Population Genetics Data for endangered species in the Lower Rio Grande Corridor

Metadata:


Identification_Information:
Citation:
Citation_Information:
Originator:
U.S. Geological Survey, National Wetlands Research Center; U.S. Fish and Wildlife Service, Corpus Christi Ecological Services; and Texas A&M University, Department of Biology
Publication_Date: unpublished material
Title:
Population Genetics Data for endangered species in the Lower Rio Grande Corridor
Geospatial_Data_Presentation_Form: digital tabular data
Description:
Abstract:
Advanced draft Recovery Plans exist for Astrophytum asterias (star cactus) and Lesquerella thamnophila (Zapata bladderpod), two endangered species endemic to South Texas and Northern Mexico. Also occurring in the same region are two other endangered species, Hoffmanseggia tenella (slender rush-pea) and Ambrosia cheiranthifolia (South Texas ambrosia). The Recovery Plans describe actions necessary for the conservation and recovery of an endangered species, which establishes criteria to downlist or delist the species. The goals of the Recovery Plans for the star cactus and Zapata bladderpod are to delist the species through discovery of more extant viable populations and/or reintroduction of the species into a suitable habitat in the historical range of the species. Before such reintroduction efforts can occur, critical genetics information is required to design populations in such a way as to maximize the probability of long-term survival. The genetics of the reintroduced populations may have to be quantitatively structured, with genetic input from several existing populations in appropriate proportion. Genetic information will also guide efforts to translocate individuals from one population to another to augment the genetic variability and viability of the population.
Purpose:
There are several objectives of this study that will benefit the endangered species: 1) to quantitatively determine genetic variation within each natural population or subpopulation, 2) to quantitatively determine genetic variation among (between) the various natural populations, and 3) to determine from the allele data whether gene flow among populations is primarily gametic (by pollen dispersal) or zygotic (by seed dispersal).
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 200404
Ending_Date: 200703
Currentness_Reference: ground condition
Status:
Progress: In work
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -100.125
East_Bounding_Coordinate: -97.150
North_Bounding_Coordinate: 28.30
South_Bounding_Coordinate: 23.00
Keywords:
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: genetic variation
Theme_Keyword: DNA
Theme_Keyword: endangered
Theme_Keyword: genetic population
Theme_Keyword: gene flow
Theme_Keyword: star cactus
Theme_Keyword: Zapata bladderpod
Theme_Keyword: slender rush-pea
Theme_Keyword: South Texas ambrosia
Theme_Keyword: recovery plan
Theme_Keyword: reintroduction
Theme_Keyword: variability
Theme_Keyword: viability
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Texas
Place_Keyword: South Texas
Place_Keyword: Mexico
Place_Keyword: Northern Mexico
Place_Keyword: TX
Place_Keyword: Rio Grande River
Place_Keyword: Lower Rio Grande Corridor
Place_Keyword: Cameron County
Place_Keyword: Hidalgo County
Place_Keyword: Jim Wells County
Place_Keyword: Kleberg County
Place_Keyword: Nueces County
Place_Keyword: Starr County
Place_Keyword: Webb County
Place_Keyword: Willacy County
Place_Keyword: Zapata County
Place_Keyword: Nuevo Leon
Place_Keyword: Tamaulipas
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Astrophytum asterias
Taxonomic_Keywords: Lesquerella thamnophila
Taxonomic_Keywords: Hoffmanseggia tenella
Taxonomic_Keywords: Ambrosia cheiranthifolia
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: Magnoliopsida
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Caryophyllidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Caryophyllales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Cactaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Astrophytum
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: asterias
Applicable_Common_Name: star cactus
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Dilleniidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Capparales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Brassicaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Lesquerella
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: thamnophila
Applicable_Common_Name: Zapata bladderpod
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Rosidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Fabales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Fabaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Hoffmanseggia
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: tenella
Applicable_Common_Name: slender rush-pea
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Asteridae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Asterales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Aseraceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Ambrosia
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: cheranthifolia
Applicable_Common_Name: South Texas ambrosia
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
Data_Set_Credit:
The National Wetlands Research Center would like to acknowledge the following organizations for their participation in this study: Texas A&M University Department of Biology, U.S Fish and Wildlife Service Corpus Christi Ecological Services, Texas Parks and Wildlife Department, Lower Rio Grande National Wildlife Refuge, Nature Conservancy, Texas Department of Transportation, San Antonio Botanical Gardens, Janssen Biological, and Universidad Autonoma de Tamaulipas Istituto de Ecologia y Alimentos
Cross_Reference:
Citation_Information:
Originator:
Reddy, B. Mohan, Alexa Pfeffer, Michael H. Crawford, and Banrida T. Langstieth
Publication_Date: 2001
Title:
Population Substructure and Patterns in Quantitative Variation among the Gollas of Southern Andhra Pradesh, India
Geospatial_Data_Presentation_Form: journal article
Publication_Information:
Publisher: Wayne State University Press
Publication_Place: Detroit, MI
Series_Information:
Series_Name:
Human Biology: The international journal of population biology and genetics
Issue_Identification: 73(2):291-306


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:
Will be reported once study is complete. Processes and methodology may change during the course of research.
Completeness_Report:
The completeness of these data is currently unknown since the project is still ongoing.
Lineage:
Methodology:
Methodology_Type: Field
Methodology_Identifier:
Methodology_Keyword_Thesaurus: None
Methodology_Keyword: leaf material
Methodology_Keyword: seasonal
Methodology_Keyword: population
Methodology_Description:
Sample collection - Leaf material will be collected from population sites within the study area and will be gathered seasonally (due to the cryptic nature of all species). 50 samples per population for all four species will be collected.
Methodology:
Methodology_Type: Lab
Methodology_Identifier:
Methodology_Keyword_Thesaurus: None
Methodology_Keyword: DNA
Methodology_Keyword: DNA extraction
Methodology_Keyword: allele
Methodology_Keyword: loci
Methodology_Keyword: primer
Methodology_Keyword: genetic diversity
Methodology_Keyword: population size
Methodology_Keyword: gene flow
Methodology_Keyword: chloroplast
Methodology_Keyword: electrophoresis
Methodology_Keyword: marker
Methodology_Keyword: nuclear
Methodology_Description:
Methods based on Reddy et al (2001) and analytical approaches for each of the species are as follows: 1) DNA will be extracted from (non-destructively) field-collected plant tissue. 2) From the DNA of one individual, a library of nuclear and chloroplast microsatellite genetic loci will be constructed, which involves sequencing of microsatellite-containing DNA fragments and designing primer pairs for a number of loci, of which 12 will be selected that amplify robustly in the polymerase chain reaction (PCR). If necessary, single nucleotide polymorphism markers from chloroplast DNA will be developed and used. 3) Using the selected microsatellite loci and non-destructive DNA sampling of each population as appropriate, allele data will be generated from all sampled individual plants using capillary acrylamide gel electrophoresis. 4) From the allele data, measures of genetic diversity within and among the populations will be obtained using measures such as FST, FIS, and FIT. 5) From FST and census data, a determination of effective population size, N will be made for each population. 6) From the allele data, information about type(s) of gene flow among population will be estimated using standard software package. The combined analysis of nuclear and chloroplast marker data will allow an estimate of relative rates of pollen and seed dispersal.
Process_Step:
Process_Description: See methodology
Process_Date: 2004-2007


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 variation within and among populations of the endangered species and determining if gene flow among populations is primarily gametic (by pollen dispersal) or zygotic (by seed dispersal).
Entity_and_Attribute_Detail_Citation: USGS Project number 2310APN Task 4 report


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.

Generated by mp version 2.7.33 on Mon Feb 13 13:42:33 2006