Coastal Louisiana Marsh Dieback Genetic Data for Spartina alterniflora (smooth cordgrass)

Metadata:

• Identification_Information
• Data_Quality_Information
• Entity_and_Attribute_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: U.S. Geological Survey

Publication_Date: 2005

Title:

Coastal Louisiana Marsh Dieback Genetic Data for Spartina alterniflora (smooth cordgrass)

Geospatial_Data_Presentation_Form: digital tabular data

Description:

Abstract:

A large-scale dieback event struck marshes along the Louisiana coast during the summer of 2000, in apparent response to a prolonged and severe drought. Large areas of the dominant marsh species, Spartina alterniflora, turned brown, followed by death of at least the aboveground structures or entire plant mortality. Genetic measures, along with some ecological parameters, were studied in the dieback-affected marsh in southwest Louisiana (Sabine National Wildlife Refuge), which was created in 1983 and for which existed predieback genetic datasets. A related study of genetic diversity was conducted on a second set of sites in southeastern Louisiana (near Bay Junop), where the dieback was more widespread. It was hypothesized that genetic diversity would be significantly reduced compared to predieback conditions and to nearby unaffected marshes. DNA extracted from leaf samples in the Sabine and Bay Junop sites was used to construct genotype profiles using AFLPs and analyzed using the complement of Simpson's Index (1-D), the richness measure G/N, average heterozygosity <H>, and the estimated proportion of polymorphic genes <P>.

Purpose:

To assess S. alterniflora population genetic diversity in predieback and postdieback conditions using genetic measures at the Sabine National Wildlife Refuge. Changes to genetic diversity were also measured in a site from the more affected areas of southeast Louisiana in order to determine whether these changes were consistent among the marshes from separate geographic regions.

Supplemental_Information:

There was an ecological component to this study, but this metadata only reflects the genetic component of the study.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1999

Ending_Date: 2001

Currentness_Reference: ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -93.50

East_Bounding_Coordinate: -91.00

North_Bounding_Coordinate: 30.00

South_Bounding_Coordinate: 29.125

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: genetic diversity

Theme_Keyword: marsh dieback

Theme_Keyword: DNA

Theme_Keyword: amplified fragment length polymorphism

Theme_Keyword: AFLP

Theme_Keyword: genetic analysis

Theme_Keyword: genotype profile

Theme_Keyword: heterozygosity

Theme_Keyword: polymorphic genes

Theme_Keyword: Simpson's Index

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Louisiana

Place_Keyword: LA

Place_Keyword: Southwest Louisiana

Place_Keyword: Southeast Louisiana

Place_Keyword: coastal Louisiana

Place_Keyword: Sabine National Wildlife Refuge

Place_Keyword: Hog Island Gully

Place_Keyword: Bay Junop

Place_Keyword: Terrebonne Bay

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:

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: Genographer version 1.6

Cross_Reference:

Citation_Information:

Originator: Edwards, Keith R., Steven E. Travis, and C. Edward Proffitt

Publication_Date: 200504

Title:

Genetic Effects of a Large-Scale Spartina alterniflora (Smooth Cordgrass) Dieback and Recovery in the Northern Gulf of Mexico

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Estuarine Research Federation

Publication_Place: Port Republic, MD

Series_Information:

Series_Name: Estuaries

Issue_Identification: 28:204-214

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

Publication_Date: 1989

Title:

Genetic diversity in a clonal narrow endemic, Erythronium propullans, and its wide-spread 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: Hartl, D.L., and A.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: 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: Montalvo, A.M., S.G. Conrad, M.T. Conkle, and P.D. Hodgekiss

Publication_Date: 1997

Title:

Population structure, genetic diversity, and clone formation in Quercus chrysolepis (Fagaceae)

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: 84:1553-1564

Cross_Reference:

Citation_Information:

Originator: E.H. Simpson

Publication_Date: 1949

Title: Measurement of Diversity

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Nature Publishing Group

Publication_Place: New York, NY

Series_Information:

Series_Name: Nature

Issue_Identification: 163:688

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 were collected from affected and reference (unaffected) areas for both sites (Sabine NWR and Bay Junop). For the Sabine marsh, samples were collected from 12 S. alterniflora ramets in each of the 20 sampling units for an overall projected number of 240 samples.

Completeness_Report:

Predieback genetic analysis was not conducted for the Bay Junop site; genetic diversity for this site was characterized only at the level of clones and populations. Pre and post analyses were conducted for just the Sabine NWR site; genetic diversity was characterized at the levels of clones and patches and over the entire marsh during the year prior to the dieback (fall 1999) and the year immediately following the dieback (summer 2001). Due to a lack of live S. alterniflora at some pre-established sampling points in the years 1999 and 2001, the projected 240 number of samples were not reached. In 1999, only 206 samples were collected; in 2001, only 205.

Lineage:

Methodology:

Methodology_Type: Field

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: sampling

Methodology_Keyword: ramets

Methodology_Keyword: grid

Methodology_Keyword: transects

Methodology_Keyword: bulls-eye

Methodology_Keyword: interval

Methodology_Description:

Sample collection - Green leaf tissue samples from both Sabine NWR and Bay Junop were collected. For the Sabine site, sampling units were laid out in the pattern of a grid on 40-m centers. Individual ramets from each sampling units were sampled in a bulls-eye pattern at three points, 1, 6, and 12m from the center, along each of four opposing compass bearings. For the Bay Junop site, individual ramets were sampled at 1-m intervals where available from transects run through each of 6 distinct patches ranging in length from 4 to 50m for an overall distance of 142m and an overall sample number of 51. Two 100-m transects, bisecting each other at right angles were run through the adjacent unaffected area and the reference area, with ramets sampled at 2-m intervals for an overall number of 76 and 60, respectively.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: DNA

Methodology_Keyword: electrophoresis

Methodology_Keyword: amplified fragment length polymorphism

Methodology_Keyword: AFLP

Methodology_Keyword: nucleotide

Methodology_Keyword: ACG

Methodology_Keyword: AGT

Methodology_Keyword: primer

Methodology_Keyword: genotype

Methodology_Keyword: Simpson's Index

Methodology_Keyword: index of fixation

Methodology_Keyword: loci

Methodology_Keyword: genetic analyzer

Methodology_Keyword: clonal diversity

Methodology_Keyword: ramet

Methodology_Keyword: richness measure

Methodology_Keyword: ANOVA

Methodology_Keyword: Genographer

Methodology_Keyword: EcoRI-primer

Methodology_Keyword: MseI-primer

Methodology_Keyword: genetic marker

Methodology_Keyword: polymorphic gene

Methodology_Keyword: Bayesian

Methodology_Keyword: genet

Methodology_Keyword: heterozygosities

Methodology_Keyword: genetic diversity

Methodology_Keyword: size standard

Methodology_Description:

Sample analysis - Molecular Protocols - DNA was extracted from all collected S. alterniflora samples (both sites) according to the methods of Travis et al. (2002), and genetic profiles were constructed using the AFLP protocol of Travis et al. (1996) with some modifications. The procedure was performed on an initial quantity of 50 ng of DNA per sample. A single primer combination consisting of the selective nucleotides ACG and AGT attached to the 3' end of the EcoRI-primer and MseI-primer, respectively was used. Electrophoresis of amplified fragments was performed on an ABI Prism 310 Genetic Analyzer in the presence of an internal size standard. This process required the use of a fluorescently labeled EcoRI-primer during the final selective restriction fragment amplification, which was performed in the presence of 1.5 mM magnesium chloride. The final reaction product was diluted 10-fold in deionized formamide prior to electrophoresis. The presence or absence of amplified fragments was tabulated on a per individual basis using Genographer ver1.6. To avoid problems of low repeatability, the illumination intensity of the software was set within a narrow range (ca. 5 units) of its lowest possible value, which had the effect of rendering 50-60% of the less intensely amplified fragments virtually invisible. Only those fragments and individuals were selected from which greater than 90% of the data could be unambiguously scored. Genetic Diversity - After all leaf tissue had been genotyped using amplified fragment length polymorphisms, common members of individual clones were identified as ramets sharing identical multilocus genotypes. The validity of this approach was assessed by calculating the random probability of separate clones sharing all population-specific markers in common. This was done by taking the product, over all loci, of the individual-locus probabilities, each calculated as the sum of squares of the expected haplotype frequencies. To be conservative, all ramets were included in the assessment with no a priori assumptions regarding clone identifies. For the Sabine marsh, clonal diversity was assessed within each sampling unit at three spatial scales, as well as over all sampling units combined within years and areas. Clonal diversity at the Bay Junop site was measured over entire area only: recovering dieback versus unaffected green zone versus reference site. Comparisons within sampling units were made on the basis of the complement of the Simpson's (1949) Index 1-D, adjusted for finite sample sizes. Broader comparisons were made on the basis of both D and the richness measure G/N (the total number of multilocus genotypes G, divided by the total number of samples N, sensu Pleasants and Wendel (1989)). Within sampling units, the diversity estimates at the larger spatial scales were inclusive of data used for the smaller-scale estimates; i.e., clonal diversity was estimated for 4 ramets at the 1-m scale, from an additional 4 ramets for a total of 8 ramets at the 6-m scale, etc. At each scale, comparisons of clonal diversity were performed across years (predieback and postdieback) using only those sampling units that came to be located in the dieback area and across zones for the postdieback year. One-way ANOVAs were used for each comparison. Patch (genotypic) structure of S. alterniflora at the Sabine marsh was characterized based on an index of fixation (Montalvo et al. 1997) using the Bayesian theta estimator of Holsinger et al. (2002). Only those patches comprised of more than one genet were included in this analysis. The level of structure apparent was determined at various local spatial scales, which corresponded to circles with radii of 1, 6, and 12m used in the analysis of clonal diversity. The level of patch structure was independently determined for the dieback area (both pre and post) and the unaffected green area (post only). The overall levels of genetic diversity across years and affected zones were compared at both the Sabine marsh and Bay Junop site on the basis of average heterozygosities (<H>) and estimated proportions of polymorphic genes (<P>); Hartl and Clark (1997). A purely phenetic measure of genetic diversity was also calculated, the average proportion of genetic markers shared in common among all individuals sampled within each population. This analysis was conducted at the level of genets.

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 determining genetic diversity of Spartina alterniflora over time (pre and post dieback) and area (southwest and southeast Louisiana). For specific parameters and results, consult the cited report for the study

Entity_and_Attribute_Detail_Citation:

Edwards, K.R. S.E. Travis, and C.E. Proffitt. 2005. Genetic effects of a large-scale Spartina alterniflora (smooth cordgrass) dieback and recovery in the Northern Gulf of Mexico. Estuarine Research Foundation, Port Republic, Maryland.

Metadata_Reference_Information:

Metadata_Date: 20060131

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.