Louisiana Marsh Dieback Genetic Similarity Matrix data

Metadata:
Identification_Information:
Citation:
Citation_Information:
Originator:
Louisiana State University, Department of Agronomy and Environmental Management
Publication_Date: 2005
Title: Louisiana Marsh Dieback Genetic Similarity Matrix data
Geospatial_Data_Presentation_Form: Digital tabular data
Larger_Work_Citation:
Citation_Information:
Originator:
Barataria-Terrebonne National Estuary Program Scientific-Technical Committee
Publication_Date: 20010207
Title:
Requests for submission of Scope of Services for Marsh Dieback and Nutria Control Emergency Response
Geospatial_Data_Presentation_Form: document
Publication_Information:
Publication_Place: Thibodaux, LA
Publisher:
Barataria-Terrebonne National Estuary Program Scientific-Technical Committee
Online_Linkage: <http://www.brownmarsh.net/reports/brown_marsh_rfp.pdf>
Description:
Abstract:
This data set consists of data matrix illustrating the similarity of the 44 brown marsh accessions. The matrix was based on Dice (1945) similarity coefficient (a measure to determine the degree of association between biotic samples.)
Purpose:
The bands in different brown marsh accession were scored and then these were analyzed using software known as NTSYS-PC to measure the genetic diversity among them. To determine those accessions with the presence of a particular band or marker can be judged similar in their genetic make up.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2001
Ending_Date: 2005
Currentness_Reference: ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Description_of_Geographic_Extent: Coastal Louisiana
Bounding_Coordinates:
West_Bounding_Coordinate: -93.910681
East_Bounding_Coordinate: -88.777417
North_Bounding_Coordinate: 30.509791
South_Bounding_Coordinate: 28.892107
Keywords:
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: emergent vegetation
Theme_Keyword: brown marsh
Theme_Keyword: dead zone
Theme_Keyword: transition zone
Theme_Keyword: dieback
Theme_Keyword: genetic diversity
Theme_Keyword: accession
Theme_Keyword: saltmarsh
Theme_Keyword: amplified fragment length polymorphism
Theme_Keyword: AFLP
Theme_Keyword: genetic similarity
Theme_Keyword: matrix
Theme_Keyword: Dice similarity coefficient
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Louisiana
Place_Keyword: Coastal Louisiana
Place_Keyword: LA
Place_Keyword: Southern Louisiana
Place_Keyword: Terrebonne Basin
Place_Keyword: Barataria Basin
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Spartina alterniflora
Taxonomic_Keywords: species
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Plantae
Taxonomic_Classification:
Taxon_Rank_Name: Division
Taxon_Rank_Value: Magnoliophyta
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Liliopsida
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Commelinidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Cyperales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Poaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Spartina
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: alterniflora
Applicable_Common_Name: smooth cordgrass
Access_Constraints:
Data generated by the Brown Marsh principal investigators will be available only to the project’s other principal investigators, following the established QA/QC review, for a period of two years. After two years from the finalization of the data, it shall be made available to the public. Please contact the principal investigator for exact date of availability. It is strongly recommended that these data be directly acquired from the Brown Marsh Database Information Management System server and not indirectly through other sources which may have changed the data in some way.
Use_Constraints:
Acknowledgement of the principal investigator as a data source would be appreciated in products developed from these data, and such acknowledgement as is standard for citation and legal practices for data source is expected by users of these data. Users should be aware that comparison with other data sets for the same area from other time periods may be inaccurate due to inconsistencies resulting from changes in mapping conventions, methodologies, data collections and computer processes over time. The principal investigator and the distributor shall not be liable for improper or incorrect use of these data, based on the description of appropriate/inappropriate uses described in this metadata document. The principal investigator and distributor make no claims as to the data’s suitability for other purposes. These data are not legal documents and are not to be used as such.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
Louisiana State University, Department of Agronomy and Environmental Management
Contact_Person: Prasanta K. Subudhi
Contact_Position: Assistant Professor
Contact_Address:
Address_Type: Physical
Address: 215 Sturgis Hall
City: Baton Rouge
State_or_Province: LA
Postal_Code: 70803
Country: USA
Contact_Voice_Telephone: 225 578-1303
Contact_Facsimile_Telephone: 225 578-1403
Contact_Electronic_Mail_Address: psubudhi@agcrt.lsu.edu
Native_Data_Set_Environment: Microsoft Excel 2000
Cross_Reference:
Citation_Information:
Originator: Dice, L.R.
Publication_Date: 194511
Title: Measures of the amount of ecologic association between species
Geospatial_Data_Presentation_Form: journal article
Publication_Information:
Publication_Place: Washington D.C.
Publisher: Ecological Society of America
Series_Information:
Series_Name: Ecology
Issue_Identification: Issue 26 297-302
Analytical_Tool:
Analytical_Tool_Description:
NTSYSpc, Version 2.1 - This software is used to discover pattern and structure in multivariate data. For this project, the software is used to determine similarities.
Tool_Access_Information:
Online_Linkage: <http://www.exetersoftware.com>
Tool_Access_Instructions: See website for information
Tool_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: Exeter Software
Contact_Address:
Address_Type: Mailing
Address: 47 Route 25A, Suite 2
City: Setauket
State_or_Province: NY
Postal_Code: 11733
Country: USA
Contact_Voice_Telephone: 800 842-5892-8437
Contact_Facsimile_Telephone: 631 689-0103
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
The accuracy of the attributes is determined by the accuracy of the statistical analysis software and the quality of the accessions marker data.
Logical_Consistency_Report:
All clear and unambiguous monomorphic and polymorphic fragments were scored.
Completeness_Report: There are no known omissions in the data.
Lineage:
Methodology:
Methodology_Type: Lab
Methodology_Identifier:
Methodology_Keyword_Thesaurus: None
Methodology_Keyword: silver stained gels
Methodology_Keyword: matrices
Methodology_Keyword: cluster analysis
Methodology_Keyword: monomorphic fragments
Methodology_Keyword: polymorphic fragments
Methodology_Keyword: NTSYSpc
Methodology_Keyword: similarity coefficient
Methodology_Keyword: presence
Methodology_Keyword: absence
Methodology_Keyword: arithmetic averages
Methodology_Description:
AFLP scoring and data analyses - Saved images of the silver stained gels of twelve primer combinations were scored as ‘1’ and ‘0’ for presence or absence of bands, respectively. All clear and unambiguous monomorphic and polymorphic fragments were scored. Binary matrices were made for statistical analyses using NTSYS-PC version 2.1 (Exeter Software, Setauket, NY, USA) (Rohlf, 1997). Dice (1945) coefficient of similarity was used to estimate similarity among the genotypes, and cluster analysis was performed following the unweighted pair group method with arithmetic averages (UPGMA) (Sneath and Sokal, 1973).
Process_Step:
Process_Description: See methodology
Process_Date: 2000-2005
Entity_and_Attribute_Information:
Overview_Description:
Entity_and_Attribute_Overview:
The tabular data for the brown marsh accessions' similarity matrix is organized according to the 44 genotype sampling areas. The similarity coefficient for each accessions vs. the other accessions is indicated within the rows and columns.
Entity_and_Attribute_Detail_Citation: Prasanta K. Subudhi, written comm. 5-27-05
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, National Wetlands Research Center
Contact_Person: Scott Wilson
Contact_Position: Electrical Engineer
Contact_Address:
Address_Type: Mailing and Physical
Address: 700 Cajundome Blvd
City: Lafayette
State_or_Province: LA
Postal_Code: 70506
Country: USA
Contact_Voice_Telephone: 337 266-8664
Contact_Facsimile_Telephone: 337 266-8513
Contact_Electronic_Mail_Address: scott_wilson@usgs.gov
Distribution_Liability:
Although these data have been processed successfully on a computer system at the designated principal investigator’s facility, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from the official Brown Marsh Database Information Management System server or from the principal investigator, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be given to the contents of the metadata file associated with these data. The Brown Marsh committee shall not be held liable for improper or incorrect use of the data described and/or contained herein. So, these data are provided as is and without any express or implied warranties. Also, use of trade names or commercial products in the metadata file is solely for the purpose of providing specific information, and does not imply recommendation or endorsement. Any downloading and use of these data signifies a user’s agreement to comprehension and compliance of the disclaimer. Insure all portions of metadata are read and clearly understood before using these data in order to protect both user and principal investigators interests.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: Microsoft Excel
Format_Version_Number: 2000+
File_Decompression_Technique: none
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: <http://www.brownmarsh.net>
Fees: None, if available online
Custom_Order_Process: None
Metadata_Reference_Information:
Metadata_Date: 20050531
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey/NWRC
Contact_Position: Metadata specialist
Contact_Address:
Address_Type: Mailing and Physical
Address: 700 Cajundome Blvd
City: Lafayette
State_or_Province: LA
Postal_Code: 70506
Country: USA
Contact_Voice_Telephone: 337 266-8500
Contact_Facsimile_Telephone: 337 266-8513
Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998
Metadata_Extensions:
Profile_Name:
Biological Data Profile of Content Standard for Digital Geospatial Metadata
Online_Linkage: <http://www.fgdc.gov/standards/status/sub5_2.html>
Metadata_Access_Constraints: None
Metadata_Use_Constraints:
Acknowledgement of the National Wetlands Research Center as the metadata source would be appreciated. Please cite the original metadata when using portions to create another record for slightly altered data, such as reprojection.
Generated by mp version 2.7.33 on Fri Jun 03 08:54:00 2005