Browsing by Author "Singh, Sohana."

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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.
Molecular phylogeny and seascape genetics of the panulirus homarus subspecies in the Western Indian Ocean.
(2016) Singh, Sohana.; Groeneveld, Johan Conrad.; Willows-Munro, Sandi.
Abstract available in PDF file.
Testing the utility of DNA barcoding for the rapid assessment of Formicidae biodiversity in the eThekwini region.
(2014) Singh, Sohana.; Willows-Munro, Sandi.
The biodiversity of Durban (eThekwini municipality) in KwaZulu Natal is primarily threatened by urbanization although other factors such as climate change and the spread of invasive species also pose a significant threat. Knowledge of what species exist within the city is important for biodiversity surveillance, detecting invasive taxa and uncovering cryptic species. Conducting a comprehensive biodiversity inventory is a daunting task, especially for hyperdiverse groups such as terrestrial arthropods, where closely related species can often only be separated by subtle morphological characters. This study investigated whether the barcoding marker, Cytochrome Oxidase C Subunit 1 (COI) can be used to efficiently and accurately delineate species of ants (family Formicidae) in comparison to traditional taxonomic approaches. The feasibility of DNA barcoding for assembling biodiversity inventories for urban areas which could be useful in conservation planning was also evaluated. A total of 619 individuals were sequenced from 23 geographic localities within the eThekwini region and surrounding regions. DNA barcoding revealed 80 provisional species/ “barcode clusters” or monophyletic lineages which could represent distinct species, while morphology revealed 51 different morphospecies. Extrapolation measures of species richness indicated that as many as 153 species of ants could occur in the city. Phylogenetic and phylogeographic analyses were performed on co-distributed species belonging to the genera Lepisiota, Camponotus, Pheidole and Pachycondyla to better understand the spatial distribution of genetic variability in the eThekwini region. Nuclear markers 18S rDNA and 28S rDNA were also sequenced and compared for a subsample of individuals from Camponotus and Pachycondyla. There was genetic variation at COI and the nuclear markers for each of the species examined. In order to fully elucidate the population genetic patterns which could be expected in eThekwini and surrounding regions, further sampling across more localities is essential. The use of more nuclear markers could also assist in uncovering these unique patterns of genetic variation in an urban setting. In this study, the utility of COI as a species diagnostic tool in ants was confirmed. The barcoding library constructed showed promise in highlighting reserves that should be preserved and possible cryptic speciation for further investigation.