Population Genetic Data of Pacific White Shrimp, Litopenaeus vannamei (Gulf of Fonseca, Honduras)

Metadata:

• Identification_Information
• Data_Quality_Information
• Entity_and_Attribute_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator:

Steve Travis, U.S. Geological Survey, National Wetlands Research Center

Publication_Date: 2005

Title:

Population Genetic Data of Pacific White Shrimp, Litopenaeus vannamei (Gulf of Fonseca, Honduras)

Geospatial_Data_Presentation_Form: digital tabular data

Description:

Abstract:

In October of 1998, Hurricane Mitch devastated parts of Central America, especially Honduras. Teams from U.S. Geological Survey traveled to Honduras to assist by improving the availability of base data/information and conducting research on the ecological/geological damage caused by the hurricane. One of the study involved the assessment of the Pacific white shrimp population in the Gulf of Fonseca. The aquaculture industry of Honduras is mostly concentrated along its Pacific coastline; the shrimp used in aquaculture are acquired from foreign sources in Panama, Ecuador, and the United States, and to a lesser extent from local estuaries. In 1998 through 2001, several extremely virulent diseases started to appear in the native Pacific white shrimp population, a possible result of the flushing of numerous aquaculture ponds containing the imported (captive) stock of shrimp by Hurricane Mitch. This study extracted the DNA of shrimp samples collected throughout the Gulf of Fonseca and analyzed population structure using several statistical methods.

Purpose:

To determine if the mixing of captive and native stocks of L. vannamei as a result of Hurricane Mitch and possibly coupled with a chronic history of smaller scale releases could be detected in the form of multiple genetically distinct subpopulations.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2001

Currentness_Reference: Ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -87.9388

East_Bounding_Coordinate: -87.2872

North_Bounding_Coordinate: 13.4658

South_Bounding_Coordinate: 12.9130

Description_of_Geographic_Extent: Gulf of Fonseca

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: genetic

Theme_Keyword: Pacific white shrimp

Theme_Keyword: estuary

Theme_Keyword: genetic structure

Theme_Keyword: aquaculture

Theme_Keyword: Hurricane Mitch

Theme_Keyword: postlarval shrimp

Theme_Keyword: population differentiation

Theme_Keyword: DNA

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Honduras

Place_Keyword: Gulf of Fonseca

Place_Keyword: Estero San Bernardo

Place_Keyword: Bahia San Lorenzo

Place_Keyword: Bahia Chismuyo

Place_Keyword: Estero el Capulin

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None

Taxonomic_Keywords: Litopenaeus vannamei

Taxonomic_Keywords: species

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom

Taxon_Rank_Value: Animalia

Taxonomic_Classification:

Taxon_Rank_Name: Division

Taxon_Rank_Value: Arthropoda

Taxonomic_Classification:

Taxon_Rank_Name: Class

Taxon_Rank_Value: Malacostraca

Taxonomic_Classification:

Taxon_Rank_Name: Subclass

Taxon_Rank_Value: Eumalacostraca

Taxonomic_Classification:

Taxon_Rank_Name: Order

Taxon_Rank_Value: Decapoda

Taxonomic_Classification:

Taxon_Rank_Name: Family

Taxon_Rank_Value: Penaeidae

Taxonomic_Classification:

Taxon_Rank_Name: Genus

Taxon_Rank_Value: Litopenaeus

Taxonomic_Classification:

Taxon_Rank_Name: Species

Taxon_Rank_Value: vannamei

Applicable_Common_Name: Pacific White Shrimp

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.

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 of 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 computer 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: Steve 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 anlaysis, 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: 800 327-3002

Contact_Facsimile_Telephone: 650 638-5800

Data_Set_Credit:

The National Wetlands Research Center would like to acknowledge the following individuals or organizations for their assistance in all aspects of this study: Philippe Hensel, Adrian Oviedo, Gerardo Pavon, the Committee for the Defense and Development of the Flora and Fauna of the Gulf of Fonseca, Juan Alberto-Vaca, Michael Antolin, Kavita Belur, Simone Stevens, Jennifer Kemmerer, Darryl Felder, Acacia Alcivar-Warren, Joseph Heigel, and the U.S. Agency for International Development.

Native_Data_Set_Environment: Genographer Ver. 1.6, Arlequin Ver. 2.0, NTSYS-pc Ver. 2.1

Cross_Reference:

Citation_Information:

Originator: Travis, Steven E.

Publication_Date: 2003

Title:

Hurricane Mitch: population genetic structure of Pacific white shrimp from the Gulf of Fonseca, Honduras

Geospatial_Data_Presentation_Form: document

Publication_Information:

Publisher: U.S. Geological Survey

Publication_Place: Lafayette, LA

Series_Information:

Series_Name: Open File Report

Issue_Identification: 2003-174

Online_Linkage: <http://pubs.er.usgs.gov/ofr/ofr03174>

Cross_Reference:

Citation_Information:

Originator: Travis, S.E., J. Maschinski, and P. Keim

Publication_Date: 1996

Title:

An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Blackwell Publishing

Publication_Place: Malden, MA

Series_Information:

Series_Name: Molecular Ecology

Issue_Identification: 5:735-745

Cross_Reference:

Citation_Information:

Originator: Coen, E.S., T. Strachan, and G.Dover.

Publication_Date: 1982

Title:

Dynamics of concerted evolution of ribosomal DNA and histone gene families in the melanogaster species subgroup of Drosophila

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Elsevier

Publication_Place: Orlando, FL

Series_Information:

Series_Name: Journal of Molecular Biology

Issue_Identification: 158:17-35

Cross_Reference:

Citation_Information:

Originator: Lynch, M.

Publication_Date: 1990

Title: The similarity index and DNA fingerprinting

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Oxford Journals

Publication_Place: Oxford, England

Series_Information:

Series_Name: Molecular Biology and Evolution

Issue_Identification: 7:478-484

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

Publication_Information:

Publisher: Blackwell Publishing

Publication_Place: Malden, MA

Series_Information:

Series_Name: Molecular Ecology

Issue_Identification: 3:91-99

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

The accuracy of the attributes are 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. Modifications to some methods were conducted to ensure a higher degree of accuracy in the results.

Logical_Consistency_Report:

Sites for sample collection were chosen opportunistically over the entire range of the gulf as it borders the country, and all sites were bordered by red mangroves-dominated intertidal swamps. For DNA analysis, the desired 8 to 50 individuals per site were collected (the number of individuals collected was based on the abundance of postlarval at each site.) The samples from sites that had less than 8 individuals were excluded from the analysis (to overcome statistical issues associated with small sample sizes).

Completeness_Report:

All sites were sampled at least at one point; some sites had multiple sampling points (to detect the possible presence of localized genetic structure within some estuaries). Initially, sample sizes were set at a minimum of 25 individuals per sites. Due to unanticipated factors (such as scarcity and small physical size of the postlarvae, contamination of samples), the number of postlarvae for which AFLP profiles were successfully constructed ranged from 2 to 22 individuals per collection site. Methodology for developing a genetic profile was modified.

Lineage:

Methodology:

Methodology_Type: Field

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: hand-held seine

Methodology_Keyword: postlarval shrimp

Methodology_Keyword: hand-sorted

Methodology_Keyword: fine mesh

Methodology_Keyword: ethanol

Methodology_Keyword: plastic screw-cap tubes

Methodology_Keyword: collection

Methodology_Keyword: sampling

Methodology_Keyword: estuary

Methodology_Keyword: red mangroves

Methodology_Description:

Sample Collection - Postlarval shrimp were collected from 33 estuarine sites surrounding the Gulf of Fonseca during January and April of 2001. Collection was conducted in shallow shoreline waters using a hand-held seine with a fine mesh sufficient to capture postlarval shrimp >3 mm in length. The shrimp were hand-sorted from fish fry and other invertebrates and placed in labeled plastic screw-cap tubes filled with absolute ethanol. The samples were shipped back to NWRC at ambient temperatures.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: DNA

Methodology_Keyword: extraction

Methodology_Keyword: deionized water

Methodology_Keyword: AFLP

Methodology_Keyword: amplified fragment length polymorphism

Methodology_Keyword: genetic analyzer

Methodology_Keyword: electrophoresis

Methodology_Keyword: loci

Methodology_Keyword: ACG

Methodology_Keyword: AGT

Methodology_Keyword: primer

Methodology_Keyword: EcoRI primer

Methodology_Keyword: MseI primer

Methodology_Keyword: haplotype

Methodology_Keyword: nucleotide

Methodology_Keyword: genetic profile

Methodology_Keyword: Genographer 1.6

Methodology_Keyword: AMOVA

Methodology_Keyword: molecular variance

Methodology_Keyword: randomization

Methodology_Keyword: comparison

Methodology_Keyword: inbreeding

Methodology_Keyword: permutation procedure

Methodology_Keyword: multivariate cluster analysis

Methodology_Keyword: UPGMA

Methodology_Keyword: numerical taxonomy and multivariate analysis

Methodology_Keyword: distribution

Methodology_Keyword: dominant marker

Methodology_Keyword: Arlequin 2.0

Methodology_Keyword: NTSYS-pc 2.1

Methodology_Description:

Sample Preparation and Analysis - In the lab, the ethanol was rinsed from the samples in deionized water for 15 minutes prior to DNA extraction. DNA was extracted from the whole postlarval up to 2 cm in length according to the procedure of Coen et al. (1982); the number of samples extracted from each site depended on the abundance of the postlarvae at the particular site. A genetic profile was developed for each individual sample from amplified fragment length polymorphisms (AFLP) according to the methods of Travis et al. (1996) with some modifications. The procedure was peformed on an initial quantity of DNA equaling 50 ng per sample. A single primer combination was used, consisting of the selective nucleotides ACG and AGT attached to the 3' end of the EcoRI- and MseI- primer, respectively. Electrophoresis of amplified fragments was conducted on an ABI Prism 310 Genetic Analyzer. A fluorescently-labeled EcoRI primer was used during the final selective restriction fragment amplification, which was performed on a 2-fold dilution (in TE, pH 8.0) of the preamplification product. A 10-fold dilution of the final reaction product was conducted in deionized formamide prior to electrophoresis. The presence or absence of amplified fragments was tabulated on a per individual basis using Genographer 1.6. To avoid problems of low repeatability associated with certain loci, the setting for the software's illumination intensity was placed within a narrow range of its lowest possible value. Only fragments and individuals for which >90% of the data could be unambiguously scored were selected for futher analysis. To avoid introducing an upward bias into the analyses of population structure, all loci for which the frequency of the dominant haplotype (x) was >0.65 were omitted according to the x<3/N rule of Lynch and Milligan (1994), where N was set at a lower bound of 8 individuals per collection site. Population structure was assessed using statistical methods specifically designed to overcome the shortcomings inherent in dominant marker data. The first method was the use of an Analysis of Molecular Variance (AMOVA) to hierarchically partition the total genetic variance within and among the estuaries using Arlequin 2.0. The second method was to compute traditional F-statistics using a newly-developed Bayesian method which requires no prior knowledge of the level of inbreeding occurring within populations. The third method computed pairwise F-statistics among all possible comparisons of collection sites using the Fst-analog, F', based on the mean similarity coefficient, S, of Lynch (1990). The significance of pairwise F-statistics was evaluated on the basis of a permutation procedure which randomized individuals over each pair of populations under comparison using Arlequin 2.0. A total of 1.023 permutations were used to obtain each null distribution for the purpose of hypothesis testing under the null hypothesis of no differentiation, with alpha set at 0.025. A multivariate (UPGMA) cluster analysis was used to provide a visual representation of population structure with the aid of NTSYS-pc (Numerical Taxonomy and Multivariate Analysis System 2.1). Clusters were formed on the basis of pairwise similarity coefficients calculated according to Lynch (1990).

Process_Step:

Process_Description: See methodology

Process_Date: 2001 - 2002

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

The attributes in this study were measured and calculated for the purpose of determining if the mixing of native and captive stocks of Pacific white shrimp through the flooding of aquacultural ponds by Hurricane Mitch and smaller scale releases could be detected in the form of multiple genetically distinct subpopulations. For specific parameters measured, the USGS Open File report 2003-0174.

Entity_and_Attribute_Detail_Citation:

Travis, Steve E., and C. Edward Proffitt. 2003. Population Genetic Structure of Pacific White Shrimp, Litopenaeus vannamei, from the Gulf of Fonseca, Honduras. U.S. Geological Survey.

Metadata_Reference_Information:

Metadata_Date: 20051221

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 created another record for slightly altered data, such as reprojection.