication
Publication_Information:

Publication_Place: Cold Spring Harbor, New York
Publisher: Cold Spring Harbor Laboratory Press

Other_Citation_Details:

Sambrook, J., Fritsch, E. R., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual (2nd ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press

Type_of_Source_Media: Digital and/or Hardcopy
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1989

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Sambrook et al. 1989
Source_Contribution: Phenol-chloroform DNA extraction method

Source_Information:

Source_Citation:

Citation_Information:

Originator: Fields, R.L.
Originator: Scribner, K.T.
Publication_Date: 2003
Title:

Isolation and Characterization of Novel Waterfowl Microsatellite Loci: Cross-Species Comparisons and Research Applications

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Molecular Ecology
Issue_Identification: 6(2):199-202

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Fields, R.L., Scribner, K.T., 2003. Isolation and characterization of novel waterfowl microsatellite loci: cross-species comparisons and research applications. Molecular Ecology 6(2):199-202 doi:10.1046/j.1365-294X.1997.d01-123.x

Online_Linkage: https://doi.org/10.1046/j.1365-294X.1997.d01-123.x

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2003

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Fields and Scribner 2003
Source_Contribution: Sfiμ1 and Sfiμ4 microsatellite loci primer sequences.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Buchholz, W.G.
Originator: Pearce, J.M.
Originator: Pierson, B.J.
Originator: Scribner, K.T.
Publication_Date: 1998
Title:

Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): characterization of a sex-linked (Z-specific) and 14 bi-parentally inherited loci

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Animal Genetics
Issue_Identification: 29(4):322-332

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Buchholz, W.G., J. M. Pearce, B.J. Pierson, K.T. Scribner., 1998. Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): characterization of a sex-linked (Z-specific) and 14 autosomal loci. Animal Genetics 29(4):322-332 doi:10.1046/j.1365-2052.1998.00247.x

Online_Linkage: https://doi.org/10.1046/j.1365-2052.1998.00247.x

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1998

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Buchholz et al. 1998
Source_Contribution: Bcaμ10, Hhiμ2, Hhiμ5 microsatellite primer sequences.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Libants, S.
Originator: Oswald, K.
Originator: Olle, E.
Originator: Scribner, K. (ORCID: 0000-0003-3416-2828)
Publication_Date: 20010210
Title:

Somateria fischeri microsatellite Sfi9 sequence and Somateria fischeri microsatellite Sfi10 sequence

Geospatial_Data_Presentation_Form: tabular digital data
Other_Citation_Details:

Sfiμ9 and Sfiμ10: Libants et al., unpublished data, GenBank accession number AF180499, AF180500

Online_Linkage:

https://www.ncbi.nlm.nih.gov/nuccore/AF180499.1 and https://www.ncbi.nlm.nih.gov/nuccore/AF180500.1

Type_of_Source_Media: Digital and/or Hardcopy
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 20010210

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Libants et al. unpubl.
Source_Contribution: Sfiμ9 and Sfiμ10 microsatellite loci primers.

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:

Detailed sample and sequence information are publicly accessible in the NCBI Genbank database (accession numbers provided in this data package: H_histrionicus_Arctic_mtDNA_Pierson_2023.csv)

Process_Step:

Process_Description:

In order to combine data collected at U.S. Geological Survey Alaska Science Center MEL with that of the Michigan State University MEL, DNA specimens were exchanged, amplified and genotyped with internal standards of known genotypes. Sizing differences were normalized for each microsatellite locus. For mtDNA haplotype data DNA specimens were also exchanged, sequenced in both labs, confirmed that both labs generated the same sequences, and finally that both labs assigned matching haplotype labels.

Process_Date: Unknown

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

Place names, geographic descriptions, and geographic coordinates do not represent exact sample collection locations. They are provided only as an indicator of the general sampling areas. The degree of geographic specificity is variable.

