Using environmental DNA metabarcoding to reveal fish biodiversity in marine ecosystems of South Africa

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dc.contributor.advisorVon der Heyden, Sophieen_ZA
dc.contributor.advisorCreer, Simonen_ZA
dc.contributor.advisorSeymour, Maten_ZA
dc.contributor.advisorCarvalho, Garyen_ZA
dc.contributor.authorCzachur, Molly Victoriaen_ZA
dc.contributor.otherStellenbosch University. Faculty of Science. Dept. of Botany and Zoology.en_ZA
dc.date.accessioned2022-03-07T06:29:09Z
dc.date.accessioned2022-04-29T12:52:38Z
dc.date.available2023-03-31T03:00:13Z
dc.date.issued2022-03
dc.descriptionThesis (PhD)--Stellenbosch University, 2022. en_ZA
dc.description.abstractENGLISH ABSTRACT: Background: South Africa is the meeting point of the Atlantic and Indian Oceans, where marine biodiversity thrives, and coastlines range from cool-temperate to tropical climates. This dynamic oceanographic regime supports over 2,000 fishes that utilise a range of habitat types, including seagrass meadows, mangrove and kelp forests, coral reefs and rocky and sandy shores. Here we describe the fish biodiversity of these coastal habitats using a metabarcoding method that, when compared with traditional methods, provides rapid species lists with reduced bias and less reliance on taxonomic expertise. Results: We applied an aquatic environmental DNA metabarcoding approach for describing the distribution of South African coastal fishes. Extensive troubleshooting and method optimisation led to a biomonitoring method that encompassed multiple coastal habitat types and allowed for large-scale datasets to be generated with a seasonal component. We have established the baseline knowledge for eDNA-based fish distribution in the region, with trends reflecting known patterns of fish biodiversity. Significance: It has been demonstrated that eDNA metabarcoding is a useful biomonitoring tool for South African coastal fishes, proving successful across large spatial scales with the use of a single method that is inclusive of different coastal habitat types and climates, and across varying levels of coastal development and marine protection. This data is a stepping-stone to producing more rapid coastal fish datasets, and an important layer for evidence-based marine spatial planning in the future.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Agtergrond: Suid-Afrika is die ontmoetingspunt van die Atlantiese en Indiese Oseaan, waar mariene biodiversiteit floreer, en kuslyne wissel van koel-gematigde tot tropiese klimate. Hierdie dinamiese oseanografiese stelsel ondersteun meer as 2 000 vis spesies wat 'n verskeidenheid habitatte gebruik, insluitend seegrasweie, mangrovewoude en rotsagtige en sandstrande. Hier beskryf ons die -biodiversiteit van die kushabitat met behulp van 'n meta- strepieskoderingsmetode wat, in vergelyking met tradisionele metodes, vinnige spesielyste bied met verminderde vooroordeel en minder afhanklikheid van taksonomiese kundigheid. Resultate: Ons het 'n water-eDNS -meta-strepieskodering -benadering toegepas om die verspreiding van Suid -Afrikaanse kusvisse te beskryf. Uitgebreide probleemoplossing en metodeoptimalisering het gelei tot 'n biomoniteringsmetode wat verskeie tipes kushabitat insluit en grootskaalse datastelle met 'n seisoenale komponent gegenereer het. Ons het die basiskennis vir eDNS-gebaseerde visverspreiding in die streek gevestig, met neigings wat bekende patrone van visdiversiteit weerspieël. Betekenis: Ons het getoon dat eDNA -meta- strepieskodering 'n nuttige biomonitoringsinstrument is vir Suid -Afrikaanse kusvisse, wat oor groot ruimtelike skale suksesvol blyk te wees met die gebruik van 'n enkele metode. Wat ook verskillende tipes en klimate van die kus insluit, en op verskillende vlakke van kusontwikkeling en mariene beskerming toegapas kan word. Hierdie gegewens is 'n wegspringblok vir die totstandkoming van vinnige kusvisdatastelle en 'n belangrike komponent vir bewys-gebaseerde mariene ruimtelike beplanning in die toekoms.af_ZA
dc.description.versionDoctorateen_ZA
dc.embargo.terms2023-03-31
dc.format.extentxvii, 119 pages : illustrations (some color), mapsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/125069
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshBiodiversity -- South Africaen_ZA
dc.subject.lcshMarine biodiversity -- Indian Oceanen_ZA
dc.subject.lcshFishes -- South Africa -- Geographical distributionen_ZA
dc.subject.lcshFishes -- Habitat -- South Africaen_ZA
dc.subject.lcshEnvironmental DNAen_ZA
dc.subject.lcshMetabarcodingen_ZA
dc.subject.lcshMarine ecosystem management -- South Africa -- Atlantic Coasten_ZA
dc.subject.nameUCTDen_ZA
dc.titleUsing environmental DNA metabarcoding to reveal fish biodiversity in marine ecosystems of South Africaen_ZA
dc.typeThesisen_ZA
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Doctoral Degrees (Botany and Zoology)