Composition and physiological roles of gut microbiota in the False Coding Moth (Thaumatotibia leucotreta)
- Authors: Richardson, Perryn Heather
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424457 , vital:72155
- Description: Gut microbiota can have a profound influence on host performance, behaviour and fitness. For False Codling Moth (FCM), Thaumatotibia leucotreta (Lepidoptera: Tortricidae), a major pest of citrus in South Africa, little work has been undertaken to date on gut microbe diversity or its influence on the host. This thesis aimed to i) characterise the gut microbiome of FCM under laboratory conditions and in FCM from the field, ii) and produce moths with reduced gut microbiota through egg dechorionation, which was followed by iii) the measurement of a suite of physiological traits, namely mass, survival and thermal stress in FCM from normal laboratory, dechorionated laboratory and field collected larvae that may be indicative of overall field performance. We aimed to directly test the hypothesis that gut microbial diversity partly determines insect performance and fitness by measuring its effects on growth, development, and tolerance to cold temperatures in FCM. FCM eggs that underwent dechorionation with sodium hypochlorite had an overall effect on larval survival, egg morphology and both larval and adult moth physiological measures. Increasing concentrations of sodium hypochlorite significantly decreased insect survival, (𝜒2(1, n = 10 850) = 21.724, p-value < 0.0001), with a concentration of ≈3.69% as the concentration limit (p-value < 0.001). Successful dechorionation of FCM was achieved with a wash of sodium hypochlorite at around 3.69% concentration and was visually confirmed by reduction of FCM egg surface area, (𝜒2(25, n = 260) p-value < 0.0001) and Scanning Electron Micrographs of the egg morphology. The gut microbiome of FCM from the different focus treatments was successfully characterized. Identification of the dominant bacterial families in these microbiomes revealed Xanthobacteraceae, Beijerinckiaceae and Burkholderiaceae in both the laboratory reared and field collected larvae, which suggests their systematic association with T. leucotreta. The most abundant genera were revealed as Bradyrhizobium, Methylobacterium and Burkholderia-Caballeronia-Paraburkholderia. Comparison of larval mass showed that treatment (dechorionated or not) had a significant effect on larval mass (𝜒2(2, n = 230) = 22.703, p-value < 0.001), field larvae were heavier than both control larvae and larvae with a disrupted gut microbiome. However, adult insects with a disrupted gut microbiome had more mass than individuals from the control and field-collected larvae with intact gut microbiomes (𝜒2(2, n = 230) = 39.074, p-value < 0.001). Despite the difference in mass between larval treatments, there was no significant difference in relative protein (𝜒2(2, n = 24) = 5.680, p-value = 0.06), carbohydrate (𝜒2(2, n = 24) = 3.940, p-value = 0.14) or lipid (𝜒2(2, n = 24) = 6.032, p-value = 0.05) content between individuals from the control and dechorionated treatments and field-collected individuals. Turning to thermal physiology, insects collected from the field took significantly longer to recover from chill coma than both laboratory treatments with intact and disrupted gut microbiomes (𝜒2(2, n = 129 = 39.659, p-value < 0.001). In addition, exposure to cold stress showed that treatment had a significant effect on insect mortality (𝜒2(2, n = 272) = 9.176, p-value = 0.01), with individuals from the control and dechorionated treatment being less likely to die after experiencing cold stress compared to field-collected individuals. Differences in the mass and thermal tolerance of insects with intact and disrupted gut microbiota suggest that gut microbiota may play an important role in the cold performance of T. leucotreta, and these findings constitute the basis for future molecular work on the functions of these bacterial taxa. This research highlights the need for consideration of the effects of T. leucotreta microbiome in current pest control programs. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Richardson, Perryn Heather
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424457 , vital:72155
- Description: Gut microbiota can have a profound influence on host performance, behaviour and fitness. For False Codling Moth (FCM), Thaumatotibia leucotreta (Lepidoptera: Tortricidae), a major pest of citrus in South Africa, little work has been undertaken to date on gut microbe diversity or its influence on the host. This thesis aimed to i) characterise the gut microbiome of FCM under laboratory conditions and in FCM from the field, ii) and produce moths with reduced gut microbiota through egg dechorionation, which was followed by iii) the measurement of a suite of physiological traits, namely mass, survival and thermal stress in FCM from normal laboratory, dechorionated laboratory and field collected larvae that may be indicative of overall field performance. We aimed to directly test the hypothesis that gut microbial diversity partly determines insect performance and fitness by measuring its effects on growth, development, and tolerance to cold temperatures in FCM. FCM eggs that underwent dechorionation with sodium hypochlorite had an overall effect on larval survival, egg morphology and both larval and adult moth physiological measures. Increasing concentrations of sodium hypochlorite significantly decreased insect survival, (𝜒2(1, n = 10 850) = 21.724, p-value < 0.0001), with a concentration of ≈3.69% as the concentration limit (p-value < 0.001). Successful dechorionation of FCM was achieved with a wash of sodium hypochlorite at around 3.69% concentration and was visually confirmed by reduction of FCM egg surface area, (𝜒2(25, n = 260) p-value < 0.0001) and Scanning Electron Micrographs of the egg morphology. The gut microbiome of FCM from the different focus treatments was successfully characterized. Identification of the dominant bacterial families in these microbiomes revealed Xanthobacteraceae, Beijerinckiaceae and Burkholderiaceae in both the laboratory reared and field collected larvae, which suggests their systematic association with T. leucotreta. The most abundant genera were revealed as Bradyrhizobium, Methylobacterium and Burkholderia-Caballeronia-Paraburkholderia. Comparison of larval mass showed that treatment (dechorionated or not) had a significant effect on larval mass (𝜒2(2, n = 230) = 22.703, p-value < 0.001), field larvae were heavier than both control larvae and larvae with a disrupted gut microbiome. However, adult insects with a disrupted gut microbiome had more mass than individuals from the control and field-collected larvae with intact gut microbiomes (𝜒2(2, n = 230) = 39.074, p-value < 0.001). Despite the difference in mass between larval treatments, there was no significant difference in relative protein (𝜒2(2, n = 24) = 5.680, p-value = 0.06), carbohydrate (𝜒2(2, n = 24) = 3.940, p-value = 0.14) or lipid (𝜒2(2, n = 24) = 6.032, p-value = 0.05) content between individuals from the control and dechorionated treatments and field-collected individuals. Turning to thermal physiology, insects collected from the field took significantly longer to recover from chill coma than both laboratory treatments with intact and disrupted gut microbiomes (𝜒2(2, n = 129 = 39.659, p-value < 0.001). In addition, exposure to cold stress showed that treatment had a significant effect on insect mortality (𝜒2(2, n = 272) = 9.176, p-value = 0.01), with individuals from the control and dechorionated treatment being less likely to die after experiencing cold stress compared to field-collected individuals. Differences in the mass and thermal tolerance of insects with intact and disrupted gut microbiota suggest that gut microbiota may play an important role in the cold performance of T. leucotreta, and these findings constitute the basis for future molecular work on the functions of these bacterial taxa. This research highlights the need for consideration of the effects of T. leucotreta microbiome in current pest control programs. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Distribution and habitat preferences of marine megafauna in Nosy Be, Madagascar
- Authors: Lubbé, Alicea
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424710 , vital:72177
- Description: Marine megafauna have important ecological roles including the top-down regulation of lower trophic levels and the transport of nutrients. They are also charismatic species of socioeconomic importance, due to their public appeal and focus for ecotourism. However, these taxa face numerous anthropogenic threats including bycatch, habitat-loss, noise disturbance, prey reductions, pollution, and vessel traffic. Northwest Madagascar has been identified as an important marine mammal area and whale shark aggregation site, yet limited information on megafauna within Madagascar exists. In this thesis, I investigated the community structure, distribution trends, related environmental factors (Chapter 2) and predicted habitat suitability (Chapter 3) using a species distribution modelling approach for marine megafauna around Nosy Be, North-west Madagascar. Data collection consisted of opportunistic boatbased surveys conducted while looking for whale sharks, mobulid rays and cetaceans. These activities were performed by dedicated ‘swim with whale shark’ tourism operators, Les Baleines Rand'eau and Safari Baleine during tourism activities directed by the Madagascar Whale Shark Project over four years (2016-2019). A total of 1792 sightings were reported with 13 identified species, including elasmobranchs: whale shark, Rhincodon typus; spinetail mobula ray, Mobula japonica; giant oceanic manta ray, Manta birostris; shortfin devil ray, Mobula kuhlii; balaenids: humpback whale, Megaptera novaeangliae; Omura's whale, Balaenoptera omurai, delphinids: Indo-Pacific bottlenose dolphin, Tursiops aduncus; spinner dolphin, Stenella longirostris; pantropical spotted dolphin, Stenella attenuata; Indian ocean humpback dolphin, Sousa plumbea; false killer whale, Pseudorca crassidens; melonheaded whale, Peponocephala electra and one cheloniid species: leatherback sea turtle, Dermochelys coriacea. Sightings were spatially analysed at a community level according to feeding guilds (i.e., filter feeders vs. predators), and distribution of the megafauna groups v were compared to selected remotely sensed physico-chemical data (sea surface temperature and chlorophyll-a concentration) and bathymetry charts (depth and slope) using generalized linear models (Chapter 2). All four variables had a significant effect on filter feeder distribution. Spatial distribution of filter feeder sightings peaked at an area of steep underwater topography (18-50m; x slope=0.5%) located on the west coast of Nosy Be, where foraging aggregations of large filter feeders (primarily R. typus and B. omurai) were frequently observed. Only SST had a significant effect on the relative abundance of animals in the predator feeding guild, which demonstrated a more longitudinal distribution along the continental shelf. The maximum entropy model (Maxent) was used for predicting habitat preference for the most frequently sighted species (Chapter 3). The distribution of whale sharks, mobulid rays and Omura’s whales were significantly overlapped as they were abundant in two main hotspots, Grand banc de l’entrée (~10 km of the west coast) and near Nosy Mitsio island, (~50 km northeast of Nosy Be). Suitable habitat for the dolphins was in relatively shallow waters in temperatures <28ºC near areas of steep changes in bathymetry. Bottlenose and spinner dolphins had a more widespread distribution across the continental shelf and humpback dolphin was closely associated with inshore reefs and occur in waters <10m. The coastal and inshore region of Nosy Be is an important habitat for a variety of megafaunal species, and the continental shelf provided essential areas for feeding and breeding. The results were similar to those presented for these species in other regions of the Indian Ocean (i.e., Eastern and Southern Africa; Western Australia; Seychelles) as well as outside of the Indian Ocean (i.e., Indonesia; Caribbean; North Atlantic). Thus the results from this thesis could be considered for management recommendations for marine conservation in the region. The value and limitations of data collected by citizen science were outlined (Chapter 4). , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Lubbé, Alicea
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424710 , vital:72177
- Description: Marine megafauna have important ecological roles including the top-down regulation of lower trophic levels and the transport of nutrients. They are also charismatic species of socioeconomic importance, due to their public appeal and focus for ecotourism. However, these taxa face numerous anthropogenic threats including bycatch, habitat-loss, noise disturbance, prey reductions, pollution, and vessel traffic. Northwest Madagascar has been identified as an important marine mammal area and whale shark aggregation site, yet limited information on megafauna within Madagascar exists. In this thesis, I investigated the community structure, distribution trends, related environmental factors (Chapter 2) and predicted habitat suitability (Chapter 3) using a species distribution modelling approach for marine megafauna around Nosy Be, North-west Madagascar. Data collection consisted of opportunistic boatbased surveys conducted while looking for whale sharks, mobulid rays and cetaceans. These activities were performed by dedicated ‘swim with whale shark’ tourism operators, Les Baleines Rand'eau and Safari Baleine during tourism activities directed by the Madagascar Whale Shark Project over four years (2016-2019). A total of 1792 sightings were reported with 13 identified species, including elasmobranchs: whale shark, Rhincodon typus; spinetail mobula ray, Mobula japonica; giant oceanic manta ray, Manta birostris; shortfin devil ray, Mobula kuhlii; balaenids: humpback whale, Megaptera novaeangliae; Omura's whale, Balaenoptera omurai, delphinids: Indo-Pacific bottlenose dolphin, Tursiops aduncus; spinner dolphin, Stenella longirostris; pantropical spotted dolphin, Stenella attenuata; Indian ocean humpback dolphin, Sousa plumbea; false killer whale, Pseudorca crassidens; melonheaded whale, Peponocephala electra and one cheloniid species: leatherback sea turtle, Dermochelys coriacea. Sightings were spatially analysed at a community level according to feeding guilds (i.e., filter feeders vs. predators), and distribution of the megafauna groups v were compared to selected remotely sensed physico-chemical data (sea surface temperature and chlorophyll-a concentration) and bathymetry charts (depth and slope) using generalized linear models (Chapter 2). All four variables had a significant effect on filter feeder distribution. Spatial distribution of filter feeder sightings peaked at an area of steep underwater topography (18-50m; x slope=0.5%) located on the west coast of Nosy Be, where foraging aggregations of large filter feeders (primarily R. typus and B. omurai) were frequently observed. Only SST had a significant effect on the relative abundance of animals in the predator feeding guild, which demonstrated a more longitudinal distribution along the continental shelf. The maximum entropy model (Maxent) was used for predicting habitat preference for the most frequently sighted species (Chapter 3). The distribution of whale sharks, mobulid rays and Omura’s whales were significantly overlapped as they were abundant in two main hotspots, Grand banc de l’entrée (~10 km of the west coast) and near Nosy Mitsio island, (~50 km northeast of Nosy Be). Suitable habitat for the dolphins was in relatively shallow waters in temperatures <28ºC near areas of steep changes in bathymetry. Bottlenose and spinner dolphins had a more widespread distribution across the continental shelf and humpback dolphin was closely associated with inshore reefs and occur in waters <10m. The coastal and inshore region of Nosy Be is an important habitat for a variety of megafaunal species, and the continental shelf provided essential areas for feeding and breeding. The results were similar to those presented for these species in other regions of the Indian Ocean (i.e., Eastern and Southern Africa; Western Australia; Seychelles) as well as outside of the Indian Ocean (i.e., Indonesia; Caribbean; North Atlantic). Thus the results from this thesis could be considered for management recommendations for marine conservation in the region. The value and limitations of data collected by citizen science were outlined (Chapter 4). , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Enteric microbial responses to host hyperthermia in southern African insectivorous bats: a test of thermal co-adaptation
- Authors: Hunter, Amy Alison
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424391 , vital:72149
- Description: Embargoed. Expected release date 2025. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Hunter, Amy Alison
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424391 , vital:72149
- Description: Embargoed. Expected release date 2025. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Evaluation of potential oviposition deterrents for false codling moth, Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae)
- Authors: Dambuza, Khalipha
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424479 , vital:72157
- Description: There has been extensive research on the use of semiochemicals as deterrents or true repellents in insect pest management, particularly in push-pull strategies. Much of this research has focused on pests of medical and veterinary importance and has been limited for agricultural pests. This means there is an opportunity to study use of deterrents to manage pests of agricultural importance. No study has been conducted on deterrents for false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a key phytosanitary pest in citrus orchards across South Africa. This study assessed FCM oviposition deterrence in botanicals (plants (n = 11) and essential oils (n = 15)), and some commercial pesticides (n = 7) used for FCM control in South Africa. All tested botanicals were selected based on an extensive literature review of plant compounds that have been reported to deter or repel lepidopteran pests. Choice and no-choice oviposition bioassays were conducted in complete darkness in a controlled environment room. Oranges treated with solutions/suspensions of potential oviposition deterrents were placed into a cage with gravid FCM females for four hours, with oviposition being recorded every hour. Of the 33 tested compounds, only eight significantly reduced FCM oviposition (P < 0.05) compared to the control in oviposition bioassays i.e. two essential oils (lavender and peppermint), two plant crude extracts (garlic and marigold), one fruit (Mango), and three commercial FCM insecticides (Delegate, Coragen, and Warlock). All identified oviposition deterrents, except for Mango, were further investigated for their ovicidal properties in concentration response bioassays, where all botanicals were identified to have dual action (both deterrent and ovicidal properties), as they significantly (P < 0.05) reduced FCM oviposition and egg hatch. Garlic was the most efficacious botanical whilst Warlock was the only commercial insecticide that did not show ovicidal activity (F = 41.17, P = 0.0622). Larval penetration of the host fruit was less than egg hatch for all tested compounds in concentration response bioassays. Oviposition, egg hatch, and larval penetration were all affected by concentration, with the higher concentrations being the most effective. The efficacy of these deterrent compounds should be further tested in semi-field and/or field trials, and they may have potential in FCM management as allomone dispensers or sprays. They can also be implemented in push-pull strategies where they can be used in conjunction with FCM attractants. Lastly, repellence studies should be conducted in absentia of the host fruit to determine whether oviposition deterrence was a result of true repellence or odour masking. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Dambuza, Khalipha
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424479 , vital:72157
- Description: There has been extensive research on the use of semiochemicals as deterrents or true repellents in insect pest management, particularly in push-pull strategies. Much of this research has focused on pests of medical and veterinary importance and has been limited for agricultural pests. This means there is an opportunity to study use of deterrents to manage pests of agricultural importance. No study has been conducted on deterrents for false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a key phytosanitary pest in citrus orchards across South Africa. This study assessed FCM oviposition deterrence in botanicals (plants (n = 11) and essential oils (n = 15)), and some commercial pesticides (n = 7) used for FCM control in South Africa. All tested botanicals were selected based on an extensive literature review of plant compounds that have been reported to deter or repel lepidopteran pests. Choice and no-choice oviposition bioassays were conducted in complete darkness in a controlled environment room. Oranges treated with solutions/suspensions of potential oviposition deterrents were placed into a cage with gravid FCM females for four hours, with oviposition being recorded every hour. Of the 33 tested compounds, only eight significantly reduced FCM oviposition (P < 0.05) compared to the control in oviposition bioassays i.e. two essential oils (lavender and peppermint), two plant crude extracts (garlic and marigold), one fruit (Mango), and three commercial FCM insecticides (Delegate, Coragen, and Warlock). All identified oviposition deterrents, except for Mango, were further investigated for their ovicidal properties in concentration response bioassays, where all botanicals were identified to have dual action (both deterrent and ovicidal properties), as they significantly (P < 0.05) reduced FCM oviposition and egg hatch. Garlic was the most efficacious botanical whilst Warlock was the only commercial insecticide that did not show ovicidal activity (F = 41.17, P = 0.0622). Larval penetration of the host fruit was less than egg hatch for all tested compounds in concentration response bioassays. Oviposition, egg hatch, and larval penetration were all affected by concentration, with the higher concentrations being the most effective. The efficacy of these deterrent compounds should be further tested in semi-field and/or field trials, and they may have potential in FCM management as allomone dispensers or sprays. They can also be implemented in push-pull strategies where they can be used in conjunction with FCM attractants. Lastly, repellence studies should be conducted in absentia of the host fruit to determine whether oviposition deterrence was a result of true repellence or odour masking. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Freshwater invasive alien crayfish species in South Africa: testing eDNA assessment and DNA barcoding
- Mdidimba, Nonkazimulo Dorothea
- Authors: Mdidimba, Nonkazimulo Dorothea
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424413 , vital:72151
- Description: The expansion of the wild populations of the two invasive alien crayfish species, i.e., Cherax quadricarinatus and Procambarus clarkii in South Africa is of high concern. Given this, innovative and improved monitoring methods are required to be explored in order to effectively detect and manage their spread. Environmental DNA (eDNA) has shown promising and reliable results to detect and monitor alien crayfish in freshwater systems even at low densities. This research study aimed to field-test the application of eDNA for detecting and monitoring invasive alien freshwater crayfish species (IAFCs) in South African freshwater systems (Chapter 2). Further, this study also aimed to confirm the true taxonomic identity of the IAFCs in South African freshwater systems by using DNA barcoding to avoid potential misidentifications with morphological identification alone (Chapter 3). Also, ectocommensal temnocephalans and leeches attached to the crayfishes were also identified with DNA barcoding. The mitochondrial COI gene fragment of the crayfishes and the ectocommensal temnocephalans and leeches was amplified, sequenced, and used for species identification. For eDNA monitoring of C. cainii, C. quadricarinatus and P. clarkii, water samples were collected from Eastern Cape, Free State and KwaZulu Natal sites that are known to house these species. The current study did not detect the eDNA of the wild populations of both C. quadricarinatus and P. clarkii. This failure was encountered despite employing several methods, such as, end-point polymerase chain reaction (PCR), quantitative PCR (qPCR) and next-generation sequencing (NGS). The eDNA assessment to detect IAFCs in the wild populations is discussed in detail, and corrective measures suggested (Chapter 2). However, only C. cainii was able to be detected by eDNA. Cherax cainii is housed/farmed in an aquaculture facility (Vaughn Bursey’s Stock Farm in Eastern Cape) with large number of individuals per pond. For this, NGS was able to detect C. cainii but the other two methods, end-point PCR and qPCR were not able to detect the species. Based on the results, refinement of eDNA monitoring methods for the South African freshwater systems is recommended. Evaluation of different DNA collection methods, preservation, DNA extraction kits and primer design to obtain effective eDNA detection is discussed as possible sources of error. Interestingly, the newly established population of P. clarkii in Mimosa Dam in Free State was infested with alien leeches, that were confirmed by DNA barcoding to be Helobdella europaea and Helobdella octatestica. Consequently, this study reports for the first time in South Africa the presence of this alien freshwater leeches. The presence of alien leeches and P. clarkii suggests a double invasion in Mimosa Dam, P. clarkii seems to continue expanding its range in the country. However, the long-established population of P. clarkii in Driehoek Farm in Mpumalanga, which has been in the country for over 30 years did not have any leech or temnocephalan infestation. This could suggest several interesting ecological phenomena, including environmental filtering over time of the co-invaders, differential source populations, and post-introduction adaptation. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Mdidimba, Nonkazimulo Dorothea
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424413 , vital:72151
- Description: The expansion of the wild populations of the two invasive alien crayfish species, i.e., Cherax quadricarinatus and Procambarus clarkii in South Africa is of high concern. Given this, innovative and improved monitoring methods are required to be explored in order to effectively detect and manage their spread. Environmental DNA (eDNA) has shown promising and reliable results to detect and monitor alien crayfish in freshwater systems even at low densities. This research study aimed to field-test the application of eDNA for detecting and monitoring invasive alien freshwater crayfish species (IAFCs) in South African freshwater systems (Chapter 2). Further, this study also aimed to confirm the true taxonomic identity of the IAFCs in South African freshwater systems by using DNA barcoding to avoid potential misidentifications with morphological identification alone (Chapter 3). Also, ectocommensal temnocephalans and leeches attached to the crayfishes were also identified with DNA barcoding. The mitochondrial COI gene fragment of the crayfishes and the ectocommensal temnocephalans and leeches was amplified, sequenced, and used for species identification. For eDNA monitoring of C. cainii, C. quadricarinatus and P. clarkii, water samples were collected from Eastern Cape, Free State and KwaZulu Natal sites that are known to house these species. The current study did not detect the eDNA of the wild populations of both C. quadricarinatus and P. clarkii. This failure was encountered despite employing several methods, such as, end-point polymerase chain reaction (PCR), quantitative PCR (qPCR) and next-generation sequencing (NGS). The eDNA assessment to detect IAFCs in the wild populations is discussed in detail, and corrective measures suggested (Chapter 2). However, only C. cainii was able to be detected by eDNA. Cherax cainii is housed/farmed in an aquaculture facility (Vaughn Bursey’s Stock Farm in Eastern Cape) with large number of individuals per pond. For this, NGS was able to detect C. cainii but the other two methods, end-point PCR and qPCR were not able to detect the species. Based on the results, refinement of eDNA monitoring methods for the South African freshwater systems is recommended. Evaluation of different DNA collection methods, preservation, DNA extraction kits and primer design to obtain effective eDNA detection is discussed as possible sources of error. Interestingly, the newly established population of P. clarkii in Mimosa Dam in Free State was infested with alien leeches, that were confirmed by DNA barcoding to be Helobdella europaea and Helobdella octatestica. Consequently, this study reports for the first time in South Africa the presence of this alien freshwater leeches. The presence of alien leeches and P. clarkii suggests a double invasion in Mimosa Dam, P. clarkii seems to continue expanding its range in the country. However, the long-established population of P. clarkii in Driehoek Farm in Mpumalanga, which has been in the country for over 30 years did not have any leech or temnocephalan infestation. This could suggest several interesting ecological phenomena, including environmental filtering over time of the co-invaders, differential source populations, and post-introduction adaptation. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Native-range studies on insect herbivores associated with African Lovegrass (Eragrostis curvula) in South Africa: prospects for biological control in Australia
- Authors: Yell, Liam Dougal
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424446 , vital:72154
- Description: Eragrostis curvula (Schrad.) Nees. (African Lovegrass) is an African native species of grass that was intentionally introduced for pasture in Australia. It has since escaped cultivation and has become widespread and highly invasive. Eragrostis curvula has been recorded in every state and territory in Australia where it has altered fire regimes, disrupted nutrient cycles and can reduce livestock carrying capacity by up to 50%. The Centre for Biological Control at Rhodes University and the New South Wales Department of Primary Industries have been working in collaboration to identify and screen herbivorous insects as biological control agents for E. curvula in Australia. Native-range surveys were conducted between 2021 and 2022 on E. curvula at twenty-two sites across South Africa to identify herbivorous natural enemies associated with it. Species accumulation curves were generated to ensure adequate sampling was performed to identify all the insects associated with E. curvula. Twenty-nine non-target grass species were surveyed simultaneously to determine the field-host range of the natural enemies associated with the target weed. Herbivorous natural enemies were prioritised as possible biological control agents against E. curvula in Australia based on field-host range, predicted efficacy and climatic suitability. Four insect species were consistently found on E. curvula, two of which were herbivorous, as well as a parasitoid and a detritivore. Species accumulation curves show that the insect community was adequately sampled in South Africa. The two herbivorous insects were identified to the lowest taxonomic level using COI barcoding. Both species are undescribed phytophagous wasps in the genus Tetramesa (Hymenoptera: Eurytomidae). Because Tetramesa species have been shown to be host specific and highly damaging in previous biological control programs for other invasive grass weeds, we assessed their suitability as candidate biological control agents for use on E. curvula in Australia. Both Tetramesa species (“sp. 4” and “sp. 5”) were found on several native congeners under field conditions in South Africa. Congeneric South African-native non-target grass species were used as phylogenetic proxies to assess the risk posed to Australian native Eragrostis species. This highlighted three non-target Australian native Eragrostis species, namely: E. parviflora (R. Br.) Trin., E. leptocarpa Benth. fl., and E. trachycarpa Benth., that are at risk of being attacked by the two candidate agents based on their phylogenetic proximity to E. curvula. Predicted efficacy trials were conducted at five long-term repeat survey sites and revealed that Tetramesa sp. 4 does not reduce the probability of E. curvula tiller survival or reproduction, while Tetramesa sp. 5 does not reduce the probability of tiller reproduction but does increase the probability of tiller survival. This result was unexpected and may be a plant compensatory response to herbivory. The sites where both Tetramesa species were collected in South Africa are climatically similar to the invaded range of E. curvula in Australia, and as such, the Tetramesa spp. are likely to be suitably adapted to the climate where they would be released in Australia. These results suggest that both Tetramesa species associated with E. curvula may have too broad a host range to be used as biological control agents in Australia. However, further quarantine-based host-range assessments on Australian native Eragrostis species are recommended to confirm this. The field-based methods used in this study have reduced the number of insect and plant species that host-range assessments will be required to be performed on, thus preventing wasted resources. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Yell, Liam Dougal
