Genetic Structure of natural and restored shoalgrass (Halodule wrightii) populations in the northwestern Gulf of Mexico Data

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:

Genetic Structure of natural and restored shoalgrass (Halodule wrightii) populations in the northwestern Gulf of Mexico Data

Geospatial_Data_Presentation_Form: digital tabular data

Description:

Abstract:

Halodule wrightii is a common seagrass inhabitant of shallow waters throughout the Caribbean region; the species can also be found in the northern Gulf of Mexico waters. Over 450 hectares of H. wrightii (and associated Thalassia testudinum) disappeared from the bay margin of western Galveston Island, Texas between 1960 and 1982; this disappearance has been attributed to waterfront dredging, wastewater discharges, and unidentified pollution. By the early 1990s, water quality had improved and dredging impacts were minimized allowing for the natural and human-assisted revegetation of seagrasses in the region. A number of these restoration efforts have provided to be viable. This data set consists of experimental data that provided information on several key attributes of these restored populations' genetic structure of Halodule wrightii and how these attributes played a role in the successful restoration of these seagrass communities (around Galveston Bay, Texas).

Purpose:

To assess the individual, clonal, and population effects on the genetic structure of natural Halodule wrightii populations in the northwestern Gulf of Mexico for comparison with a series of restoration ranging in age from 2-7 yrs by using molecular markers in the form of amplified fragment length polymorphisms (AFLPs).

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2001

Ending_Date: 2004

Currentness_Reference: ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -96.50

East_Bounding_Coordinate: -94.625

North_Bounding_Coordinate: 29.625

South_Bounding_Coordinate: 28.50

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: seagrass

Theme_Keyword: genetic structure

Theme_Keyword: clonal reproduction

Theme_Keyword: genetic diversity

Theme_Keyword: AFLP

Theme_Keyword: restoration

Theme_Keyword: shoalgrass

Theme_Keyword: amplified fragment length polymorphism

Theme_Keyword: molecular marker

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: northwestern Gulf of Mexico

Place_Keyword: Texas

Place_Keyword: Galveston Bay

Place_Keyword: Galveston Island

Place_Keyword: TX

Place_Keyword: Redfish Cove

Place_Keyword: Christmas Bay

Place_Keyword: East Matagorda

Place_Keyword: Matagorda Bay

Place_Keyword: Dana Cove

Place_Keyword: Cold Pass

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None

Taxonomic_Keywords: Halodule wrightii

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: Alismatidae

Taxonomic_Classification:

Taxon_Rank_Name: Order

Taxon_Rank_Value: Najadales

Taxonomic_Classification:

Taxon_Rank_Name: Family

Taxon_Rank_Value: Cymodoceaceae

Taxonomic_Classification:

Taxon_Rank_Name: Genus

Taxon_Rank_Value: Halodule

Taxonomic_Classification:

Taxon_Rank_Name: Species

Taxon_Rank_Value: wrightii

Applicable_Common_Name: shoalgrass

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 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 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: Garmin GPS Model 38: used to acquire geographic coordinates

Tool_Access_Information:

Online_Linkage: <http://www.garmin.com>

Tool_Access_Instructions: See website for information - Model has been discontinued

Tool_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: Garmin International, Inc.

Contact_Address:

Address_Type: Physical

Address: 1200 East 151st Street

City: Olathe

State_or_Province: KS

Postal_Code: 66062-3426

Country: USA

Contact_Voice_Telephone: 913 397-8200

Contact_Facsimile_Telephone: 913 397-8282

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: 800 327-3002

Contact_Facsimile_Telephone: 650 638-5800

Data_Set_Credit:

The National Wetlands Research Center would like to acknowledge the following individuals and organizations for their assistance in all aspects of this study: J. Kemmerer, S. Stevens, J. Doerr, S. King, J. Salas, S. Hillen, National Oceanic and Atmospheric Administration Restoration Center, Texas Parks and Wildlife Commission, and Texas Commission on Environmental Quality's Galveston Bay Estuary Program.

Cross_Reference:

Citation_Information:

Originator: Travis, S.E., C.E. Proffitt, R.C. Lowenfeld, and T.W. Mitchell

Publication_Date: 2002

Title:

A comparative assessment of genetic diversity among differently-aged populations of Spartina alterniflora on restored versus natural wetlands

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Blackwell Publishing

Publication_Place: Malden, MA

Series_Information:

Series_Name: Restoration Ecology

Issue_Identification: 10:37-42

Cross_Reference:

Citation_Information:

Originator: Pleasants, J.M, and J.F. Wendell

Publication_Date: 1989

Title:

Genetic diversity in a clonal narrow endemic, Erythronium propullans, and its widespread progenitor, Erythronium albidium

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Botanical Society of America

Publication_Place: St. Louis, MO

Series_Information:

Series_Name: American Journal of Botany

Issue_Identification: 76:1136-1151

Cross_Reference:

Citation_Information:

Originator: Holsinger, K.E., P.O. Lewis, and D.K. Dey

Publication_Date: 2002

Title:

A Bayesian approach to inferring population structure from dominant markers

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Blackwell Publishing

Publication_Place: Malden, MA

Series_Information:

Series_Name: Molecular Ecology

Issue_Identification: 11:1157-1164

Cross_Reference:

Citation_Information:

Originator: Hartl, Daniel, L. and Andrew G. Clark

Publication_Date: 1997

Title: Principles of Population Genetics

Edition: 3rd

Geospatial_Data_Presentation_Form: book

Publication_Information:

Publisher: Sinauer Associates, Inc

Publication_Place: Sunderland, MA

Cross_Reference:

Citation_Information:

Originator: E.C. Pielou

Publication_Date: 1969

Title: An Introduction to Mathematical Ecology

Geospatial_Data_Presentation_Form: book

Publication_Information:

Publisher: Wiley-Interscience

Publication_Place: New York, NY

Cross_Reference:

Citation_Information:

Originator: Weir, B.S. and C.C. Cockerham

Publication_Date: 1984

Title:

Estimation of F statistics for the analysis of population structure

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Society for the Study of Evolution

Publication_Place: Lancaster, PA

Series_Information:

Series_Name: Evolution: international journal of organic evolution

Issue_Identification: 38:1358-1370

Cross_Reference:

Citation_Information:

Originator: Travis, S.E., C.E. Proffitt, and K.Ritland

Publication_Date: 2004

Title:

Population structure and inbreeding vary with successional stage in created Spartina alterniflora marshes

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Ecological Society of America

Publication_Place: Washington, DC

Series_Information:

Series_Name: Ecological Applications

Issue_Identification: 14:1189-1202

Cross_Reference:

Citation_Information:

Originator:

Vos, P. R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau

Publication_Date: 1995

Title: AFLP: a new technique for DNA fingerprinting

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Oxford Journals

Publication_Place: Oxford, England

Series_Information:

Series_Name: Nucleic Acids Research

Issue_Identification: 23:4407-4414

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.

Logical_Consistency_Report:

For sample collection, sites were chosen based on the nature of beds; samples were collected from four natural sites (found in sheltered bays and channels), two restoration sites, and a volunteer site.

Completeness_Report:

For the volunteer beds, the coordinates were collected for the center of the bed and not the location of the collected fragment. Leaf tissue was omitted from the extraction of DNA to avoid contamination with epiphytic algae.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:

The accuracy of the horizontal positions is based on the accuracy of the GPS equipment used to gather coordinates. According to the owner's manual for the Garmin Model 38, position accuracy is 5-10 meters with DGPS corrections or 15 meters without corrections.

Lineage:

Methodology:

Methodology_Type: Field

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: sampling

Methodology_Keyword: natural site

Methodology_Keyword: restoration site

Methodology_Keyword: volunteer site

Methodology_Keyword: GPS

Methodology_Keyword: 15cm diameter plastic corer

Methodology_Keyword: rhizome

Methodology_Keyword: fragment

Methodology_Keyword: planting site

Methodology_Keyword: global positioning system

Methodology_Keyword: shoots

Methodology_Keyword: perimeter

Methodology_Description:

Collection of samples - Material for genetic analyses was collected from beds in Redfish Cove, Dana Cove, Cold Pass, Christmas Bay, East Matagorda Bay, and Matagorda in 2001 and 2002. At each site, a 15 cm diameter plastic corer was used to retrieve specimens consisting of 100-150 mm long fragments having 3 to 5 shoots attached to a section of rhizome (one per core). For the volunteer site, seven fragments were collected within the perimeter of the bed. 42 beds were randomly selected from among the 90 beds in Redfish Cove. For all other restored and natural beds except for those at Cold Pass, fragments at 12-42 locations spaced 10-100 m apart were collected, with up to four replicates within the locations except where beds were distributed in small patches of <1-2 , diameter. Locations of each collected fragment were recorded with a hand-held Garmin GPS unit. Samples were placed in labeled plastic bags, stored on ice while in the field, and subsequently frozen in the lab prior to genetic analysis.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: multilocus genotype

Methodology_Keyword: AFLP

Methodology_Keyword: DNA

Methodology_Keyword: CTAB

Methodology_Keyword: PCR primer

Methodology_Keyword: ACG

Methodology_Keyword: AGG

Methodology_Keyword: ACA

Methodology_Keyword: ACG

Methodology_Keyword: heterozygosities

Methodology_Keyword: polymorphic alleles

Methodology_Keyword: differentiation

Methodology_Keyword: F-statistics

Methodology_Keyword: Bayesian approach

Methodology_Keyword: nucleotide

Methodology_Keyword: fragment

Methodology_Keyword: selective restriction fragment amplification

Methodology_Keyword: SRFA

Methodology_Keyword: polymerase chain reaction

Methodology_Keyword: PCR

Methodology_Keyword: EcoRI

Methodology_Keyword: MseI

Methodology_Description:

Sample preparation and analyses - DNA was extracted from seagrass rhizomes by using a standard CTAB-based method as described in Travis et al. (2002). A multilocus genotype for each seagrass sample was constructed on the basis of AFLPs generated according to the methods of Vos et al. (1995) as modified by Travis et al. (2004). This involved two successive polymerase chain reactions (PCR): a selective preamplification, involving one selective nucleotide, and a more stringent selective restriction fragment amplification (SRFA), with three selective nucleotides. In all, four combinations of PCR primers were used to generate AFLP markers in four separate SRFA reactions. A single primer containing a restriction site for EcoRI and the selective nucleotides ACG was paired with each of four primers containing a restriction site for MseI and the selective nucleotides ACC, AGG, ACA, or ACG. Identical multilocus genotypes were searched for among replicate seagrass fragments collected within locations in order to compare clonal richness and diversity among sites and to reduce the overall data set down to the level of genets for an evaluation of genetic population structure. The overall clonal richness at each location was computed as G/N, or the number of genotypes (genets), G, divided by the number of ramets sampled, N (senus Pleasants and Wendel 1989); this measure was used primarily for large samples, since its lower bound approaches zero as sample sizes approach infinity (upper bound=1). For comparisons of clonal diversity at the scale of individual beds, the complement of the Simpson Index, 1-D (Pielou 1969), averaged over beds within locations was used. Genetic diversity was assessed from the entire group of genets identified within each population on the basis of average heterozygosities and proportions of polymorphic alleles (Hartl and Clark 1997), as well as the inverse of the average proportion of markers shared between pairs of individuals, which was denoted as 1-S. Population differentiation was estimated by using the Bayesian approach of Holsinger et al. (2002), which provided traditional F-statistics equivalent to the 0-statistics of Weir and Cockerham (1984), and ranged from 0 to 1.

Process_Step:

Process_Description: See methodology

Process_Date: 2002-2004

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

The attributes in this study were measured and calculated for the purpose of assessing the individual, clonal, and population effects on the genetic structure of natural Halodule wrightii populations in the northwestern Gulf of Mexico for comparison with a series of restoration ranging in age from 2-7 yrs by using molecular markers in the form of amplified fragment length polymorphisms (AFLPs). For specific parameters measured, consult the Marine Ecology progress series on this research (once it is published).

Entity_and_Attribute_Detail_Citation:

Travis, S.E. and P. Sheridan. A comparative analysis of genetic population structure among natural and restored shoalgrass (Hadodule wrightii) populations along the northwest Gulf of Mexico Coast. Marine Ecology Progress Series: in preparation.

Metadata_Reference_Information:

Metadata_Date: 20060105

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.