Within-watershed genetic variation of coastal cutthroat trout in Camp Creek, Oregon

Metadata:

• Identification_Information
• Data_Quality_Information
• Spatial_Data_Organization_Information
• Entity_and_Attribute_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: John Wofford and Robert Gresswell

Publication_Date: 2004

Title:

Within-watershed genetic variation of coastal cutthroat trout in Camp Creek, Oregon

Geospatial_Data_Presentation_Form: spreadsheet

Larger_Work_Citation:

Citation_Information:

Originator: Wofford, J.E.B.

Publication_Date: 2004

Title:

Factors influencing within-watershed genetic variation of coastal cutthroat trout in Camp Creek, Oregon.

Geospatial_Data_Presentation_Form: thesis

Publication_Information:

Publication_Place: Corvallis, OR

Publisher: Oregon State University

Other_Citation_Details: MS thesis

Description:

Abstract:

Data are in the form of an Excel spreadsheet and contain Camp Creek coastal cutthroat trout (Oncorhynchus clarki clarki) genotypes at 8 microsatellite loci. These coastal cutthroat trout were collected from 10 locations above an anadromous barrier in Camp Creek, Oregon during the summer of 2002 and spring of 2003.

Purpose:

These data were collected in order to evaluate the dispersal and gene flow between coastal cutthroat trout populations in Camp Creek and to investigate the influence of fish passage barriers on coastal cutthroat trout genetic heterogeneity.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 200208

Beginning_Time: Unknown

Ending_Date: 200305

Ending_Time: Unknown

Currentness_Reference:

Fin tissue was collected during field visits and genetic information was quantified in the lab

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

Camp Creek, a tributary of Mill Creek in the lower Umpqua drainage of western Oregon

Bounding_Coordinates:

West_Bounding_Coordinate: -123.72

East_Bounding_Coordinate: -123.66

North_Bounding_Coordinate: 43.56

South_Bounding_Coordinate: 43.53

Keywords:

Theme:

Theme_Keyword_Thesaurus: Biocomplexity Thesaurus

Theme_Keyword: population genetics

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Oregon

Place_Keyword: OR

Place_Keyword: western Oregon

Place_Keyword: Umpqua River

Place_Keyword: Camp Creek

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: Biocomplexity Thesaurus

Taxonomic_Keywords: fish

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator:

National Oceanic and Atmospheric Administration (NOAA) , United States Geological Survey (USGS), Environmental Protection Agency (EPA) , Agriculture Research Service (ARS), Natural Resources Conservation Service (NRCS), National Museum of Natural History (NMNH)

Publication_Date: 1999

Title: Integrated Taxonomic Identification System (ITIS)

Geospatial_Data_Presentation_Form: web site

Online_Linkage: <http://www.itis.usda.gov>

Taxonomic_Procedures: Refer to methods

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom

Taxon_Rank_Value: Animalia

Taxonomic_Classification:

Taxon_Rank_Name: Phylum

Taxon_Rank_Value: Chordata

Taxonomic_Classification:

Taxon_Rank_Name: Sub Phylum

Taxon_Rank_Value: Vertebrata

Taxonomic_Classification:

Taxon_Rank_Name: Class

Taxon_Rank_Value: Actinopterygii

Taxonomic_Classification:

Taxon_Rank_Name: Order

Taxon_Rank_Value: Salmoniformes

Taxonomic_Classification:

Taxon_Rank_Name: Family

Taxon_Rank_Value: Salmonidae

Taxonomic_Classification:

Taxon_Rank_Name: Genus

Taxon_Rank_Value: Oncorhynchus

Taxonomic_Classification:

Taxon_Rank_Name: Species

Taxon_Rank_Value: Oncorhynchus clarkii

Taxonomic_Classification:

Taxon_Rank_Name: Sub Species

Taxon_Rank_Value: Oncorhynchus clarkii clarkii

Applicable_Common_Name: coastal cutthroat trout

Access_Constraints: Data are available after research results have been published

Use_Constraints:

Use with permission of the Cooperative Forest Ecosystem Research Program

Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Gresswell, Robert

Contact_Address:

Address_Type: Mailing and Physical Address

Address: Northern Rocky Mountain Science Center

City: Bozeman

State_or_Province: Montana

Postal_Code: 59715

Country: USA

Contact_Voice_Telephone: 406-994-7544

Contact_Electronic_Mail_Address: robert_gresswell@usgs.gov

Data_Set_Credit:

This research was produced through the Cooperative Forest Ecosystem Research (CFER) program, with funding provided by the USGS Forest and Rangeland Ecosystem Science Center and the Oregon Department of Forestry.

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report: No tests for attribute accuracy were conducted

Logical_Consistency_Report:

Data have been sorted by code for each field to check for typographical errors. Numeric data has been sorted to evaluate extreme values to check for typographical errors. Data have been scanned for missing values. DNA that contained unusual alleles was reanalyzed for confirmation.

Completeness_Report: Refer to methods

Lineage:

Methodology:

Methodology_Type: Field

Methodology_Description:

All genetic sampling locations were determined by tributary junctions or fish passage barriers, excluding sites MS3 and MS4. Sites MS3 and MS4 were selected because it was important to sample the entire watershed, and no tributaries or passage barriers occurred in the relatively extensive upper portions of Camp Creek. In all, genetic sampling occurred at ten sites in the Camp Creek watershed.

Coastal cutthroat trout were captured using one-pass electrofishing or with a hook and line. In sections MS1, T1, T2, and T3, up to ten fin clips and scale samples were taken from trout (>50 mm in length) in each 10 mm size class until 100 samples were collected or until sampling crews reached the end of trout distribution. At site MS0 and at all sites above barrier 3, fin clips were obtained from every captured trout and scale samples were collected from age 1+ fish. All sites were sampled during the summer of 2002 with the exception of MS0 and MS1.1 which were sampling during the spring of 2003. Fish were assigned to age classes based on length frequency analysis.

Methodology:

Methodology_Type: Lab

Methodology_Description:

Genomic DNA was extracted from small portions of tissue (0.5 mm2) in 200 µL of 5% Chelex®100 (Biorad) in 96-well PCR trays (0.2 µL) using a MJ research PT-100 thermocycler. 8 microsatellites were used to quantify coastal cutthroat trout genetic variation: Ots-209 and Ots-212 (Greig et al. 2003), One-102, One-103, and One-108 (Olsen et al. 2000)), Ots-9,-10 (Banks et al. 1999), and Omy-1046 (Rexroad et al. 2002).

Methodology_Citation:

Citation_Information:

Originator:

Banks, M. A., M. S. Blouin, B. A. Baldwin, V. K. Rashbrook, H. A. Fitzgerald, S. M. Blankenship, and D. Hedgecock

Publication_Date: 1999

Title:

Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha)

Geospatial_Data_Presentation_Form: Journal article

Series_Information:

Series_Name: Journal of Heredity

Issue_Identification: 90:281-288

Methodology_Citation:

Citation_Information:

Originator: Greig, C., D. P. Jacobson, and M. A. Banks

Publication_Date: 2003

Title:

New tetranucleotide microsatellites for fine-scale discrimination among endangered chinook salmon (Oncorhynchus tshawytscha)

Geospatial_Data_Presentation_Form: Journal article

Series_Information:

Series_Name: Molecular Ecology Notes

Issue_Identification: 3:376-379

Methodology_Citation:

Citation_Information:

Originator:

Olsen, J. B., S. L. Wilson, E. J. Kretschmer, K. C. Jones, and J. E. Seeb

Publication_Date: 2000

Title:

Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon

Geospatial_Data_Presentation_Form: Journal article

Series_Information:

Series_Name: Molecular Ecology

Issue_Identification: 9:2185-2187

Methodology_Citation:

Citation_Information:

Originator:

Rexroad, C. E., R. L. Coleman, A. L. Gustafson, W. K. Hershberger, and J. Killefer

Publication_Date: 2000

Title:

Development of rainbow trout microsatellite markers from repeat enriched libraries

Geospatial_Data_Presentation_Form: Journal article

Series_Information:

Series_Name: Marine Biotechnology

Issue_Identification: 4:12-16

Process_Step:

Process_Description: original data collection, no processing

Process_Date: Unknown

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

Camp Creek, a tributary of Mill Creek in the lower Umpqua drainage of western Oregon

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: camp_creek_genotype.xls

Entity_Type_Definition: Microsoft Excel spreadsheet

Entity_Type_Definition_Source: Microsoft

Attribute:

Attribute_Label: Age

Attribute_Definition:

age class assigned to captured fish based on length frequency analysis

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0

Enumerated_Domain_Value_Definition: fish is less than one year of age

Enumerated_Domain:

Enumerated_Domain_Value: 1

Enumerated_Domain_Value_Definition: fish is older than one year of age

Attribute:

Attribute_Label: Ots9, Ots209, Ots212, Omy1046, Ots10, One102, One108, One103

Attribute_Definition:

This field indicates the genotypes of coastal cutthroat trout at the specified locus (Oxxnnnn)

Attribute_Domain_Values:

Unrepresentable_Domain:

The six digit number represents the two alleles that compose the genotype. Individual alleles are listed as three digit numbers indicating the number of base pairs in the respective allele. For example, an individual with a genotype of 115117, has an allele of 115 base pairs and an allele of 117 base pairs at the respective locus. Zeros indicate failure to score genotypes for the respective individual

Attribute:

Attribute_Label: Population

Attribute_Definition: name of population

Attribute_Domain_Values:

Unrepresentable_Domain: unbounded list of population names

Attribute:

Attribute_Label: Reach

Attribute_Definition: stream reach number where fish was captured

Attribute_Domain_Values:

Unrepresentable_Domain:

unbounded list of reach numbers; NA indicates that reach # was unknown

Attribute:

Attribute_Label: Sample #

Attribute_Definition: unique identification number assigned to each fish

Attribute_Domain_Values:

Unrepresentable_Domain: unbounded list of unique integers

Attribute:

Attribute_Label: Sample period

Attribute_Definition: sampling period when fish were captured

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: August 2002

Enumerated_Domain:

Enumerated_Domain_Value: March 2003

Attribute:

Attribute_Label: ScaleCard number

Attribute_Definition:

number of scale card and idenifier of cell on card where scales are stored

Attribute_Domain_Values:

Unrepresentable_Domain:

unbounded list of scale cards; this field lists the scale card followed by an underscore and the scale card cell where fish scales are stored. NA indicates that scales were not collected from that individual

Attribute:

Attribute_Label: Segment

Attribute_Definition: stream segment number where fish was captured

Attribute_Domain_Values:

Unrepresentable_Domain: unbounded list of stream segment numbers

Attribute:

Attribute_Label: Tray

Attribute_Definition: the PCR tray in which extracted DNA was stored

Attribute_Domain_Values:

Unrepresentable_Domain: unbounded list of tray numbers

Attribute:

Attribute_Label: Unit

Attribute_Definition: stream habitat unit number where fish was captured

Attribute_Domain_Values:

Unrepresentable_Domain:

unbounded list of habitat unit numbers; NA indicates that unit # was unknown

Metadata_Reference_Information:

Metadata_Date: 20040416

Metadata_Review_Date: 20040423

Metadata_Future_Review_Date:

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Metadata Coordinator

Contact_Organization:

U.S. Geological Survey Forest and Rangeland Ecosystem Science Center

Contact_Address:

Address_Type: mailing and physical address

Address: 3200 SW Jefferson Way

City: Corvallis

State_or_Province: OR

Postal_Code: 97331

Contact_Voice_Telephone: 541-750-7343

Contact_Facsimile_Telephone: 541-758-7761

Contact_Electronic_Mail_Address: george_lienkaemper@usgs.gov

Metadata_Standard_Name:

FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001.1-1999