A molecular investigation of stem-galling Tetramesa Walker (Hymenoptera: Eurytomidae) on African grasses: applications to biological control
- Van Steenderen, Clarke Julian Mignon
- Authors: Van Steenderen, Clarke Julian Mignon
- Date: 2023-10-13
- Subjects: Grasses Africa , Tetramesa , Invasive plants Biological control , DNA barcoding , Weeds Biological control , Eragrostis curvula , Sporobolus pyramidalis , Sporobolus natalensis
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/432565 , vital:72881 , DOI 10.21504/10962/432565
- Description: South Africa is a larger donor than receiver of alien grasses, where approximately 15% (_ 165 spp.) of the country's native grass species have become naturalised elsewhere. Many of these grasses have become serious invaders, causing significant damage to native species, habitat structure, and ecosystem functioning. Biological control is a sustainable and cost-effective method for the control of invasive weeds, but its application to invasive grasses has been approached with trepidation in the past due to the fears of a lack of host-specific herbivores that may cause non-target damage to agriculturally-important crops. The Tetramesa Walker genus (Hymenoptera: Eurytomidae) is one of three genera in the family that feed exclusively on grasses, and have a record of being host-specific to a particular species, or complex of closely-related congeners. There are over 200 described Tetramesa species, but this taxonomic effort has occurred almost exclusively in the Northern Hemisphere. Only about 2% of the described species are from Africa, with none from southern Africa despite the high diversity of grasses in the region. The low morphological variability between many Tetramesa groups has made identification difficult, where there may in fact be multiple undiscovered cryptic species. This thesis generated genetic sequence data (mitochondrial COI and nuclear 28S) that revealed at least eight native southern African Tetramesa taxa that are new to science, focusing particularly on the assemblages associated with Eragrostis curvula Nees (African lovegrass) and Sporobolus pyramidalis Beauv. and S. natalensis Steud. (giant rat's tail grass) which are alien invasive pests in Australia. Approximately 200 eurytomid wasps were collected and sequenced from 19 grass species across six South African provinces. Additionally, 27 grass species were sequenced using four gene regions (rps16-trnK, rps16, rpl32-trnL, and ITS), which were added to existing sequence data to build a dataset comprising over 700 sequences. Field host ranges and the use of host grass genetic proxies were important in making inferences about the host-specificity of eurytomid wasps of interest. Nine Tetramesa groups appeared to be host-specific to a single grass species, while six Tetramesa were associated with multiple species in a single grass genus. Since S. pyramidalis, S. natalensis, S. africanus, Hyparrhenia hirta, E. trichophora, and Andropogon gayanus are weeds elsewhere, there are at least six potential Tetramesa biological control agents that have been identified. A high diversity of Tetramesa on grasses within the Eragrostis genus was reported, with at least four taxa associated with E. curvula. It is currently uncertain whether these taxa represent different cryptic species or intraspecific populations that are the result of geographic sub-structuring. No-choice host-specificity testing using Tetramesa sp. 4 on E. curvula revealed that the wasp could complete its lifecycle on two non-target African grasses; namely E. plana and E. planiculmis. The wasp was also recorded on other Eragrostis species in the field (namely E. biflora and E. capensis). Using grass genetic sequences obtained in this study, it was found that there are four native Australian Eragrostis species that are more closely related to target E. curvula than to the non-target E. plana and E. planiculmis. This suggests that Tetramesa sp. 4 may not be suitably host-specific for use as a biological control agent. Further host-specificity testing on these native Australian species is required, however, before this insect is ruled out completely. The Tetramesa on S. pyramidalis (Tetramesa sp. 1), and the unidentified Sporobolus species presumed to be S. africanus, were suitably host-specific to be used as biological control agents. Since it was unclear whether some phylogenetic clades were true species or intraspecific populations, which is essential to understand when selecting agents for biological control, a new piece of software, SPEDE-sampler", was developed. It offers users of the Generalised Mixed Yule Coalescent (GMYC) species delimitation model a means of assessing the degree to which sampling effects such as data size and parameter choice can influence species diversity estimates. When applied to the Tetramesa data set, the software assisted in identifying which groups may contain cryptic species, uncovering that the COI marker is affected more by singletons than the 28S marker (i.e. species diversity tends to be overestimated), and confirming putative Tetramesa taxa that could be useful for biological control programmes going forward. This thesis has provided evidence that South Africa contains a diverse assemblage of Tetramesa and other eurytomids that are closely associated with their grass hosts, and that many of these taxa hold promise for grass biological control. This work has also highlighted the importance of integrative taxonomy in the discovery of novel taxa, and that biological control practitioners need to be aware of the caveats of each line of evidence used in the delimitation of putative species. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Van Steenderen, Clarke Julian Mignon
- Date: 2023-10-13
- Subjects: Grasses Africa , Tetramesa , Invasive plants Biological control , DNA barcoding , Weeds Biological control , Eragrostis curvula , Sporobolus pyramidalis , Sporobolus natalensis
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/432565 , vital:72881 , DOI 10.21504/10962/432565
- Description: South Africa is a larger donor than receiver of alien grasses, where approximately 15% (_ 165 spp.) of the country's native grass species have become naturalised elsewhere. Many of these grasses have become serious invaders, causing significant damage to native species, habitat structure, and ecosystem functioning. Biological control is a sustainable and cost-effective method for the control of invasive weeds, but its application to invasive grasses has been approached with trepidation in the past due to the fears of a lack of host-specific herbivores that may cause non-target damage to agriculturally-important crops. The Tetramesa Walker genus (Hymenoptera: Eurytomidae) is one of three genera in the family that feed exclusively on grasses, and have a record of being host-specific to a particular species, or complex of closely-related congeners. There are over 200 described Tetramesa species, but this taxonomic effort has occurred almost exclusively in the Northern Hemisphere. Only about 2% of the described species are from Africa, with none from southern Africa despite the high diversity of grasses in the region. The low morphological variability between many Tetramesa groups has made identification difficult, where there may in fact be multiple undiscovered cryptic species. This thesis generated genetic sequence data (mitochondrial COI and nuclear 28S) that revealed at least eight native southern African Tetramesa taxa that are new to science, focusing particularly on the assemblages associated with Eragrostis curvula Nees (African lovegrass) and Sporobolus pyramidalis Beauv. and S. natalensis Steud. (giant rat's tail grass) which are alien invasive pests in Australia. Approximately 200 eurytomid wasps were collected and sequenced from 19 grass species across six South African provinces. Additionally, 27 grass species were sequenced using four gene regions (rps16-trnK, rps16, rpl32-trnL, and ITS), which were added to existing sequence data to build a dataset comprising over 700 sequences. Field host ranges and the use of host grass genetic proxies were important in making inferences about the host-specificity of eurytomid wasps of interest. Nine Tetramesa groups appeared to be host-specific to a single grass species, while six Tetramesa were associated with multiple species in a single grass genus. Since S. pyramidalis, S. natalensis, S. africanus, Hyparrhenia hirta, E. trichophora, and Andropogon gayanus are weeds elsewhere, there are at least six potential Tetramesa biological control agents that have been identified. A high diversity of Tetramesa on grasses within the Eragrostis genus was reported, with at least four taxa associated with E. curvula. It is currently uncertain whether these taxa represent different cryptic species or intraspecific populations that are the result of geographic sub-structuring. No-choice host-specificity testing using Tetramesa sp. 4 on E. curvula revealed that the wasp could complete its lifecycle on two non-target African grasses; namely E. plana and E. planiculmis. The wasp was also recorded on other Eragrostis species in the field (namely E. biflora and E. capensis). Using grass genetic sequences obtained in this study, it was found that there are four native Australian Eragrostis species that are more closely related to target E. curvula than to the non-target E. plana and E. planiculmis. This suggests that Tetramesa sp. 4 may not be suitably host-specific for use as a biological control agent. Further host-specificity testing on these native Australian species is required, however, before this insect is ruled out completely. The Tetramesa on S. pyramidalis (Tetramesa sp. 1), and the unidentified Sporobolus species presumed to be S. africanus, were suitably host-specific to be used as biological control agents. Since it was unclear whether some phylogenetic clades were true species or intraspecific populations, which is essential to understand when selecting agents for biological control, a new piece of software, SPEDE-sampler", was developed. It offers users of the Generalised Mixed Yule Coalescent (GMYC) species delimitation model a means of assessing the degree to which sampling effects such as data size and parameter choice can influence species diversity estimates. When applied to the Tetramesa data set, the software assisted in identifying which groups may contain cryptic species, uncovering that the COI marker is affected more by singletons than the 28S marker (i.e. species diversity tends to be overestimated), and confirming putative Tetramesa taxa that could be useful for biological control programmes going forward. This thesis has provided evidence that South Africa contains a diverse assemblage of Tetramesa and other eurytomids that are closely associated with their grass hosts, and that many of these taxa hold promise for grass biological control. This work has also highlighted the importance of integrative taxonomy in the discovery of novel taxa, and that biological control practitioners need to be aware of the caveats of each line of evidence used in the delimitation of putative species. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-10-13
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: Introduced organisms South Africa , Crayfish , Leeches , Rhabdocoelida , Environmental DNA , DNA barcoding
- 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:
- Date Issued: 2023-10-13
- Authors: Mdidimba, Nonkazimulo Dorothea
- Date: 2023-10-13
- Subjects: Introduced organisms South Africa , Crayfish , Leeches , Rhabdocoelida , Environmental DNA , DNA barcoding
- 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:
- Date Issued: 2023-10-13
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:
- Date Issued: 2022-10-14
- 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:
- Date Issued: 2022-10-14
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