Population estimates and spatial ecology of brown hyaenas in Kwandwe private game reserve
- Authors: Welch, Rebecca Jane
- Date: 2015
- Subjects: Brown hyaena -- Reintroduction -- South Africa , Kwandwe Private Game Reserve
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5932 , http://hdl.handle.net/10962/d1017810
- Description: During the last 25 years, the Eastern Cape Province of South Africa has seen the establishment of many small to medium sized (≤ 440km2) game reserves. These reserves have reintroduced many of the larger indigenous wildlife that had been extirpated by the early 20th century. As such, these reserves and wildlife introductions have created many research opportunities, including investigations on the ecology of reintroduced carnivores in the Thicket biome. Brown hyaenas (Hyaena brunnea) are one of the large carnivore species that have been reintroduced into the area. As these animals have predominantly been studied in more open, arid systems, their reintroduction has provided an excellent opportunity to study the species in an alternate natural habitat. Information gathered from such investigations adds to our knowledge of the species and also provides information for the management of brown hyaenas within small, enclosed reserves. Data were collected over the period of one calendaryear, from February 2013 to February 2014 at Kwandwe Private Game Reserve in the Eastern Cape, South Africa. Brown hyaena population estimates were calculated using capture-recapture methods from individually identifiable images captured during a three month camera trapping survey. Images of brown hyaenas were separated into left- and right-side profiles. Twenty-eight individuals were positively identified from left-side images and 27 from right-side images. Non-spatial and spatially explicit capture-recapture analyses were both run in the program DENSITY 5.0. Density estimates ranged from 14 to 20 individuals/100km2 (equivalent to a total abundance of 26-37 individuals) depending on the method used. Despite the range of estimates, all are considerably higher than in other areaswhere densities have been calculated. Satellite/GPS collars were fitted to three individual brown hyaenas (two males and one female) to measure their home range size and use of space. Home range size was calculated using two different methods, Kernel utilisation distributions and Brownian bridges. Home range estimates were similar using both methods; however Brownian bridge methods appeared to exaggerate the use of space by individuals. Kernel home range sizes for the three individuals ranged between 42.62km2 and 79.88km2. These estimates are considerably smaller than previous findings from other parts of Africa and suggest that sufficient resources may be available within this enclosed system. The results from this study suggest that brown hyaenas are successful generalists in this enclosed system and are able to persist at high densities and occupy relatively small home ranges. This information is important for the managers of small reserves who wish to reintroduce brown hyaenas. Should brown hyaenas be introduced into reserves in the Thicket biome with sufficient resources, the numbers are likely to increase rapidly. If high numbers are not desired then preventative measures (e.g. contraception) should be investigated before release.
- Full Text:
- Date Issued: 2015
- Authors: Welch, Rebecca Jane
- Date: 2015
- Subjects: Brown hyaena -- Reintroduction -- South Africa , Kwandwe Private Game Reserve
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5932 , http://hdl.handle.net/10962/d1017810
- Description: During the last 25 years, the Eastern Cape Province of South Africa has seen the establishment of many small to medium sized (≤ 440km2) game reserves. These reserves have reintroduced many of the larger indigenous wildlife that had been extirpated by the early 20th century. As such, these reserves and wildlife introductions have created many research opportunities, including investigations on the ecology of reintroduced carnivores in the Thicket biome. Brown hyaenas (Hyaena brunnea) are one of the large carnivore species that have been reintroduced into the area. As these animals have predominantly been studied in more open, arid systems, their reintroduction has provided an excellent opportunity to study the species in an alternate natural habitat. Information gathered from such investigations adds to our knowledge of the species and also provides information for the management of brown hyaenas within small, enclosed reserves. Data were collected over the period of one calendaryear, from February 2013 to February 2014 at Kwandwe Private Game Reserve in the Eastern Cape, South Africa. Brown hyaena population estimates were calculated using capture-recapture methods from individually identifiable images captured during a three month camera trapping survey. Images of brown hyaenas were separated into left- and right-side profiles. Twenty-eight individuals were positively identified from left-side images and 27 from right-side images. Non-spatial and spatially explicit capture-recapture analyses were both run in the program DENSITY 5.0. Density estimates ranged from 14 to 20 individuals/100km2 (equivalent to a total abundance of 26-37 individuals) depending on the method used. Despite the range of estimates, all are considerably higher than in other areaswhere densities have been calculated. Satellite/GPS collars were fitted to three individual brown hyaenas (two males and one female) to measure their home range size and use of space. Home range size was calculated using two different methods, Kernel utilisation distributions and Brownian bridges. Home range estimates were similar using both methods; however Brownian bridge methods appeared to exaggerate the use of space by individuals. Kernel home range sizes for the three individuals ranged between 42.62km2 and 79.88km2. These estimates are considerably smaller than previous findings from other parts of Africa and suggest that sufficient resources may be available within this enclosed system. The results from this study suggest that brown hyaenas are successful generalists in this enclosed system and are able to persist at high densities and occupy relatively small home ranges. This information is important for the managers of small reserves who wish to reintroduce brown hyaenas. Should brown hyaenas be introduced into reserves in the Thicket biome with sufficient resources, the numbers are likely to increase rapidly. If high numbers are not desired then preventative measures (e.g. contraception) should be investigated before release.
- Full Text:
- Date Issued: 2015
Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae)
- Authors: Riddin, Megan Amy
- Date: 2015
- Subjects: River sardine , Molecular evolution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5930 , http://hdl.handle.net/10962/d1017808
- Description: The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.
- Full Text:
- Date Issued: 2015
- Authors: Riddin, Megan Amy
- Date: 2015
- Subjects: River sardine , Molecular evolution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5930 , http://hdl.handle.net/10962/d1017808
- Description: The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.
- Full Text:
- Date Issued: 2015
The cheetahs of the Northern Tuli Game Reserve, Botswana: population estimates, monitoring techniques and human-predator conflict
- Authors: Brassine, Eleanor I
- Date: 2015
- Subjects: Cheetah -- Botswana , Northern Tuli Game Reserve , Animal populations -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5922 , http://hdl.handle.net/10962/d1017800
- Description: Remaining viable cheetah (Acinonyx jubatus) populations in Africa are threatened by direct persecution through conflict with farmers and habitat degradation and fragmentation. Botswana is considered a stronghold for free roaming cheetahs in Africa, yet the country has had relatively limited research on its cheetahs, and information from the east of the country is lacking. Data on the current status of populations is thus required to make informed management decisions. My study provides estimates of population density, abundance, distribution and status for the demographically open cheetah population of the Northern Tuli Game Reserve (NOTUGRE) in Botswana. The effectiveness of two population monitoring methods, namely camera trapping and a photographic survey, were also investigated. Moreover, I report on the level of conflict between livestock farmers and predators on rural communal farmlands within and adjacent to NOTUGRE. Data were collected between May 2012 and November 2013. Results indicate a low population density of 0.61 ± 0.18 adult cheetahs per 100 km² and a minimum population size of 10 individuals (nine adults and one cub). Camera traps placed at cheetah scent-marking posts increased detection rates and provided ideal set up locations. This approach, together with Spatial Explicit Capture- Recapture (SECR) models, is recommended for future studies. The long-term studies that are required to better understand the status of cheetahs in Botswana do not exist. Thus, photographic surveys may provide an alternative method for providing baseline data on population numbers, distribution and demography. The third aspect of my study gathered information on levels of livestock loss and human tolerance of predators through the use of interviews (n = 80). Conflict with subsistence farmers is a concern as livestock depredation is relatively high (9.1% of total livestock owned) and farmers had an overall negative attitude towards conservation of large predators. My results suggest that human-predator conflict in this area is more complex than the direct financial loss from depredation. Hence, reducing depredation rates alone is unlikely to change farmer tolerance of wildlife on farmlands. Improved, responsible farm management, including self-responsibility for livestock rearing, and positive appreciation for wildlife are necessary. The NOTUGRE cheetah population requires further research to understand possible threats to the population. Furthermore, a better understanding of the connectivity between cheetahs of NOTUGRE, South Africa and Zimbabwe is required. The number of cheetahs within NOTUGRE is too small to sustain a viable population, hence conserving cheetahs outside of the protected area should be a priority for the conservation of the population. This can only be achieved through assistance and involvement from national authorities, local people and conservation organisations.
- Full Text:
- Date Issued: 2015
- Authors: Brassine, Eleanor I
- Date: 2015
- Subjects: Cheetah -- Botswana , Northern Tuli Game Reserve , Animal populations -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5922 , http://hdl.handle.net/10962/d1017800
- Description: Remaining viable cheetah (Acinonyx jubatus) populations in Africa are threatened by direct persecution through conflict with farmers and habitat degradation and fragmentation. Botswana is considered a stronghold for free roaming cheetahs in Africa, yet the country has had relatively limited research on its cheetahs, and information from the east of the country is lacking. Data on the current status of populations is thus required to make informed management decisions. My study provides estimates of population density, abundance, distribution and status for the demographically open cheetah population of the Northern Tuli Game Reserve (NOTUGRE) in Botswana. The effectiveness of two population monitoring methods, namely camera trapping and a photographic survey, were also investigated. Moreover, I report on the level of conflict between livestock farmers and predators on rural communal farmlands within and adjacent to NOTUGRE. Data were collected between May 2012 and November 2013. Results indicate a low population density of 0.61 ± 0.18 adult cheetahs per 100 km² and a minimum population size of 10 individuals (nine adults and one cub). Camera traps placed at cheetah scent-marking posts increased detection rates and provided ideal set up locations. This approach, together with Spatial Explicit Capture- Recapture (SECR) models, is recommended for future studies. The long-term studies that are required to better understand the status of cheetahs in Botswana do not exist. Thus, photographic surveys may provide an alternative method for providing baseline data on population numbers, distribution and demography. The third aspect of my study gathered information on levels of livestock loss and human tolerance of predators through the use of interviews (n = 80). Conflict with subsistence farmers is a concern as livestock depredation is relatively high (9.1% of total livestock owned) and farmers had an overall negative attitude towards conservation of large predators. My results suggest that human-predator conflict in this area is more complex than the direct financial loss from depredation. Hence, reducing depredation rates alone is unlikely to change farmer tolerance of wildlife on farmlands. Improved, responsible farm management, including self-responsibility for livestock rearing, and positive appreciation for wildlife are necessary. The NOTUGRE cheetah population requires further research to understand possible threats to the population. Furthermore, a better understanding of the connectivity between cheetahs of NOTUGRE, South Africa and Zimbabwe is required. The number of cheetahs within NOTUGRE is too small to sustain a viable population, hence conserving cheetahs outside of the protected area should be a priority for the conservation of the population. This can only be achieved through assistance and involvement from national authorities, local people and conservation organisations.
- Full Text:
- Date Issued: 2015
Using the larval parasitoid, Agathis bishopi (Nixon) (Hymenoptera: Braconidae), for early detection of false codling moth, Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) infested fruit
- Authors: Zimba, Kennedy Josaya
- Date: 2015
- Subjects: Cryptophlebia leucotreta , Citrus -- Diseases and pests -- South Africa , Pests -- Biological control -- South Africa , Cryptophlebia leucotreta -- Detection , Parasitoids -- Hosts , Braconidae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5919 , http://hdl.handle.net/10962/d1017186
- Description: Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is one of the major citrus pests of economic importance for South Africa’s citrus industry. It is endemic to Africa, and therefore a phytosanitary pest with zero tolerance by most export markets. The cryptic nature of T. leucotreta makes visual inspection an inefficient method for detecting neonate larvae in fruit in the packhouse. Therefore, a more accurate method for sorting infested fruit at the packhouse, particularly for newly infested fruit could ensure market access. A recent study showed that fruit infested by T. leucotreta emit a chemical profile different from that of a healthy fruit. Several studies provide evidence that parasitoids locate their hosts feeding on fruit by exploiting the novel chemical profiles produced due to host herbivory. The aim of this study was to evaluate the potential of using the naturally occurring behaviour of a larval parasitoid Agathis bishopi (Nixon) (Hymenoptera: Braconidae) for detection of T. leucotreta infested fruit, by determining which compound in infested fruit is attractive to parasitoids. Ytube olfactometer and flight-tunnel bioassays with healthy and T. leucotreta infested fruit showed a significantly stronger response of A. bishopi female parasitoids to infested fruit. Among the volatile compounds associated with T. leucotreta infested fruit, D-limonene elicited the strongest attraction to A. bishopi female parasitoids. Attraction of mated A. bishopi female parasitoids to T. leucotreta infested fruit and D-limonene significantly increased after oviposition experience. Behavioural responses of A. bishopi female parasitoids that were associated with T. leucotreta infested fruit were investigated to determine which behaviours are distinct and interpretable. Probing and oviposition behaviours were the most noticeable and were only elicited on infested fruit when parasitoids contacted T. leucotreta frass, indicating that chemical compounds in frass are short-range cues used for final host location. Since production of D-limonene by fruit is elevated due to herbivory by different pests including mechanical injury on fruit, response of A. bishopi female parasitoids to compounds in frass offers a more specific and potentially useful mechanism for development of a detection system for T. leucotreta infested fruit. Chemical analysis of T. leucotreta frass and conditioning A. bishopi parasitoids to respond behaviourally to compounds in frass is proposed.
- Full Text:
- Date Issued: 2015
- Authors: Zimba, Kennedy Josaya
- Date: 2015
- Subjects: Cryptophlebia leucotreta , Citrus -- Diseases and pests -- South Africa , Pests -- Biological control -- South Africa , Cryptophlebia leucotreta -- Detection , Parasitoids -- Hosts , Braconidae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5919 , http://hdl.handle.net/10962/d1017186
- Description: Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is one of the major citrus pests of economic importance for South Africa’s citrus industry. It is endemic to Africa, and therefore a phytosanitary pest with zero tolerance by most export markets. The cryptic nature of T. leucotreta makes visual inspection an inefficient method for detecting neonate larvae in fruit in the packhouse. Therefore, a more accurate method for sorting infested fruit at the packhouse, particularly for newly infested fruit could ensure market access. A recent study showed that fruit infested by T. leucotreta emit a chemical profile different from that of a healthy fruit. Several studies provide evidence that parasitoids locate their hosts feeding on fruit by exploiting the novel chemical profiles produced due to host herbivory. The aim of this study was to evaluate the potential of using the naturally occurring behaviour of a larval parasitoid Agathis bishopi (Nixon) (Hymenoptera: Braconidae) for detection of T. leucotreta infested fruit, by determining which compound in infested fruit is attractive to parasitoids. Ytube olfactometer and flight-tunnel bioassays with healthy and T. leucotreta infested fruit showed a significantly stronger response of A. bishopi female parasitoids to infested fruit. Among the volatile compounds associated with T. leucotreta infested fruit, D-limonene elicited the strongest attraction to A. bishopi female parasitoids. Attraction of mated A. bishopi female parasitoids to T. leucotreta infested fruit and D-limonene significantly increased after oviposition experience. Behavioural responses of A. bishopi female parasitoids that were associated with T. leucotreta infested fruit were investigated to determine which behaviours are distinct and interpretable. Probing and oviposition behaviours were the most noticeable and were only elicited on infested fruit when parasitoids contacted T. leucotreta frass, indicating that chemical compounds in frass are short-range cues used for final host location. Since production of D-limonene by fruit is elevated due to herbivory by different pests including mechanical injury on fruit, response of A. bishopi female parasitoids to compounds in frass offers a more specific and potentially useful mechanism for development of a detection system for T. leucotreta infested fruit. Chemical analysis of T. leucotreta frass and conditioning A. bishopi parasitoids to respond behaviourally to compounds in frass is proposed.
- Full Text:
- Date Issued: 2015
A flight of fancy in the Chorister Robin-Chat (Cossypha dichroa) : an isotopic standpoint
- Wolmarans, Milena Helena Louise
- Authors: Wolmarans, Milena Helena Louise
- Date: 2015
- Subjects: Muscicapidae -- South Africa , Muscicapidae -- Food , Muscicapidae -- Habitat , Muscicapidae -- Habitat -- Conservation , Forest birds -- South Africa , Isotopes , Stable isotope tracers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5920 , http://hdl.handle.net/10962/d1017207
- Description: Forested areas have been cited for their highly diverse floral and faunal assemblages, which are currently under threat from anthropogenic activities that restrict their range and deplete the resources produced within these naturally fragmented patches. Historically, up to 67 percent of avifaunal species associated with well-treed areas have undergone localised extinctions, consequentially affecting biodiversity as a measure of species richness and ecosystem functionality. To date, more than 900 of the bird species affiliated with forests are under threat and despite the theory surrounding functional redundancy, the mass extinction that is currently underway poses considerable limitations on the ecological integrity of these biomes. In South Africa, indigenous forest (one of the rarest biomes), occurs predominantly in small isolated patches along the eastern escarpment. With mountainous terrain emphasised as ‘prominent hotspots of extinction’, the limited dispersal and habitat sensitivity of montane forest fauna renders these species more prone to localised extinctions. BirdLife International, the IUCN and SABAP2 all indicate reductions in the range and abundance of the Chorister Robin-Chat (Cossypha dichroa) - an endemic forest specialist that is reported to move seasonally between high-altitude forest patches where they breed in summer, and lowland coastal forests where they overwinter. Beyond diet, body morphology and vocalisations, much of the information available on the altitudinal movements of C. dichroa is based on secondary sources and the assumptions therein. This study aimed to investigate the potential utilisation of δ13C and δ15N stable isotopes in determining the dietary niche width and altitudinal movements of C. dichroa. Feathers obtained in forested patches of the Limpopo, KwaZulu-Natal and Eastern Cape provinces exhibited a wide trophic niche width and generalised diet. Strong regional separation is apparent in the isotopic signatures suggesting little movement between provinces. A comparison of 13C-isotopes showed minimal variation that point to a uniformity in the carbon-base utilised by C. dichroa across their range. The 15N-signatures obtained in Limpopo, however, revealed a distinct trophic segregation between the northern-most Chorister populations and their southern counterparts. No altitudinal movements were detected in the isotopic signatures of recaptured Choristers, but more research is needed to investigate the long-term accuracy of these results and the breeding potential of resident Choristers in lowland coastal forests; especially when considering the reduced range and abundance reported for this endemic species.
- Full Text:
- Date Issued: 2015
- Authors: Wolmarans, Milena Helena Louise
- Date: 2015
- Subjects: Muscicapidae -- South Africa , Muscicapidae -- Food , Muscicapidae -- Habitat , Muscicapidae -- Habitat -- Conservation , Forest birds -- South Africa , Isotopes , Stable isotope tracers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5920 , http://hdl.handle.net/10962/d1017207
- Description: Forested areas have been cited for their highly diverse floral and faunal assemblages, which are currently under threat from anthropogenic activities that restrict their range and deplete the resources produced within these naturally fragmented patches. Historically, up to 67 percent of avifaunal species associated with well-treed areas have undergone localised extinctions, consequentially affecting biodiversity as a measure of species richness and ecosystem functionality. To date, more than 900 of the bird species affiliated with forests are under threat and despite the theory surrounding functional redundancy, the mass extinction that is currently underway poses considerable limitations on the ecological integrity of these biomes. In South Africa, indigenous forest (one of the rarest biomes), occurs predominantly in small isolated patches along the eastern escarpment. With mountainous terrain emphasised as ‘prominent hotspots of extinction’, the limited dispersal and habitat sensitivity of montane forest fauna renders these species more prone to localised extinctions. BirdLife International, the IUCN and SABAP2 all indicate reductions in the range and abundance of the Chorister Robin-Chat (Cossypha dichroa) - an endemic forest specialist that is reported to move seasonally between high-altitude forest patches where they breed in summer, and lowland coastal forests where they overwinter. Beyond diet, body morphology and vocalisations, much of the information available on the altitudinal movements of C. dichroa is based on secondary sources and the assumptions therein. This study aimed to investigate the potential utilisation of δ13C and δ15N stable isotopes in determining the dietary niche width and altitudinal movements of C. dichroa. Feathers obtained in forested patches of the Limpopo, KwaZulu-Natal and Eastern Cape provinces exhibited a wide trophic niche width and generalised diet. Strong regional separation is apparent in the isotopic signatures suggesting little movement between provinces. A comparison of 13C-isotopes showed minimal variation that point to a uniformity in the carbon-base utilised by C. dichroa across their range. The 15N-signatures obtained in Limpopo, however, revealed a distinct trophic segregation between the northern-most Chorister populations and their southern counterparts. No altitudinal movements were detected in the isotopic signatures of recaptured Choristers, but more research is needed to investigate the long-term accuracy of these results and the breeding potential of resident Choristers in lowland coastal forests; especially when considering the reduced range and abundance reported for this endemic species.
- Full Text:
- Date Issued: 2015
What limits an invasive biotic and abiotic effects on the distribution of the invasive mussel mytilus galloprovincialis on the South African coastline
- Authors: Hall, Madison
- Date: 2015
- Subjects: Perna , Mytilus galloprovincialis , Mussels -- South Africa , Introduced organisms -- Environmental aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5927 , http://hdl.handle.net/10962/d1017805
- Full Text:
- Date Issued: 2015
- Authors: Hall, Madison
- Date: 2015
- Subjects: Perna , Mytilus galloprovincialis , Mussels -- South Africa , Introduced organisms -- Environmental aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5927 , http://hdl.handle.net/10962/d1017805
- Full Text:
- Date Issued: 2015
The roles of black-backed jackals and caracals in issues of human-wildlife conflict in the Eastern Cape, South Africa
- Authors: Murison, Megan Kate
- Date: 2015
- Subjects: Black-backed jackal -- South Africa -- Eastern Cape , Human-animal relationships -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Black-backed jackal -- Food -- South Africa -- Eastern Cape , Black-backed jackal -- Effect of human beings on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5939 , http://hdl.handle.net/10962/d1018667
- Description: [Partial abstract]: Human-wildlife conflict is a widely observed phenomenon and encompasses a range of negative interactions between humans and wildlife. Depredation upon livestock and game species proves to be the prevalent form of this conflict and often results in the killing of carnivores. Within the South African context, despite intense lethal control, two sympatric mesopredators, the blackbacked jackal (Canis mesomelas) and the caracal (Caracal caracal), remain common enough to be considered a major threat to human livelihoods through depredation. Wildlife ranches and livestock farms dominate the landscape in the Eastern Cape Province. Moreover, human-predator conflict within the region is extensive as both the black-backed jackal and caracal are seen to be inimical by landowners. Understanding this conflict is essential for mitigating any potential adverse environmental reactions (i.e. range collapses or extinctions) and requires knowledge of anthropogenic, ecological and environmental factors. I interviewed 73 land owners across five municipal boundaries in the Eastern Cape to quantify perceptions of predator control methods.
- Full Text:
- Date Issued: 2015
- Authors: Murison, Megan Kate
- Date: 2015
- Subjects: Black-backed jackal -- South Africa -- Eastern Cape , Human-animal relationships -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Black-backed jackal -- Food -- South Africa -- Eastern Cape , Black-backed jackal -- Effect of human beings on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5939 , http://hdl.handle.net/10962/d1018667
- Description: [Partial abstract]: Human-wildlife conflict is a widely observed phenomenon and encompasses a range of negative interactions between humans and wildlife. Depredation upon livestock and game species proves to be the prevalent form of this conflict and often results in the killing of carnivores. Within the South African context, despite intense lethal control, two sympatric mesopredators, the blackbacked jackal (Canis mesomelas) and the caracal (Caracal caracal), remain common enough to be considered a major threat to human livelihoods through depredation. Wildlife ranches and livestock farms dominate the landscape in the Eastern Cape Province. Moreover, human-predator conflict within the region is extensive as both the black-backed jackal and caracal are seen to be inimical by landowners. Understanding this conflict is essential for mitigating any potential adverse environmental reactions (i.e. range collapses or extinctions) and requires knowledge of anthropogenic, ecological and environmental factors. I interviewed 73 land owners across five municipal boundaries in the Eastern Cape to quantify perceptions of predator control methods.
- Full Text:
- Date Issued: 2015
The influence of the physical environment, topography and time on the inshore distribution of invertebrate larvae : a multi-taxon approach
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
- Date Issued: 2015
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
- Date Issued: 2015
The trophic ecology of the endangered endemic Barau's Petrel (Pterodroma baraui) from Reunion Island, south-western Indian Ocean
- Authors: Danckwerts, Daniel Keith
- Date: 2015
- Subjects: Petrels -- Réunion , Pterodroma baraui , Ecology -- Réunion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5925 , http://hdl.handle.net/10962/d1017803
- Description: Réunion is the only tropical island that supports two endemic gadfly petrels. Population modelling has indicated that the current threats to the Barau’s Petrel (Pterodroma baraui) may drive it to extinction; this fate is almost definite for the Mascarene Petrel (Pseudobulweria aterrima). Management interventions have therefore been implemented, but conservation potential is handicapped since virtually nothing is known about the former species’ at-sea biology. Thus, following numerous recommendations, this study aimed to combine stomach content, stable isotope, and fatty acid analyses so to provide new information on the at-sea ecology of Barau’s Petrel. Breeding colonies were repeatedly visited over the same season and samples gathered from adults, fledglings, and downy chicks. Stomach contents consisted mostly of accumulated cephalopod beaks whereas structures from fishes, molluscs, arthropods, and crustaceans were less frequently encountered. Fatty acid profiles of blood varied greatly among individuals and the lowincidences of monounsaturated and n-3 fatty acids discounted fish as an important dietary component. δ¹⁵N of blood indicated a niche between the fourth and fifth trophic levels, which proposes that these birds scavenge to a greater degree than other sympatric seabirds and suggests that adults are also reliant on their endogenous reserves during breeding. δ¹³C values confirmed the migratory behaviour of adults since birds returning from the non-breeding grounds were enriched relative to individuals sampled through the breeding period. Significant intra-breeding season variations in δ13C were also observed, which matched this species’ patterns of habitat use as have recently described. These results collectively indicate an opportunistic behaviour, which implies some degree of resilience against shifts in prey availability/accessibility, and suggest that this species’ reproduction isdependent on distant foraging areas. This breeding strategy is synonymous with great vulnerability as over-investing into a single breeding episode may jeopardize future survival and fecundity. Thus, in light of environmental conditions that are becoming increasingly more susceptible to dramatic changes, the birds could rather be prioritising adult survival, over reproductive output. Further work is obviously necessary and should benefit from databases of fatty acid profiles and isotope signatures of potential prey species.
- Full Text:
- Date Issued: 2015
- Authors: Danckwerts, Daniel Keith
- Date: 2015
- Subjects: Petrels -- Réunion , Pterodroma baraui , Ecology -- Réunion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5925 , http://hdl.handle.net/10962/d1017803
- Description: Réunion is the only tropical island that supports two endemic gadfly petrels. Population modelling has indicated that the current threats to the Barau’s Petrel (Pterodroma baraui) may drive it to extinction; this fate is almost definite for the Mascarene Petrel (Pseudobulweria aterrima). Management interventions have therefore been implemented, but conservation potential is handicapped since virtually nothing is known about the former species’ at-sea biology. Thus, following numerous recommendations, this study aimed to combine stomach content, stable isotope, and fatty acid analyses so to provide new information on the at-sea ecology of Barau’s Petrel. Breeding colonies were repeatedly visited over the same season and samples gathered from adults, fledglings, and downy chicks. Stomach contents consisted mostly of accumulated cephalopod beaks whereas structures from fishes, molluscs, arthropods, and crustaceans were less frequently encountered. Fatty acid profiles of blood varied greatly among individuals and the lowincidences of monounsaturated and n-3 fatty acids discounted fish as an important dietary component. δ¹⁵N of blood indicated a niche between the fourth and fifth trophic levels, which proposes that these birds scavenge to a greater degree than other sympatric seabirds and suggests that adults are also reliant on their endogenous reserves during breeding. δ¹³C values confirmed the migratory behaviour of adults since birds returning from the non-breeding grounds were enriched relative to individuals sampled through the breeding period. Significant intra-breeding season variations in δ13C were also observed, which matched this species’ patterns of habitat use as have recently described. These results collectively indicate an opportunistic behaviour, which implies some degree of resilience against shifts in prey availability/accessibility, and suggest that this species’ reproduction isdependent on distant foraging areas. This breeding strategy is synonymous with great vulnerability as over-investing into a single breeding episode may jeopardize future survival and fecundity. Thus, in light of environmental conditions that are becoming increasingly more susceptible to dramatic changes, the birds could rather be prioritising adult survival, over reproductive output. Further work is obviously necessary and should benefit from databases of fatty acid profiles and isotope signatures of potential prey species.
- Full Text:
- Date Issued: 2015
The diets of co-occuring anurans in a small South African river: assessments using stomach contents, stable isotope ratios and fatty acid profiles
- Authors: Sikutshwa, Likho
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54405 , vital:26562
- Description: During their life cycle amphibians change their habitat and feeding, and are important consumers in both terrestrial and aquatic habitats. The trophic ecology of anurans has been studied intensively using gut content analysis, but very little work has been done using biochemical techniques such as stable isotope and fatty acid analyses. These biochemical techniques produce data that allow for additional inferences about the trophic ecology of anurans, as they reveal what the organisms assimilated over time rather than what was recently ingested. The investigation of the feeding ecology and trophic interactions of anurans using gut content analyses together with stable isotope and fatty acid analyses will help us to better understand their ecological roles. The objective of this thesis was to assess the feeding ecology of four anurans (Amietia angolensis, Amietophyrnus rangeri, Strongylopus grayii and Xenopus laevis) in a temperate river using a combination of gut content, stable isotope and fatty acid analyses. Frogs, tadpoles and potential food sources were sampled in two sites (upstream and downstream) in the Kowie River, Eastern Cape Province, South Africa. Gut content analyses identified 147 prey items belonging to 12 prey orders in the stomachs of the sampled specimens. In both A. angolensis and S. grayii the most important prey category was Coleoptera, followed by Hemiptera, Diptera and Hymenoptera at both sites. Aquatic prey items (aquatic hemipterans, chirinomids and blackflies) were the most important food sources for X. laevis (Alimentary Index (IAi) = 6.4; 5.2; 4.2). In Am. rangeri, Hymenoptera was the most important prey category (IAi = 8.3). The trophic niche overlap between A. angolensis and S. grayii was biologically significant (> 0.6), and in the remaining species there was no significant trophic niche overlap. Amietia angolensis showed a larger trophic niche (Levin’s measure; B = 7.7 and Bst = 0.84 downstream, and upstream B = 7.6 (Bst = 0.82) compared to the other species. The gut content analyses showed that frogs feed on a variety of prey items that constitutes food sources from both aquatic and terrestrial habitats. Stable isotopes indicated that aquatic derived sources contributed significantly more towards the diets of X. laevis, A. angolensis tadpoles and S. grayii tadpoles compared with the other anurans, whereas aquatic and terrestrial derived food sources contributed equally to the diets of A. angolensis and S. grayii. Increased trophic positions in A. angolensis and S. grayii occurred throughout their development. The four different species had similar fatty acid profiles in the upstream region, and fairly similar δ13C values, suggesting that they probably consumed similar food. Fatty acid profiles of anurans in the downstream region showed distinct separations among the species. Tadpoles had high levels of diatom-associated fatty acids (20:5ω3; A. angolensis tadpole – 8.4 %, S. grayii tadpole – 9.4 % upstream and downstream; 9.1 and 6.1 % total fatty acids (TFA), respectively). All four species had substantial contributions from bacterial fatty acids, and large proportions of saturated fatty acids (30.6 - 50.0 %) including those with 14 and 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. The fatty acid profiles revealed high proportions of polyunsaturated fatty acids (PUFAs) and essential fatty acids (EFAs) in all species, indicating a good quality of food and that the quality of food consumed was similar among species. The results demonstrated the usefulness of a combination of traditional techniques (gut content techniques) and biochemical techniques (stable isotopes and fatty acid analysis) for assessing consumption and assimilation. The amphibian assemblages examined derived much of their energy from terrestrial and aquatic sources. This information will allow more precise and comprehensive assessments of trophic interactions in freshwater habitats, along with aiding in future amphibian conservation and management efforts.
- Full Text:
- Date Issued: 2015
- Authors: Sikutshwa, Likho
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54405 , vital:26562
- Description: During their life cycle amphibians change their habitat and feeding, and are important consumers in both terrestrial and aquatic habitats. The trophic ecology of anurans has been studied intensively using gut content analysis, but very little work has been done using biochemical techniques such as stable isotope and fatty acid analyses. These biochemical techniques produce data that allow for additional inferences about the trophic ecology of anurans, as they reveal what the organisms assimilated over time rather than what was recently ingested. The investigation of the feeding ecology and trophic interactions of anurans using gut content analyses together with stable isotope and fatty acid analyses will help us to better understand their ecological roles. The objective of this thesis was to assess the feeding ecology of four anurans (Amietia angolensis, Amietophyrnus rangeri, Strongylopus grayii and Xenopus laevis) in a temperate river using a combination of gut content, stable isotope and fatty acid analyses. Frogs, tadpoles and potential food sources were sampled in two sites (upstream and downstream) in the Kowie River, Eastern Cape Province, South Africa. Gut content analyses identified 147 prey items belonging to 12 prey orders in the stomachs of the sampled specimens. In both A. angolensis and S. grayii the most important prey category was Coleoptera, followed by Hemiptera, Diptera and Hymenoptera at both sites. Aquatic prey items (aquatic hemipterans, chirinomids and blackflies) were the most important food sources for X. laevis (Alimentary Index (IAi) = 6.4; 5.2; 4.2). In Am. rangeri, Hymenoptera was the most important prey category (IAi = 8.3). The trophic niche overlap between A. angolensis and S. grayii was biologically significant (> 0.6), and in the remaining species there was no significant trophic niche overlap. Amietia angolensis showed a larger trophic niche (Levin’s measure; B = 7.7 and Bst = 0.84 downstream, and upstream B = 7.6 (Bst = 0.82) compared to the other species. The gut content analyses showed that frogs feed on a variety of prey items that constitutes food sources from both aquatic and terrestrial habitats. Stable isotopes indicated that aquatic derived sources contributed significantly more towards the diets of X. laevis, A. angolensis tadpoles and S. grayii tadpoles compared with the other anurans, whereas aquatic and terrestrial derived food sources contributed equally to the diets of A. angolensis and S. grayii. Increased trophic positions in A. angolensis and S. grayii occurred throughout their development. The four different species had similar fatty acid profiles in the upstream region, and fairly similar δ13C values, suggesting that they probably consumed similar food. Fatty acid profiles of anurans in the downstream region showed distinct separations among the species. Tadpoles had high levels of diatom-associated fatty acids (20:5ω3; A. angolensis tadpole – 8.4 %, S. grayii tadpole – 9.4 % upstream and downstream; 9.1 and 6.1 % total fatty acids (TFA), respectively). All four species had substantial contributions from bacterial fatty acids, and large proportions of saturated fatty acids (30.6 - 50.0 %) including those with 14 and 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. The fatty acid profiles revealed high proportions of polyunsaturated fatty acids (PUFAs) and essential fatty acids (EFAs) in all species, indicating a good quality of food and that the quality of food consumed was similar among species. The results demonstrated the usefulness of a combination of traditional techniques (gut content techniques) and biochemical techniques (stable isotopes and fatty acid analysis) for assessing consumption and assimilation. The amphibian assemblages examined derived much of their energy from terrestrial and aquatic sources. This information will allow more precise and comprehensive assessments of trophic interactions in freshwater habitats, along with aiding in future amphibian conservation and management efforts.
- Full Text:
- Date Issued: 2015
Gene expression analysis of Thaumatotibia leucotreta in response to the Cryptophlebia leucotreta granulovirus
- Authors: Ridgeway, Jaryd Antony
- Date: 2015
- Subjects: Gene expression , Insects -- Viruses , Tortricidae -- Viruses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5931 , http://hdl.handle.net/10962/d1017809
- Description: Gene expression studies provide baseline information on the interactions of insects with their environment. Despite the importance of this information, limited gene expression data are available for most insect pests, including the family Tortricidae (Lepidoptera), which includes Thaumatotibia leucotreta (Meyr), an important agricultural pest in Africa. Because T. leucotreta can be controlled successfully by a granulovirus, this system is a good model for exploring insect-virus susceptibility. The main aim of this study was to investigate gene expression of T. leucotreta in responce to virus infection. However, before pursuing this aim, two objectives required completion. First, the most suitable RNA extraction method for insects needed to be determined and second, the most suitable reference genes for qPCR for Tortricidae pests needed to be identified. Once these objectives were accomplished, the response of T. leucotreta to its granulovirus was evaluated at different temperatures and points after infection.Four RNA extraction methods, the RNeasy® Mini Kit, SV Total RNA isolation system, TRIzol® reagent, and a CTAB-based method, were compared using two beetle and two moth species, including T. leucotreta. The quality of extracted RNA was similar for all four species for all extraction methods. Based on several criteria, the best RNA extraction method was the SV Total RNA isolation system. Six candidate reference genes were evaluated for qPCR using different tissue types of T. leucotreta and two other Tortricidae pests. Additionally, reference genes were evaluated for T. leucotreta with and without its granulovirus at different temperatures. Reference gene stability was found to be dependent on species and tissue type. Overall the most suitable combination of reference genes for T. leucotreta were α-actin, arginine kinase and elongation factor 1-α.Gene expression of T. leucotreta in response to granulovirus infection at different temperatures and intervals after infection was evaluated by qPCR using 13 target genes associated with the infection process. Most genes were down-regulated after 24 and 48 h.p.i. However, after 72 h.p.i most genes were up-regulated. The same trend was observed at different temperatures, where most genes were down-regulated at 15°C and 25°C but up-regulated at 35°C. These results show that there is a dynamic gene expression response in T. leucotreta due to granulovirus infection under different conditions. Not only do these findings provide insight into the control of this tortricid pest, they also contribute further to our knowledge of insect-virus interactions.
- Full Text:
- Date Issued: 2015
- Authors: Ridgeway, Jaryd Antony
- Date: 2015
- Subjects: Gene expression , Insects -- Viruses , Tortricidae -- Viruses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5931 , http://hdl.handle.net/10962/d1017809
- Description: Gene expression studies provide baseline information on the interactions of insects with their environment. Despite the importance of this information, limited gene expression data are available for most insect pests, including the family Tortricidae (Lepidoptera), which includes Thaumatotibia leucotreta (Meyr), an important agricultural pest in Africa. Because T. leucotreta can be controlled successfully by a granulovirus, this system is a good model for exploring insect-virus susceptibility. The main aim of this study was to investigate gene expression of T. leucotreta in responce to virus infection. However, before pursuing this aim, two objectives required completion. First, the most suitable RNA extraction method for insects needed to be determined and second, the most suitable reference genes for qPCR for Tortricidae pests needed to be identified. Once these objectives were accomplished, the response of T. leucotreta to its granulovirus was evaluated at different temperatures and points after infection.Four RNA extraction methods, the RNeasy® Mini Kit, SV Total RNA isolation system, TRIzol® reagent, and a CTAB-based method, were compared using two beetle and two moth species, including T. leucotreta. The quality of extracted RNA was similar for all four species for all extraction methods. Based on several criteria, the best RNA extraction method was the SV Total RNA isolation system. Six candidate reference genes were evaluated for qPCR using different tissue types of T. leucotreta and two other Tortricidae pests. Additionally, reference genes were evaluated for T. leucotreta with and without its granulovirus at different temperatures. Reference gene stability was found to be dependent on species and tissue type. Overall the most suitable combination of reference genes for T. leucotreta were α-actin, arginine kinase and elongation factor 1-α.Gene expression of T. leucotreta in response to granulovirus infection at different temperatures and intervals after infection was evaluated by qPCR using 13 target genes associated with the infection process. Most genes were down-regulated after 24 and 48 h.p.i. However, after 72 h.p.i most genes were up-regulated. The same trend was observed at different temperatures, where most genes were down-regulated at 15°C and 25°C but up-regulated at 35°C. These results show that there is a dynamic gene expression response in T. leucotreta due to granulovirus infection under different conditions. Not only do these findings provide insight into the control of this tortricid pest, they also contribute further to our knowledge of insect-virus interactions.
- Full Text:
- Date Issued: 2015
DNA-based identification of forensically significant beetles from Southern Africa
- Authors: Collett, Isabel Judith
- Date: 2015
- Subjects: Carrion insects , Forensic entomology , Cleridae , Dermestidae , Silphidae , Staphylinidae , Scarabaeidae , Histeridae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5923 , http://hdl.handle.net/10962/d1017801
- Description: Necrophilous insects, if correctly identified, can provide useful forensic information. Research in this area has focussed on flies and beetles remain comparatively under-studied, partly because some adult carrion beetles are difficult to identify morphologically, as are their juvenile stages, often requiring specialist expertise in both cases. Molecular taxonomy has been proposed as a solution to these problems. DNA “barcodes" are short fragments of mitochondrial cytochrome oxidase I (COI) DNA that are anticipated to delineate species. This approach is becoming increasingly popular, but has been met with varying enthusiasm from taxonomists. This thesis examines their use in identifying forensically significant beetles.The DNA barcodes of 234 specimens of 25 forensically significant southern African beetle species from seven families (Cleridae, Dermestidae, Silphidae, Staphylinidae, Scarabaeidae, Trogidae and Histeridae) were obtained. Thirty-three initial barcode amplification failures were overcome by using primers other than the standard Folmer pair, undermining the barcode concept’s hope of universal primers that would allow even non-specialists to produce barcodes. Another 150 specimens (64%) entirely failed to yield barcodes, including 18 fresh specimens of three species of Trogidae, implying another lack of universality of the barcoding protocol. The majority of the beetles clustered with confamilials on neighbour-joining and maximum likelihood trees, but 1.3% of the barcodes failed to cluster with their respective families, raising questions concerning the associating power of barcodes. The identification tools of the GenBank and BOLD on-line DNA sequence databases identified 21% of the specimens to the species level, 6% of them correctly. There was evidence of a paralogous sequence in the Cleridae that, while supporting identification now that it has been associated with a morphological identification, would hamper attempts at identification by clustering or phylogenetic analysis.Distance and haplotype network analyses of the barcodes of six widespread species showed that they are not geographically structured. Barcodes are thus unlikely to be indicators of the region of origin of a species and will not determine whether a corpse has been relocated after death. To assess whether a different mitochondrial DNA fragment might address (some of) these problems, a 2.2 kb fragment extending from the 5’ end of the COI gene to the 3’ end of the Cytochrome Oxidase II (COII) gene was analysed for nine species. It was found that, for Dermestidae, Scarabaeidae and Histeridae, higher degrees of diversity occurred downstreamof the barcode region, but the region of highest diversity in the Cleridae was in the barcode region. Thus, finding a more reliable fragment along the COI-COII region for each family may make robust and guaranteed DNA-based identification of these beetles more likely. The possibility of a forensic specimen being incorrectly or not identified based on its barcode alone exists in about 40% of cases, even with the new barcodes reported here. Forensic science sets a very high bar in assessing the performance of its techniques, and it is concluded that barcodes currently have unsettling failure rates as court-worthy evidence.
- Full Text:
- Date Issued: 2015
- Authors: Collett, Isabel Judith
- Date: 2015
- Subjects: Carrion insects , Forensic entomology , Cleridae , Dermestidae , Silphidae , Staphylinidae , Scarabaeidae , Histeridae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5923 , http://hdl.handle.net/10962/d1017801
- Description: Necrophilous insects, if correctly identified, can provide useful forensic information. Research in this area has focussed on flies and beetles remain comparatively under-studied, partly because some adult carrion beetles are difficult to identify morphologically, as are their juvenile stages, often requiring specialist expertise in both cases. Molecular taxonomy has been proposed as a solution to these problems. DNA “barcodes" are short fragments of mitochondrial cytochrome oxidase I (COI) DNA that are anticipated to delineate species. This approach is becoming increasingly popular, but has been met with varying enthusiasm from taxonomists. This thesis examines their use in identifying forensically significant beetles.The DNA barcodes of 234 specimens of 25 forensically significant southern African beetle species from seven families (Cleridae, Dermestidae, Silphidae, Staphylinidae, Scarabaeidae, Trogidae and Histeridae) were obtained. Thirty-three initial barcode amplification failures were overcome by using primers other than the standard Folmer pair, undermining the barcode concept’s hope of universal primers that would allow even non-specialists to produce barcodes. Another 150 specimens (64%) entirely failed to yield barcodes, including 18 fresh specimens of three species of Trogidae, implying another lack of universality of the barcoding protocol. The majority of the beetles clustered with confamilials on neighbour-joining and maximum likelihood trees, but 1.3% of the barcodes failed to cluster with their respective families, raising questions concerning the associating power of barcodes. The identification tools of the GenBank and BOLD on-line DNA sequence databases identified 21% of the specimens to the species level, 6% of them correctly. There was evidence of a paralogous sequence in the Cleridae that, while supporting identification now that it has been associated with a morphological identification, would hamper attempts at identification by clustering or phylogenetic analysis.Distance and haplotype network analyses of the barcodes of six widespread species showed that they are not geographically structured. Barcodes are thus unlikely to be indicators of the region of origin of a species and will not determine whether a corpse has been relocated after death. To assess whether a different mitochondrial DNA fragment might address (some of) these problems, a 2.2 kb fragment extending from the 5’ end of the COI gene to the 3’ end of the Cytochrome Oxidase II (COII) gene was analysed for nine species. It was found that, for Dermestidae, Scarabaeidae and Histeridae, higher degrees of diversity occurred downstreamof the barcode region, but the region of highest diversity in the Cleridae was in the barcode region. Thus, finding a more reliable fragment along the COI-COII region for each family may make robust and guaranteed DNA-based identification of these beetles more likely. The possibility of a forensic specimen being incorrectly or not identified based on its barcode alone exists in about 40% of cases, even with the new barcodes reported here. Forensic science sets a very high bar in assessing the performance of its techniques, and it is concluded that barcodes currently have unsettling failure rates as court-worthy evidence.
- Full Text:
- Date Issued: 2015
The biology, behaviour and survival of pupating false codling moth, Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), a citrus pest in South Africa
- Authors: Love, Claire Natalie
- Date: 2015
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Larvae -- Behavior , Citrus -- Diseases and pests , Citrus -- Diseases and pests -- Biological control , Biological pest control agents , Entomopathogenic fungi , Insect nematodes , Pupae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5941 , http://hdl.handle.net/10962/d1018907
- Description: Control of the citrus pest, false codling moth (FCM), Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is crucial for the South African citrus industry. The economic losses and phytosanitary status of this pest, coupled with increased consumer awareness and demands, has created a need for effective, IPM-compatible control measures for use against the soil-dwelling life stages of FCM. Promising developments in the field of microbial control through the use of entomopathogenic fungi (EPF) and entomopathogenic nematodes (EPNs) have highlighted the need for research regarding pupation biology, behaviour and survival of FCM, as a good understanding of biology of the target organism is an important component of any biological control programme. The aim of this study was to improve the current understanding of FCM pupation habits through the manipulation of soil texture class, ground cover, shading, soil compaction, air temperature, and soil moisture in the laboratory. These findings would then be used to aid the biological control programmes using EPF and EPNs against FCM in the soil. Three soil texture classes (sandy loam, silt loam and silty clay loam) were obtained from orchards for use in the study. FCM larvae were allowed to drop into the soil of their own accord and the pupation behaviour that followed was then captured on film with pupae formed in the soil being kept in order to measure adult eclosion. In general, very few abiotic factors had a clear influence on FCM pupation. Larval wandering time and distance was short, but also variable between individuals. Distance did increase when soils were moist. Pupation depth was shallow, with pupal cocoons generally being formed on the soil surface. Depth of pupation was less than one centimetre for all abiotic conditions, with little burrowing into soil. Eclosion success was higher for sandier soils when these were dry and uncompacted, but the addition of both moisture and soil compaction increased FCM eclosion success. FCM was sensitive to desiccation when the soils were dry and temperature limits of 15 °C and 32 °C had a strongly negative impact on eclosion success. Preferences for particular abiotic conditions were limited to only certain moisture conditions when interacting with soil texture class and a preference for pupating in soil when it is available. Limited preference was found for particular soil textures despite this having a strong influence on eclosion success, but individuals did appear to pupate in close proximity to one another. Viable direct habitat manipulation for FCM control could not be identified. These results and all of the abiotic variables measured have important implications for EPF and EPN application, survival and persistence in the soil in order to improve the ability of these biological control agents to control FCM. These are discussed in each chapter.
- Full Text:
- Date Issued: 2015
- Authors: Love, Claire Natalie
- Date: 2015
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Larvae -- Behavior , Citrus -- Diseases and pests , Citrus -- Diseases and pests -- Biological control , Biological pest control agents , Entomopathogenic fungi , Insect nematodes , Pupae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5941 , http://hdl.handle.net/10962/d1018907
- Description: Control of the citrus pest, false codling moth (FCM), Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is crucial for the South African citrus industry. The economic losses and phytosanitary status of this pest, coupled with increased consumer awareness and demands, has created a need for effective, IPM-compatible control measures for use against the soil-dwelling life stages of FCM. Promising developments in the field of microbial control through the use of entomopathogenic fungi (EPF) and entomopathogenic nematodes (EPNs) have highlighted the need for research regarding pupation biology, behaviour and survival of FCM, as a good understanding of biology of the target organism is an important component of any biological control programme. The aim of this study was to improve the current understanding of FCM pupation habits through the manipulation of soil texture class, ground cover, shading, soil compaction, air temperature, and soil moisture in the laboratory. These findings would then be used to aid the biological control programmes using EPF and EPNs against FCM in the soil. Three soil texture classes (sandy loam, silt loam and silty clay loam) were obtained from orchards for use in the study. FCM larvae were allowed to drop into the soil of their own accord and the pupation behaviour that followed was then captured on film with pupae formed in the soil being kept in order to measure adult eclosion. In general, very few abiotic factors had a clear influence on FCM pupation. Larval wandering time and distance was short, but also variable between individuals. Distance did increase when soils were moist. Pupation depth was shallow, with pupal cocoons generally being formed on the soil surface. Depth of pupation was less than one centimetre for all abiotic conditions, with little burrowing into soil. Eclosion success was higher for sandier soils when these were dry and uncompacted, but the addition of both moisture and soil compaction increased FCM eclosion success. FCM was sensitive to desiccation when the soils were dry and temperature limits of 15 °C and 32 °C had a strongly negative impact on eclosion success. Preferences for particular abiotic conditions were limited to only certain moisture conditions when interacting with soil texture class and a preference for pupating in soil when it is available. Limited preference was found for particular soil textures despite this having a strong influence on eclosion success, but individuals did appear to pupate in close proximity to one another. Viable direct habitat manipulation for FCM control could not be identified. These results and all of the abiotic variables measured have important implications for EPF and EPN application, survival and persistence in the soil in order to improve the ability of these biological control agents to control FCM. These are discussed in each chapter.
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- Date Issued: 2015
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