Direct_Spatial_Reference_Method: Point

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Geographic:

Latitude_Resolution: 0.1
Longitude_Resolution: 0.1
Geographic_Coordinate_Units: Decimal degrees

Geodetic_Model:

Horizontal_Datum_Name: World Geodetic System of 1984 (WGS84)
Ellipsoid_Name: World Geodetic System of 1984 (WGS84)
Semi-major_Axis: 6378137
Denominator_of_Flattening_Ratio: 298.257223563

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: harlequinDuck_sampleLocation_holarctic_pierson.csv
Entity_Type_Definition:

Table with sample location details, including geographic descriptions and approximate geographic coordinates. The degree of geographic specificity is variable and geographic coordinates do not represent exact sample collection locations. They are provided only as an indicator of the general sampling areas. Location details of sample locales in Iceland could not be resolved or confirmed and are presented generally for the entire island. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: locale
Attribute_Definition:

Place name of sampling location, as provided with the sample. The degree of geographic specificity is highly variable. Corresponds with the "locale" column in all tables included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Place name of sampling location, as provided with the sample.

Attribute:

Attribute_Label: state_province
Attribute_Definition:

The governmental region of the sampling location, if provided with the sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

The governmental region of the sampling location, if provided with the sample.

Attribute:

Attribute_Label: country
Attribute_Definition: Name of the country where the sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Name of the country where the sample was collected.

Attribute:

Attribute_Label: locale_description
Attribute_Definition:

A brief generalized geographic description of the sampling location. The degree of geographic specificity is highly variable and does not represent exact sample collection locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

A brief generalized geographic description of the sampling location.

Attribute:

Attribute_Label: approximate_lat
Attribute_Definition:

Approximate latitude of the sampling location. The degree of geographic specificity is highly variable and does not represent exact sample collection locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 44.01
Range_Domain_Maximum: 65.7
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Attribute:

Attribute_Label: approximate_lon
Attribute_Definition:

Approximate longitude of the sampling locale. The degree of geographic specificity is highly variable and does not represent exact sample collection locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -171.8
Range_Domain_Maximum: 174.1
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Detailed_Description:

Entity_Type:

Entity_Type_Label: harlequinDuck_microsat_holarctic_pierson.csv
Entity_Type_Definition:

Table sample details, associated manuscripts, population, and allele scores (in base pairs) for 6 autosomal and 1 z-linked (Sfiµ1) microsatellite loci and mtDNA control region haplotype designation. Locus names and order of presentation: Sfiµ1, Sfiµ4, Sfiµ9, Sfiµ10, Bcaµ10, Hhiµ2, Hhiµ5, mtDNA haplotype. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: country
Attribute_Definition: Name of the country where the sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Name of the country where the sample was collected.

Attribute:

Attribute_Label: state_province
Attribute_Definition:

The governmental region of the sampling location, if provided with sample. Blank cells indicate that data were not provided with the sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

The governmental region of the sampling location, if provided with sample.

Attribute:

Attribute_Label: locale
Attribute_Definition:

Place name of sampling locale, as provided with the sample. The degree of geographic specificity is highly variable. Additional details, including geographic descriptions and approximate coordinates are provided in the table "harlequinDuck_sampleLocation_holarctic_pierson.csv" included with this data package. Blank cells indicate that data were not provided with the sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place name of sampling locale, as provided with the sample. Corresponds with the "locale" attribute in all tables included with this data package.

Attribute:

Attribute_Label: sampling_date
Attribute_Definition:

The sampling date or date range provided with samples. Dates provided vary from 4 digit years represented in YYYY form to specific dates represented by YYYYMMDD or date range in YYYYMMDD-YYMMDD form.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 1945
Range_Domain_Maximum: 2006
Attribute_Units_of_Measure: date

Attribute:

Attribute_Label: manuscript
Attribute_Definition:

This indicates which data were used in analyses found in Scribner et al. in prep.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: notincld
Enumerated_Domain_Value_Definition:

This indicates data that were not included in Scribner et al. in prep.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: mtnuc
Enumerated_Domain_Value_Definition:

This indicates that both mitochondrial DNA haplotype and nuclear microsatellite data were included in analyses in Scribner et al. in prep.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: mt
Enumerated_Domain_Value_Definition:

This indicates that only mitochondrial DNA haplotype was included in analyses in Scribner et al. in prep.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: nuc
Enumerated_Domain_Value_Definition:

This indicates that only nuclear microsatellite data were included in analyses in Scribner et al. in prep.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: disconly
Enumerated_Domain_Value_Definition:

This indicates that the mitochondrial DNA haplotype was not included in population analyses, but was included for haplotype distribution context in Scribner et al. in prep.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: population
Attribute_Definition:

The population groupings to which samples were assigned for population genetic analyses (based on sampling location).

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: The population groupings to which samples were assigned.

Attribute:

Attribute_Label: field_ID
Attribute_Definition:

The field_ID provided to the lab with the sample (such as the last 5 digits of the USGS tarsal band, or other marker). Blank cells indicate that the field_ID provided was used as the lab_ID.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

These are any combination of numeric or alphanumeric labels on the samples at time of receipt in the lab.

Attribute:

Attribute_Label: lab_ID
Attribute_Definition:

Labels assigned to samples and used to track samples through laboratory analyses.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

These are any combination of numeric or alphanumeric labels on the samples used in laboratory analyses.

Attribute:

Attribute_Label: sex
Attribute_Definition: Sex provided with samples.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: U
Enumerated_Domain_Value_Definition: Sex unknown
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: sample_ID
Attribute_Definition:

Labels assigned to samples and used to track samples in data analyses.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

These are any combination letter code for the population and unique number.

Attribute:

Attribute_Label: Sfiµ1_allele1 through Hhiµ5_allele2
Attribute_Definition:

These 14 columns represent 7 microsatellite loci. Each microsatellite locus genotype is represented by two adjacent columns (i.e., allele1 and allele2) each containing one allele score. Blank cells indicate that data were not collected for the sample.

Genotype numbers were determined by scoring based on allele size relative to an M13 DNA sequence ladder and to samples established as size standards that were run on each gel. A blank cell indicates data were not collected at this locus for that sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Allele scores (nucleotide base pairs) for each microsatellite locus.

Attribute:

Attribute_Label: mtDNA
Attribute_Definition:

Unique identifiers for 17 mtDNA haplotypes based on site substitutions at 18 sites in 162 base pairs sequenced from harlequin ducks referenced in Lanctot et al. 1999 and Scribner et al. in prep. Blank cells indicate that an mtDNA haplotype was not assigned for the sample.

Haplotype details (including NCBI Genbank Accession numbers and mtDNA control region sequences) are provided in the table "harlequinDuck_mtDNA_holarctic_pierson.csv" included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifiers for 17 mtDNA haplotypes (A-R). Haplotype IDs correspond with IDs in all tables included with this data package.

Detailed_Description:

Entity_Type:

Entity_Type_Label: harlequinDuck_mtDNA_holarctic_pierson.csv
Entity_Type_Definition:

Table with mtDNA haplotype details, including Genbank_accession and sequences for 17 mtDNA control region sequences delineated for this data release. mtDNA haplotypes were assigned based on site substitutions at 18 sites in 162 base pairs sequenced from harlequin ducks referenced in Lanctot et al. 1999 and Scribner et al. in prep. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: haplotype
Attribute_Definition:

Unique identifiers for 17 mtDNA haplotypes (A-R). Haplotype IDs correspond with IDs in all tables included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifiers for 17 mtDNA haplotypes (A-R). Haplotype IDs correspond with IDs in all tables included with this data package.

Attribute:

Attribute_Label: GenBank_accession
Attribute_Definition:

GenBank Accession Number. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) of the Harlequin Duck mtDNA 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 haplotypes that were not submitted to Genbank before sequences less than 250 base pairs were no longer accepted by NCBI.

Attribute_Definition_Source: NCBI GenBank
Attribute_Domain_Values:

Unrepresentable_Domain:

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

Attribute:

Attribute_Label: sequence
Attribute_Definition:

Nucleotide sequence for 162 base pairs of mtDNA control region mtDNA.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Nucleotide sequence for 162 base pairs of mtDNA control region mtDNA.

Harlequin Duck Genetic Data, North America, Greenland, and Iceland, 1945-2006

Metadata: