Scoter (Melanitta sp.) ddRAD SNP and Microsatellite Genetic Data, North America and Europe, 1977-2012

Identification_Information:

Citation:

Citation_Information:

Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Pierson, B.J. (ORCID: 0000-0001-8233-874X)
Originator: Wilson, R.E. (ORCID: 0000-0003-1800-0183)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 20200710
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., Pierson, B.J., Wilson, R.E., and Talbot, S.L., 2020, Scoter (Melanitta sp.) ddRAD SNP and microsatellite genetic data, North America and Europe, 1977-2012: U.S. Geological Survey data release, https://doi.org/10.5066/P9W7H2JK

Online_Linkage: https://doi.org/10.5066/P9W7H2JK
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 set contains sampling information, allele sizes of 11 microsatellite loci, and Genbank accession numbers of ddRAD seq results for scoters (Melanitta sp.). Microsatellite data is provided for three North American species of scoter (black scoter, M. americana n = 61; white-winged scoter, M. deglandi, n = 208 ; surf scoter, M. perspicillata, n = 145) and their European congeners (common scoter, M. nigra, n = 19; velvet scoter, M. fusca, n = 20 ). Individuals with ddRAD results include 27 black scoters, 4 common scoters, 32 surf scoters, 28 white-winged scoters, and 4 velvet scoters.

Purpose:

These data were gathered in support of a study examining the population connectivity of North American scoters.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1977
Ending_Date: 2012

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

Western Alaska north to Cardinal Lake NWT, east to Denmark, and south to Baja California.

Bounding_Coordinates:

West_Bounding_Coordinate: -163.9
East_Bounding_Coordinate: 12.2
North_Bounding_Coordinate: 67.6
South_Bounding_Coordinate: 30.3

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC279

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota

Theme:

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

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Waterfowl
Theme_Keyword: Seasonal distribution
Theme_Keyword: Seasonal movement
Theme_Keyword: Gene Flow
Theme_Keyword: Migratory birds

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Wildlife
Theme_Keyword: Terrestrial ecosystems
Theme_Keyword: Coastal ecosystems
Theme_Keyword: Wetland ecosystems
Theme_Keyword: Population dynamics
Theme_Keyword: Genetics
Theme_Keyword: Polymerase chain reaction

Theme:

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

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: Melanitta americana
Theme_Keyword: Melanitta deglandi
Theme_Keyword: Melanitta perspicillata
Theme_Keyword: Melanitta nigra
Theme_Keyword: Melanitta fusca
Theme_Keyword: Genetic structure

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System (GNIS)
Place_Keyword: Alaska
Place_Keyword: Rhode Island
Place_Keyword: Virginia
Place_Keyword: Washington

Place:

Place_Keyword_Thesaurus: NGA GEOnet Names Server
Place_Keyword: Canada
Place_Keyword: Nova Scotia
Place_Keyword: British Columbia
Place_Keyword: New Brunswick
Place_Keyword: Newfoundland and Labrador
Place_Keyword: Northwest Territories
Place_Keyword: Quebec
Place_Keyword: Saskatchewan
Place_Keyword: Denmark
Place_Keyword: Midtjylland
Place_Keyword: Sjælland
Place_Keyword: Syddanmark
Place_Keyword: Mexico
Place_Keyword: Baja California

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals
Taxonomic_Keywords: Birds
Taxonomic_Keywords: Waterfowl

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: database
Series_Information:

Series_Name: Taxonomic Serial Number
Issue_Identification: TSN 175163, 175167, 175171, 714092, 175170

Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomic details for birds retrieved January 6, 2020, from the Integrated Taxonomic Information System on-line database https://www.itis.gov

Online_Linkage: https://www.itis.gov

Classification_System_Modifications:

In accordance with the American Ornithologists' Union 7th edition, including the 60th supplement (AOS 2019), Melanitta deglandi (White-winged Scoter) and M. americana (Black Scoter) are recognized species. We have retained ITIS taxonomic serial numbers (TSN) for these species, though ITIS currently considers Melanitta deglandi and M. americana invalid.

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: 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: Melanitta
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta fusca
Applicable_Common_Name: TSN: 175163
Applicable_Common_Name: Velvet Scoter

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta deglandi
Applicable_Common_Name: TSN: 175167
Applicable_Common_Name: White-winged Scoter

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta nigra
Applicable_Common_Name: TSN: 175171
Applicable_Common_Name: Common Scoter

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta americana
Applicable_Common_Name: TSN: 714092
Applicable_Common_Name: Black Scoter

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Melanitta perspicillata
Applicable_Common_Name: TSN: 175170
Applicable_Common_Name: Surf Scoter

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:

Samples were provided through projects that were funded by the Sea Duck Joint Venture: R.Alisauskas, T. Bowman, F. Broerman, S. De La Cruz, D. Esler, P. Flint, T. Hollman, D. Kraege, C. Lepage, M. Luckenbach, B. McClymont, D. Mullcahy, D. Nysewander, J. Osenkowski, J. Pearce, M. Petrula, D. Rosenberg, P. Ross, D. Rudis, J. Schamber, S. Slattery, C. Swoboda, D. Ward, and the numerous biologists, graduate students, and technicians who assisted on those projects. Thomas Kjær Christensen, Aarhus University (Denmark) provided European samples. Sequencing was performed at the Tufts University Core Genomics Facility, Boston, Massachusetts, USA.

Cross_Reference:

Citation_Information:

Originator: Sonsthagen, S.A.
Originator: Wilson, R.E.
Originator: Lavretsky, P.
Originator: Talbot, S.L.
Publication_Date: 2019
Title:

Coast to coast: High genomic connectivity in North American scoters

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Ecology and Evolution
Issue_Identification: 9(12):7246-7261

Publication_Information:

Publication_Place: online
Publisher: John Wiley and Sons, Inc

Other_Citation_Details:

Sonsthagen, S.A., Wilson, R.E., Lavretsky, P., Talbot, S.L. 2019. Coast to coast: high genomic connectivity in North American scoters. Ecology and Evolution 9(12):7246-7261 doi:10.1002/ece3.5297

Online_Linkage: https://doi.org/10.1002/ece3.5297

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Individual sample ID's, collection dates, sampling locations, band numbers, and reported sex of individual samples provided by collectors were cross-checked and verified to match the accompanying worksheet. Some band numbers on data sheets accompanying samples had discrepancies with sample labels, but records preclude identifying the source of the recording error. Band number discrepancies were not critical to parameters of the genetic investigation since geographic sampling locale was not disputed. Sampling locations were verified with collectors and formally labeled and cross-referenced to the Geographic Names Information Service (GNIS) or NGA GEOnet Names Server when possible. Species identification by collectors were informally verified by confirming genetic "signatures" (e.g. microsatellite size or DNA sequence) fell within expected values for that species. Field sex was not confirmed with a laboratory analysis. Genbank accession numbers were cross-referenced to the appropriate samples in attributes. Quality control (QC) included a minimum of 10% 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.

Logical_Consistency_Report:

For microsatellite loci, reported allele sizes were reviewed to confirm that 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, and single occurrences of an allele size were scrutinized).

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. Not all samples originated from a banded bird. If known, band information has been provided.

Lineage:

Methodology:

Methodology_Type: Lab
Methodology_Description:

DNAs for ddRAD were extracted using a QIAamp DNA Stool Kit (Qiagen, Valencia, CA) or Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Valencia, CA) following manufacturer’s protocol, quantified using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific Inc.), and diluted to 0.02 ug/ul. Library prep followed DaCosta and Sorenson (2014) and Lavretsky et al (2015, 2016) as detailed in Sonsthagen et al (2019). Samples were pooled in equimolar concentrations and 150 bp, single-end sequencing was completed on an Illumina HiSeq 2500 at the Tufts University Core Genomics Facility.

Methodology:

Methodology_Type: Lab
Methodology_Description:

DNAs for microsatellites were extracted using a modified salt extraction technique (Medrano et al. 1990; Sonsthagen et al. 2004), quantified using fluorometry, and diluted to 50 ng/ul working solutions. Polymerase chain reaction (PCR) amplification and scoring of microsatellites followed Talbot et al.(2011). Microsatellite alleles were resolved on a 25 cm 6% polyacrylamide gel using a LI-COR (IR 4200) automated DNA sequencer.

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.

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: ddRAD library prep methods

Source_Information:

Source_Citation:

Citation_Information:

Originator: Lavretsky, P.
Originator: Dacosta, J.M.
Originator: Hernández-Baños, B.E.
Originator: Engilis, A. jr.
Originator: Sorenson, M.D.
Originator: Peters, J.L.
Publication_Date: 2015
Title:

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Molecular Ecology
Issue_Identification: 24(21):5364-5378

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Lavretsky, P., Dacosta, J.M., Hernández-Baños, B.E., Engilis, A. jr., Sorenson, M.D., Peters, J.L. 2015. Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards. Molecular Ecology 24(21):5364-5378 doi:10.1111/mec.13402

Online_Linkage: https://doi.org/10.1111/mec.13402

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2015

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Lavretsky et al 2015
Source_Contribution: ddRAD library prep methods

Source_Information:

Source_Citation:

Citation_Information:

Originator: Lavretsky, P.
Originator: Peters, J.L.
Originator: Winker, K.
Originator: Bahn, V.
Originator: Kulikova, I.
Originator: Zhuravlev, Y.N.
Originator: Wilson, R.E.
Originator: Barger, C.
Originator: Gurney, K.
Originator: McCracken, K.G.
Publication_Date: 2016
Title:

Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Molecular Ecology
Issue_Identification: 25(3):661-674

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Lavretsky, P., Peters, J.L., Winker, K., Bahn, V., Kulikova, I., Zhuravlev, Y.N., Wilson, R.E., Barger, C., Gurney, K., McCracken, K.G. 2016. Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations. Molecular Ecology 25(3):661-674 doi:10.1111/mec.13487

Online_Linkage: https://doi.org/10.1111/mec.13487

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2016

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Lavretsky et al 2016
Source_Contribution: ddRAD library prep methods

Source_Information:

Source_Citation:

Citation_Information:

Originator: Medrano, J.F.
Originator: Aasen, E.
Originator: Sharrow, L.
Publication_Date: 1990
Title: DNA extraction from nucleated red blood cells
Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Biotechniques
Issue_Identification: 8(1):43

Publication_Information:

Publication_Place: online
Publisher: Future Science, Ltd.

Other_Citation_Details:

Medrano, J.F., Aasen, E., Sharrow, L. 1990. DNA extraction from nucleated red blood cells. Biotechniques 8(1):43

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1990

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Medrano et al 1990
Source_Contribution:

Laboratory Technique Citation: describes DNA extraction technique.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Sonsthagen, S.A.
Originator: Talbot, S.L.
Originator: White, C.M.
Publication_Date: 2004
Title:

Gene flow and genetic characterization of Northern Goshawks breeding in Utah.

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Condor
Issue_Identification: 106(4):826–836

Publication_Information:

Publication_Place: Oxford, UK
Publisher: Oxford University Press

Other_Citation_Details:

Sonsthagen, S.A., Talbot, S.L., White, C.M. 2004. Gene flow and genetic characterization of Northern Goshawks breeding in Utah. Condor 106(4):826–836

Online_Linkage: http://www.jstor.org/stable/3247787

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2004

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Sonsthagen et al 2004
Source_Contribution:

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

Source_Information:

Source_Citation:

Citation_Information:

Originator: Talbot, S.L.
Originator: Palmer, A.G.
Originator: Sage, G.K.
Originator: Sonsthagen, S.A.
Originator: Swem, T.
Originator: Brimm, D.J.
Originator: White, C.M.
Publication_Date: 2011
Title:

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Journal of Avian Biology
Issue_Identification: 42(5):415-428

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Talbot, S.L., Palmer, A.G., Sage, G.K., Sonsthagen, S.A., Swem, T., Brimm, D.J., White, C.M. 2011. Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji. Journal of Avian Biology 42(5):415-428 doi:10.1111/j.1600-048x.2011.05280.x

Online_Linkage: https://doi.org/10.1111/j.1600-048x.2011.05280.x

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2011

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Talbot et al 2011
Source_Contribution: PCR parameters

Source_Information:

Source_Citation:

Citation_Information:

Originator: Chesser, R.T.
Originator: Burns, K.J.
Originator: Cicero, C.
Originator: Dunn, J.L.
Originator: Kratter, A.W.
Originator: Lovette, I.J.
Originator: Rasmussen, P.C.
Originator: Remsen, J.V. Jr.
Originator: Stotz, D.F.
Originator: Winker, K.
Publication_Date: 2019
Title:

Sixtieth Supplement to the American Ornithological Society's Check-list of North American Birds

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: The Auk
Issue_Identification: 136(3)

Publication_Information:

Publication_Place: online
Publisher: American Ornithological Society

Other_Citation_Details:

Chesser, R.T., Burns, K.J., Cicero, C., Dunn, J.L., Kratter, A.W., Lovette, I.J., Rasmussen, P.C., Remsen, J.V. Jr., Stotz, D.F., Winker, K. 2019. Sixtieth Supplement to the American Ornithological Society's Check-list of North American Birds. The Auk 136(3) doi:10.1093/auk/ukz042

Online_Linkage: https://doi.org/10.1093/auk/ukz042

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2019

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: AOS 2019
Source_Contribution:

American Ornithologist Union recognized taxonomy of the genus Melanitta.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Sonsthagen, S.A.
Originator: Wilson, R.E.
Originator: Lavretsky, P.
Originator: Talbot, S.L.
Publication_Date: 2019
Title:

Coast to coast: High genomic connectivity in North American scoters

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Ecology and Evolution
Issue_Identification: 9(12):7246-7261

Publication_Information:

Publication_Place: online
Publisher: John Wiley and Sons, Inc

Other_Citation_Details:

Sonsthagen, S.A., Wilson, R.E., Lavretsky, P., Talbot, S.L. 2019. Coast to coast: high genomic connectivity in North American scoters. Ecology and Evolution 9(12):7246-7261 doi:10.1002/ece3.5297

Online_Linkage: https://doi.org/10.1002/ece3.5297

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2019

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Sonsthagen et al (2019)
Source_Contribution: Detailed methods.

Process_Step:

Process_Description:

Raw Illumina reads were de-multiplexed and processed using DaCosta and Sorenson (2014) pipelines, stepwise according to Lavretsky et al (2015). Additional details in Sonsthagen et al (2019).

Process_Date: Unknown

Process_Step:

Process_Description:

For microsatellite data, a small subset of individuals was run on an initial gel for each locus alongside an M13 sequence ladder of known size and allele sizes assigned using Gene Profiler 4.05 (Scanalytics, Inc.). Subsequent gels included these known size individuals on every gel from which relative sizes of unknown individuals were assigned, using Gene Profiler 4.05 (Scanalytics).

Process_Date: Unknown

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

Countries and regions are listed to describe generalized field sampling locations.

Direct_Spatial_Reference_Method: Point

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Geographic:

Latitude_Resolution: 0.01
Longitude_Resolution: 0.01
Geographic_Coordinate_Units: Decimal degrees

Geodetic_Model:

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

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: scoter_ddRAD_microsatellites_northAmericaEurope_sonsthagen
Entity_Type_Definition:

Table with sample ID, species, band numbers, sampling locale, sampling dates, population grouping, BioSample accession numbers, and allele scores (in base pairs) for 11 autosomal microsatellite loci. Presented in a Comma Separated Value (CSV) formatted table.

Locus names and order of presentation: APH02, APH04.1, APH07, APH08, Bcaµ11, CRG, Hhi3, Sfi10, Sfi11, Smo7, ANAS

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: species
Attribute_Definition: Species abbreviation for each sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: BLSC
Enumerated_Domain_Value_Definition:

Indicates sample is from a North American Black Scoter (Melanitta americana).

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: BLSC/Common
Enumerated_Domain_Value_Definition:

Indicates sample is from a European Common Scoter (Melanitta nigra).

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: SUSC
Enumerated_Domain_Value_Definition:

Indicates sample is from a North American Surf Scoter (Melanitta perspicillata).

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: WWSC
Enumerated_Domain_Value_Definition:

Indicates sample is from a North American White-Winged Scoter (Melanitta deglandi).

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: WWSC/Velvet
Enumerated_Domain_Value_Definition:

Indicates sample is from a European Velvet Scoter (Melanitta fusca).

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: band_id
Attribute_Definition:

Unique field identification code, used to mark individual birds in the field such as a coded plastic neck collar, tarsal flag, or the final 5 digits of the metal leg band issued by the USGS Bird Banding Lab. Blank cells indicate the individual did not have a band.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Unique field identifier

Attribute:

Attribute_Label: sex
Attribute_Definition:

This indicates the sex reported to the laboratory by the source providing the DNA or DNA source tissue to the laboratory. Blank cells indicate information was not provided.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition:

Sample was identified as a female in the field. This information provided to, but not generated by the laboratory.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition:

Sample was identified as a male in the field. This information provided to, but not generated by the laboratory.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: country
Attribute_Definition: Country where sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place names within the United States follow the USGS Geographic Names Information System (GNIS) https://geonames.usgs.gov/apex/f?p=138

Attribute_Domain_Values:

Unrepresentable_Domain:

Place names outside the United States follow the National Geospatial-Intelligence Agency (NGA) GEOnet Names Server https://geonames.nga.mil/namesgaz

Attribute:

Attribute_Label: region
Attribute_Definition:

The state (USA/Mexico), territory or province (Canada), or region (Denmark) where sample was collected.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place names within the United States follow the USGS Geographic Names Information System (GNIS) https://geonames.usgs.gov/apex/f?p=138

Attribute_Domain_Values:

Unrepresentable_Domain:

Place names outside the United States follow the National Geospatial-Intelligence Agency (NGA) GEOnet Names Server https://geonames.nga.mil/namesgaz

Attribute:

Attribute_Label: locale
Attribute_Definition:

Site name for sample collection locations. Corresponds to the "locale" attribute in the other table included with this data package.

The complete list of all site names and approximate geographic coordinates are provided in the other table ("scoter_samplingLocales_northAmericaEurope_sonsthagen.csv") included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Site name for sample collection location

Attribute:

Attribute_Label: field_collection_start
Attribute_Definition:

This indicates the specific date (month/day/year) the individual was collected from the field when known. If a less specific date is known, this represents the start date of the field collection effort (see "Field _collection_end" for end date of the field effort). Black Scoters from Sheet Harbour, Nova Scotia, Canada have an uncertain, non-specific collection date sometime in 1999 or 2000 and have been left blank. A blank cell indicates a specific date or date range is not available.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 05/28/1977
Range_Domain_Maximum: 10/11/2010
Attribute_Units_of_Measure: Date (MM/DD/YYYY)

Attribute:

Attribute_Label: field_collection_end
Attribute_Definition:

If a specific field collection date is unknown, this represents the end date of the field collection effort (see "Field _collection_start" for start date of the field effort). A blank cell indicates a specific date is entered in the Field_collection_start or date of collection is not available.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 06/08/1977
Range_Domain_Maximum: 04/09/2011
Attribute_Units_of_Measure: Date (MM/DD/YYYY)

Attribute:

Attribute_Label: pub_genepop_id
Attribute_Definition:

If present, this indicates the population assigned in Sonsthagen et al 2019. Blank cells indicate sample was not used in population analyses in Sonsthagen et al 2019.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Alphanumeric identifier for population analyses.

Attribute:

Attribute_Label: biosample_accession
Attribute_Definition:

This is the NCBI Biosample accession number for Bioproject PRJNA541567 Coast to Coast: High Genomic Connectivity in North American Scoters. A blank cell indicates the sample was not included in the ddRAD portion of the study.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Alphanumeric label assigned by NCBI to the sequence data associated with this individual.

Attribute:

Attribute_Label: APH02_allele1 through ANAS_allele2
Attribute_Definition:

These 22 columns represent 11 autosomal 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 data were not collected for the sample.

Locus names and order of presentation: APH02, APH4.1, APH07, APH08, Bcaµ11, CRG, Hhiµ3, Sfi10, Sfi11, Smo7, ANAS.

These microsatellite data cannot be combined with data generated outside the Alaska Science Center without molecular size calibration between laboratories.

Details and full citations for microsatellite loci are available at https://doi.org/10.5066/P9GJEX8Y

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Allele scores (in base pairs) for each microsatellite locus.

Detailed_Description:

Entity_Type:

Entity_Type_Label: scoter_samplingLocales_northAmericaEurope_sonsthagen
Entity_Type_Definition:

Table providing site names and approximate geographic coordinates of locales where scoters were sampled. Coordinates are for general location only and are not actual sampling locations. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: locale
Attribute_Definition:

Site name for sample collection locations. Corresponds to the "Collection_location" attribute in the other table included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

The complete list of all site names included with this data package

Attribute:

Attribute_Label: region
Attribute_Definition:

The state (USA/Mexico), territory or province (Canada), or region (Denmark) where sample was collected.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place names within the United States follow the USGS Geographic Names Information System (GNIS) https://geonames.usgs.gov/apex/f?p=138

Attribute_Domain_Values:

Unrepresentable_Domain:

Place names outside the United States follow the National Geospatial-Intelligence Agency (NGA) GEOnet Names Server https://geonames.nga.mil/namesgaz

Attribute:

Attribute_Label: country
Attribute_Definition: Country where sample was collected.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Place names within the United States follow the USGS Geographic Names Information System (GNIS) https://geonames.usgs.gov/apex/f?p=138

Attribute_Domain_Values:

Unrepresentable_Domain:

Place names outside the United States follow the National Geospatial-Intelligence Agency (NGA) GEOnet Names Server https://geonames.nga.mil/namesgaz

Attribute:

Attribute_Label: latitude
Attribute_Definition:

Latitude of sample collection. Coordinates are for general location only and are not actual sampling locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 30.46
Range_Domain_Maximum: 67.60
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Attribute:

Attribute_Label: longitude
Attribute_Definition:

Longitude of sample collection. Coordinates are for general location only and are not actual sampling locations.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -164.80
Range_Domain_Maximum: 12.25
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Scoter (Melanitta sp.) ddRAD SNP and Microsatellite Genetic Data, North America and Europe, 1977-2012

Metadata: