Molecular investigation data for Purshia X subintegra.

Metadata:

• Identification_Information
• Data_Quality_Information
• Entity_and_Attribute_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: U.S. Geological Survey and the Arboretum at Flagstaff

Publication_Date: 2005

Title: Molecular investigation data for Purshia X subintegra.

Geospatial_Data_Presentation_Form: digital tabular data

Description:

Abstract:

Purshia X subintegra (Kearney) Henrickson (Arizona cliffrose) is an endangered xerophytic shrub of the transition zone geological province in central Arizona. It is believed that the species arose during a hybridization event occurring near the end of the last glacial maximum between 11,000 and 13,000 years before present. Although hybridization can be a major force in the evolution of many plant taxa, it can also represent a conservation issue if the hybrid species is difficult to discern based on morphology or if secondary range overlap with one of its progenitors places it in danger of re-assimilation. Molecular investigations indicate that hybrids identified using DNA markers are often mistaken for one of their progenitors based solely on morphology. This molecular investigation of Purshia X subintegra was conducted to assist in the clarification of the species. A reliable field method was devised for differentiating relatively pure stands of P. subintegra from stands that have been heavily influenced by introgression through secondary contact with P. stansburiana. Comparisons were also conducted among all surviving populations of P. subintegra and its rare progenitor, P. pinkavae, and with populations of P. stansburiana both inside and outside the current zone of sympatry. A hybrid index for each sampled individual based on the relative number of P. pinkavae - versus P. stansburiana specific markers in its genetic profile was calculated, and a stepwise discriminant function analysis was used to identify 4 morphological characters from among a group of 11, capable of correctly assigning Purshia individuals to one of three species categories with a 74% accuracy.

Purpose:

To reconcile discrepancies between the prevailing taxonomic view that Purshia X subintegra is a hybrid species of the rare P. pinkavae and the common P. stansburiana and the historical view that this species and the rare P. pinkavae species represent a single species of unknown origin.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2000

Currentness_Reference: ground condition

Status:

Progress: complete

Maintenance_and_Update_Frequency: none planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -113.50

East_Bounding_Coordinate: -110.50

North_Bounding_Coordinate: 36.25

South_Bounding_Coordinate: 33.25

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: hybridization

Theme_Keyword: introgression

Theme_Keyword: amplified fragment length polymorphisms

Theme_Keyword: AFLP

Theme_Keyword: stepwise discriminant function analysis

Theme_Keyword: transition zone

Theme_Keyword: rosaceae

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Arizona

Place_Keyword: AZ

Place_Keyword: San Carlos Basin

Place_Keyword: Sonoran Desert

Place_Keyword: Verde Valley

Place_Keyword: Bylas

Place_Keyword: Burro Creek

Place_Keyword: Horseshoe Lake

Place_Keyword: Dead Horse Ranch State Park

Place_Keyword: central Arizona

Place_Keyword: Grand Canyon

Place_Keyword: Walnut Canyon

Place_Keyword: Tonto National Forest

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None

Taxonomic_Keywords: Purshia x subintegra

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: Rosidae

Taxonomic_Classification:

Taxon_Rank_Name: Order

Taxon_Rank_Value: Rosales

Taxonomic_Classification:

Taxon_Rank_Name: Family

Taxon_Rank_Value: Rosaceae

Taxonomic_Classification:

Taxon_Rank_Name: Genus

Taxon_Rank_Value: Purshia DC. ex Poir

Taxonomic_Classification:

Taxon_Rank_Name: Species

Taxon_Rank_Value: Purshia x subintegra (Kearney) Henrickson

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: 800 327-3002

Contact_Facsimile_Telephone: 650 638-5800

Data_Set_Credit: *

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

Cross_Reference:

Citation_Information:

Originator: Huang, J., X. Ge, and M. Sun

Publication_Date: 2000

Title:

Modified CTAB protocol using a silica matrix for isolation of plant genomic DNA

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publisher: Biotechniques

Publication_Place: Westborough, MA

Series_Information:

Series_Name: Biotechniques

Issue_Identification: 28:432-434

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: Baggs, J.E., and J. Maschinski

Publication_Date: 2001

Title:

From the greenhouse to the field: cultivation requirements of Purshia subintegra, Arizona cliffrose