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424446 , vital:72154
- Description: Eragrostis curvula (Schrad.) Nees. (African Lovegrass) is an African native species of grass that was intentionally introduced for pasture in Australia. It has since escaped cultivation and has become widespread and highly invasive. Eragrostis curvula has been recorded in every state and territory in Australia where it has altered fire regimes, disrupted nutrient cycles and can reduce livestock carrying capacity by up to 50%. The Centre for Biological Control at Rhodes University and the New South Wales Department of Primary Industries have been working in collaboration to identify and screen herbivorous insects as biological control agents for E. curvula in Australia. Native-range surveys were conducted between 2021 and 2022 on E. curvula at twenty-two sites across South Africa to identify herbivorous natural enemies associated with it. Species accumulation curves were generated to ensure adequate sampling was performed to identify all the insects associated with E. curvula. Twenty-nine non-target grass species were surveyed simultaneously to determine the field-host range of the natural enemies associated with the target weed. Herbivorous natural enemies were prioritised as possible biological control agents against E. curvula in Australia based on field-host range, predicted efficacy and climatic suitability. Four insect species were consistently found on E. curvula, two of which were herbivorous, as well as a parasitoid and a detritivore. Species accumulation curves show that the insect community was adequately sampled in South Africa. The two herbivorous insects were identified to the lowest taxonomic level using COI barcoding. Both species are undescribed phytophagous wasps in the genus Tetramesa (Hymenoptera: Eurytomidae). Because Tetramesa species have been shown to be host specific and highly damaging in previous biological control programs for other invasive grass weeds, we assessed their suitability as candidate biological control agents for use on E. curvula in Australia. Both Tetramesa species (“sp. 4” and “sp. 5”) were found on several native congeners under field conditions in South Africa. Congeneric South African-native non-target grass species were used as phylogenetic proxies to assess the risk posed to Australian native Eragrostis species. This highlighted three non-target Australian native Eragrostis species, namely: E. parviflora (R. Br.) Trin., E. leptocarpa Benth. fl., and E. trachycarpa Benth., that are at risk of being attacked by the two candidate agents based on their phylogenetic proximity to E. curvula. Predicted efficacy trials were conducted at five long-term repeat survey sites and revealed that Tetramesa sp. 4 does not reduce the probability of E. curvula tiller survival or reproduction, while Tetramesa sp. 5 does not reduce the probability of tiller reproduction but does increase the probability of tiller survival. This result was unexpected and may be a plant compensatory response to herbivory. The sites where both Tetramesa species were collected in South Africa are climatically similar to the invaded range of E. curvula in Australia, and as such, the Tetramesa spp. are likely to be suitably adapted to the climate where they would be released in Australia. These results suggest that both Tetramesa species associated with E. curvula may have too broad a host range to be used as biological control agents in Australia. However, further quarantine-based host-range assessments on Australian native Eragrostis species are recommended to confirm this. The field-based methods used in this study have reduced the number of insect and plant species that host-range assessments will be required to be performed on, thus preventing wasted resources. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Phylogeography of two small owl species in South Africa: population genetics and phenotypic variation in the African Barred Owlet (Glaucidium capense) and the African Scops Owl (Otus senegalensis)
- Authors: Balmer, Jonathan Peter
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424369 , vital:72147
- Description: Embargoed. Expected release date in 2025. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Balmer, Jonathan Peter
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424369 , vital:72147
- Description: Embargoed. Expected release date in 2025. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Phytoplankton and aquatic macroinvertebrate assemblages from coastal and inland lakes of South Africa
- Authors: Nkibi, Esethu
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424435 , vital:72153
- Description: Freshwater lakes are generally defined as permanent natural standing water bodies, with some of them having a direct and indirect connection with groundwater, rivers, and the ocean. Freshwater lakes provide essential socio-economic and ecological goods and services including recreation, aesthetic, support aquatic biodiversity, food in a form of fisheries and water for domestic use. Given their critical role in sustainability in providing socio-economic services, freshwater lakes are among the most threatened ecosystems globally due to intense human impacts over the last decades. South Africa has limited freshwater lakes, which according to the National Biodiversity Assessment (NBA 2018), we know little about their current biology except historic aquatic biodiversity studies conducted in the early 1940s. There are no management strategies in place to protect and conserve freshwater lake biodiversity and important ecosystem services. This thesis aims to: (1) produce a biodiversity inventory of phytoplankton and aquatic macroinvertebrate species and, (2) investigate important environmental drivers responsible for phytoplankton and aquatic macroinvertebrate species composition from six South African freshwater lakes. It was hypothesized that the three lake types will show different phytoplankton and aquatic macroinvertebrates species composition attributed by the geographical region (coastal and inland lake) and related physico-chemical parameters. Study sites consisted of two Northern KwaZulu-Natal coastal lakes (hereafter Coastal Lakes, CL) i.e., Lake Sibaya, Lake Mzingazi; two fresh inland lakes (hereafter Fresh Inland Lakes, FIL) i.e., Lake Banagher fresh and Lake Tevrede Se Pan; and two inland salt lakes (hereafter Salt Inland Lakes, SIL) i.e., Lake Banagher salt and Lake Chrissiesmeer, all inland lakes are situated in Mpumalanga province, together with other Pans making up the Mpumalanga Lake District of South Africa. The study sites were categorized based on their geographical position i.e., coastal vs inland and physico-chemical characteristics i.e., the presence and absence of aquatic vegetation, dominate substrate, salinity and different physico-chemical concentration i.e., Temperature, Dissolved Oxygen. Aquatic macroinvertebrates were collected from four littoral zone sites (< 1-meter depth) around each lake, whereas phytoplankton samples were collected from four water column sites (> 5-meters depth) and (0.5-meter depth) from the water surface at each lake during summer and winter season. The results were consistent with our hypothesis that both phytoplankton and aquatic macroinvertebrate species composition were influenced by physico-chemical parameters and that the differences in salinity concentration and aquatic vegetation between CL, FIL, and SIL were the driving factors for phytoplankton and aquatic macroinvertebrate species composition. In summary, one hundred and twenty-two phytoplankton taxa were collected and identified during this study, belonging to seven Phyla which included Chlorophyta, Bacillariophyta, Cyanophyta, Chrysophyta, Dinophyta, Euglenophyta, and Cryptophyta. The most abundant phytoplankton groups were Bacillariophyta and Chlorophyta. Phytoplankton relative taxa abundance, Pielou’s evenness, taxa richness, and Shannon diversity were significantly different between lake types. Aquatic macroinvertebrates, on the other hand, summed up to 10 orders, 67 families, and 80 taxa. The most abundant group were the order Coleoptera, Hemiptera, Odonata, and Gastropoda. Aquatic macroinvertebrate relative taxa abundance, taxa richness, and Shannon diversity were also significantly different between lake types. Aquatic macroinvertebrate relative taxa abundance, Pielous evenness, and Shannon diversity index were not significant between seasons, and only taxa richness was significant. Canonical analysis of principal coordinates (CAP) results further showed unique and distinct phytoplankton and aquatic macroinvertebrates community composition between lake types. The present study provides baseline biodiversity inventory (or species list) for important lake ecosystems biological indicators i.e., phytoplankton and aquatic macroinvertebrates and species composition in relation to lake type for six freshwater lakes in South Africa. Furthermore, the study provides empirical evidence that will inform policy and the development of management strategies for freshwater lakes in South Africa which is currently missing. The current study will also contribute to the next National Biodiversity Assessment Report (2024), concerning the freshwater lakes biological data deficiency noted in the previous NBA (2018) report. The study will also fill up the gaps to better understand species composition in lake systems and how they function which is currently limited. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Nkibi, Esethu
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424435 , vital:72153
- Description: Freshwater lakes are generally defined as permanent natural standing water bodies, with some of them having a direct and indirect connection with groundwater, rivers, and the ocean. Freshwater lakes provide essential socio-economic and ecological goods and services including recreation, aesthetic, support aquatic biodiversity, food in a form of fisheries and water for domestic use. Given their critical role in sustainability in providing socio-economic services, freshwater lakes are among the most threatened ecosystems globally due to intense human impacts over the last decades. South Africa has limited freshwater lakes, which according to the National Biodiversity Assessment (NBA 2018), we know little about their current biology except historic aquatic biodiversity studies conducted in the early 1940s. There are no management strategies in place to protect and conserve freshwater lake biodiversity and important ecosystem services. This thesis aims to: (1) produce a biodiversity inventory of phytoplankton and aquatic macroinvertebrate species and, (2) investigate important environmental drivers responsible for phytoplankton and aquatic macroinvertebrate species composition from six South African freshwater lakes. It was hypothesized that the three lake types will show different phytoplankton and aquatic macroinvertebrates species composition attributed by the geographical region (coastal and inland lake) and related physico-chemical parameters. Study sites consisted of two Northern KwaZulu-Natal coastal lakes (hereafter Coastal Lakes, CL) i.e., Lake Sibaya, Lake Mzingazi; two fresh inland lakes (hereafter Fresh Inland Lakes, FIL) i.e., Lake Banagher fresh and Lake Tevrede Se Pan; and two inland salt lakes (hereafter Salt Inland Lakes, SIL) i.e., Lake Banagher salt and Lake Chrissiesmeer, all inland lakes are situated in Mpumalanga province, together with other Pans making up the Mpumalanga Lake District of South Africa. The study sites were categorized based on their geographical position i.e., coastal vs inland and physico-chemical characteristics i.e., the presence and absence of aquatic vegetation, dominate substrate, salinity and different physico-chemical concentration i.e., Temperature, Dissolved Oxygen. Aquatic macroinvertebrates were collected from four littoral zone sites (< 1-meter depth) around each lake, whereas phytoplankton samples were collected from four water column sites (> 5-meters depth) and (0.5-meter depth) from the water surface at each lake during summer and winter season. The results were consistent with our hypothesis that both phytoplankton and aquatic macroinvertebrate species composition were influenced by physico-chemical parameters and that the differences in salinity concentration and aquatic vegetation between CL, FIL, and SIL were the driving factors for phytoplankton and aquatic macroinvertebrate species composition. In summary, one hundred and twenty-two phytoplankton taxa were collected and identified during this study, belonging to seven Phyla which included Chlorophyta, Bacillariophyta, Cyanophyta, Chrysophyta, Dinophyta, Euglenophyta, and Cryptophyta. The most abundant phytoplankton groups were Bacillariophyta and Chlorophyta. Phytoplankton relative taxa abundance, Pielou’s evenness, taxa richness, and Shannon diversity were significantly different between lake types. Aquatic macroinvertebrates, on the other hand, summed up to 10 orders, 67 families, and 80 taxa. The most abundant group were the order Coleoptera, Hemiptera, Odonata, and Gastropoda. Aquatic macroinvertebrate relative taxa abundance, taxa richness, and Shannon diversity were also significantly different between lake types. Aquatic macroinvertebrate relative taxa abundance, Pielous evenness, and Shannon diversity index were not significant between seasons, and only taxa richness was significant. Canonical analysis of principal coordinates (CAP) results further showed unique and distinct phytoplankton and aquatic macroinvertebrates community composition between lake types. The present study provides baseline biodiversity inventory (or species list) for important lake ecosystems biological indicators i.e., phytoplankton and aquatic macroinvertebrates and species composition in relation to lake type for six freshwater lakes in South Africa. Furthermore, the study provides empirical evidence that will inform policy and the development of management strategies for freshwater lakes in South Africa which is currently missing. The current study will also contribute to the next National Biodiversity Assessment Report (2024), concerning the freshwater lakes biological data deficiency noted in the previous NBA (2018) report. The study will also fill up the gaps to better understand species composition in lake systems and how they function which is currently limited. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
The activity and foraging patterns of the western rock elephant shrew (Elephantulus rupestris)
- Authors: Jackson, Emily Anne
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424402 , vital:72150
- Description: The increase, and prolonged periods, of high ambient temperatures are cause for concern for small mammals living in arid areas of Southern Africa. In this study, I aimed to determine the effect of high environmental temperatures on the activity, body temperature maintenance and foraging behaviour in a population of Western rock elephant shrew, Elephantulus rupestris, in the Eastern Cape, South Africa. I found that E. rupestris maintained stable body temperatures (Tb = 37.31 °C ± 0.64) over a range of environmental temperatures (Tair = 5° to 33.9 °C), indicating their ability to remain normothermic during the heat of the day. Under cool, mild and hot air temperatures, E. rupestris were predominantly active in the morning and night, being the least active during midday. This shift in activity time, known as polyphasic activity, is common amongst Macroscelidea species and is a mechanism for escaping thermal extremes. To determine the effect of temperature on foraging behaviour, I ran giving-up density (GUD) experiments on E. rupestris under a range of environmental conditions. GUD experiments yielded no conclusive results as animals did not show a significant preference for foraging under certain thermal conditions, and rather foraged under a variety of air temperatures. Overall, E. rupestris showed risk adverse behaviour, trading-off thermoregulation with foraging and activity for self-preservation during hot periods of the day. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Jackson, Emily Anne
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424402 , vital:72150
- Description: The increase, and prolonged periods, of high ambient temperatures are cause for concern for small mammals living in arid areas of Southern Africa. In this study, I aimed to determine the effect of high environmental temperatures on the activity, body temperature maintenance and foraging behaviour in a population of Western rock elephant shrew, Elephantulus rupestris, in the Eastern Cape, South Africa. I found that E. rupestris maintained stable body temperatures (Tb = 37.31 °C ± 0.64) over a range of environmental temperatures (Tair = 5° to 33.9 °C), indicating their ability to remain normothermic during the heat of the day. Under cool, mild and hot air temperatures, E. rupestris were predominantly active in the morning and night, being the least active during midday. This shift in activity time, known as polyphasic activity, is common amongst Macroscelidea species and is a mechanism for escaping thermal extremes. To determine the effect of temperature on foraging behaviour, I ran giving-up density (GUD) experiments on E. rupestris under a range of environmental conditions. GUD experiments yielded no conclusive results as animals did not show a significant preference for foraging under certain thermal conditions, and rather foraged under a variety of air temperatures. Overall, E. rupestris showed risk adverse behaviour, trading-off thermoregulation with foraging and activity for self-preservation during hot periods of the day. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
The effect of piospheres on the ecology of insectivorous birds and their arthropod prey
- Authors: Balmer, Natasha Louise
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424380 , vital:72148
- Description: Desertification is the degradation of arid ecosystems that result in the loss of biodiversity. Piospheres are areas of local degradation around a central point due to overgrazing and increased herbivore presence. There is a paucity of information regarding the effect of localised degradation on arthropods and insectivorous birds. Both of these organisms play crucial roles in ecosystem functioning and stability and can be used as models to study ecosystem functioning. I investigated the effect of piospheres on arthropods and birds in the Eastern Cape province of South Africa. I found that the abundance and diversity of arthropods were significantly reduced inside the piospheres due to the lack of vegetation. Termites were a group specifically negatively impacted by piospheres, with a significant reduction in their presence inside the piosphere. The family composition of arthropods also changed inside and outside the piospheres, with Caelifera, Diptera and Formicidae being the most dominant groups. The diversity of birds was also significantly reduced due to the degradation inside the piospheres. Looking at insectivorous birds, I found that the reduction in both vegetation and arthropod prey availability resulted in non-random avoidance of piospheres. This shows that piospheres negatively impact both arthropods and birds. The results from my study are supported by other literature studying the effects of habitat degradation associated with desertification. Due to the similarities of degradation between piospheres and desertification I make the argument that piospheres can be studied as localised models of desertification. The decrease in vegetation and arthropod abundance and diversity was found to further impact the feeding success of insectivorous birds. Using piospheres as a model for desertification, I found that the foraging effort of birds is significantly reduced within a degraded area due to the lack of vegetation providing safety to arthropod prey species. In addition to this, the foraging efficiency of insectivorous birds is significantly reduced inside the piospheres due to the decreased arthropod abundance and diversity. This shows that inside the piospheres birds spend less time searching for insects and have fewer successful feeds. This has implications for desertification of arid environments where birds face hyperthermia. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Balmer, Natasha Louise
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424380 , vital:72148
- Description: Desertification is the degradation of arid ecosystems that result in the loss of biodiversity. Piospheres are areas of local degradation around a central point due to overgrazing and increased herbivore presence. There is a paucity of information regarding the effect of localised degradation on arthropods and insectivorous birds. Both of these organisms play crucial roles in ecosystem functioning and stability and can be used as models to study ecosystem functioning. I investigated the effect of piospheres on arthropods and birds in the Eastern Cape province of South Africa. I found that the abundance and diversity of arthropods were significantly reduced inside the piospheres due to the lack of vegetation. Termites were a group specifically negatively impacted by piospheres, with a significant reduction in their presence inside the piosphere. The family composition of arthropods also changed inside and outside the piospheres, with Caelifera, Diptera and Formicidae being the most dominant groups. The diversity of birds was also significantly reduced due to the degradation inside the piospheres. Looking at insectivorous birds, I found that the reduction in both vegetation and arthropod prey availability resulted in non-random avoidance of piospheres. This shows that piospheres negatively impact both arthropods and birds. The results from my study are supported by other literature studying the effects of habitat degradation associated with desertification. Due to the similarities of degradation between piospheres and desertification I make the argument that piospheres can be studied as localised models of desertification. The decrease in vegetation and arthropod abundance and diversity was found to further impact the feeding success of insectivorous birds. Using piospheres as a model for desertification, I found that the foraging effort of birds is significantly reduced within a degraded area due to the lack of vegetation providing safety to arthropod prey species. In addition to this, the foraging efficiency of insectivorous birds is significantly reduced inside the piospheres due to the decreased arthropod abundance and diversity. This shows that inside the piospheres birds spend less time searching for insects and have fewer successful feeds. This has implications for desertification of arid environments where birds face hyperthermia. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
The enigmatic subterranean amphipod genus (sternophysinx: sternophysingidae): conservation and systematics
- Authors: Mlungu, Zizile
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424424 , vital:72152
- Description: Sternophysingidae Holsinger, 1992 is a monotypic subterranean amphipod family endemic to Namibia and South Africa. It currently has eight described species under the genus Sternophysinx. The species in this family are considered narrow endemics, having only been identified using morphological characters. However, the apparent wide distribution of certain species, reported in several subterranean waters in different provinces, suggests that our current taxonomic understanding of these species needs to be completed, thus needing revision. Further, detailed knowledge of the distribution and phylogenetic relationship between species of this taxon still needs to be improved. This study aimed to use integrative taxonomy to analyse both morphology and molecular biology to study hidden diversity and to further our understanding of the distribution in this taxon. The available morphological keys were used to identify species, and 12S rRNA was also used to investigate the relationships of Sternophysinx species and delimit species boundaries. The study primarily aimed to use mitochondrial cytochrome c oxidase subunit I (COI). However, due to technical issues such as getting the correct primers, this study's aims were altered, and 12S was used instead of CO1. However, the process of getting CO1 sequences is still ongoing, and the results will be made available elsewhere. The current study aimed to visit all the type localities of the seven species of Sternophysinx reported in South Africa, including all known localities in which these amphipods have been recorded in the past. Nevertheless, this study did not get samples from Nelspruit, De Hoop Nature Reserve, and Nash Nature Reserve, which cover type localities of S. travaleensis, Matlapitse and Chaos cave that harbours S. calceola. Instead, the current study added five new localities Graaff-Reinet, Beaufort West, Hogsback, Makhambathi Nature Reserve and Ntsikeni Nature Reserve, for the distribution, including two new provinces (i.e., Eastern Cape and KwaZulu-Natal) that had records of this genus in the country. Three delimitation methods, Assemble Species by Automatic Partitioning (ASAP), Bayesian implementation of the Poison Tree Processor (bPTP) and Automatic Barcode Gap Discovery (ABGD), were used to identify cryptic species within Sternophysinx. Phylogenetic analyses and three delimitation methods (ASAP, bPTP and ABGD) revealed considerable hidden cryptic diversity within this Sternophysinx. Preliminary morphological examination revealed at least two species as undescribed from Bakwena and Sterkfontein caves, and several that were morphologically identified using the current taxonomic keys did not match with the molecular analysis. For example, S. basilobata from three different systems, Boesmansgat cave (Northern Cape), Beaufort West (Western Cape) and Potchefstroom (North West), was in genetically different putative species. The same is true for S. robertsi and S. alca in Ficus and Peppercorn cave in Limpopo. Overall, the results of the current study demonstrate the need for a comprehensive integrative taxonomic revision of Sternophysinx. These findings suggest that S. basilobata is a complex of distinct lineages and requires further study. On the other hand, species delimitation methods suggested that there are 12- 14 candidate species (Figure 2.5). Lastly, this study investigated the threat posed by the invasive koi fish introduced to an important cave, Boesmansgat cave in the Northern Cape, which is a type locality of two endemic species (S. megacheles and S. basilobata). Stable isotope (δ13C and δ15N) and gut content analyses of the fish were investigated to establish whether this invasive fish feed on these critical creatures, thus endangering their long-term survival. Stable isotope signatures and the stomach gut content proved to be helpful in determining the diet of the koi fish, revealing it to be an omnivorous feeder with high invertebrate preference, including amphipods. These results indicate that the introduction of koi fish in the Boesmansgat cave threatens the long-term sustainability of these amphipods and other invertebrate assemblages in this cave. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Mlungu, Zizile
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424424 , vital:72152
- Description: Sternophysingidae Holsinger, 1992 is a monotypic subterranean amphipod family endemic to Namibia and South Africa. It currently has eight described species under the genus Sternophysinx. The species in this family are considered narrow endemics, having only been identified using morphological characters. However, the apparent wide distribution of certain species, reported in several subterranean waters in different provinces, suggests that our current taxonomic understanding of these species needs to be completed, thus needing revision. Further, detailed knowledge of the distribution and phylogenetic relationship between species of this taxon still needs to be improved. This study aimed to use integrative taxonomy to analyse both morphology and molecular biology to study hidden diversity and to further our understanding of the distribution in this taxon. The available morphological keys were used to identify species, and 12S rRNA was also used to investigate the relationships of Sternophysinx species and delimit species boundaries. The study primarily aimed to use mitochondrial cytochrome c oxidase subunit I (COI). However, due to technical issues such as getting the correct primers, this study's aims were altered, and 12S was used instead of CO1. However, the process of getting CO1 sequences is still ongoing, and the results will be made available elsewhere. The current study aimed to visit all the type localities of the seven species of Sternophysinx reported in South Africa, including all known localities in which these amphipods have been recorded in the past. Nevertheless, this study did not get samples from Nelspruit, De Hoop Nature Reserve, and Nash Nature Reserve, which cover type localities of S. travaleensis, Matlapitse and Chaos cave that harbours S. calceola. Instead, the current study added five new localities Graaff-Reinet, Beaufort West, Hogsback, Makhambathi Nature Reserve and Ntsikeni Nature Reserve, for the distribution, including two new provinces (i.e., Eastern Cape and KwaZulu-Natal) that had records of this genus in the country. Three delimitation methods, Assemble Species by Automatic Partitioning (ASAP), Bayesian implementation of the Poison Tree Processor (bPTP) and Automatic Barcode Gap Discovery (ABGD), were used to identify cryptic species within Sternophysinx. Phylogenetic analyses and three delimitation methods (ASAP, bPTP and ABGD) revealed considerable hidden cryptic diversity within this Sternophysinx. Preliminary morphological examination revealed at least two species as undescribed from Bakwena and Sterkfontein caves, and several that were morphologically identified using the current taxonomic keys did not match with the molecular analysis. For example, S. basilobata from three different systems, Boesmansgat cave (Northern Cape), Beaufort West (Western Cape) and Potchefstroom (North West), was in genetically different putative species. The same is true for S. robertsi and S. alca in Ficus and Peppercorn cave in Limpopo. Overall, the results of the current study demonstrate the need for a comprehensive integrative taxonomic revision of Sternophysinx. These findings suggest that S. basilobata is a complex of distinct lineages and requires further study. On the other hand, species delimitation methods suggested that there are 12- 14 candidate species (Figure 2.5). Lastly, this study investigated the threat posed by the invasive koi fish introduced to an important cave, Boesmansgat cave in the Northern Cape, which is a type locality of two endemic species (S. megacheles and S. basilobata). Stable isotope (δ13C and δ15N) and gut content analyses of the fish were investigated to establish whether this invasive fish feed on these critical creatures, thus endangering their long-term survival. Stable isotope signatures and the stomach gut content proved to be helpful in determining the diet of the koi fish, revealing it to be an omnivorous feeder with high invertebrate preference, including amphipods. These results indicate that the introduction of koi fish in the Boesmansgat cave threatens the long-term sustainability of these amphipods and other invertebrate assemblages in this cave. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
The possible effect of insecticide drift from citrus orchards, and acute toxicity of insecticides on the biocontrol agents of Pontederia crassipes (Mart.) Solms-Laub (Pontederiaceae) established along citrus orchards in the Lowveld region of Mpumalanga Province, South Africa
- Authors: Mabuza, Mefika Michael
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424468 , vital:72156
- Description: This study investigated the possible effect of insecticide drift on naturalized biological control agents of Pontederia crassipes (Mart.) Solms-Laub (Pontederiaceae), in the Lowveld region of Mpumalanga Province of South Africa. Occurrence and abundance of biocontrol agents were recorded at three sites on the Crocodile River and at three dams adjacent to citrus orchards. Leaves of P. crassipes and water samples were collected for insecticide residues and also nutrient status of the water and plants. Eccritotarsus catarinensis Carvalho (Hemiptera: Miridae), Neochetina spp. (combined) (Coleoptera: Curculionidae), and Orthogalumna terebrantis Wallwork (Sarcoptiformes: Galumnidae) were recorded with notable variation in abundance between the river and dams across regions. Insecticide residues were not detected on all leaves sampled across study regions, however, nutrients were detected with nitrate ranging between oligotrophic and mesotrophic. Phosphorus was also detected, but, neither of the nutrients correlated with the occurrence and abundance of naturalized biological control agents of P. crassipes. Bioassays were conducted to measure the effect of commonly used insecticides (viz. Methomyl and Chlorpyrifos) on the survival and feeding damage of biological control agents of P. crassipes. Survival of individual insects was recorded between 0.5 and 120 hours for Megamelus scutellaris and Neochetina eichhorniae Warner (Coleoptera: Curculionidae) adults for treatments where insecticides were topically applied onto the insects or leaves were dipped into the pesticides. Concentrations below field rates, recommended and above field rates of Methomyl and Chlorpyrifos on either exposure techniques significantly reduced survival and feeding of biocontrol agents. Methomyl was more toxic compared to Chlorpyrifos and it significantly reduced the survival of M. scutellaris and N. eichhorniae. In conclusion, in this study, population abundance of biocontrol agents of P. crassipes at the Lowveld region of Mpumalanga was not influenced by pesticide drift, but, insecticides commonly used in the citrus orchards has the potential to negatively impact naturalized biological control of P. crassipes as demonstrated by the bioassays. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Mabuza, Mefika Michael
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424468 , vital:72156
- Description: This study investigated the possible effect of insecticide drift on naturalized biological control agents of Pontederia crassipes (Mart.) Solms-Laub (Pontederiaceae), in the Lowveld region of Mpumalanga Province of South Africa. Occurrence and abundance of biocontrol agents were recorded at three sites on the Crocodile River and at three dams adjacent to citrus orchards. Leaves of P. crassipes and water samples were collected for insecticide residues and also nutrient status of the water and plants. Eccritotarsus catarinensis Carvalho (Hemiptera: Miridae), Neochetina spp. (combined) (Coleoptera: Curculionidae), and Orthogalumna terebrantis Wallwork (Sarcoptiformes: Galumnidae) were recorded with notable variation in abundance between the river and dams across regions. Insecticide residues were not detected on all leaves sampled across study regions, however, nutrients were detected with nitrate ranging between oligotrophic and mesotrophic. Phosphorus was also detected, but, neither of the nutrients correlated with the occurrence and abundance of naturalized biological control agents of P. crassipes. Bioassays were conducted to measure the effect of commonly used insecticides (viz. Methomyl and Chlorpyrifos) on the survival and feeding damage of biological control agents of P. crassipes. Survival of individual insects was recorded between 0.5 and 120 hours for Megamelus scutellaris and Neochetina eichhorniae Warner (Coleoptera: Curculionidae) adults for treatments where insecticides were topically applied onto the insects or leaves were dipped into the pesticides. Concentrations below field rates, recommended and above field rates of Methomyl and Chlorpyrifos on either exposure techniques significantly reduced survival and feeding of biocontrol agents. Methomyl was more toxic compared to Chlorpyrifos and it significantly reduced the survival of M. scutellaris and N. eichhorniae. In conclusion, in this study, population abundance of biocontrol agents of P. crassipes at the Lowveld region of Mpumalanga was not influenced by pesticide drift, but, insecticides commonly used in the citrus orchards has the potential to negatively impact naturalized biological control of P. crassipes as demonstrated by the bioassays. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Implications of changing land use and introducing extralimital giraffe on vegetation in the subtropical thicket, South Africa
- Authors: Trafford, Bronwyn Kate
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422356 , vital:71935
- Description: Land use change has increased in southern Africa as many livestock farms convert to game reserves, to restore degraded and overgrazed lands. This leads to a change in herbivore communities with potential positive and negative consequences for vegetation and landscape productivity. This study aimed to look at the effect of land use change and subsequent herbivore community changes, on thicket vegetation structure, composition, and landscape productivity. To attain the study objectives, data were collected from four game reserves and their adjacent livestock farms within the Eastern Cape province in South Africa. These sites were selected because they are within the Subtropical Thicket biome (similar vegetation) and were once used for livestock farming. At each study site, vegetation composition and structure were assessed using a unique bush clump sampling technique along fence line contrasts. Six plots were sampled at each site, three plots on the game reserve lands and three plots on the adjacent livestock farmlands during the dry (July/August 2020) and wet (January/February 2021) seasons. The Normalized Difference Vegetation Index (NDVI), in-situ leaf area index (LAI) and the fraction of intercepted photosynthetically active radiation (FIPAR), were used to assess vegetation productivity between the two land use types. Additionally, diet of an extralimital herbivore, giraffe (Giraffa camelopardalis), was assessed during contrasting seasons (dry and wet) to infer the role this species might have on these landscapes. The diet of giraffes was assessed through field observations, recording plant species that giraffes were feeding on. Floristic results showed that there were no differences in vegetation structure, species composition and richness between the two land types. There was no difference in the overall diversity of plant species on the game reserves than in the adjacent livestock farms. The primary productivity was greater on the game reserves compared to the livestock farms. Field observations of giraffe feeding showed that they fed predominantly on Vachellia karroo followed by Searsia longispina. Their diets did not differ between the two seasons. My study provides an insight into the effects of changing land use and this information can be used to infer the extent to which these changes might have on restoration of degraded landscape and how land use changes may be effective in restoring the degraded thicket vegetation caused by overgrazing and overstocking of domestic livestock. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Trafford, Bronwyn Kate
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422356 , vital:71935
- Description: Land use change has increased in southern Africa as many livestock farms convert to game reserves, to restore degraded and overgrazed lands. This leads to a change in herbivore communities with potential positive and negative consequences for vegetation and landscape productivity. This study aimed to look at the effect of land use change and subsequent herbivore community changes, on thicket vegetation structure, composition, and landscape productivity. To attain the study objectives, data were collected from four game reserves and their adjacent livestock farms within the Eastern Cape province in South Africa. These sites were selected because they are within the Subtropical Thicket biome (similar vegetation) and were once used for livestock farming. At each study site, vegetation composition and structure were assessed using a unique bush clump sampling technique along fence line contrasts. Six plots were sampled at each site, three plots on the game reserve lands and three plots on the adjacent livestock farmlands during the dry (July/August 2020) and wet (January/February 2021) seasons. The Normalized Difference Vegetation Index (NDVI), in-situ leaf area index (LAI) and the fraction of intercepted photosynthetically active radiation (FIPAR), were used to assess vegetation productivity between the two land use types. Additionally, diet of an extralimital herbivore, giraffe (Giraffa camelopardalis), was assessed during contrasting seasons (dry and wet) to infer the role this species might have on these landscapes. The diet of giraffes was assessed through field observations, recording plant species that giraffes were feeding on. Floristic results showed that there were no differences in vegetation structure, species composition and richness between the two land types. There was no difference in the overall diversity of plant species on the game reserves than in the adjacent livestock farms. The primary productivity was greater on the game reserves compared to the livestock farms. Field observations of giraffe feeding showed that they fed predominantly on Vachellia karroo followed by Searsia longispina. Their diets did not differ between the two seasons. My study provides an insight into the effects of changing land use and this information can be used to infer the extent to which these changes might have on restoration of degraded landscape and how land use changes may be effective in restoring the degraded thicket vegetation caused by overgrazing and overstocking of domestic livestock. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Microbial and extracellular polymeric substance dynamics in arid–zone temporary pan ecosystems
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422258 , vital:71925
- Description: Microbial communities of bacteria, viruses, algae, protozoans and fungi participate profoundly in aquatic systems, particularly in mediating processes such as primary production, decomposition, and biogeochemical cycles. In addition, microbiomes produce extracellular polymeric substances (EPS) which encompass a hydrated exopolymer mainly constituted of carbohydrates and proteins. The exopolymer aid proliferation and persistence of biofilms on their resident surfaces. There is however paucity of data on functional diversity of microbiomes in arid zone temporary wetlands with previous research having mainly focused on permanent systems in the northern hemisphere. In the face of ongoing climatic changes and anthropogenic threats to wetlands, it is imperative to assess the health status of aquatic systems in relation to microbial productivity dynamics. In this thesis, colorimetric methods and sequence–based metagenomics were conducted to quantify microbial EPS production and bacterial metagenome functions, respectively. This study was conducted in Khakhea–Bray region (North–West, South Africa) in June 2021 and January 2022 with a focus on evaluating microbial patterns of distribution between seasons (i.e., Dry and Wet) and varying depth i.e., deepest zones (Deep), intermediate depth (Mid) and shallowest regions (Edge). Additionally, potential relationships between EPS and either water content or organic matter content (OM content) were evaluated. In this study it was hypothesized that wet phases and deeper zones will have high EPS production and support more functions in comparison to shallowest regions and dry phases. Carbohydrates and proteins were quantified using the Dubois method and modified Lowry procedure, respectively. Carbohydrates generally occurred in higher proportions than proteins, suggesting that EPS found in these systems was largely diatom produced. The wet phases (wet season and inundation periods) supported more EPS production compared to the dry phases. The results of principal components analysis (PCA) and Spearman’s correlations suggested that EPS was highly correlated with sediment water content among other assessed variables. No significant associations were established between EPS and organic matter content. Spatial distribution of EPS demonstrated similar patterns between the deepest (Deep) and the intermediate depth zones (Mid) however the shallow regions (Edge) had significantly lower concentrations. Bacterial characterization was established by amplification of the 16S rRNA gene using illumina–sequencing protocol. Enzyme functions associated with biogeochemical pathways were predicted in PICRUSt2 bioinformatics pipeline. A total of 15 042 Unique Amplicon Sequence Variants (ASVs) were observed to be affiliated to 51 bacterial phyla and 1 127 genera. All top genera had commonality in heat tolerance. Firmicutes, dominated at phyla level with 59 % (mean ± sd, 19 ± 13 %) relative abundance followed by Actinobacteria and Proteobacteria both at 34 % (18 ± 7 %) and (18 ± 6 %), respectively. Microbial diversity matrices highlighted significant differences in beta diversity more than alpha diversity. Bacterial microbiomes were more distinct between seasons compared to within season, suggesting that functions were seasonally driven. These findings were supported by highest rates of denitrification, carbohydrate degradation and EPS production by core microbiomes in the wet season as compared to low rates of nitrogen mineralisation, carbon fixation and nitrification in the dry season. The present findings represent a first attempt in evaluating sequence–based metagenomics in semi–arid southern African temporary pan ecosystem. Both microbial EPS and bacterial functional potential were highly driven by water availability, with highest rates mainly associated with maximum inundation compared to dry states of pans. It can therefore be suggested that extended dry periods are threatening to microbially mediated processes in temporary wetlands, with implications to loss of biodiversity due to desiccation resulting in poor nutrient cycling. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422258 , vital:71925
- Description: Microbial communities of bacteria, viruses, algae, protozoans and fungi participate profoundly in aquatic systems, particularly in mediating processes such as primary production, decomposition, and biogeochemical cycles. In addition, microbiomes produce extracellular polymeric substances (EPS) which encompass a hydrated exopolymer mainly constituted of carbohydrates and proteins. The exopolymer aid proliferation and persistence of biofilms on their resident surfaces. There is however paucity of data on functional diversity of microbiomes in arid zone temporary wetlands with previous research having mainly focused on permanent systems in the northern hemisphere. In the face of ongoing climatic changes and anthropogenic threats to wetlands, it is imperative to assess the health status of aquatic systems in relation to microbial productivity dynamics. In this thesis, colorimetric methods and sequence–based metagenomics were conducted to quantify microbial EPS production and bacterial metagenome functions, respectively. This study was conducted in Khakhea–Bray region (North–West, South Africa) in June 2021 and January 2022 with a focus on evaluating microbial patterns of distribution between seasons (i.e., Dry and Wet) and varying depth i.e., deepest zones (Deep), intermediate depth (Mid) and shallowest regions (Edge). Additionally, potential relationships between EPS and either water content or organic matter content (OM content) were evaluated. In this study it was hypothesized that wet phases and deeper zones will have high EPS production and support more functions in comparison to shallowest regions and dry phases. Carbohydrates and proteins were quantified using the Dubois method and modified Lowry procedure, respectively. Carbohydrates generally occurred in higher proportions than proteins, suggesting that EPS found in these systems was largely diatom produced. The wet phases (wet season and inundation periods) supported more EPS production compared to the dry phases. The results of principal components analysis (PCA) and Spearman’s correlations suggested that EPS was highly correlated with sediment water content among other assessed variables. No significant associations were established between EPS and organic matter content. Spatial distribution of EPS demonstrated similar patterns between the deepest (Deep) and the intermediate depth zones (Mid) however the shallow regions (Edge) had significantly lower concentrations. Bacterial characterization was established by amplification of the 16S rRNA gene using illumina–sequencing protocol. Enzyme functions associated with biogeochemical pathways were predicted in PICRUSt2 bioinformatics pipeline. A total of 15 042 Unique Amplicon Sequence Variants (ASVs) were observed to be affiliated to 51 bacterial phyla and 1 127 genera. All top genera had commonality in heat tolerance. Firmicutes, dominated at phyla level with 59 % (mean ± sd, 19 ± 13 %) relative abundance followed by Actinobacteria and Proteobacteria both at 34 % (18 ± 7 %) and (18 ± 6 %), respectively. Microbial diversity matrices highlighted significant differences in beta diversity more than alpha diversity. Bacterial microbiomes were more distinct between seasons compared to within season, suggesting that functions were seasonally driven. These findings were supported by highest rates of denitrification, carbohydrate degradation and EPS production by core microbiomes in the wet season as compared to low rates of nitrogen mineralisation, carbon fixation and nitrification in the dry season. The present findings represent a first attempt in evaluating sequence–based metagenomics in semi–arid southern African temporary pan ecosystem. Both microbial EPS and bacterial functional potential were highly driven by water availability, with highest rates mainly associated with maximum inundation compared to dry states of pans. It can therefore be suggested that extended dry periods are threatening to microbially mediated processes in temporary wetlands, with implications to loss of biodiversity due to desiccation resulting in poor nutrient cycling. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Source of introduced populations of Hemidactylus mabouia (Moreau de Jonnès, 1818) into the Eastern Cape Province and the potential spread to other South African regions
- Authors: Jeme, Alungile
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422334 , vital:71933
- Description: Human movements globally have resulted in dispersal and introduction of terrestrial and marine organisms into areas outside of their native range. Species that have been introduced to new habitats can either be alien (not causing any harm to the new environment) or invasive alien species (destroying or competing with the indigenous species for resources). Investigating the source of these introductions is important as it provides baseline information about their biology and evolution. It also allows for better prevention measures for future invasions and for effective conservation strategies. In this study, I investigate the source of the introduced populations of tropical house geckos Hemidactylus mabouia in the Eastern Cape Province using two mitochondrial gene regions, ribosomal 16S and NADH dehydrogenase subunit 4 (ND4). We also look at the potential spread of these species using species distribution models (SDMs). The phylogeny showed that the introduced populations into the Eastern Cape were genetically similar to both H. mabouia lineages found in Central & Southern Africa. The phylogeny produced two clades from which the majority of the introduced samples were grouped in a clade with samples from Angola, DRC, and Mozambique, and only a few nested within the second clade with the South African native population. Haplotype networks from both genes also showed two clades, matching those found in the phylogeny. The introduced samples were associated with samples from Angola and those from South Africa (native) as these localities had a number of shared haplotypes. SDMs showed less evidence that these individuals could naturally move west down the coast as the probability of occurrence was below 0.4 from the Eastern Cape to the Western Cape. Our conclusion was that the introductions may be due to multiple avenues like species moving down the east coast or human translocation including trade routes. From this we can conclude that geckos are largely translocated through human movement as they are known for their opportunistic behaviours as they are commensal with humans. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Jeme, Alungile
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422334 , vital:71933
- Description: Human movements globally have resulted in dispersal and introduction of terrestrial and marine organisms into areas outside of their native range. Species that have been introduced to new habitats can either be alien (not causing any harm to the new environment) or invasive alien species (destroying or competing with the indigenous species for resources). Investigating the source of these introductions is important as it provides baseline information about their biology and evolution. It also allows for better prevention measures for future invasions and for effective conservation strategies. In this study, I investigate the source of the introduced populations of tropical house geckos Hemidactylus mabouia in the Eastern Cape Province using two mitochondrial gene regions, ribosomal 16S and NADH dehydrogenase subunit 4 (ND4). We also look at the potential spread of these species using species distribution models (SDMs). The phylogeny showed that the introduced populations into the Eastern Cape were genetically similar to both H. mabouia lineages found in Central & Southern Africa. The phylogeny produced two clades from which the majority of the introduced samples were grouped in a clade with samples from Angola, DRC, and Mozambique, and only a few nested within the second clade with the South African native population. Haplotype networks from both genes also showed two clades, matching those found in the phylogeny. The introduced samples were associated with samples from Angola and those from South Africa (native) as these localities had a number of shared haplotypes. SDMs showed less evidence that these individuals could naturally move west down the coast as the probability of occurrence was below 0.4 from the Eastern Cape to the Western Cape. Our conclusion was that the introductions may be due to multiple avenues like species moving down the east coast or human translocation including trade routes. From this we can conclude that geckos are largely translocated through human movement as they are known for their opportunistic behaviours as they are commensal with humans. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
The influence of immuno-contraception on the ecology of African savanna elephants (Loxodonta africana) in a small game reserve in the Eastern Cape, South Africa
- Authors: Fowler, Natalie
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422269 , vital:71926
- Description: African savanna elephants (Loxodonta africana) can alter the vegetation structure on a landscape which has both positive and negative consequences for biodiversity. This ecological role can be dependent on the density of elephants in a given area and how the area is transformed. Elephants are currently listed as an endangered species on the International Union for Conservation of Nature (IUCN) global red list. Despite this endangered status, strong conservation efforts in southern Africa have increased elephant numbers in protected areas. In South Africa, many of these protected areas are small (<1000 km2) and fenced. Thus, without the freedom to roam over large areas, elephant impacts on vegetation and other ecosystem processes may be exacerbated. Increased growth rates and higher population densities, have prompted wildlife managers to explore several population-level management techniques to slow elephant growth rates in small, protected areas. One such technique is the use of immuno-contraception. My study focused on three datasets (Pre, During and Post porcine zona pellucida (PZP) treatments) of one elephant population over an 18-year period in a small game reserve in the Eastern Cape, South Africa. The first aim of my study was to compare the female demography and reproductive parameters of treated (with PZP) and non-treated females (no PZP). I predicted that the population growth would decrease as more elephant cows were contracepted as well as them having longer inter-calving intervals than non-treated cows. Further, I predicted that there would be a skewed sex ratio of male calves born to treated cows. Lastly, I predicted that fertility rates would be lower in treated cows than in non-treated cows. I calculated the annual population growth rates, inter-calving intervals, sex ratios, age at first calving, fecundity rates and fertility rates of all breeding cows. Population growth rates were similar to other managed populations although, compared to a relatively untouched elephant population, annual growth rates in my study site were high. The inter-calving intervals and age at first birth were low compared to other African protected areas which were most likely influenced by the use of PZP, rainfall and a lack of density dependence. Treated cows did not have longer inter-calving intervals compared to non-treated cows nor was there a male biased sex ratio of the offspring of treated cows. The second aim was to assess the spatial ecology of this elephant population and how it may be influenced by immuno-contraception. I predicted that the use of PZP would increase the elephant herd’s core range as there were fewer reproducing cows. I also predicted that PZP would alter the elephant’s habitat use making them less selective in terms of the vegetation types they selected. I compared the home ranges of the elephant population among the three treatments (Pre PZP, During PZP and Post PZP treatment). Home ranges were larger when elephants were treated with PZP compared to the Pre and Post treatments. The herd utilized most of the reserve during the use of PZP whereas prior to contraception, their space use was mostly concentrated on the eastern side of the reserve. Additionally, the vegetation utilization was inconsistent across the differing timeframes, specifically between pre PZP and during PZP. Prior to the use of PZP, the elephant herd utilized the old lands and riverine thicket the most whereas during the use of PZP, the grasslands and karroid habitats were used the most. The most likely influence of the changes in home ranges and vegetation utilization were rainfall, the use of PZP and resource availability. My results suggest that the use of PZP is essential for controlling elephant population numbers. However, there may be some long-term effects (e.g., behavioural changes) of the use of PZP in elephant populations in small game reserves. Thus, I recommend continued monitoring of all aspects of elephant ecology on reserves where PZP is used as a contraceptive technique. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Authors: Fowler, Natalie
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422269 , vital:71926
- Description: African savanna elephants (Loxodonta africana) can alter the vegetation structure on a landscape which has both positive and negative consequences for biodiversity. This ecological role can be dependent on the density of elephants in a given area and how the area is transformed. Elephants are currently listed as an endangered species on the International Union for Conservation of Nature (IUCN) global red list. Despite this endangered status, strong conservation efforts in southern Africa have increased elephant numbers in protected areas. In South Africa, many of these protected areas are small (<1000 km2) and fenced. Thus, without the freedom to roam over large areas, elephant impacts on vegetation and other ecosystem processes may be exacerbated. Increased growth rates and higher population densities, have prompted wildlife managers to explore several population-level management techniques to slow elephant growth rates in small, protected areas. One such technique is the use of immuno-contraception. My study focused on three datasets (Pre, During and Post porcine zona pellucida (PZP) treatments) of one elephant population over an 18-year period in a small game reserve in the Eastern Cape, South Africa. The first aim of my study was to compare the female demography and reproductive parameters of treated (with PZP) and non-treated females (no PZP). I predicted that the population growth would decrease as more elephant cows were contracepted as well as them having longer inter-calving intervals than non-treated cows. Further, I predicted that there would be a skewed sex ratio of male calves born to treated cows. Lastly, I predicted that fertility rates would be lower in treated cows than in non-treated cows. I calculated the annual population growth rates, inter-calving intervals, sex ratios, age at first calving, fecundity rates and fertility rates of all breeding cows. Population growth rates were similar to other managed populations although, compared to a relatively untouched elephant population, annual growth rates in my study site were high. The inter-calving intervals and age at first birth were low compared to other African protected areas which were most likely influenced by the use of PZP, rainfall and a lack of density dependence. Treated cows did not have longer inter-calving intervals compared to non-treated cows nor was there a male biased sex ratio of the offspring of treated cows. The second aim was to assess the spatial ecology of this elephant population and how it may be influenced by immuno-contraception. I predicted that the use of PZP would increase the elephant herd’s core range as there were fewer reproducing cows. I also predicted that PZP would alter the elephant’s habitat use making them less selective in terms of the vegetation types they selected. I compared the home ranges of the elephant population among the three treatments (Pre PZP, During PZP and Post PZP treatment). Home ranges were larger when elephants were treated with PZP compared to the Pre and Post treatments. The herd utilized most of the reserve during the use of PZP whereas prior to contraception, their space use was mostly concentrated on the eastern side of the reserve. Additionally, the vegetation utilization was inconsistent across the differing timeframes, specifically between pre PZP and during PZP. Prior to the use of PZP, the elephant herd utilized the old lands and riverine thicket the most whereas during the use of PZP, the grasslands and karroid habitats were used the most. The most likely influence of the changes in home ranges and vegetation utilization were rainfall, the use of PZP and resource availability. My results suggest that the use of PZP is essential for controlling elephant population numbers. However, there may be some long-term effects (e.g., behavioural changes) of the use of PZP in elephant populations in small game reserves. Thus, I recommend continued monitoring of all aspects of elephant ecology on reserves where PZP is used as a contraceptive technique. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
Genetic analysis and field application of a UV-tolerant strain of CrleGV for improved control of Thaumatotibia leucotreta
- Authors: Bennett, Tahnee Tashia
- Date: 2022-10-14
- Subjects: Cryptophlebia leucotreta Biological control , Pests Integrated control , Biological pest control agents , Ultraviolet radiation , Oligonucleotides
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362741 , vital:65358
- Description: Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), also known as false codling moth (FCM), is indigenous to sub-Saharan Africa. Thaumatotibia leucotreta has been controlled through an integrated pest management (IPM) programme, which includes chemical control, sterile insect technique (SIT), cultural and biological control. As part of the biological control, a key component is the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA). Currently, CryptogranTM, a commercial formulation of CrleGV, is the preferred product to use in South Africa for the control of T. leucotreta. The registration of the biopesticide Cryptogran (River bioscience, South Africa) was established after conducting extensive field trials with CrleGV-SA. One of the major factors affecting the baculovirus efficacy in the field is UV irradiation. A UV-tolerant Cryptophlebia leucotreta granulovirus (CrleGV-SA-C5) isolate was isolated after consecutive cycles of UV exposure. This UV-tolerant isolate is genetically distinct from the CrleGV-SA isolate. The CrleGV-SA-C5 isolate has the potential as a biological control agent. The control of T. leucotreta in South Africa could be improved by the development of novel isolates into new biopesticide formulations. To date, there has not been any field trials conducted on the CrleGV-SA-C5 isolate. Therefore, it is important to determine the biological and genetic stability of this isolate and to conduct field trials with CrleGV-SA- C5 to test the efficacy of the isolate before possible production into a biopesticide. A de novo assembly was conducted to reassemble the genome of CrleGV-SA-C5 which was followed by a sequence comparison with the CrleGV-SA genome. The identification of SNPs, led to the design of oligonucleotides flanking the regions where the SNPs were detected. Polymerase chain reaction amplification of the target regions was conducted using the oligonucleotides. After sequence comparison, seven SNPs were detected and PCR amplification was successful using the three oligonucleotides, Pif-2, HypoP and Lef-8/HP. To differentiate between CrleGV-SA-C5 and CrleGV-SA genomes and confirm the presence of the SNPs, two methods of screening were conducted. The first was the construction of six plasmids, the plasmids contained the targeted pif-2, HypoP, and the Lef-8/HP insert regions from both the CrleGV-SA-C5 and CrleGV-SA genome region where the SNPs were identified, followed by sequencing. The Five recombinant plasmids, pC5_Pif-2, pSA_Pif-2, pC5_HypoP, pSA_HypoP, and pC5_Lef-8/HP were successfully sequenced. No amplicon was obtained for one of the plasmids used as template (pSA_Lef-8/HP) and therefore the PCR product used for cloning was sequenced instead. Sequence alignment confirmed the presence of four of the five targeted SNPs in the genome of the CrleGV-SA-C5 isolate. However, of these only one SNP (UV_7) rendered a suitable marker for the differentiation between the CrleGV-SA-C5 and CrleGV-SA isolates as the SNPs, UV_2, UV_3 and UV_5, were also present in the CrleGV- SA sequences. The second screening method was a quantitative polymerase chain reaction (qPCR) melt curve analysis to differentiate between the CrleGV-SA-C5 and CrleGV-SA isolates. qPCR melt curve analysis was done using the CrleGV-SA-C5 and CrleGV-SA HypoP PCR products. This technique was unable to differentiate between the CrleGV-SA-C5 and CrleGV-SA isolates. However, this may be as a result of sequence data confirming that SNP UV_5 originally identified in the CrleGV-SA-C5 HypoP region was identical to the SNP at the same position in the CrleGV-SA HypoP region. Following the differentiation of the CrleGV-SA-C5 and CrleGV-SA isolates through two screening methods, the genetic integrity of the CrleGV-SA-C5 isolate after two virus bulk-ups was determined by PCR amplification of the target regions in the bulk-up virus followed by sequencing. Prior to virus bulk-up, surface dose bioassays were conducted on 4th instar larvae and LC50 and LC90 values of 4.01 x 106 OBs/ml and 8.75 x 109 OBs/ml respectively were obtained. The CrleGV-SA-C5 isolate was then bulked up in fourth instar T. leucotreta larvae using the LC90 value that was determined. Sequencing of the target regions from the CrleGV- SA-C5_BU2 (bulk-up 2) was conducted. Sequencing results confirmed the presence of the target SNPs in the CrleGV-SA-C5_BU2 genome. The UV-tolerance of the CrleGV-SA-C5 isolate in comparison to the CrleGV-SA isolate was evaluated by detached fruit bioassays under natural UV irradiation. Two detached fruit bioassays were set-up, a UV exposure and a non-UV exposure bioassay set-up. Three treatments were used for each bioassay set-up which were the viruses CrleGV-SA-C5 and CrleGV-SA and a ddH2O control. Statistical analysis indicated that there was no significant difference between the virus treatments in both the UV exposed detached fruit bioassay and the non-UV exposed detached fruit bioassay. This study is the second study to report on the de novo assembly of the CrleGV-SA-C5 and sequence comparison with the CrleGV-SA genome, and the first to report on the UV-tolerance of the CrleGV-SA-C5 isolate by detached fruit bioassays. Future work could involve further evaluation of intraspecific genetic variability in the CrleGV-SA-C5 isolate and to identify any additional SNPs present within the genome that can be used as suitable markers for differentiation between the CrleGV-SA-C5 and CrleGV-SA isolates. It was recognised that it is required to conduct further detached fruit bioassays and field trials, but with improved protocols, for the efficacy and UV-tolerance of the CrleGV-SA-C5 isolate to be conclusively determined. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Authors: Bennett, Tahnee Tashia
- Date: 2022-10-14
- Subjects: Cryptophlebia leucotreta Biological control , Pests Integrated control , Biological pest control agents , Ultraviolet radiation , Oligonucleotides
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362741 , vital:65358
- Description: Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), also known as false codling moth (FCM), is indigenous to sub-Saharan Africa. Thaumatotibia leucotreta has been controlled through an integrated pest management (IPM) programme, which includes chemical control, sterile insect technique (SIT), cultural and biological control. As part of the biological control, a key component is the use of Cryptophlebia leucotreta granulovirus (CrleGV-SA). Currently, CryptogranTM, a commercial formulation of CrleGV, is the preferred product to use in South Africa for the control of T. leucotreta. The registration of the biopesticide Cryptogran (River bioscience, South Africa) was established after conducting extensive field trials with CrleGV-SA. One of the major factors affecting the baculovirus efficacy in the field is UV irradiation. A UV-tolerant Cryptophlebia leucotreta granulovirus (CrleGV-SA-C5) isolate was isolated after consecutive cycles of UV exposure. This UV-tolerant isolate is genetically distinct from the CrleGV-SA isolate. The CrleGV-SA-C5 isolate has the potential as a biological control agent. The control of T. leucotreta in South Africa could be improved by the development of novel isolates into new biopesticide formulations. To date, there has not been any field trials conducted on the CrleGV-SA-C5 isolate. Therefore, it is important to determine the biological and genetic stability of this isolate and to conduct field trials with CrleGV-SA- C5 to test the efficacy of the isolate before possible production into a biopesticide. A de novo assembly was conducted to reassemble the genome of CrleGV-SA-C5 which was followed by a sequence comparison with the CrleGV-SA genome. The identification of SNPs, led to the design of oligonucleotides flanking the regions where the SNPs were detected. Polymerase chain reaction amplification of the target regions was conducted using the oligonucleotides. After sequence comparison, seven SNPs were detected and PCR amplification was successful using the three oligonucleotides, Pif-2, HypoP and Lef-8/HP. To differentiate between CrleGV-SA-C5 and CrleGV-SA genomes and confirm the presence of the SNPs, two methods of screening were conducted. The first was the construction of six plasmids, the plasmids contained the targeted pif-2, HypoP, and the Lef-8/HP insert regions from both the CrleGV-SA-C5 and CrleGV-SA genome region where the SNPs were identified, followed by sequencing. The Five recombinant plasmids, pC5_Pif-2, pSA_Pif-2, pC5_HypoP, pSA_HypoP, and pC5_Lef-8/HP were successfully sequenced. No amplicon was obtained for one of the plasmids used as template (pSA_Lef-8/HP) and therefore the PCR product used for cloning was sequenced instead. Sequence alignment confirmed the presence of four of the five targeted SNPs in the genome of the CrleGV-SA-C5 isolate. However, of these only one SNP (UV_7) rendered a suitable marker for the differentiation between the CrleGV-SA-C5 and CrleGV-SA isolates as the SNPs, UV_2, UV_3 and UV_5, were also present in the CrleGV- SA sequences. The second screening method was a quantitative polymerase chain reaction (qPCR) melt curve analysis to differentiate between the CrleGV-SA-C5 and CrleGV-SA isolates. qPCR melt curve analysis was done using the CrleGV-SA-C5 and CrleGV-SA HypoP PCR products. This technique was unable to differentiate between the CrleGV-SA-C5 and CrleGV-SA isolates. However, this may be as a result of sequence data confirming that SNP UV_5 originally identified in the CrleGV-SA-C5 HypoP region was identical to the SNP at the same position in the CrleGV-SA HypoP region. Following the differentiation of the CrleGV-SA-C5 and CrleGV-SA isolates through two screening methods, the genetic integrity of the CrleGV-SA-C5 isolate after two virus bulk-ups was determined by PCR amplification of the target regions in the bulk-up virus followed by sequencing. Prior to virus bulk-up, surface dose bioassays were conducted on 4th instar larvae and LC50 and LC90 values of 4.01 x 106 OBs/ml and 8.75 x 109 OBs/ml respectively were obtained. The CrleGV-SA-C5 isolate was then bulked up in fourth instar T. leucotreta larvae using the LC90 value that was determined. Sequencing of the target regions from the CrleGV- SA-C5_BU2 (bulk-up 2) was conducted. Sequencing results confirmed the presence of the target SNPs in the CrleGV-SA-C5_BU2 genome. The UV-tolerance of the CrleGV-SA-C5 isolate in comparison to the CrleGV-SA isolate was evaluated by detached fruit bioassays under natural UV irradiation. Two detached fruit bioassays were set-up, a UV exposure and a non-UV exposure bioassay set-up. Three treatments were used for each bioassay set-up which were the viruses CrleGV-SA-C5 and CrleGV-SA and a ddH2O control. Statistical analysis indicated that there was no significant difference between the virus treatments in both the UV exposed detached fruit bioassay and the non-UV exposed detached fruit bioassay. This study is the second study to report on the de novo assembly of the CrleGV-SA-C5 and sequence comparison with the CrleGV-SA genome, and the first to report on the UV-tolerance of the CrleGV-SA-C5 isolate by detached fruit bioassays. Future work could involve further evaluation of intraspecific genetic variability in the CrleGV-SA-C5 isolate and to identify any additional SNPs present within the genome that can be used as suitable markers for differentiation between the CrleGV-SA-C5 and CrleGV-SA isolates. It was recognised that it is required to conduct further detached fruit bioassays and field trials, but with improved protocols, for the efficacy and UV-tolerance of the CrleGV-SA-C5 isolate to be conclusively determined. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
Larval assemblages in intertidal habitats: the use of artificial and natural microhabitats
- Authors: Reddy, Seshnee
- Date: 2022-10-14
- Subjects: Larvae Habitat , Niche (Ecology) , Intertidal ecology South Africa Eastern Cape , Light trap , DNA barcoding , Artificial habitat , Larvae Effect of human beings on South Africa Eastern Cape , Urbanization South Africa Eastern Cape
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/364992 , vital:65668
- Description: Coastal habitats, and more specifically, intertidal habitats, host a unique range of biodiversity and are key areas for many fish and invertebrate species across one or more of their life stages. This is due to the provision of microhabitats which offer an escape from harsh environmental stressors and predation as well as increased food supply, hence increasing chances of survival. Due to the growing human population however, coastal habitats are being replaced by artificial structures (jetties, seawalls, piers, breakwaters) which partially or heavily fragment the natural environment through urbanisation-related expansion processes. These coastal infrastructures also have different physical properties from the natural environment and therefore tend to support different biological assemblages and can potentially alter the existing biodiversity and its functionality. The overall aim of this project was therefore to evaluate the use of artificial and natural intertidal microhabitats by fish and invertebrate larvae along the South African, Eastern Cape coastline. As independent case studies, fieldwork was conducted at an urban (Port Alfred Marina) and rocky shore (Kenton-on-Sea) site. Within each of these study sites, two replicated sheltered subsites were selected, which represented microhabitats. Samples were collected from these replicated microhabitats from September 2019 to February 2020 using light traps which targeted phototactic larval species, as well as a portable pump, for photo-neutral/negative taxa. All samples were preserved onsite in 99% ethanol and specimens were later counted and identified in the laboratory to the lowest possible taxonomic level using a stereomicroscope. Additionally, DNA barcoding was conducted on selected larval taxa for verification of morphological identification as well as contributing to the field of larval taxonomy through development of public database records. The barcoding technique was effective in positively identifying 96% and 58% of fish and invertebrate larvae sampled, respectively (overall identification success of 86%), to either family, genus or species level. Results of microhabitat use indicate higher larval abundances associated with artificial structures as compared to natural structures, with significant differences between the selected microhabitats within the rocky shores and the marina respectively, across months. High numbers of several early stage taxa were observed within the selected microhabitats in the marina, with Pinnotheres sp. (zoea) (Family: Pinnotheridae) being the most abundant invertebrate larval taxon collected at the artificial microhabitats of jetties and vertical walls. Fish larvae of Omobranchus woodi (preflexion) and Etrumeus whiteheadi (postflexion) were the most dominant at the selected artificial microhabitats within the marina. The DNA barcoding tool used in the current study to verify morphological identification proved to be instrumental in the accuracy of the reliable data collection of the early life stages present in these habitats. These results suggest that artificial structures may provide refugia for the vulnerable very early life stages of species and, in turn, play a potential facilitative role in reproductive and population connectivity which could result in replenishment of natural populations. It is therefore possible that these urban habitats could be considered as hubs for maintenance of coastal biodiversity. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Authors: Reddy, Seshnee
- Date: 2022-10-14
- Subjects: Larvae Habitat , Niche (Ecology) , Intertidal ecology South Africa Eastern Cape , Light trap , DNA barcoding , Artificial habitat , Larvae Effect of human beings on South Africa Eastern Cape , Urbanization South Africa Eastern Cape
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/364992 , vital:65668
- Description: Coastal habitats, and more specifically, intertidal habitats, host a unique range of biodiversity and are key areas for many fish and invertebrate species across one or more of their life stages. This is due to the provision of microhabitats which offer an escape from harsh environmental stressors and predation as well as increased food supply, hence increasing chances of survival. Due to the growing human population however, coastal habitats are being replaced by artificial structures (jetties, seawalls, piers, breakwaters) which partially or heavily fragment the natural environment through urbanisation-related expansion processes. These coastal infrastructures also have different physical properties from the natural environment and therefore tend to support different biological assemblages and can potentially alter the existing biodiversity and its functionality. The overall aim of this project was therefore to evaluate the use of artificial and natural intertidal microhabitats by fish and invertebrate larvae along the South African, Eastern Cape coastline. As independent case studies, fieldwork was conducted at an urban (Port Alfred Marina) and rocky shore (Kenton-on-Sea) site. Within each of these study sites, two replicated sheltered subsites were selected, which represented microhabitats. Samples were collected from these replicated microhabitats from September 2019 to February 2020 using light traps which targeted phototactic larval species, as well as a portable pump, for photo-neutral/negative taxa. All samples were preserved onsite in 99% ethanol and specimens were later counted and identified in the laboratory to the lowest possible taxonomic level using a stereomicroscope. Additionally, DNA barcoding was conducted on selected larval taxa for verification of morphological identification as well as contributing to the field of larval taxonomy through development of public database records. The barcoding technique was effective in positively identifying 96% and 58% of fish and invertebrate larvae sampled, respectively (overall identification success of 86%), to either family, genus or species level. Results of microhabitat use indicate higher larval abundances associated with artificial structures as compared to natural structures, with significant differences between the selected microhabitats within the rocky shores and the marina respectively, across months. High numbers of several early stage taxa were observed within the selected microhabitats in the marina, with Pinnotheres sp. (zoea) (Family: Pinnotheridae) being the most abundant invertebrate larval taxon collected at the artificial microhabitats of jetties and vertical walls. Fish larvae of Omobranchus woodi (preflexion) and Etrumeus whiteheadi (postflexion) were the most dominant at the selected artificial microhabitats within the marina. The DNA barcoding tool used in the current study to verify morphological identification proved to be instrumental in the accuracy of the reliable data collection of the early life stages present in these habitats. These results suggest that artificial structures may provide refugia for the vulnerable very early life stages of species and, in turn, play a potential facilitative role in reproductive and population connectivity which could result in replenishment of natural populations. It is therefore possible that these urban habitats could be considered as hubs for maintenance of coastal biodiversity. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
Puma (Puma concolor) diet and habitat use in south-west New Mexico
- Authors: Bernard, Kelly Monica Tandi
- Date: 2022-10-14
- Subjects: Puma Food New Mexico , Puma Habitat New Mexico , Puma Nutrition New Mexico , Puma Conservation New Mexico , Carnivorous animals New Mexico , Red deer , Elk , Mule deer , Ungulates
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362752 , vital:65359
- Description: The puma (Puma concolor) is a wide-ranging large felid species occupying an extensive geographic range throughout North and South America, and site-specific research on their diet is important for local management. Like other large felids, puma diet may differ between sexes due to size dimorphism, and between seasons due to changes in prey vulnerability and availability. This study assessed the influence of sex and season on puma diet in south-west New Mexico in terms of prey species and prey size categories. Pumas specialised on mule deer and elk throughout the year, and killed a range of other species of different sizes. The diet of the smaller female puma was nested within the diet of males, supporting the size-nested strategy. The effect of puma sex on prey species and size categories was independent of season, and vice versa, and the probability of a female making a medium-sized kill such as mule deer was higher than for males, while the probability of an extra-large kill such as elk was substantially greater for males. The probability of pumas killing either mule deer or elk in each season was similar, and greater than other species categories. Additionally, individual puma strongly influenced all prey species and size categories killed. The results from this study concur with previous findings on the importance of mule deer and elk in puma diet, and suggest that puma predation may also impact a number of other species, particularly smaller herbivores like collared peccary, and mesocarnivores such as skunks. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Authors: Bernard, Kelly Monica Tandi
- Date: 2022-10-14
- Subjects: Puma Food New Mexico , Puma Habitat New Mexico , Puma Nutrition New Mexico , Puma Conservation New Mexico , Carnivorous animals New Mexico , Red deer , Elk , Mule deer , Ungulates
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362752 , vital:65359
- Description: The puma (Puma concolor) is a wide-ranging large felid species occupying an extensive geographic range throughout North and South America, and site-specific research on their diet is important for local management. Like other large felids, puma diet may differ between sexes due to size dimorphism, and between seasons due to changes in prey vulnerability and availability. This study assessed the influence of sex and season on puma diet in south-west New Mexico in terms of prey species and prey size categories. Pumas specialised on mule deer and elk throughout the year, and killed a range of other species of different sizes. The diet of the smaller female puma was nested within the diet of males, supporting the size-nested strategy. The effect of puma sex on prey species and size categories was independent of season, and vice versa, and the probability of a female making a medium-sized kill such as mule deer was higher than for males, while the probability of an extra-large kill such as elk was substantially greater for males. The probability of pumas killing either mule deer or elk in each season was similar, and greater than other species categories. Additionally, individual puma strongly influenced all prey species and size categories killed. The results from this study concur with previous findings on the importance of mule deer and elk in puma diet, and suggest that puma predation may also impact a number of other species, particularly smaller herbivores like collared peccary, and mesocarnivores such as skunks. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
The biology of Oreochromis mossambicus and vulnerability to the invasion of Oreochromis niloticus
- Authors: Mpanza, Nobuhle Phumzile
- Date: 2022-10-14
- Subjects: Ecomorphology , Mozambique tilapia , Nile tilapia , Introduced fishes , Predatory aquatic animals , Predation (Biology) , Otoliths , Von Bertalanffy function
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362983 , vital:65380
- Description: Mozambique tilapia, Oreochromis mossambicus, a native southern African species now co-occurs with invasive Nile tilapia, Oreochromis niloticus throughout much of the distribution of the former. The spread of O. niloticus in South Africa has been attributed to escapees from aquaculture facilities, placing O. mossambicus at risk through competition for habitat and food resources, as well as through hybridisation. To better manage invasions, a comprehensive understanding of the biology, ecology and behaviour of both native and invasive species is required. The aim of this research was to comparatively assess the biology of O. mossambicus and O. niloticus, their food resource use characteristics and potential competitive interactions to infer impact risks associated with O. niloticus invasion dynamics. In addition to lack of sufficient autecological knowledge on O. niloticus in general, the challenge in the Eastern Cape is that relatively little regional knowledge is available on the biology and ecology of the native O. mossambicus. To address this, a total of 101 O. mossambicus individuals (32 - 297 mm LT) were sampled from the Sunday River catchment and their age and growth determined using sectioned sagittal otoliths. The largest female was 288.8 mm with a parameter estimate of LT (mm) = 272 (1-e-0.331(t=0.772)) and the largest male was 297 mm described as LT (mm) = 331.9 (1-e-0.167(t=1.192)). The growth parameter estimate age for combined sexes was best described as LT (mm) = 322.5 (1-e-0.201(t=1.027)). The growth rate was initially rapid for O. mossambicus and the asymptotic length reached after four years. The length-at-50% maturity was reached at 106.45 mm LT (R2 = 0.57) for the entire population. There was a significant difference (ᵡ2 = 8,047, df = 1, p-value = 0.0045) in the sex ratio between males and females which was skewed towards males 1:1.89 (F:M). Comparisons with O. niloticus were based on literature and these showed that O. niloticus had faster growth rates than O. mossambicus. These results serve as a baseline study in predicting the potential impacts of O. niloticus if it was to be introduced in the Eastern Cape region. Furthermore, although these two species are known to share habitat and food resources, feeding dynamics within the context of relative impact on prey resources, and competition potential between the species, are largely lacking. I used experimental functional response procedures to contrast the food consumption dynamics of each species and to assess for any multiple predator effects (MPEs) between these two closely related fishes. This was done by contrasting functional responses between individual species under single predator scenarios, predicted multiple predator functional response dynamics based on the individual species outputs, and actually observed functional responses under multiple predator conditions. Results showed that both Nile tilapia and Mozambique tilapia depicted a destabilizing Type II functional response. In both single and conspecific pairing Nile tilapia had significantly greater functional responses than Mozambique tilapia, hence greater overall predatory potential than its native congeneric Mozambique tilapia. Attack rates were also greater for Nile tilapia than Mozambique tilapia with both species showing similar handling times in single trials. However, no evidence for MPEs were detected, given lack of differences between predicted and observed functional responses under heterospecific conditions. These results suggest that Nile tilapia do not adjust their food intake in the presence of heterospecific competitors, but do consume more than Mozambique tilapia and are better at finding food when it is present at low densities. Feeding-related morphological characteristics may influence predatory performance of a species and can further provide information on the species’ capacity to locate, attack and consume different prey items. The feeding capacities between O. mossambicus and O. niloticus were compared based on morphological traits in order to determine whether differences existed, and if these differences place the invasive O. niloticus at an advantageous position in terms of resource acquisition and consumption over its native congener. Principal component analysis for functional morphology traits showed overlap between O. niloticus and O. mossambicus. Oreochromis niloticus had distinctively larger lower jaw closing force, gill resistance and gill raker length which facilitated greater feeding capacities for the invasive species over the native O. mossambicus. Trophic profiles depicted high dietary overlap between the two species. Although O. niloticus had a greater feeding capacity towards phytoplankton, plants, fish (ambush), fish (pursuit) and larvae, while O. mossambicus only showed greater feeding capacity towards zooplankton. While dietary overlap and similarities in morphological traits between native and invasive species may result in exploitative competition between the species, O. niloticus seems to be more versatile in its feeding and capable of consuming food web components that O. mossambicus may not be able to handle. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Authors: Mpanza, Nobuhle Phumzile
- Date: 2022-10-14
- Subjects: Ecomorphology , Mozambique tilapia , Nile tilapia , Introduced fishes , Predatory aquatic animals , Predation (Biology) , Otoliths , Von Bertalanffy function
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362983 , vital:65380
- Description: Mozambique tilapia, Oreochromis mossambicus, a native southern African species now co-occurs with invasive Nile tilapia, Oreochromis niloticus throughout much of the distribution of the former. The spread of O. niloticus in South Africa has been attributed to escapees from aquaculture facilities, placing O. mossambicus at risk through competition for habitat and food resources, as well as through hybridisation. To better manage invasions, a comprehensive understanding of the biology, ecology and behaviour of both native and invasive species is required. The aim of this research was to comparatively assess the biology of O. mossambicus and O. niloticus, their food resource use characteristics and potential competitive interactions to infer impact risks associated with O. niloticus invasion dynamics. In addition to lack of sufficient autecological knowledge on O. niloticus in general, the challenge in the Eastern Cape is that relatively little regional knowledge is available on the biology and ecology of the native O. mossambicus. To address this, a total of 101 O. mossambicus individuals (32 - 297 mm LT) were sampled from the Sunday River catchment and their age and growth determined using sectioned sagittal otoliths. The largest female was 288.8 mm with a parameter estimate of LT (mm) = 272 (1-e-0.331(t=0.772)) and the largest male was 297 mm described as LT (mm) = 331.9 (1-e-0.167(t=1.192)). The growth parameter estimate age for combined sexes was best described as LT (mm) = 322.5 (1-e-0.201(t=1.027)). The growth rate was initially rapid for O. mossambicus and the asymptotic length reached after four years. The length-at-50% maturity was reached at 106.45 mm LT (R2 = 0.57) for the entire population. There was a significant difference (ᵡ2 = 8,047, df = 1, p-value = 0.0045) in the sex ratio between males and females which was skewed towards males 1:1.89 (F:M). Comparisons with O. niloticus were based on literature and these showed that O. niloticus had faster growth rates than O. mossambicus. These results serve as a baseline study in predicting the potential impacts of O. niloticus if it was to be introduced in the Eastern Cape region. Furthermore, although these two species are known to share habitat and food resources, feeding dynamics within the context of relative impact on prey resources, and competition potential between the species, are largely lacking. I used experimental functional response procedures to contrast the food consumption dynamics of each species and to assess for any multiple predator effects (MPEs) between these two closely related fishes. This was done by contrasting functional responses between individual species under single predator scenarios, predicted multiple predator functional response dynamics based on the individual species outputs, and actually observed functional responses under multiple predator conditions. Results showed that both Nile tilapia and Mozambique tilapia depicted a destabilizing Type II functional response. In both single and conspecific pairing Nile tilapia had significantly greater functional responses than Mozambique tilapia, hence greater overall predatory potential than its native congeneric Mozambique tilapia. Attack rates were also greater for Nile tilapia than Mozambique tilapia with both species showing similar handling times in single trials. However, no evidence for MPEs were detected, given lack of differences between predicted and observed functional responses under heterospecific conditions. These results suggest that Nile tilapia do not adjust their food intake in the presence of heterospecific competitors, but do consume more than Mozambique tilapia and are better at finding food when it is present at low densities. Feeding-related morphological characteristics may influence predatory performance of a species and can further provide information on the species’ capacity to locate, attack and consume different prey items. The feeding capacities between O. mossambicus and O. niloticus were compared based on morphological traits in order to determine whether differences existed, and if these differences place the invasive O. niloticus at an advantageous position in terms of resource acquisition and consumption over its native congener. Principal component analysis for functional morphology traits showed overlap between O. niloticus and O. mossambicus. Oreochromis niloticus had distinctively larger lower jaw closing force, gill resistance and gill raker length which facilitated greater feeding capacities for the invasive species over the native O. mossambicus. Trophic profiles depicted high dietary overlap between the two species. Although O. niloticus had a greater feeding capacity towards phytoplankton, plants, fish (ambush), fish (pursuit) and larvae, while O. mossambicus only showed greater feeding capacity towards zooplankton. While dietary overlap and similarities in morphological traits between native and invasive species may result in exploitative competition between the species, O. niloticus seems to be more versatile in its feeding and capable of consuming food web components that O. mossambicus may not be able to handle. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text: