Snowy Plover Inter Simple Sequence Repeat (ISSR)

Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Leah R. Gorman and Susan M. Haig
Publication_Date: 2001
Title: Snowy Plover Inter Simple Sequence Repeat (ISSR)
Geospatial_Data_Presentation_Form: data file
Larger_Work_Citation:
Citation_Information:
Originator: Gorman, L. R.
Publication_Date: 2001
Title:
Population differentiation among Snowy Plovers (Charadrius alexandrinus) across North America
Geospatial_Data_Presentation_Form: M.S. Thesis
Publication_Information:
Publication_Place: Corvallis, OR
Publisher: Oregon State University
Description:
Abstract:
This data set contains Inter Simple Sequence Repeat band frequencies (ISSR) for eight Snowy Plover sampling areas in North America and Puerto Rico. The sampling areas are Puerto Rico, Florida, Texas, Great Plains, Utah, Eastern Oregon, Oregon Coast, and California.
Purpose:
Data were collected to describe population structure for Snowy Plovers in North America and the Caribbean.
Supplemental_Information: Science Information System Project #: 70-40
Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 1999
Currentness_Reference: date of laboratory analysis
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Description_of_Geographic_Extent:
The geographic range of samples collected included continental North America and Puerto Rico.
Bounding_Coordinates:
West_Bounding_Coordinate: -124.3
East_Bounding_Coordinate: -75.3
North_Bounding_Coordinate: 45.8
South_Bounding_Coordinate: 17.7
Keywords:
Theme:
Theme_Keyword_Thesaurus: none
Theme_Keyword: Snowy Plover
Theme_Keyword: Inter-simple sequence repeat
Theme_Keyword: ISSR
Theme_Keyword: population differentiation
Theme:
Theme_Keyword_Thesaurus: ISO19115 Topic Categories
Theme_Keyword: biota
Theme_Keyword: 002
Place:
Place_Keyword_Thesaurus: none
Place_Keyword: Puerto Rico
Place_Keyword: Florida
Place_Keyword: Texas
Place_Keyword: Great Plains
Place_Keyword: Utah
Place_Keyword: Oregon
Place_Keyword: California
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: none
Taxonomic_Keywords: Charadrius alexandrinus
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: 1997
Title: ITIS (Integrated Taxonomic Identification System)
Geospatial_Data_Presentation_Form: Database
Other_Citation_Details:
ITIS Taxonomic Serial Numbers (TSN) may be included under applicable common name.
Online_Linkage: <http://www.itis.usda.gov/plantproj/itis/index.html>
Taxonomic_Procedures: Refer to Methodology
General_Taxonomic_Coverage: ITIS Taxonomic Serial Number 176510
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: Aves
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Ciconiiformes
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Charadriidae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Charadrius
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: alexandrinus
Applicable_Common_Name: Snowy Plover
Access_Constraints:
Data are available only after research results have been published.
Use_Constraints: None
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Haig, Susan M.
Contact_Organization:
US 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) 750-7482
Contact_Facsimile_Telephone: (541) 758-7761
Contact_Electronic_Mail_Address: susan_haig@usgs.gov
Data_Set_Credit:
Funding was provided thanks to USGS Forest and Rangeland Ecosytem Science Center, USGS Species at Risk Program, and US Fish and Wildlife Service.
Cross_Reference:
Citation_Information:
Originator: Haig, S.M., C.L. Gratto-Trevor, T.D. Mullins, and M.A. Colwell
Publication_Date: 1997
Title:
Population identification of western hemisphere shorebirds throughout the annual cycle
Geospatial_Data_Presentation_Form: Journal article
Series_Information:
Series_Name: Molecular Ecology
Issue_Identification: 6: 413-427
Cross_Reference:
Citation_Information:
Originator: Lynch, M., and B.G. Milligan
Publication_Date: 1994
Title: Analysis of population genetic structure with RAPD markers
Geospatial_Data_Presentation_Form: Journal article
Series_Information:
Series_Name: Molecular Ecology
Issue_Identification: 3: 91-99
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report: No tests for attribute accuracy were conducted
Logical_Consistency_Report:
DNA was amplified from single extractions to minimize variation in DNA quality and concentration. Negative controls were run to prevent scoring artifact bands. Low quality DNA samples were eliminated from the analyses.
Completeness_Report: See methods
Lineage:
Methodology:
Methodology_Type: Lab
Methodology_Description:
Genomic DNA was extracted from Snowy Plover blood and tissue samples as described in Gorman, 2001. The ISSR method utilizes a single primer anchored to a simple sequence repeat (SSR), or microsatellite, to amplify the region between adjacent repeats. Amplifications were carried out in 10X buffer (20 mM Tris-C2H3O2, pH 9.0; 10 mM NH4SO4 sulfate; 75 mM KC2H3O2; 0.05% Tween® 20); 1.5 mM MgCl2; 5 mg/mL acetamide; 100 µM dNTPs; 0.15 µM primer; 50 ng of genomic DNA; fluorescent dUTPs (0.2 mM [R110]dUTP or 0.2 mM [R6G]dUTP or 0.8 mM dUTP [TAMRA]); and 1.9 units of Taq polymerase (Promega) per 25 µL reaction. A PTC-100 thermal cycler (MJ Research) was programmed for 34 cycles of the following parameters: denaturation for 30 s at 93°C, annealling for 30 s at 45°C, and elongation for 2 min at 72°C. A single 10 min elongation at 72°C followed the cycles, and reactions were held at 4°C until removed from the thermal cycler. Two methods of electrophoresis were utilized to visualize bands of different sizes. First, we loaded 15 µL of each reaction into a 2% agarose gel stained with EtBr, and electrophoresed for 4 h in TBE (90 mM Tris base; 90 mM Boric Acid; 2 mM EDTA, pH 8.0). A one Kb ladder (GibcoBRL) served as a molecular size standard. Amplification products between 1000 and 1400 bp were scored as present (1) or absent (0) from the agarose gel. Further, PCR products were electrophoresed on an ABI Prism 377 automated sequencer (Applied Biosystems) at the Central Services Laboratory at Oregon State University. Briefly, amplification products were loaded in a 5% LongRanger (6 M Urea) denaturing gel, and run for 5 h with Filter Wheel A, and Genescan 2500 [Rox] as an internal lane standard. Gels were analyzed utilizing GeneScan Analysis 2.1 software (Applied Biosystems). Fragments between 400 and 1000 bp were scored as present (1) or absent (0) using Genotyper software (Applied Biosystems). Ninety primers from the University of British Columbia Biotechnology Laboratory (UBCBL) primer set #9 were initially screened for PCR amplification on agarose gels. Of these, 44 with distinct, well separated bands were screened for variability using 4 individuals from across the North American range (Cabo Rojo, Puerto Rico; St. George Island, Florida; Lower Rio Grande Valley NWR, Texas; San Diego County, California). We chose 16 bright, reproducible bands from eight primers for scoring in the final analysis. The primers utilized in the final analysis were UBC826: (AC)8T; UBC846: (CA)8RT; UBC848:(CA)8RG; UBC849: (GT)8YA; UBC850: (GT)8YC; UBC857 (AC)8YG; UBC859: (TG)8RC; and UBC886: VDV(CT)7. Band frequencies for each sampling area (Puerto Rico, Florida, Texas, Great Plains, Utah, Eastern Oregon, Oregon Coast, and California)) were calcuated using Lynch and Milligan’s (1994) Taylor expansion.
Methodology_Citation:
Citation_Information:
Originator: Gorman, L. R.
Publication_Date: 2001
Title:
Population differentiation among Snowy Plovers (Charadrius alexandrinus) across North America
Geospatial_Data_Presentation_Form: M.S. Thesis
Publication_Information:
Publication_Place: Corvallis, OR
Publisher: Oregon State University
Process_Step:
Process_Description: Refer to methods
Process_Date: Unknown
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: issr
Entity_Type_Definition:
ASCII file containing attributes describing the sequence locus and band frequency of each Snowy Plover population
Attribute:
Attribute_Label: Frequency
Attribute_Definition: band frequency in each population
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.0
Range_Domain_Maximum: 1.0
Attribute:
Attribute_Label: ISSR locus
Attribute_Definition:
Code for each locus (University of British Columbia (UBC) primer number and band length in base pairs)
Attribute_Domain_Values:
Unrepresentable_Domain: List of locus codes (refer to methods)
Attribute:
Attribute_Label: Population
Attribute_Definition: Snowy Plover population coded by geographic area
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PR
Enumerated_Domain_Value_Definition: Puerto Rico
Enumerated_Domain_Value: FL
Enumerated_Domain_Value_Definition: Florida
Enumerated_Domain_Value: TX
Enumerated_Domain_Value_Definition: Texas
Enumerated_Domain_Value: UT
Enumerated_Domain_Value_Definition: Utah
Enumerated_Domain_Value: GP
Enumerated_Domain_Value_Definition: Great Plains
Enumerated_Domain_Value: EO
Enumerated_Domain_Value_Definition: eastern Oregon
Enumerated_Domain_Value: OC
Enumerated_Domain_Value_Definition: Oregon Coast
Enumerated_Domain_Value: CA
Enumerated_Domain_Value_Definition: California
Metadata_Reference_Information:
Metadata_Date: 20050818
Metadata_Review_Date: 20001006
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: USGS Forest & Rangeland Ecosystem Science Center (FRESC)
Contact_Address:
Address_Type: Mailing and Physical Address
Address:
777 NW 9th St. Ste. 400
City: Corvallis
State_or_Province: Oregon
Postal_Code: 97330
Country: USA
Contact_Voice_Telephone: (541) 750-1030
Metadata_Standard_Name:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FFGDC-STD-001.1-1999
Generated by mp version 2.8.10 on Thu Aug 18 07:47:56 2005