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Nutria Population Estimation Genetic Data

Metadata:
Identification_Information:
Citation:
Citation_Information:
Originator:
U.S. Geological Survey, National Wetlands Research Center, and University of Louisiana at Lafayette, Biology Department
Publication_Date: 2006
Title: Nutria Population Estimation Genetic Data
Geospatial_Data_Presentation_Form: digital tabular data
Description:
Abstract:
The nutria (Myocastor coypus) is a large South American rodent that was widely introduced throughout Europe, Asia, and North America during the early 20th Century for its value to the fur trade. It is now considered a pest in many parts of the world due to its overgrazing of native wetland plant species. In North America, the problem is most notable in the states bordering the northern Gulf of Mexico, especially Louisiana. Population size for the nutria in this region was estimated at 20 million individuals by mid-century. Overgrazing by this species, in combination of human activity (such as flood control, maintenance dredging, and oil extraction) has contributed to loss of wetland habitat. A variety of government agencies have been charged with implementing nutria control measures in an effort to offset this wetland loss. Facing resource managers who have been charged with this task, is the challenge of accurately evaluating alternative control measures. Traditional sampling, such as mark-recapture techniques, can lead to significant bias into calculations of population size with trap shyness. This data set consists of genetic results based on non-invasive methodologies of sampling, using hair and feces. The methodology strives to track changes in population sizes over time to gauge their responses to control measures.
Purpose:
To develop the molecular and field-sampling protocols for acccurately estimating population sizes of the invasive nutria, Myocastor coypus from fecal and/or hair samples.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates_Times:
Beginning_Date: 200401
Ending_Date: 200604
Currentness_Reference: ground condition
Status:
Progress: In work
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -93.910660
East_Bounding_Coordinate: -88.777351
North_Bounding_Coordinate: 30.507537
South_Bounding_Coordinate: 28.892102
Keywords:
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: nutria
Theme_Keyword: population estimates
Theme_Keyword: genetics
Theme_Keyword: molecular marker
Theme_Keyword: DNA
Theme_Keyword: DNA extraction
Theme_Keyword: genotype
Theme_Keyword: non-invasive sampling
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Louisiana
Place_Keyword: LA
Place_Keyword: Coastal Louisiana
Place_Keyword: Jean Lafitte National Historical Park and Preserve
Place_Keyword: Rockefeller State Wildlife Refuge
Place_Keyword: Southern Louisiana
Taxonomy:
Keywords_Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Myocastor coypus
Taxonomic_Keywords: species
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:
Taxon_Rank_Name: Division
Taxon_Rank_Value: Chordata
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: Order
Taxon_Rank_Value: Rodentia
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Echimyidae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Myocastor
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: coypus
Applicable_Common_Name: nutria
Access_Constraints:
Any downloading and use of these data signifies a user's agreement to comprehension and compliance of the NWRC Standard Disclaimer. Insure all portions of metadata are read and clearly understood before using these data in order to protect both user and NWRC interests. See section 6.3 Distribution Liability.
Use_Constraints:
Acknowledgement of the National Wetlands Research Center 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 this data. Sharing new data layers developed directly from these data would also be appreciated by NWRC staff. Users should be aware that comparisons with other data sets for the same area from other time periods may be inaccurate due to inconsistencies resulting from changes in analyses and digital processes over time. These data are not legal documents and are not to be used as such.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, National Wetlands Research Center
Contact_Person: Steven Travis
Contact_Position: Ecologist
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: 337 266-8583
Contact_Facsimile_Telephone: 337 266-8592
Contact_Electronic_Mail_Address: steven_travis@usgs.gov
Analytical_Tool:
Analytical_Tool_Description:
ABI Prism 310 Genetic Analyzer: performs a variety of applications such as comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, and mutation detection.
Tool_Access_Information:
Online_Linkage:
http://www.appliedbiosystems.com
Tool_Access_Instructions: See website for information
Tool_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: Applied Biosystems, Inc
Contact_Address:
Address_Type: Physical
Address: 850 Lincoln Centre Drive
City: Foster City
State_or_Province: CA
Postal_Code: 94404
Country: USA
Contact_Voice_Telephone: 800 327-3302
Contact_Facsimile_Telephone: 650 638-5800
Native_Data_Set_Environment: unknown
Cross_Reference:
Citation_Information:
Originator: Callahan, C.R., A.P. Henderson, M.S. Eackels, and T.L. King
Publication_Date: 2005
Title:
Microsatelite DNA markers for the study of population structure and dynamics in nutria (Myocastor coypus)
Geospatial_Data_Presentation_Form: journal article
Publication_Information:
Publisher: Blackwell Publishing
Publication_Place: Malden, MA
Series_Information:
Series_Name: Molecular Ecology Notes
Issue_Identification: 5:124-126
Cross_Reference:
Citation_Information:
Originator: Miller, C.R., P. Joyce, and L.P. Waits
Publication_Date: 2002
Title:
Assessing allelic drop-out and genotype reliability using maximum likelihood
Geospatial_Data_Presentation_Form: journal article
Publication_Information:
Publisher: Genetics Society of America
Publication_Place: Bethesda, MD
Series_Information:
Series_Name: Genetics
Issue_Identification: 160:357-366
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Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
The accuracy of the attributes is dependent on the instrumentation and statistical software used for analyses. An exact accuracy value can not be determined due to the procedures and software used.
Logical_Consistency_Report:
Samples are collected and handled/stored separately to prevent cross-contamination. Three preservation methods have been evaluated along with three DNA extraction methods to determine the optimal combination. Because fecal samples generally yield small quantities of relatively low quality DNA, a "multiple-tubes" approach was taken to avoid committing genotyping errors. The maximum likelihood method of Miller et al. (2002) was used based on early multiple-tubes results; this would optimize the actual number of separate reactions required to assure appropriate accuracy.
Completeness_Report:
The completeness of these data are currently unknown since the project is still ongoing.
Lineage:
Methodology:
Methodology_Type: Field/Lab
Methodology_Identifier:
Methodology_Keyword_Thesaurus: None
Methodology_Keyword: DNA extraction
Methodology_Keyword: sampling
Methodology_Keyword: sample preservation
Methodology_Keyword: DET
Methodology_Keyword: buffering
Methodology_Keyword: freezing
Methodology_Keyword: preparation
Methodology_Keyword: fecal matter
Methodology_Keyword: hair
Methodology_Description:
Sample collection/preparation and DNA extraction - For 2004 and 2005, fecal samples were collected from different sites (a captive population at a research facility in New Iberia and Rockefeller State Wildlife Refuge). Each sample was handled with discardable weigh paper and placed in a separate sterile centrifuge tube. The samples were preserved according to three methods: 1) buffering in 70-100% ethanol, 2) freezing at -20 degrees Celsius, and 3) buffering in DETs (20% Dimethyl Sulfoxide, 0.25M ethylenediaminetetraacetic acid, 100 mM Tris, pH 7.5, and Sodium Chloride to saturation). DNA was extracted from the samples using three common methods: 1) buffering in GuSCN to suspend the DNA in solution, and capture of the DNA using a silica matrix, 2) extraction with the QIAamp DNA Stool Mini-kit manufactured by Qiagen, and 3) buffering in a salt solution and DNA capture using Chelex resin beads. The quality and yield of DNA resulting from each of these nine preservation/extraction combinations were evaluated on 0.7% Agarose gels in the presence of ethidium bromide, using the feces from 13 individuals. Once the optimal combination of preservation and extraction was determined, the length of time that fecal DNA remains viable in the field was determined by collecting fresh feces from 15 captive animals and storing them under ambient environmental conditions for 12, 24, 48, 72, and 168 hours prior to the preservation/extraction procedures. For the 2006 collection, samples of hair were collected from individuals (extraction of DNA from fecal matter was not consistently successful). Hair capture methods were developed for the field and include, but are not limited to, sticky tape, barbed wire, and wire brushes.
Methodology:
Methodology_Type: Lab
Methodology_Identifier:
Methodology_Keyword_Thesaurus: None
Methodology_Keyword: genotype
Methodology_Keyword: accuracy
Methodology_Keyword: differentiation
Methodology_Keyword: DNA
Methodology_Keyword: allele
Methodology_Keyword: microsatellite loci
Methodology_Keyword: blood sample
Methodology_Keyword: fecal sample
Methodology_Description:
Genetic analysis - all samples will be genotyped, and data on the number of distinct individuals represented in the first and second samples will be used to estimate population size. To determine statistical accuracy of differentiating among individual nutria from fecal DNA, these results will be compared to the results generated from blood samples of the captive animals. The high quality DNA yielded by these blood samples will first be used to find a subset of the microsatellite loci developed in the initial phase of the study that can be used to differentiate among individuals with a minimum accuracy of 99% based on their respective numbers and frequencies of allele.
Process_Step:
Process_Description: See methodology
Process_Date: 2004-2006
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Entity_and_Attribute_Information:
Overview_Description:
Entity_and_Attribute_Overview:
The attributes in this study were measured and calculated for the purpose of developing molecular and field-sampling protocols for accurately estimating population sizes of nutria from fecal and hair samples.
Entity_and_Attribute_Detail_Citation: USGS Project number 8343BBF Task 3 plan
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Metadata_Reference_Information:
Metadata_Date: 20060213
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey, National Wetlands Research Center
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_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.
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