Department of Genetics

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Browsing Department of Genetics by browse.metadata.advisor "Bolton, John"

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    DNA barcoding of South African red seaweeds (Rhodophyta)
    (2020-12) du Plessis, Jamie Cristen; Roodt-Wilding, Rouvay; Bolton, John; Anderson, Robert; Reddy, Maggie; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    ENGLISH ABSTRACT: On the rocky shoreline of South Africa, red algae are thriving, representing more than two-thirds of the diverse seaweed flora, forming species-rich communities as well as displaying high levels of endemism. The seaweed flora is well-studied and traditionally identified based on morphological characteristics, including characteristics such as life history, thalli type, basic anatomy, cell structures and post-fertilisation events. However, this mode of species identification can be complicated and erroneously implemented due to confounding attributes in many species of Rhodophyta. This includes factors such as simple morphology and anatomy, phenotypic plasticity due to environmental conditions and poor knowledge of female reproductive morphology and life history stages of some species. Accordingly, algal biosystematics have become more reliant on molecular techniques to aid in species identification, the discovery of cryptic species or confirming new distribution records. The research presented in the current study forms part of a preliminary investigation to add to the DNA barcoding reference database for macroalgae present in South Africa. Firstly, the utility of three unlinked barcodes, LSU D2/D3, COI-5P, and rbcL-3P, in the identification of genetic species groups were assessed on a diverse range of Rhodophyta species. A significant amount of the specimens was sourced from the main study area, Port Alfred, obtained in two sampling trips. A third sampling trip was focused on collecting specific species that proved difficult in obtaining molecular data for, sourced from localities these species are known to occur along the coast of South Africa. Initial identification of specimens, based on morphological and anatomical features, was performed in the field and a portion of each specimen was preserved for DNA analysis. DNA barcodes were generated using published primers, T16N and T24U for LSU D2/D3, M13LF3 and M13Rx for COI-5P and TLF1/TLF5 and rbcLrevNEW for rbcL-3P. This study generated 213 barcodes from the three gene regions, with the rbcL-3P barcode being the most efficient in the species- level identification of a diverse group of red seaweeds. The COI-5P was the most variable of the barcodes, thus being the most promising in species identification of closely related or cryptic species. In the current study, the LSU D2/D3 barcode was not reliable in the identification of closely related red algae species, therefore, caution should be taken when applying this marker in future studies. As a secondary aim, the monophyly of species and the phylogenetic placement of anomalous genetic species groups (e.g. Dichotomaria, Plocamium) were assessed implementing Bayesian Inference analyses. Molecular phylogenies highlighted possible new species and/or genera, hidden species diversity as well as misapplied species names. The application of DNA barcoding has emphasised the poor taxonomic state of certain groups in the Rhodophyta, therefore suggesting the dire need for taxonomic revision for some South African taxa. Accordingly, the research presented in this thesis provided valuable insights into algal biodiversity in South Africa and provided a reliable means of identification.