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FBIP: Population genetics and morphological dataset for Helichrysum taxonomic Group 4

Latest version published by South African National Biodiversity Institute on Jun 28, 2019 South African National Biodiversity Institute

Morphological and molecular data to delineate possible speciation events and gene flow among species.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 346 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 346 records in English (12 KB) - Update frequency: unknown
Metadata as an EML file download in English (14 KB)
Metadata as an RTF file download in English (12 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Goodman-Cron G (2019): FBIP: Population genetics and morphological dataset for Helichrysum taxonomic Group 4. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip&v=1.0

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 3fd87f77-1da0-44c7-b5e7-5c33103ca18c.  South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.

Keywords

polyploidy; population genetics; everlasting daisy; morphometrics; Specimen

Contacts

Who created the resource:

Glynis Goodman-Cron
Associate Professor
University of the Witwatersrand Animal, Plant and Environmental Sciences, Private Bag 3 2050 Johannesburg Gauteng ZA 0117176480
https://www.wits.ac.za/staff/academic-a-z-listing/g/glynisgoodmanwitsacza/

Who can answer questions about the resource:

Glynis Goodman-Cron
Associate Professor
University of the Witwatersrand Animal, Plant and Environmental Sciences, Private Bag 3 2050 Johannesburg Gauteng ZA 0117176480
https://www.wits.ac.za/staff/academic-a-z-listing/g/glynisgoodmanwitsacza/
Kelsey Glennon
Senior Lecturer
University of the Witwatersrand Animal, Plant and Environmental Sciences, Private Bag 3 2050 Johannesburg Gauteng ZA 0117176428
https://kelseylglennon.weebly.com/

Who filled in the metadata:

Glynis Goodman-Cron
Associate Professor
University of the Witwatersrand Animal, Plant and Environmental Sciences, Private Bag 3 2050 Johannesburg Gauteng ZA 0117176480
https://www.wits.ac.za/staff/academic-a-z-listing/g/glynisgoodmanwitsacza/

Who else was associated with the resource:

Content Provider
Mahlatse Kgatla
FBIP Data Specialist
SANBI 2 Cussonia Avenue, Brummeria 0184 Pretoria Gauteng ZA 0128435196
http://fbip.co.za/contact/

Geographic Coverage

South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)

Bounding Coordinates South West [-34.742, 17.139], North East [-24.207, 34.233]

Taxonomic Coverage

All everlasting daisies identified to genus level

Genus  Helichrysum (Everlasting Daisies)

Temporal Coverage

Start Date / End Date 2013-01-01 / 2015-01-01

Project Data

Morphological and molecular data to delineate possible speciation events and gene flow among species

Title Population genetics and morphological dataset for Helichrysum taxonomic Group 4 (Morphology)
Identifier IBSG13052718273
Funding Foundational Biodiversity Information Programme
Study Area Description South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)

The personnel involved in the project:

Principal Investigator
Glynis Goodman-Cron

Sampling Methods

Survey and loans of specimens

Study Extent South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)

Method step description:

  1. Field collections: (on-going) Collections of individuals from populations of Helichrysum Group 4 species across South Africa are currently underway with appropriate permits. Previous work was used to identify target populations where ploidy-level has been established 1,2,3. PRECIS data was used to identify additional populations. Population locality information is collected with a hand-held GPS unit, and leaf tissue samples are collected for DNA analyses (vouchers will be deposited at J and the appropriate provincial herbarium). Currently, ~100 individuals have been collected all of the six provinces where Group 4 species occur. The investigators K. Glennon (co-) and G. Cron (PI) are conducting field collections and collections will be completed by March 2014. Ploidy-level determination: (on-going) Ploidy-level of collected populations for all species will be determined using chromosome squash (karyotype) protocols previously established in the lab and complemented with DNA content quantification using a flow cytometer (available at the Wits Medical School), whereby nuclei are stained and quantified via fluorescence. DNA content is a fast and reliable method to establish ploidy level in plants4,5. K. Glennon will carry out flow cytometry analyses and is starting to optimize the protocol. This work will be completed by June 2014. Phylogenetics and population genetics: (on-going) Molecular data will be used to examine relationships among currently named species and to identify potential new species. We will generate DNA barcode data and use these sequences to estimate relationships and investigate cryptic species. Amplified fragment length polymorphism (AFLP) profiles will also be generated using a modified protocol6 to obtain additional genome-wide markers for species identification. Further, microsatellite primers will be developed for H. odoratissimum using available protocols7 to estimate gene flow among populations and calculate genetic diversity estimates, both of which are important measures for determining extinction risks due to global change. Currently, AFLP profiles are being generated, and preliminary data suggest that there are at least four useful polymorphic primer pairs for this project. An additional two primer pairs have been identified to include in the dataset. These data will be analysed according to recently published protocols8. AFLP and microsatellite data will be collected by K. Glennon and nuclear and plastid sequence data by G. Cron (including other EMR species of Helichrysum). Phylogenetic analyses will be performed in collaboration with Dr. Nicola Bergh (Compton Herbarium, Kirstenbosch) on larger data sets of Helichrysum, including as many EMR species as possible. Given that some pilot data are already collected, we expect these data to be collected and analysed by September 2014. Morphological Measurements & Population Abundance: Floral trait measurements will be recorded following established protocols9. The height and width of the synflorescences of the capitula and the diameter of the capitula will be measured. In addition, the number of florets in the capitula will be counted, and determine whether the capitula are homogamous or heterogamous. Further, the height of the stems with capitula will be recorded, as this trait has been shown to vary between ploidies in other species (e.g. North American Heuchera grossulariifolia). In addition, vegetative traits (pubescence of leaves, stem thickness, leaf shape, odour) will be recorded to examine differences among populations and between ploidies. Representatives of floral visitors will be collected, identified and quantified at each selected population per Segraves and Thompson (1999). Permits for the collection of insects will be obtained from provincial authorities. K. Glennon will conduct measurements of plants in the field with the assistance of a postgraduate student. Measurement data will be completed by October 2014. In addition, population abundance will be estimated at each selected population. These data will indicate the prevalence of different ploidy-levels and species across different provinces, as well as in the EMR. Chemical analyses of H. odoratissimum: In collaboration with Prof. Alvaro Viljoen of Tshwane University of Technology, K. Glennon and a postgraduate (M.Sc.) student (should funds become available) will assess the presence and quantity of biochemical compounds among ploidy-levels with H. odoratissimum. A variety of biochemical compounds are present in Helichrysum species that are known to be important for medicinal purposes10. Previous work has shown that secondary chemistry can vary between ploidies11. Chemical compounds will be extracted from fresh tissue and analyzed using mass spectrometry and gas chromatography for volatile oils (e.g. flavonoids and terpenes) content. The presence and quantity of each volatile will be compared between ploidy-levels using appropriate statistical tests to determine whether compounds statistically significantly differ between ploidies. Quantifying and comparing chemical compounds between ploidies will be beneficial for those who use this plant for medical purposes. Chemical analyses are expected to be completed by August 2014.

Additional Metadata

Alternative Identifiers http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip