Author: Mahlatse Kgatla
Keywords: polyploidy, population genetics, everlasting daisy, morphometrics, Specimen

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

Glynis Goodman-Cron^1, Mahlatse Kgatla^2

1 University of the Witwatersrand, Animal, Plant and Environmental Sciences, Private Bag 3, 2050, Johannesburg, South Africa; 2 SANBI, 2 Cussonia Avenue, Brummeria, 0184, Pretoria, South Africa

Corresponding author(s): Glynis Goodman-Cron (Glynis.Goodman@wits.ac.za)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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

Keywords: polyploidy, population genetics, everlasting daisy, morphometrics, Specimen

Project details

Project title: Population genetics and morphological dataset for Helichrysum taxonomic Group 4 (Morphology)
Personnel: Glynis Goodman-Cron
Funding: Foundational Biodiversity Information Programme
Study area descriptions/descriptor: South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)

Data published through GBIF: http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip

Taxonomic coverage

General taxonomic coverage description: All everlasting daisies identified to genus level
Taxonomic ranks
Genus: Helichrysum
Common names: Everlasting Daisies

Spatial coverage

General spatial coverage: South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)
Coordinates: 34°44'31.2''S and 24°12'25.2''S Latitude; 17°8'20.4''E and 34°13'58.8''E Longitude 

Temporal coverage: 2013 - 2015

Methods

Method step description: 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.
Study extent description: South Africa (Mpumalanga, KwaZulu Natal, Eastern Cape, Western Cape)
Sampling description: Survey and loans of specimens

Datasets

Dataset description
Object name: Darwin Core Archive FBIP: Population genetics and morphological dataset for Helichrysum taxonomic Group 4
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.sanbi.org.za/iptsanbi/archive.do?r=fbip
Publication date of data: 2019-06-28
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2019-05-15
Hierarchy level: Dataset