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Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding
Thesis (MSc)--Stellenbosch University, 2025.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613962443423744 |
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| access_status_str | Open Access |
| author | Courtaillac, Kira-Lee |
| author2 | Von der Heyden, Sophie |
| author_browse | Courtaillac, Kira-Lee Von der Heyden, Sophie |
| author_facet | Von der Heyden, Sophie Courtaillac, Kira-Lee |
| author_sort | Courtaillac, Kira-Lee |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132112 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:44:27.789Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132112 Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding Courtaillac, Kira-Lee Von der Heyden, Sophie Landschoff, Jannes Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology. Marine biodiversity -- South Africa Great African Seaforest -- Ecology Environmental monitoring -- Data processing Kelp bed ecology -- Africa, Southern Environmental DNA metabarcoding -- Technique Bioinformatics UCTD Thesis (MSc)--Stellenbosch University, 2025. Courtaillac, K. 2025. Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/933b9d7c-720d-4398-afae-40ee6f296c5b ENGLISH ABSTRACT: Popularised as the ‘Great African Seaforest’ (GASF), kelp forest ecosystems in southwestern South Africa span across one third of the country’s coastline and provide a complex habitat of ecological significance. Due to the many benefits that kelp forests provide, such as supporting high levels of biodiversity, research and conservation interest in the GASF is increasing, although contemporary studies on the biodiversity and biogeographic patterns of the GASF as a large-scale ecosystem are lacking. This thesis explores the potential of environmental DNA (eDNA) metabarcoding to capture fish biodiversity patterns within South Africa’s kelp forest ecosystems, to potentially contribute to improved ecosystem-scale monitoring. To maximise the detection of biodiversity, an optimised sampling framework is established in Chapter 1, through an analysis of eDNA signal variability across small spatiotemporal scales in two coastal kelp forest sites. Seawater sampling at two shoreline stations, depths, and time-points detected 113 operational taxonomic units (OTUs) across 32 families. Our findings revealed significant variations in community composition over spatial scales under 600 meters and within 24 hours, suggesting that sampling at multiple points and times within a site of interest is necessary to account for spatiotemporal variability in eDNA signals. For comprehensive biodiversity detection, including low-abundance species, it is recommended to maximise biological replication within the constraints of logistical capacity. While individual replicates yielded higher OTU richness than pooled samples, pooling still captured valuable broad-scale patterns suitable for ongoing monitoring efforts. These insights establish a sampling foundation for eDNA-based fish surveys in southern Africa’s kelp forests, that considers eDNA transport and persistence. Building on this framework, the second chapter applies eDNA metabarcoding to assess fish biodiversity across an extensive range of kelp forest ecosystems (~1000 km) in South Africa, establishing a contemporary baseline that reflects biogeographical patterns and captures the effects of the eastern leading-edge expansion of the GASF. Spanning two ecoregions (Southern Benguela and Agulhas) and three purported kelp forest types (Namaqua, Cape, and Agulhas), we analysed 192 eDNA samples, capturing diversity from eight sites with intra-site sampling to account for small-scale spatiotemporal variability. A total of 140 OTUs representing 39 functionally diverse marine fish families were detected. OTU richness increased significantly from west to east, and community composition differed markedly among biogeographical and intra-site predictors. Distinct biodiversity patterns were especially evident at De Hoop, a site marking the edge of kelp forest expansion, suggesting potential regional biodiversity shifts. While OTU accumulation curves did not reach saturation, intensive spatiotemporal sampling at sites with lower richness captured a larger proportion of the expected diversity. These findings confirm the effectiveness of eDNA metabarcoding as a complementary biomonitoring tool for detecting fish communities across large-scale ecosystems, offering valuable insights into the biodiversity dynamics of South Africa’s kelp forests. The results highlight the importance of continuing eDNA applications to enhance biodiversity monitoring in these critical marine habitats, thereby advancing our capacity to track shifting biological baselines. AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar. Masters 2025-05-23T18:23:08Z 2025-05-23T18:23:08Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132112 Stellenbosch University xx, 119 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Marine biodiversity -- South Africa Great African Seaforest -- Ecology Environmental monitoring -- Data processing Kelp bed ecology -- Africa, Southern Environmental DNA metabarcoding -- Technique Bioinformatics UCTD Courtaillac, Kira-Lee Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title | Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title_full | Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title_fullStr | Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title_full_unstemmed | Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title_short | Diving into the biodiversity of the Great African Seaforest using environmental DNA metabarcoding |
| title_sort | diving into the biodiversity of the great african seaforest using environmental dna metabarcoding |
| topic | Marine biodiversity -- South Africa Great African Seaforest -- Ecology Environmental monitoring -- Data processing Kelp bed ecology -- Africa, Southern Environmental DNA metabarcoding -- Technique Bioinformatics UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132112 |
| work_keys_str_mv | AT courtaillackiralee divingintothebiodiversityofthegreatafricanseaforestusingenvironmentaldnametabarcoding |