Genetic Data from Cooper's Hawks (Accipiter cooperii), North America

Identification_Information:

Citation:

Citation_Information:

Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Talbot, S.L. (ORCID: 0000-0002-3312-721)
Publication_Date: 20200101
Title:

Geospatial_Data_Presentation_Form: tabular digital data
Series_Information:

Series_Name:

Genetic data from Cooper's Hawks (Accipiter cooperii), North America

Issue_Identification: ver 2.0, February 2022

Publication_Information:

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

Other_Citation_Details:

Suggested Citation: Sonsthagen, S.A., Talbot, S.L., 2020, Genetic data from Cooper's Hawks (Accipiter cooperii), North America (ver 2.0, February 2022): U.S. Geological Survey data release, https://doi.org/10.5066/P914SGB1

Online_Linkage: https://doi.org/10.5066/P914SGB1
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 describes nuclear microsatellite genotypes derived from six autosomal loci (AgCA222, Age7.1JT, BV13, BV20, NVH206, NVH195-2) in Cooper's Hawks. Samples originated from blood samples collected from live trapped birds.

Purpose: To examine familial relationships within Cooper's Hawks.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2011
Ending_Date: 2019

Currentness_Reference: Observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent: Wisconsin, USA, west to British Columbia, Canada.
Bounding_Coordinates:

West_Bounding_Coordinate: -123.37
East_Bounding_Coordinate: -87.90
North_Bounding_Coordinate: 48.43
South_Bounding_Coordinate: 43.04

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC334

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: Eagles/Falcons/Hawks and Allies

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Birds of prey
Theme_Keyword: Site Fidelity
Theme_Keyword: Gene Flow
Theme_Keyword: Population Genetics

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Wildlife
Theme_Keyword: Terrestrial ecosystems
Theme_Keyword: Genetics
Theme_Keyword: Polymerase chain reaction

Theme:

Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: DNA
Theme_Keyword: Alleles
Theme_Keyword: Genetic Markers
Theme_Keyword: Microsatellite Repeats
Theme_Keyword: Genotype

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: Raptors
Theme_Keyword: Cooper's Hawk
Theme_Keyword: Accipiter cooperii

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: AgCA222
Theme_Keyword: Age7.1JT
Theme_Keyword: BV13
Theme_Keyword: BV20
Theme_Keyword: NVH195-2
Theme_Keyword: NVH206

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System (GNIS)
Place_Keyword: Wisconsin
Place_Keyword: North Dakota
Place_Keyword: British Columbia

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals
Taxonomic_Keywords: Birds
Taxonomic_Keywords: Raptors

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
Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomic details retrieved December 10, 2021, from the Integrated Taxonomic Information System on-line database https://www.itis.gov

Online_Linkage: https://www.itis.gov

Taxonomic_Procedures:

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

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:

Taxon_Rank_Name: 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: Accipitriformes
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Accipitridae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Accipiter
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Accipiter cooperii
Applicable_Common_Name: Cooper's Hawk
Applicable_Common_Name: TSN 175309

Access_Constraints: None
Use_Constraints:

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

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

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

Contact_Address:

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

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

Cross_Reference:

Citation_Information:

Originator: Rosenfield, R.N.
Originator: Sonsthagen, S.A. (ORCID: 0000-0001-6215-5874)
Originator: Riddle-Berntsen, A.E. (ORCID: 0000-0002-1925-0849)
Originator: Kuhel, E.
Publication_Date: 2020
Title:

Record fledging count from a seven-egg clutch in the Cooper’s Hawk (Accipiter cooperii)

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Wilson Journal of Ornithology
Issue_Identification: 132(2):460-463

Publication_Information:

Publication_Place: online
Publisher: Springer Nature

Other_Citation_Details:

Rosenfield, R.N., Sonsthagen, S.A., Riddle-Berntsen, A.E., Kuhel, E., 2020. Record fledging count from a seven-egg clutch in the Cooper’s Hawk (Accipiter cooperii). Wilson Journal of Ornithology 132(2):460-463 doi:10.1676/1559-4491-132.2.460

Online_Linkage: https://doi.org/10.1676/1559-4491-132.2.460

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Identifying information about samples were cross-checked with original field data. Polymerase chain reaction (PCR) amplification and electrophoresis followed protocols described in Sonsthagen et al 2004. Quality control (QC) included a minimum of 20% re-extraction and PCR replication for each locus and all laboratory techniques were performed using sterile procedures. All duplicate characterizations of the same individual resulted in concordant data.

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 by laboratory personnel, gaps in allele sizes were reviewed, and single occurrences of an allele size were scrutinized). No inconsistencies in genotype scores were observed between replicates. Tests for null alleles and allelic dropout were implemented in MicroChecker (van Oosterhout et al 2004).

Completeness_Report:

No data were omitted. Blank cells are described for each attribute.

Lineage:

Methodology:

Methodology_Type: Field
Methodology_Description:

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

Methodology:

Methodology_Type: Lab
Methodology_Description:

DNA was extracted using a modified salt extraction technique (Medrano et al 1990; Sonsthagen et al 2004) or using a Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Düsseldorf, Germany) following manufacturer’s protocol.

Methodology:

Methodology_Type: Lab
Methodology_Description:

Polymerase chain reaction (PCR) amplification and scoring of microsatellites followed Sonsthagen et al 2004 except the thermocycler parameters consisted of a 2 min denaturation at 94 °C, followed 40 cycles at 94°C for 15 seconds, 50°C for 15 seconds and 72 °C for 30 seconds with a final extension at 72 °C for 30 min. Microsatellite alleles were resolved on a 25 cm 6% polyacrylamide gel using a LI-COR (IR 4200) automated DNA sequencer. For quality control purposes, we extracted, amplified, and sequenced, 20% of the samples in duplicate.

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: van Oosterhout, C.
Originator: Hutchinson, W.F.
Originator: Wills, D.P.M.
Originator: Shipley, P.
Publication_Date: 2004
Title:

MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Molecular Ecology Notes
Issue_Identification: 4(3):535-538

Publication_Information:

Publication_Place: online
Publisher: Wiley Online Library

Other_Citation_Details:

van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M., Shipley, P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4(3):535-538 doi:10.1111/j.1471-8286.2004.00684.x

Online_Linkage: https://doi.org/10.1111/j.1471-8286.2004.00684.x

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: van Oosterhout et al 2004
Source_Contribution:

Laboratory Technique Citation: describes tool used to identify potential scoring errors and null alleles of microsatellite loci.

Process_Step:

Process_Description:

Initial microsatellite allele sizes were determined by scoring based on PCR product size relative to an M13 DNA sequence ladder using Gene Profiler 4.05 (Scanalytics, Inc., Fairfax, VA). Subsequent gels included these known size individuals from which relative sizes of unknown individuals were assigned using Gene Profiler 4.05. For this reason, these microsatellite data cannot be combined with data generated outside the USGS Alaska Science Center without molecular size calibration between laboratories. MtDNA sequences from opposite strands were reconciled using Sequencher 4.1.2 (Gene Codes Corporation, Ann Arbor, MI). Tests for null alleles and allelic dropout were implemented in MicroChecker (van Oosterhout et al 2004).

Process_Date: Unknown

Process_Step:

Process_Description:

Sequences of novel microsatellite loci developed in this study were submitted to the NCBI Genbank publicly available genetic sequence data database.

Process_Date: Unknown
Source_Produced_Citation_Abbreviation: NCBI GenBank

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

States are listed to describe generalized field sampling locations.

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: coopersHawk_microsatellite_sonsthagen.csv
Entity_Type_Definition:

Table with sample identifying information, collection data, and genotype numbers for six autosomal microsatellite loci (AgCA222, Age7.1JT, BV13, BV20, NVH206, NVH195-2). Genotype numbers (nucleotide base pairs) 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. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: Sample_Name
Attribute_Definition:

Unique identification code used to mark individual samples collected in the field.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Unique field indentification.

Attribute:

Attribute_Label: Nest_Name
Attribute_Definition:

Unique name to identify each nest from which blood were collected.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier; a name to identify each nest from which blood were collected.

Attribute:

Attribute_Label: Sample_Location
Attribute_Definition: Place names of sample collection sites.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Wisconsin
Enumerated_Domain_Value_Definition: Samples collected in Wisconsin (approx 44.5N, 89.6W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: North Dakota
Enumerated_Domain_Value_Definition: Samples collected in North Dakota (approx 46.9N, 96.8W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: British Columbia
Enumerated_Domain_Value_Definition: Samples collected in British Columbia (approx 48.4N, 123.4W)
Enumerated_Domain_Value_Definition_Source: Geographic Names Information System (GNIS)

Attribute:

Attribute_Label: Collection_Year
Attribute_Definition: Year that sample was collected in the field.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 2011
Range_Domain_Maximum: 2019
Attribute_Units_of_Measure: Year (YYYY)

Attribute:

Attribute_Label: Sex
Attribute_Definition:

Sex of bird sampled; identified in the field by morphological characteristics. Blank cells indicate that sex information was not collected for this sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: female
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: male
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Age
Attribute_Definition: Age class of bird, identified in the field.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Adult
Enumerated_Domain_Value_Definition: Sampled individual greater than 12 months in age.
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Nestling
Enumerated_Domain_Value_Definition: Sampled individual less than 4 months of age.
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Version
Attribute_Definition:

The data package version that was current at the time each record was originally released by the USGS Alaska Science Center.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: v 1.0
Enumerated_Domain_Value_Definition: Version 1.0, December 2020
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: v 2.0
Enumerated_Domain_Value_Definition: Version 2.0, January 2022
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: AgCA222_allele1 through NVH206_allele2
Attribute_Definition:

These 12 columns present the genotype number (nucleotide base pairs) for each of six autosomal microsatellite loci. Each microsatellite locus genotype is represented by two adjacent columns (i.e., allele1 and allele2). Blank cells indicate that the genotype number of this locus was not collected for this sample.

Locus names and order of presentation: AgCA222, Ag7.1JT, BV13, BV20, NVH195-2, NVH206

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:

Genotype number (nucleotide base pairs) for each microsatellite locus from each sample.

Distribution_Information:

Distributor:

Contact_Information:

Contact_Organization_Primary:

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

Contact_Address:

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

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

Resource_Description:

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

Distribution_Liability:

Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name: CSV
Format_Information_Content:

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

File_Decompression_Technique:

Compression applied by the 7-Zip utility using default compression (5). The Zip package can be decompressed and unpacked by open source or commercially available unzip tools.

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name: https://doi.org/10.5066/P914SGB1

Fees: None

Genetic Data from Cooper's Hawks (Accipiter cooperii), North America

Metadata: