Investigating fine-scale population dynamics in the threatened Cape Dwarf eelgrass, Zostera capensis, using RADseq

Thesis (MSc)--Stellenbosch University, 2021.

ENGLISH ABSTRACT: Seagrasses are the foundational species of one of the world’s most productive and valuable coastal ecosystems, however they are also among the most highly threatened. Zostera capensis is the dominant seagrass in South African estuaries where it enhances local biodiversity and performs essential ecosystem services. It is currently listed as vulnerable on the IUCN Red List of Threatened Species, because of numerous anthropogenic pressures that threaten estuarine systems in the region. Utilising genomic tools can potentially help underpin conservation decision making through identifying important population structure and diversity, essential components of resistance and resilience to on-going disturbances. The goal of this project was to assess genomic diversity and population structure of Z. capensis, with the intention of informing management plans for the effective conservation and potential restoration of this important ecosystem engineer. To do this, DNA was extracted and sequenced from 96 individuals collected from eight populations of Z. capensis from the three largest marine biogeographic regions along the South African coastline. A double digest RAD sequencing approach was used to generate 5 208 Single Nucleotide Polymorphisms (SNPs), based on a de novo assembly. Outlier analyses identified 71 outlier SNPs, which were then removed from the complete dataset to create “neutral” and “adaptive” datasets. Surprisingly, there were no clones, despite it being widely believed that the species primarily reproduces through clonal propagation. and. Overall, genomic diversity was higher on the east coast of South Africa, contrary to previous findings, and there were limited indications of inbreeding although heterozygosity levels were low compared to other seagrass species. There is likely limited dispersal between disparate estuaries as there was a strong indication of isolation by distance between populations. In addition, associations between morphology, diversity and environmental variables were tested. Leaf length and leaf width were greater in all subtidal populations and varied across estuaries. Leaf area was shown to be associated with variation in environmental conditions and genomic diversity along the South African coastline. Shoot density was typically higher in intertidal populations and was influence by FIS values across populations. This suggests that both genomic processes and phenotypic plasticity act as adaptive mechanisms to local conditions in Z. capensis.

AFRIKAANSE OPSOMMING: Seegrasse is die fondasie spesies van een van die wêreld se mees produktiewe en waardevolle kus-ekosisteme, maar is egter ook een van die mees bedreigde spesies. Zostera capensis is ‘n dominante seegras in Suid-Afrikaanse riviermondings waar dit die inheemse biodiversiteit ondersteun en noodsaaklike ekosisteemdienste verskaf. Dit is tans gelys as kwesbaar op die IUCN Rooi Lys van Bedreigde Spesies, as gevolg van talle antropogeniese druk wat riviermondingstelsels in die streek bedreig. Die gebruik van genomiese gereedskap kan moontlik help om bewaringsbesluitneming te ondersteun deur belangrike bevolkingstruktuur en diversiteit, asook die noodsaaklike komponente wat weerstand en veerkrag verskaf teen voortdurende versteurings te identifiseer. Die doel van hierdie projek was om die genomiese diversiteit en bevolkingstruktuur van Z. capensis te evalueer, met die doel om bestuursplanne in te lig oor die effektiewe bewaring en potensiële herstel van hierdie belangrike ekosisteemingenieur. Om dit te bewerkstelig, is DNS uit 96 individue ge-ekstraheer en opgevolg, versamel uit agt populasies van Z. capensis vanuit die drie grootste mariene biogeografiese streke langs die Suid-Afrikaanse kuslyn. 'n Dubbelvertering-RAD-opvolgings metode was gebruik om 5 208 Enkel Nukleotied Polimorfismes (SNPs) te genereer, gebaseer op 'n de novo samestelling. Uitskieter analise het 71 uitskieter-SNP's geïdentifiseer wat uit die volledige datastel verwyder was om "neutrale" en "adaptiewe" datastelle te skep. Onverwags was daar geen klone nie, ten spyte daarvan dat dit wyd geglo word dat die spesie hoofsaaklik deur klonale voortplanting propageer. Oor die algemeen was die genomiese diversiteit hoër aan die ooskus van Suid-Afrika in teenstelling met vorige bevindings, en daar was beperkte indukasies van inteling alhoewel heterosigositeitsvlakke laer was in vergelyking met ander seegraspesies. Waarskynlik is daar beperkte verspreiding tussen uiteenlopende riviermondings aangesien daar 'n sterk indukasie was van isolasie deur afstand tussen die bevolkings. Daarbenewens is assosiasies tussen morfologie, diversiteit en omgewingsveranderlikes getoets. Blaarlengte en blaarwydte was groter in alle subgetypopulasies en het oor riviermondings gevarieer. Dit was gevind dat blaararea geassosieer is met variasie in omgewingstoestande en genomiese diversiteit langs die Suid- Afrikaanse kuslyn. Lootdigtheid was tipies hoër in tussengety populasies was beïnvloed was deur FIS waardes dwarsoor die populasies. Dit stel voor dat beide genomiese prosesse en fenotipiese plastisiteit dien as aanpassingsmeganismes by die plaaslike toestande van Z. capensis.

Masters