Browsing by Author "Govender, Ashrenee."

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DNA metabarcoding of zooplankton enhances community-level analyses of connectivity in a marine pelagic environment.
(2021) Govender, Ashrenee.; Willows-Munro, Sandi.; Groeneveld, Johan Conrad.; Singh, Sohana.
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.
Testing the utility of DNA barcoding in South African Hemiptera: using eThekwini species as a case study.
(2017) Govender, Ashrenee.; Willows-Munro, Sandi.; Rouget, Mathieu.
The eThekwini municipal region and surrounding areas (Durban, Kwazulu-Natal, South Africa) are situated within the globally important Maputaland-Pondoland-Albany biodiversity hotspot. The biodiversity present in this region is under significant pressure from urbanization and climate change. This highlights the need to provide tools that can assist in the discovery and identification of species at an accelerated pace, to create biodiversity inventories which can be used for appropriate conservation planning. The creation of species inventories is a difficult task, more especially for hyper-diverse groups such as terrestrial arthropods. These groups can be morphologically cryptic or difficult to identify using traditional morphology-based taxonomy. Therefore, molecular-based methods of species identification have been proposed to assist in traditional taxonomy. DNA barcoding has been suggested as a mechanism which enables biologists to “label” or “tag” species, using nucleotide variations in short sequences known as DNA barcodes. This study investigates the utility of DNA barcoding and the use of the mitochondrial cytochrome oxidase c subunit 1 (COI) marker to identify species of Hemiptera efficiently and accurately. This study presents a preliminary DNA barcode reference library for Hemiptera collected from 18 different localities within and around the eThekwini municipal region. To test the success of DNA barcoding and the COI marker, matches between morphospecies and barcode clusters (BINs) were analyzed and the presence of the DNA barcode gap in the data was examined. The DNA barcode gap is the gap between the intraspecific and interspecific genetic distances, the lack of the DNA barcode gap suggests that taxa cannot be reliably sorted into species based on the genetic data. Analyses revealed that DNA barcoding using the COI marker is a successful method of identifying Hemiptera species in this study. Thereafter, a case study was selected within the Buffelsdraai Landfill Site Community Reforestation Project, to test whether DNA barcoding could be used to assess the potential of Hemiptera as an indicator of ecological restoration success. The Hemiptera species composition and assembly were assessed by analyzing multiple diversity indices, ordination, UPGMA cluster analysis and phylogenetic analysis. Hemiptera was seen to be sensitive to changes in an ecosystem which make this order an effective environmental and biological indicator. With the help of DNA barcoding, specific families of Hemiptera were identified as habitat-specific and good biological indicators for future studies of ecological restoration and reforestation.