Biogeography, biodiversity, and barcodes: accounting for seagrass associated biodiversity along the South African coastline

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dc.contributor.advisorVon der Heyden, Sophieen_ZA
dc.contributor.authorFagg, Courtneyen_ZA
dc.contributor.otherStellenbosch University. Faculty of Science. Dept. of Botany and Zoology.en_ZA
dc.date.accessioned2022-03-04T15:15:34Z
dc.date.accessioned2022-04-29T09:35:40Z
dc.date.available2022-03-04T15:15:34Z
dc.date.available2022-04-29T09:35:40Z
dc.date.issued2022-04
dc.descriptionThesis (MSc)--Stellenbosch University, 2022.en_ZA
dc.description.abstractENGLISH ABSTRACT: Environmental DNA metabarcoding is gaining momentum for global biodiversity studies. Many studies have demonstrated the ability of metabarcoding to characterize communities for biodiversity surveys, biogeographical analyses, and impact assessments. However, few studies have been performed along the complex coastline of South Africa, which is influenced by two current systems that shape three highly diverse biogeographic regions (the subtropical and warm temperate regions on the east coast, and cool temperate region on the west coast); especially in highly variable estuarine systems. Given the important ecological and economic services that estuaries, their seagrasses and their associated biodiversity provide, it is important that metabarcoding is assessed as a tool for biodiversity studies in South African estuaries. Yet there are still many unknowns surrounding metabarcoding in estuaries, such as the effect of sampling substrate choice on the communities returned, and the ability of metabarcoding to capture biogeographical variation. As such, this study aimed to investigate metabarcoding using a partial fragment of the mitochondrial cytochrome oxidase 1 (CO1) gene in six estuaries containing the seagrass, Zostera capensis, along the coastline of South Africa, with two estuaries per biogeographic region. Broadly, this project compared the multicellular, eukaryotic communities returned by different sampling substrates (water and three different sediment samples, including intertidal vegetated and unvegetated sediments, and subtidal vegetated sediment). There were some differences in community composition from water and sediment samples, likely due to the different communities harboured by the environments. It was expected that sediment substrates from different environments (intertidal and subtidal, and vegetated and unvegetated seagrass beds) would also capture different communities, yet there was no difference between them, which may likely reflect patchiness and insufficient sampling replication. This study further aimed to explore whether eDNA metabarcoding would capture the biogeographical signals associated with the South African coastline. Indeed, this approach was sufficient to detect variation in communities along the coastline to delineate biogeographic regions. The communities returned by regions were significantly different, with the strongest biogeographic differentiation between the east and west coast sites. Furthermore, species richness was found to be greatest in the warm temperate region as has been shown by previous studies. Finally, a redundancy analysis was used to explore the environmental variables that could explain the variation in communities between regions, which showed that nitrate, mean sea surface temperate and water quality were the three most powerful explanatory variables. In all, this study showed that selection of sampling substrate is critical for determining community structuring, and that overall metabarcoding is a useful tool to provide insights into biogeographical structuring of communities.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.af_ZA
dc.description.versionMastersen_ZA
dc.format.extentix, 100 pages : illustrations (some color)en_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/124828
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subjectBiodiversity -- South Africaen_ZA
dc.subjectDNA metabarcodingen_ZA
dc.subjectSeagrassen_ZA
dc.subjectBiogeography -- South Africaen_ZA
dc.subjectSampling substratesen_ZA
dc.subjectCytochrome oxidase -- Genetic aspectsen_ZA
dc.subjectMitochondrial DNAen_ZA
dc.subjectUCTDen_ZA
dc.titleBiogeography, biodiversity, and barcodes: accounting for seagrass associated biodiversity along the South African coastlineen_ZA
dc.typeThesisen_ZA
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Masters Degrees (Botany and Zoology)