Genetic Microsatellite Data from Sorex, Based on Holarctic Sampling

Identification_Information:

Citation:

Citation_Information:

Originator: Hope, Andrew G. (ORCID: 0000-0003-3814-2891)
Originator: Sage, G. Kevin (ORCID: 0000-0003-1431-2286)
Originator: Talbot, Sandra L. (ORCID: 0000-0002-3312-7214)
Publication_Date: 20220504
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: Hope, A.G., Sage, G.K., Talbot, S.L. 2022, Genetic microsatellite data from Sorex, based on Holarctic sampling: U.S. Geological Survey data release, https://doi.org/10.5066/P9DJQFH8

Online_Linkage: https://doi.org/10.5066/P9DJQFH8
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 17 autosomal loci (Sug001, Sug002, Sug003, Sug006, Sug007, Sug008, Sug009, Sug010, Sug011, Sug012, Sug019, Sug021, Sug022, Sug023, Sug024, Sug029, Sug038) in shrews, Sorex spp.

Purpose: To examine familial relationships within the genus Sorex.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2022

Currentness_Reference: publication date

Status:

Progress: In work
Maintenance_and_Update_Frequency: As needed

Spatial_Domain:

Description_of_Geographic_Extent: Alaska and eastern Russia
Bounding_Coordinates:

West_Bounding_Coordinate: 150.85
East_Bounding_Coordinate: -150.44
North_Bounding_Coordinate: 70.72
South_Bounding_Coordinate: 54.5

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC458

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: Mammals

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Gene Flow

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Wildlife
Theme_Keyword: Terrestrial ecosystems
Theme_Keyword: Tundra ecosystems
Theme_Keyword: Genetics
Theme_Keyword: Genetic diversity
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: Insectivora
Theme_Keyword: Shrews
Theme_Keyword: Sorex jacksoni
Theme_Keyword: Sorex cinereus
Theme_Keyword: Sorex pribilofensis
Theme_Keyword: Sorex ugyunak
Theme_Keyword: Sorex portenkoi
Theme_Keyword: Sorex camtschatica

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System (GNIS)
Place_Keyword: Alaska
Place_Keyword: Pribilof Islands

Place:

Place_Keyword_Thesaurus: NGA GEOnet Names Server
Place_Keyword: Russia
Place_Keyword: Kamchatka Peninsula
Place_Keyword: Chukotka
Place_Keyword: Anadyr

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals
Taxonomic_Keywords: Mammals

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 25, 2022, from the Integrated Taxonomic Information System online database https://www.itis.gov

Online_Linkage: https://www.itis.gov

Taxonomic_Procedures:

Species identifications were determined by the Museums that provided the tissue samples.

Taxonomic_Completeness: Taxonomy is complete for all samples.

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: Mammalia
Taxonomic_Classification:

Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Theria
Taxonomic_Classification:

Taxon_Rank_Name: Infraclass
Taxon_Rank_Value: Eutheria
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Soricomorpha
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Soricidae
Taxonomic_Classification:

Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Soricinae
Taxonomic_Classification:

Taxon_Rank_Name: Tribe
Taxon_Rank_Value: Soricini
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Sorex
Taxonomic_Classification:

Taxon_Rank_Name: Subgenus
Taxon_Rank_Value: Sorex (Otisorex)
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex jacksoni
Applicable_Common_Name: St. Lawrence Island Shrew
Applicable_Common_Name: TSN: 179931

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex cinereus
Applicable_Common_Name: Common Shrew
Applicable_Common_Name: Masked Shrew
Applicable_Common_Name: Cinereus Shrew
Applicable_Common_Name: TSN: 179929

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex pribilofensis
Applicable_Common_Name: Pribilof Island Shrew
Applicable_Common_Name: TSN: 179930

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex ugyunak
Applicable_Common_Name: Barren Ground Shrew
Applicable_Common_Name: TSN: 552509

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex portenkoi
Applicable_Common_Name: Portenko's Shrew
Applicable_Common_Name: TSN: 633803

Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Sorex camtschatica
Applicable_Common_Name: Kamchatka Shrew
Applicable_Common_Name: TSN: 633784

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:

The Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico; Museum of the North, University of Alaska, Fairbanks, Alaska

Cross_Reference:

Citation_Information:

Originator: Wiens, B.J.
Originator: Combe, F.J.
Originator: Dickerson, B.
Originator: Divine, L.M.
Originator: Padula, V.A.
Originator: Sage, G.K.
Originator: Talbot, S.L.
Originator: Hope, A.G.
Publication_Date: 2022
Title:

Genetic Drift Drives Rapid Speciation of an Arctic Insular Endemic Shrew (Sorex pribilofensis)

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Molecular Ecology
Issue_Identification: 31(20):5231-5248

Publication_Information:

Publication_Place: online
Publisher: Wiley

Other_Citation_Details:

Wiens, B.J., Combe, F.J., Dickerson, B., Divine, L.M., Padula, V.A., Sage, G.K., Talbot, S.L., Hope, A.G. 2022. Genetic drift drives rapid speciation of an Arctic insular endemic shrew (Sorex pribilofensis). Molecular Ecology 31(20):5231-5248 doi:10.1111/mec.16658

Online_Linkage: https://doi.org/10.1111/mec.16658

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

All identifying information corresponding to 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 conformed 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 indicate no data were collected.

Lineage:

Methodology:

Methodology_Type: Field
Methodology_Description:

All genetic samples were obtained from collections at The Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico or the Museum of the North, University of Alaska, Fairbanks, Alaska.

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, Germantown, MD) 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: Sonsthagen, S.A.
Originator: Sage, G.K.
Originator: Fowler, M.
Originator: Hope, A.G.
Originator: Cook, J.A.
Originator: Talbot, S.L.
Publication_Date: 2013
Title:

Development and Characterization of 21 Polymorphic Microsatellite Markers for the Barren-ground Shrew, Sorex ugyunak (Mammalia: Soricidae), through Next-Generation Sequencing, and Cross-Species Amplification in the Masked Shrew, S. cinereus

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Conservation Genetics Resources
Issue_Identification: 5(2):315–318

Publication_Information:

Publication_Place: online
Publisher: Springer Nature

Other_Citation_Details:

Sonsthagen, S.A., Sage, G.K., Fowler, M., Hope, A.G., Cook, J.A., Talbot, S.L. 2013. Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Soricidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus. Conservation Genetics Resources 5(2):315–318 doi:10.1007/s12686-012-9792-5

Online_Linkage: https://doi.org/10.1007/s12686-012-9792-5

Type_of_Source_Media: publication
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2013

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Sonsthagen et al. 2013
Source_Contribution: Laboratory Technique Citation: details of microsatellite loci

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.

Source_Information:

Source_Citation:

Citation_Information:

Originator:

Mammal Collection - Museum of Southwestern Biology, Albuquerque, New Mexico

Publication_Date: Unpublished material
Title: Shrew Specimens
Geospatial_Data_Presentation_Form: Preserved physical samples

Type_of_Source_Media: Tissue for genetic analyses
Source_Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: Unknown
Ending_Date: Unknown

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: Museum of Southwestern Biology
Source_Contribution: Source of preserved shrew specimens used in the study.

Source_Information:

Source_Citation:

Citation_Information:

Originator: University of Alaska Museum of the North
Publication_Date: Unpublished material
Title: Shrew Specimens
Geospatial_Data_Presentation_Form: Preserved physical samples

Type_of_Source_Media: Tissue for genetic analyses
Source_Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: Unknown
Ending_Date: Unknown

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: University of Alaska Museum of the North
Source_Contribution: Source of preserved shrew specimens used in the study.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Arctos
Publication_Date: Unknown
Title: Arctos - collaborative collection management solution
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://arctos.database.museum

Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2022

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: Arctos
Source_Contribution:

Database of museum collections; queried to identify appropriate shrew specimens for this study.

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. Tests for null alleles and allelic dropout were implemented in MicroChecker (van Oosterhout et al. 2004).

Process_Date: Unknown

Spatial_Data_Organization_Information:

Direct_Spatial_Reference_Method: Point

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Geographic:

Latitude_Resolution: 0.001
Longitude_Resolution: 0.001
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: sorex_microsatellite_holarctic_hope.csv
Entity_Type_Definition:

Table with identifying information for each sample, including collection data, and genotype numbers for 17 autosomal microsatellite loci (Sug001, Sug002, Sug003, Sug006, Sug007, Sug008, Sug009, Sug010, Sug011, Sug012, Sug019, Sug021, Sug022, Sug023, Sug024, Sug029, Sug038). Data include museum collection identification and species as cataloged. 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_ID
Attribute_Definition: Unique identifier for each sample.
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier for each sample. A concatenation of four-letter species code and Arctos accession number.

Attribute:

Attribute_Label: Arctos_Museum_Catalog
Attribute_Definition:

The Arctos database identifier of the museum collections from which specimens were selected.

Attribute_Definition_Source: Author Defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: UAM:Mamm:[accession number]
Enumerated_Domain_Value_Definition:

The Arctos database identifier (Mammal Collection - University of Alaska Museum of the North, Fairbanks, Alaska) and unique identifying accession number

Enumerated_Domain_Value_Definition_Source: Arctos

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: MSB:Mamm:[accession number]
Enumerated_Domain_Value_Definition:

The Arctos database identifier (Mammal Collection - Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico) and unique identifying accession number

Enumerated_Domain_Value_Definition_Source: Arctos

Attribute:

Attribute_Label: Collection_Tissue_Catalog
Attribute_Definition: The Arctos database institutional collection acronym.
Attribute_Definition_Source: Author Defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: AF
Enumerated_Domain_Value_Definition:

Alaska Frozen Tissue Collection, University of Alaska Museum of the North, Fairbanks, Alaska

Enumerated_Domain_Value_Definition_Source: Arctos

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: UAM
Enumerated_Domain_Value_Definition: University of Alaska Museum of the North, Fairbanks, Alaska
Enumerated_Domain_Value_Definition_Source: Arctos

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: NK
Enumerated_Domain_Value_Definition:

"New Mexico Karytoype Number," a frozen tissue collection number for the Museum of Southwestern Biology

Enumerated_Domain_Value_Definition_Source: Arctos

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: IF
Enumerated_Domain_Value_Definition: Idaho Frozen Tissue Collection
Enumerated_Domain_Value_Definition_Source: Arctos

Attribute:

Attribute_Label: Collection_Tissue_Number
Attribute_Definition:

The Arctos database collection number associated with Collection Tissue Catalog Number.

Attribute_Definition_Source: Author Defined
Attribute_Domain_Values:

Unrepresentable_Domain: Unique sample identifier in Arctos database

Attribute:

Attribute_Label: Species
Attribute_Definition:

Species identification of individual as cataloged at time of data retrieval from Arctos

Attribute_Definition_Source: Author Defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Sorex jacksoni
Enumerated_Domain_Value_Definition: