Dictionary of Microsatellite Loci from the U.S. Geological Survey, Alaska Science Center, Molecular Ecology Laboratory

Identification_Information:

Citation:

Citation_Information:

Originator: Talbot, Sandra L. (ORCID: 0000-0002-3312-7214)
Originator: Pierson, Barbara J. (ORCID: 0000-0001-8233-874X)
Originator: Sage, G. Kevin (ORCID: 0000-0003-1431-2286)
Publication_Date: 20240411
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: Talbot, S.L., Pierson, B.J., and Sage, G.K., 2024, Dictionary of microsatellite loci from the U.S. Geological Survey, Alaska Science Center, Molecular Ecology Laboratory: U.S. Geological Survey data release, https://doi.org/10.5066/P9GJEX8Y

Online_Linkage: https://doi.org/10.5066/P9GJEX8Y

Description:

Abstract:

This data package provides a dictionary of microsatellite locus primers used by the USGS Alaska Science Center, Molecular Ecology Laboratory (MEL). It is a look-up file of microsatellite locus names and citations to the original publication or source where additional information about the locus primers may be found.

Purpose:

This dictionary was compiled to serve as a source for citation information about microsatellite locus primers used by the MEL.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2024

Currentness_Reference: publication date

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC614

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: Data Analysis and Visualization
Theme_Keyword: Reference and Information Services
Theme_Keyword: Animals/Vertebrates
Theme_Keyword: Birds

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Genetics
Theme_Keyword: Genetic Screening
Theme_Keyword: Laboratory methods

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Genetics
Theme_Keyword: Polymerase chain reaction
Theme_Keyword: Genetic diversity

Theme:

Theme_Keyword_Thesaurus: MeSH-National Library of Medicine
Theme_Keyword: Alleles
Theme_Keyword: Genetic markers
Theme_Keyword: Microsatellite Repeats
Theme_Keyword: Genetic Variation
Theme_Keyword: Polymorphism, Genetic
Theme_Keyword: Genetics, Population

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals

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 April 11, 2024, from the Integrated Taxonomic Information System online database https://www.itis.gov

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

Classification_System_Modifications:

Taxonomic rank above the class aves (birds) follow the most current (as of February 2023) taxonomic designation by the ITIS

Taxonomic_Procedures:

Species were identified by skilled observers in the field based on morphology and habitat.

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
Applicable_Common_Name: Birds

Access_Constraints: None
Use_Constraints:

It is requested that the suggested citation for this USGS data release be included in any publications that reference or utilize these data.

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_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Microsatellite locus names have been cross-referenced and verified. No formal quality control has been applied to the data summarized in this release. Any uncertainties are described in the Notes attributes of each worksheet. Summary descriptions provided have been compiled from across multiple laboratory notebooks and every effort has been made to make the information useful and accurate.

Logical_Consistency_Report:

Occasionally, microsatellite locus primer sequences are/were obtained from researchers prior to publication. This situation may result in differences between 'MEL_locusName' and 'published_locusName'. This may also lead to incomplete marker information and an inability to provide primer sequences developed by other researchers and subsequently not published by the original researcher. At other times, published sequences are used to redesign original primers for a cleaner and/or smaller product more easily characterized on the equipment in our lab. Citations for the original publications or sources of the microsatellite locus primers were compiled into a single look-up file, available in the "microsatDictionary" included with this data package.

Completeness_Report:

Blank cells are described in attribute definitions. No attempt to describe the quality of non-variable products was made.

Lineage:

Methodology:

Methodology_Type: Lab
Methodology_Description:

Methods for identifying specific microsatellite loci are detailed by the original authors, users are referred to the citations provided in the "microsatDictionary_molecularEcologyLab.csv" table included with this data package.

Source_Information:

Source_Citation:

Citation_Information:

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

Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2020

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI GenBank
Source_Contribution:

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

Process_Step:

Process_Description:

Microsatellite loci names and source citations were collected and entered in a CSV table.

Process_Date: Unknown

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: microsatDictionary_molecularEcologyLab.csv
Entity_Type_Definition:

A dictionary of microsatellite loci used by the USGS Alaska Science Center, Molecular Ecology Laboratory (MEL). It is a look-up file of microsatellite locus names and citations to their original publication where additional information about the loci can be found. Presented in a Comma Separated Value (CSV) formatted table.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: published_locusName
Attribute_Definition:

Microsatellite locus name as given in the original publication or source. Corresponds to the 'published_locusName' field in all tables included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Microsatellite locus name as given in the original publication or source.

Attribute:

Attribute_Label: MEL_locusName
Attribute_Definition:

Microsatellite locus name used by the MEL, if different from published locus name. Corresponds to the 'MEL_locusName' field in all tables included with this data package.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Microsatellite locus name used by the MEL, if different from published locus name.

Attribute:

Attribute_Label: GenBank_Accession
Attribute_Definition:

GenBank Accession Number. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) assigned to the microsatellite locus nucleotide sequence. This number may be used to retrieve detailed sample and sequence information from the NCBI GenBank database https://www.ncbi.nlm.nih.gov/genbank Blank cells indicate that there is no GenBank Accession Number for the locus.

Attribute_Definition_Source: NCBI GenBank accession
Attribute_Domain_Values:

Unrepresentable_Domain:

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

Attribute:

Attribute_Label: Citation_short
Attribute_Definition:

Authors' last names and publication year for the original publication or source of the microsatellite locus primer.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier for the original publication or source of the microsatellite locus primer.

Attribute:

Attribute_Label: DOI
Attribute_Definition:

Digital Object Identifier (DOI) for the original publication of the microsatellite locus primer. Blank cells indicate that the source citation has not been assigned a DOI.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier for the original publication of the microsatellite locus primer.

Attribute:

Attribute_Label: Notes
Attribute_Definition:

Additional information about the microsatellite locus primer source or citation. Not all cells contain notes.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain: Additional relevant information.

Attribute:

Attribute_Label: Citation_full
Attribute_Definition:

The complete citation for the original publication or source of the microsatellite locus primer. In most instances, this is the journal publication describing the development and testing in source species. Some unpublished markers were obtained via GenBank or collaborators and have been indicated as such.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Citation for the original publication or source of the microsatellite locus primer.

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 the default compression level [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/P9GJEX8Y

Fees: None

Dictionary of Microsatellite Loci from the U.S. Geological Survey, Alaska Science Center, Molecular Ecology Laboratory

Metadata: