DNA metabarcoding of zooplankton enhances community-level analyses of connectivity in a marine pelagic environment.
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Zooplankton are abundant and diverse marine organisms that form ecologically important communities in marine pelagic ecosystems. They are well-suited for biomonitoring of ecosystem health and changes in biodiversity because their community structure and biomass respond rapidly to environmental variation. Biomonitoring of zooplankton communities using traditional morphology-based species identification methods is labor-intensive due to their cryptic morphology, high diversity and small body size. Fast-developing molecular techniques such as DNA metabarcoding (large-scale, high-throughput DNA sequencing of targeted gene regions to simultaneously identify multiple species present in samples) may provide higher resolution, accurate, faster and more cost-effective biomonitoring tools. The primary objectives of this dissertation were to develop and test a novel DNA metabarcoding approach for biomonitoring of marine zooplankton over the continental shelf of eastern South Africa. Novel taxon-specific DNA mini-barcode primers were designed to increase species identification rates of selected taxa. Artificially assembled mock communities with known composition and relative abundances were then used in an experimental setup to test detection rates and the accuracy of designed and published primers. The DNA metabarcoding protocol was then used to assess connectivity among zooplankton communities over the narrow KwaZulu-Natal continental shelf. Plankton tow nets were used to sample cross-shelf transects at three sites (uThukela, Durban and Aliwal), which are strongly influenced by the Agulhas Current but differ in shelf width, seafloor substrate and benthic habitat structures. Connectivity network analysis detected distinct clustering of zooplankton communities associated with each transect. The hypothesis that a dynamic ocean current regime associated with the offshore Agulhas Current (nearby and flowing parallel to the shelf-edge) would result in similar well-mixed alongshore zooplankton communities was rejected. A strong benthicpelagic coupling effect was inferred based on the species composition of planktonic larvae and benthic adults occurring at the respective transects. This dissertation provides a refined and novel method for biomonitoring of marine pelagic environments in coastal waters, based on taxonspecific DNA metabarcoding of zooplankton communities. The approach is well-suited to measuring the long-term effects of climate change on marine pelagic ecosystems and ocean productivity.