Geospatial_Data_Presentation_Form: conference proceedings

Publication_Information:

Publisher:

U.S Department of Agriculture, Forest Service, Rocky Mountain Research Station

Publication_Place: Fort Collins, CO

Series_Information:

Series_Name: Southwestern Rare and Endangered Plants Third Conference

Issue_Identification: 176-185

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: Martin, L.J., and M. B. Cruzan

Publication_Date: 1999

Title:

Patterns of hybridization in the Piriqueta caroliniana complex in Central Florida: evidence for an expanding hybrid zone

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: 53:1037-1049

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

The accuracy of the attributes is dependent on the instrumentation and statistical software used for analyses. The exact accuracy value is not known.

Logical_Consistency_Report:

Sites for collection were chosen based on observed morphology, introgressed or non-introgressed. Samples were collected from: sites where morphologies were deemed to be most characteristic of P. subintegra; sites where distributional overlap between the rare and common species and the presence of apparently introgressed morphologies suggested that the re-assimilation of P. subintegra by P. stansburiana may be underway; and sites where typological morphologies were observed. In designating markers, markers were considered species-diagnostic if they occurred in >75% of the individuals from at least one population of the first species, and none of the individuals from at least one population of the second species.

Completeness_Report:

Due to isolated, rugged terrain, and low population densities, the number of samples per collection site was variable, ranging from 10 to 23, with a mean of 15 and an overall number of 219. Putatively introgressed populations from the Verde Valley were not include in the principal coordinates analysis to visualize the degree of genetic isolation between certain Purshia populations.

Lineage:

Methodology:

Methodology_Type: Field

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: sampling

Methodology_Keyword: leaf tissue

Methodology_Keyword: collection

Methodology_Keyword: endangered population

Methodology_Keyword: introgressed

Methodology_Keyword: morphology

Methodology_Description:

Field collection - Leaf tissue samples were collected from each of the three endangered Purshia populations existing outside of the Verde Valley, as well as from five sites within the Verde Valley. In addition, introgressed individuals were collected from three sites in the Verde Valley. For P. stansburiana, samples were collected from two populations bordering the Verde Valley and from two non-Verde Valley populations.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: DNA

Methodology_Keyword: primer

Methodology_Keyword: genetic profile

Methodology_Keyword: leaf tissue

Methodology_Keyword: selective restriction fragment amplification

Methodology_Keyword: amplified fragment

Methodology_Keyword: electrophoresis

Methodology_Keyword: GeneScan 400HD ROX

Methodology_Keyword: size standard

Methodology_Keyword: AAA

Methodology_Keyword: AGC

Methodology_Keyword: AGG

Methodology_Keyword: AGT

Methodology_Keyword: ATG

Methodology_Keyword: ATT

Methodology_Keyword: nucleotide

Methodology_Keyword: marker

Methodology_Keyword: AFLP

Methodology_Keyword: amplified fragment length polymorphism

Methodology_Keyword: agarose

Methodology_Keyword: CTAB

Methodology_Keyword: cetlytrimethylammonium bromide

Methodology_Keyword: buffer

Methodology_Keyword: Genographer

Methodology_Keyword: genetic analyzer

Methodology_Description:

Molecular Marker Development - DNA was extracted from the leaf tissue according to the methods of Huang et al. (2000) with minor modifications. Specifically, 0.3-0.5 g of leaf material was grounded in liquid nitrogen, which was then suspended in 7mL of a CTAB homogenization buffer with 0.05% 2-mercaptoethanol. After a 20 minute incubation at 65 degrees Celsius, an equal volume of chloroform:isoamyl alcohol (24:1) was added to the reaction, which was mixed by inversion for 1 minute and then centrifuged at 4000 rpm for a hour. All subsequent steps were conducted in accordance with the cited methodology. The quality and yield of DNA via ethidium bromide staining in 0.7% agarose was estimated. Genetic profiles for each sample were developed on the basis of amplified fragment length polymorphisms in accordance with Travis et al. (1996) with the following modifications. The procedure was performed on 50ng of DNA per sample. Electrophoresis was performed 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 performed in deionized formamide prior to electrophoresis. The presence or absence of amplified fragments was tabulated on a per-individual basis using Genographer Version 1.6.0. Sizes, in base pairs, of all fragments were determined by comparison to an internal size standard, GeneScan 400 HD ROX. Six primer combinations were used to compare individuals from each Purshia population. The primers include a single EcoRI primer containing the selective nucleotide ACG in combination with six MseI primers, including the selective nucleotides AAA, AGC, AGG, AGT, ATG, and ATT. Only the markers thus generated that unambiguously scored for presence or absence in >90% of individuals were kept.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: stem cutting

Methodology_Keyword: perlite

Methodology_Keyword: heating mats

Methodology_Keyword: transplant

Methodology_Keyword: stalked gland

Methodology_Keyword: relative density

Methodology_Keyword: leaf width

Methodology_Keyword: leaf length

Methodology_Keyword: leaf area

Methodology_Keyword: leaf perimeter

Methodology_Keyword: leaf lobes

Methodology_Keyword: punctate gland

Methodology_Keyword: soil type

Methodology_Keyword: soil treatment

Methodology_Description:

Morphological Measurements - Rooted stem cuttings were cross-fostered in three different soil types in a common garden setting at the Arboretum at Flagstaff, Az according to the methods of Baggs and Maschinski (2001). Stem cuttings (ca. 10cm) were soaked in dilute bleach and dipped in Hormex 8 prior to placing them in perlite on heating mats for up to one year until good root growth had emerged. The cuttings were then tranplanted into their respective soil treatments. After approximately 20 months of growth, cuttings representing 166 of the 219 Purshia individuals included in our molecular survey were measured for the following variables: presence or absence of stalked glands on stems, relative density of stalked glands on stems, relative density of hairs on stems, leaf area, leaf length, leaf width, ratio of leaf length to leaf width, length of leaf perimeter, number of leaf lobes, relative density of hairs on leaves, and relative density of punctate glands on leaves. All measurements were averaged over soil types; leaf measurements were further averaged over 3-10 leaves per cutting. Relative densities of hairs and glands were scored on a scale of 0-5.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: species-diagnostic marker

Methodology_Keyword: genetic isolation

Methodology_Keyword: morphological character

Methodology_Keyword: introgression

Methodology_Keyword: regression analysis

Methodology_Keyword: discriminant analysis

Methodology_Keyword: hybrid status

Methodology_Keyword: genetic hybrid index

Methodology_Keyword: stepwise analysis

Methodology_Keyword: score

Methodology_Keyword: principal coordinates analysis

Methodology_Keyword: NTSYS

Methodology_Description:

Genetic Analysis - Species-diagnostic markers were developed to test the hypothesis that P. stansburiana and P. pinkavae are the true progenitors of P. subintegra. Based on these markers, the degrees of genetic isolation between Purshia populations inside and outside the distributional overlap of P. subintegra and P. stansburiana in the Verde Valley were further visualized using a principal coordinates analysis (using NTSYS ver. 2.1 and including calculation of a pairwise similarity matrix using the similarity coefficient of Lynch (1990)). All individuals collected from Verde Valley sites were lumped together by species. The putatively introgressed populations from Verde Valley were not included. To reveal morphological characters that could be reliably be used to determine the hybrid status of Purshia stands from Central Arizona, the species-diagnostic markers were used in calculations of a genetic hybrid index for each individual sampled, as described in Martin and Cruzan (1999). A stepwise regression analysis and a stepwise discriminant function analysis were conducted to determine which subset of the morphological measures was the most reliable at predicting either the actual hybrid index of each individual (regression analysis) or their hybrid status (discriminant analysis).

Process_Step:

Process_Description: See methodology

Process_Date: 2000-2004

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

The attributes in this study were measured and calculated for the purpose of deterimining if Purshia X subintegra is a hybrid of the species, P. pinkavae and P. stansburiana or is a representative of a single species of unknown origin. For specific parameters measured, consult the cited report for the study.

Entity_and_Attribute_Detail_Citation:

Travis, Steven E., Joanne E. Baggs, Joyce Maschinski, and Darren Johnson. Using molecular and morphological data to elucidate historic and current patterns of introgression in an endangered shrub (Purshia X subintegra; Rosaceae). in preparation.

Metadata_Reference_Information:

Metadata_Date: 20060124

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.