Theses and Dissertations (Zoology and Entomology)

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Population and individual life history consequences of polygyny in male southern elephant seals
(University of Pretoria, 2019-11) De Bruyn, P.J. Nico; Oosthuizen, W.C. (Wessel Christiaan); kyle.john.lloyd@gmail.com; Lloyd, Kyle John
Our understanding of polygynous life history is biased towards females. Few studies investigate the processes governing male life history because of the difficulty in measuring male reproductive effort, and because population growth is thought to be limited only by females. Therefore, clarity is needed on the drivers and predictors of polygynous male life history and the long-term consequences this has for male fitness. My thesis achieves this overall aim by answering specific questions about the life history of male southern elephant seals at Marion Island using a 34-year mark-recapture dataset. The male elephant seal served as a model organism to investigate the most important life stages of polygynous males in general. For pre-breeders that survived their first year of life, individual heterogeneity in survival probabilities was expressed from age 2. Males born in years with relatively few pups were more likely to be robust in quality than males born in years with many pups. Survival probabilities of robust individuals and the population average became more similar as pre-breeders aged, suggesting that frail individuals were preferentially removed from the population during development. Therefore, the majority of pre-breeders that survived to breed successfully were robust in quality. Pre-breeder recruitment probabilities increased with age. In addition, pre-breeders of the same age often recruited as first-time subordinate breeders than as first-time dominant breeders. First-time subordinate breeders started recruiting from a younger age than first-time dominant breeders. Males likely need time to socially mature or require some breeding experience to outcompete older breeders. Pre-breeders expressed individual heterogeneity in recruitment probabilities, with robust individuals (i.e. higher survival) being more likely to recruit than frail individuals (i.e. lower survival). This supports the individual quality theory, which predicts that life-history traits are positively, rather than negatively, correlated. Pre-breeders born during low pup production years generally recruited at younger ages than pre-breeder born during high pup production years. Males attending breeding events did not suffer lower survival probabilities than same aged males that were still pre-breeders, suggesting that there was no reproductive cost for attending breeding events for early recruits. However, all males attending breeding events experienced actuarial senescence from recruitment age, with subordinate males suffering higher baseline mortalities. Given that this coincided with breeding improvement (the probability of becoming dominant), males appear to pay a reproductive cost for attempting to obtain dominance. When comparing survival probabilities between individual dominant males, there was also a reproductive cost for breeding successfully that accumulated with age. Males that were dominant at beaches with above average harem sizes accumulated higher reproductive costs than males that were dominant at beaches with below average harem sizes. Nevertheless, dominant males still maintained higher survival probabilities than subordinate males of the same age. Therefore, individual quality (inferred from breeding state) may play an important role in modifying resource allocation trade-offs between reproduction and survival. Future breeding success (measured as social status) increased with age for both subordinate and dominant males, but dominant males were more likely to remain dominant than subordinate males were in obtaining dominance. This apparent improvement in breeding success with age was predicted by birth cohort size, again suggesting that males born into cohorts with few conspecifics performed better as adults. In conclusion, I provide support for several population theories and show how they shaped male elephant seal demographics from birth to death. My findings provide valuable insight into the drivers and predictors of male life history in a highly polygynous breeding system.
Phenotypic and genotypic sources of variation in the thermal physiology of a passerine bird
(University of Pretoria, 2020-01) McKechnie, Andrew E.; noakesmatthewj@gmail.com; Noakes, Matthew Jason
There is considerable variation in avian thermal physiology, with traits such as metabolic rates correlated with climate at both inter- and intraspecific levels. However, it is often unclear whether these correlations result from genotypic adaptation, developmental plasticity or phenotypic flexibility. Seasonal acclimatization is a frequently cited example of phenotypic flexibility, with small, temperate-zone birds typically increasing metabolic rates in response to low winter air temperatures (Ta). Recent studies suggest considerable variation in patterns of seasonal acclimatization in birds inhabiting lower latitudes with milder winters, with variation also reported among populations of subtropical species such as the white-browed sparrow-weaver (Plocepasser mahali). To gain insights into the sources of intraspecific variation, I investigated phenotypic flexibility in the thermal physiology of Afrotropical passerine birds, using sparrow-weavers as a model species. I measured seasonal variation in basal metabolic rate (BMR) and summit metabolism (Msum) over a four-year period in arid-zone populations of sparrow-weavers and scaly-feathered weavers (Sporopipes squamifrons; chapter 1). Patterns of acclimatization varied substantially among years in both species, for example, sparrow-weaver BMR ranged from ~ 20 % lower to 68 % higher during winter compared to summer. In contrast to higher-latitude species, interannual metabolic variation was never related to minimum Ta or enhanced cold tolerance, but metabolic rates were significantly lower in seasons with lower food abundance. I also investigated seasonal changes in the body composition of sparrow-weavers, focusing on traits commonly correlated with BMR and Msum in temperate-zone birds (chapter 2). As expected, a lack of seasonal variation in BMR during the study period was associated with no significant variation in the dry mass of digestive and excretory organs. However, despite significant winter increases in pectoral muscle (~ 9 % higher; primary muscle for avian shivering thermogenesis) and heart mass (~ 18 % higher), there was a winter decrease in Msum. These findings support the idea that factors other than enhanced cold tolerance drive patterns of metabolic variation in subtropical birds. I used short-term (~ 30 days) thermal acclimation experiments to investigate whether phenotypic flexibility in thermoregulatory responses of sparrow-weaver varies among populations across a climatic gradient (~ 8 °C and 11 °C in mean daily winter minimum and summer maximum Ta respectively). I measured BMR and Msum after acclimating individuals to one of three acclimation Ta (Taccl) treatments (5 °C, 15 °C or 35 °C; chapter 3). There was ~ 12 % lower BMR and 25 % lower evaporative water loss in birds at the hottest Taccl compared to cooler treatments, with no interpopulation variation after acclimation (i.e., similar reaction norms). In contrast to the findings of most studies on temperate-zone birds, Msum did not vary with Taccl regardless of population. I also investigated flexibility in heat tolerance and evaporative cooling capacity of sparrow-weavers, measuring their ability to handle high Ta (~ 38 °C to 54 °C) after acclimation to one of three treatments (day-time Taccl = 30 °C, 36 °C or 42 °C; chapter 4). Birds at the hottest Taccl coped better with high Ta than those at milder Taccl, maintaining lower body temperatures and reaching Ta ≈ 2 °C higher before the onset of severe hyperthermia. There was no variation among populations after acclimation, suggesting similar reaction norms for heat tolerance and evaporative cooling capacity. These findings suggest previously documented interpopulation differences in sparrow-weaver thermal physiology is largely the result of phenotypic flexibility rather than local adaptation. In conclusion, I found considerable flexibility in the thermal physiology of an Afrotropical passerine bird, both within and among populations. My data support the idea that enhancing winter cold tolerance is less important in subtropical birds compared to higher-latitude species. Moreover, similar thermoregulatory reaction norms among populations highlights the importance of phenotypic flexibility as a source of variation in avian physiology.
Monitoring of large carnivores in Botswana for conservation management
(University of Pretoria, 2019-10) Somers, Michael J.; christiaan.winterbach@gmail.com; Winterbach, Christiaan Willem
Assessing the range, population size and trend of large carnivores are required for conservation management at global to local scales. Survey techniques should be precise with low bias, detect population trends and cover large areas efficiently. Track surveys may be used to monitor populations of lion (Panthera leo), leopard (Panthera pardus), spotted hyaena (Crocuta crocuta), brown hyaena (Parahyaena brunnea), cheetah (Acinonyx jubatus) and African wild dog (Lycaon pictus) in Botswana. Call up surveys is an alternative to survey lion and spotted hyaena. I recalibrated the published relationships between track density and true density. Linear regression through the origin was justified over linear regression with intercept for all models tested. Models through the origin fitted better and Akaike Information Criteria showed that these models were more robust. A review of the track survey method clarified ambiguous terminology and inappropriate analyses of data. This allows others to replicate track surveys in a way that improves inter-survey comparisons of results. I calculated species-specific calibrations to estimate confidence intervals of track densities from track incidence frequencies, and thus carnivore densities, for the entire southern African large carnivore guild. Calibration of carnivore response is required to estimate density from call up surveys. There correlation between the mean number of lions per calling station and reference density was significant (P < 0.05). Response probability did not differ by sex and age among surveys (call duration 90 minutes). Site-specific calibrations performed better than published calibrations. Call up surveys are unlikely to detect population trends in the Okavango Delta due to the high coefficient of variation (>200%). I collated data from various sources and conducted track surveys to assess brown hyaena distribution and density across land uses in Botswana. Density ranged from 0 brown hyaena / 100 km² in parts of northern Botswana, to 2.94 (2.16–3.71) brown hyaena / 100 km² in the southern Central Kalahari Game Reserve. The estimated brown hyaena population is 4642 (3133–5993). Agricultural land in Botswana is important to link populations in South Africa, Namibia and Zimbabwe. In 2005, Botswana implemented a minimum age threshold strategy to manage sustainable trophy hunting of male lions. I evaluated tooth: pulp width and area ratios to estimate age of trophy-hunted male lions in Botswana as a post hoc monitoring of compliance (2005 – 2007) to the 6-year minimum-age threshold. I used digital radiographs of the second premolar for measurements and cementum annuli analysis to calculate reference ages. The linear regression y = 0.990 x + 2.512 (r² = 0.647), between the tooth root area: root pulp cavity area ratio (R: RPA) and reference ages < 10 years (F1, 23 = 42.244, P < 0.001), was used to estimate age from R: RPA ratios. The 95% confidence intervals of age estimates from R: RPA ratios for the reference age classes 4 - 5 years and 6 - 7 years were mutually exclusive, showing the methods ability to distinguish between animals older and younger than the minimum age threshold. Wildlife tourism can provide economic incentives for conservation. I evaluated tourism potential in the Northern Conservation Zone of Botswana, using wildlife biomass and diversity estimates from aerial survey data as indicators of tourism potential. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. Tourists will have significantly better wildlife sightings in areas with high tourism potential compared to low potential areas. Although the largest part of the Northern Conservation Zone has low tourism potential, it has a high conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana.
Using functional genomics to provide insights into social parasitism by Cape honey bee clonal workers based on mandibular gland pheromones (Apis mellifera capensis Eschscholtz)
(University of Pretoria, 2019-04) Crewe, Robin M.; Pirk, Christian Walter Werner; Yusuf, Abdullahi Ahmed; fiona.mumoki@up.ac.za; Mumoki, Fiona Nelima
The queen mandibular gland pheromone (QMP) enables the queen to maintain reproductive dominance by inhibiting worker ovary activation and production of queen-like multi-glandular secretions. While the queen is typically able to maintain the reproductive role in most colonies, some rogue workers evade this strict control to become reproductively active. An extreme form of this evasion is seen in Apis mellifera capensis (Eschscholtz 1822) where, through a short-sighted evolutionary process, a specific invasive lineage of the A. m. capensis workers developed into facultative social parasites. These parasitic workers (A. m. capensis clones) infest susceptible honey bee colonies and develop into pseudo-queens, taking over the role of reproduction. While relatively more has been described regarding the behavioural basis accompanying reproductive parasitism, the genetic basis describing how these morphologically-worker honey bees become pseudo-queens still requires more investigation. Here, the composition of the mandibular gland secretions from young, old and field-collected (age-unspecified) A. m. capensis clones from queenright and queenless social environments was investigated and compared to the mandibular secretions of A. m. scutellata workers (a subspecies with a comparatively lower reproductive potential). Techniques in gas chromatography and functional genomics were used to investigate the chemical composition of the mandibular gland secretions and the molecular pathways involved in the biosynthesis of mandibular gland fatty acid components, respectively. In the first part of this work, it is shown that even at less than 24 hours old, queenless A. m. capensis clones show queen-like signatures in their pheromone profiles through the production of 9-HDA, the precursor to the ‘queen-substance’ 9-ODA. Using high-throughput RNA sequencing technology, about 48 differentially expressed transcripts (DEGs) directly associated with the mandibular gland pheromone biosynthetic pathway in Apis mellifera, were identified. Of these DEGs, 25 were orthologues to Cytochrome P450s, enzymes involved in the caste-specific hydroxylation of acylated stearic acid, a major regulatory point in the biosynthesis of mandibular gland fatty acids. The in-situ biosynthesis and activation of stearic acid, uncompleted β- oxidation and the oxidative conversion of 9-HDA to 9-ODA were also identified as putative points of queen-associated regulation in the multi-step biosynthetic pathway. Finally, using field-collected A. m. capensis clones, it is shown that some host queens can suppress reproductive parasitism in clones by regulating the synthesis of multiple enzymes key in the production of mandibular gland components, such as Cytochrome P450 enzymes and alcohol dehydrogenases, leading to a multi-step regulation of worker reproduction. This work contributes to our understanding of the molecular-level mechanisms related to regulation of reproductive dominance and deepens our understanding of the evolution of reproductive division of labour.
Constitutive chemical defense of Eucalyptus against herbivory by Gonipterus sp. n. 2
(University of Pretoria, 2019) Hammerbacher, Almuth; Hurley, Brett P.; Schröder, Michelle; u14029406@tuks.co.za; Joubert, Johannes Christoff
The Gonipterus scutellatus species complex Gyllenhaal, 1833 (Curculionidae, Coleoptera) is comprised of 8 cryptic species native to East Australia and Tasmania. Of these 8 species only G. platensis, G. pulverulentus and Gonipterus sp. n. 2 are invasive pests. Gonipterus sp. n. 2 was first discovered outside of its native range in 1916 in South Africa, and caused widespread defoliation of Eucalyptus trees, preferentially feeding on young leaves and new shoots. In 1926 Anaphes nitens Girault, 1928 (Hymenoptera: Mymaridae), an egg parasitoid, was discovered and released in South Africa. Anaphes nitens was historically very effective until the early 2000’s when large outbreaks of the beetle were occurring with increasing frequency. Therefore, investigations for alternative management options were initiated. Both biopesticides and pesticides were tested. However, biopesticides showed little reduction in beetle populations and pesticides are expensive and under legislative control, thus lowering accessibility and hampering large scale use, which results in inefficient control of the beetle. However, Gonipterus sp. n. 2 shows a very distinct host selection behavior, preferentially feeding on certain Eucalyptus species and not at all on others. Several studies have indicated Eucalyptus defense compounds, (such as 1,8-cineole) which may be able to repel Gonipterus sp. n. 2 and could partially explain this selective feeding behavior. Therefore, understanding these compounds which potentially mediate the feeding behavior of Gonipterus sp. n. 2 can offer an alternative control strategy for these beetles. However, this feeding preference has not been studied in depth and more research is needed to understand how these compounds can be developed into a control measure for commercial Eucalyptus plantations. Therefore, the inherent resistance mechanisms of the plant against feeding by Gonipterus sp. n. 2 should further investigated.
Temporal changes in food resource availability between two karst bat assemblages
(University of Pretoria, 2020) Keith, Mark; Seamark, Ernest; tlaishegonkoana@gmail.com; Nkoana, Tlaishego Tedson
The temporal availability of arthropods varies in response to changing quality of vegetation which is influenced by climatic conditions. Climate in the Savanna and Grassland biomes is defined by wet and dry cycles. Bats (Chiroptera) are major consumers of nocturnal flying arthropods and respond to temporal fluctuations of their arthropod prey as well as climatic conditions. My study is undertaken in two karst landscapes within two biomes, Savanna (Meletse) and Grassland (Cradle of Humankind World Heritage Site-CoH WHS). The migratory Miniopterus natalensis utilizes Madimatle cave (Meletse –Thabazimbi) for maternity roosting (October-February/March) whilst caves in the CoH WHS provide hibernacula (winter) roosts (April-September) for this population. Migration in bats has been linked to changing climatic conditions for temperate species and food availability in tropical species. The factors driving the migration of Min. natalensis population are not yet understood. The temporal changes of bat assemblages and their arthropod prey from dry to wet season climatic regimes are of interest. To test this, I collected arthropods and recorded bat echolocation calls from dry to wet season (June-February), using malaise traps and Anabat SD2 bat detectors, respectively. Different bat species are adapted to forage within different levels of vegetation clutter. Traps and bat detectors were therefore spatially placed across different levels of vegetation clutter at the study sites. Arthropods were caught, measured (size and biomass) and capture success (CS=individuals/trap-hours) were calculated monthly. An Acoustic Activity Index (AAI) of recorded bats was also used to obtain monthly relative activity. My results show that bat activity corresponds to arthropod availability on a temporal basis with wet season highs and dry season lows, at both study sites. When comparing Grassland and Savanna sites, arthropod CS was significantly higher (P<0.01) at the grassland (mean CS=0.248 ind./trap) whilst biomass was greater at the savanna site. In addition, the Grassland had higher CS with lower biomass for the arthropods Diptera and Lepidoptera, whilst the larger biomass taxa, Coleoptera and Hemiptera, had higher CS at the savanna. The frequency of larger arthropods was higher in November and corresponded with peak biomass measured that month. At Meletse, significant increases (P<0.05) for bat activity and arthropod CS were recorded in August/September (late dry season) and November (wet season). Species level bat activity increases corresponded with increases in arthropod CS and biomass. The matching between bat activity patterns and arthropod availability is important for the maternity season when pregnant females have to meet increased energy demands. Indeed, the maternity season matched with periods of highest food resources expressed as increased arthropod abundance and biomass. Greater bat activity during the maternity period places Meletse as an important food resource reservoir both supporting resident and the migratory species. As bats are major predators of several taxa of nocturnal flying arthropods amongst which are agricultural pests, the ecological and economic implications of maintaining healthy bat assemblages remain of importance. Careful and effective monitoring of bat assemblages and arthropod prey will further increase understanding of the temporal dynamics between predator activity and prey abundance within habitats. Knowledge on the effects of land-use change on habitats will develop a better understanding of impacts on species and broader ecological systems.
Drivers of leopard population dynamics in the Kruger National Park, South Africa
(University of Pretoria, 2014-08) Ferreira, Sam M.; Chimimba, Christian Timothy; nmaputla@awf.org; Maputla, Nakedi Walter
In the Kruger National Park (KNP), South Africa, five of the six extant members of the large carnivore guild: lions, Panthera leo, spotted hyaenas, Crocuta crocuta, leopards, P. pardus, cheetahs, Acynonyx jubatus, and wild dogs, Lycaon pictus, are sympatric. A priori and posteriori deductions dictate that lions maintain a balance in the top-down processes in the KNP ecosystem including population abundances and behaviour of the subordinate predators. The recent discovery of the extrinsic disease, bovine tuberculosis (bTB) caused by a bacterium Mycobacterium bovis, in lions suggests that potentially, lion population may decline. Further deductions dictate that the leopard population whereas at individual level may be affected, does not appear to be challenged by the disease. This presupposes that the balance in the top-down processes will potentially be affected. By specifically assessing how this change may affect the leopard population, two mechanisms, which in the context of the KNP are contradictory were invoked. The first mechanism is the meso-predator release hypothesis, which predicts that should the lion population decline, the leopard population would increase as a consequence. The second mechanism, niche packing hypothesis, predicts that the leopard population will not experience a change as a result of the lion population declining; it argues that leopards and lions have co-evolved and as a result have developed conflict avoidance life history, morphological and ecological patterns. Consequently, the thesis set out to investigate if these mechanisms were in effect in the KNP by: (i) designing a robust method to estimate leopard abundances; (ii) estimating leopard abundances throughout the KNP; (iii) comparing leopard abundances with abundances of other members of the large carnivore guild; and (iv) assessing how leopard movements responded to indices of resource distribution and models that predicted space use by lions. Results revealed that leopards responded to resource distribution more than in response to other carnivores and especially lions as was predicted. Accordingly, niche packing theory was selected over meso-predator release theory on the grounds that at population level leopards, at least as far as the KNP is concerned, are not affected by other carnivores. This study therefore, has direct implications on the large carnivore management in KNP. The present study suggests that the leopard population is mainly driven by resources and secondarily by lions. That means in the absence of factors such as human-induced effects, and diseases that are likely to threaten their resource base and them as a result, leopard population is likely to self-regulate in KNP.
Evolution and recent speciation in two disparate endemic South African insect genera: Macroderes (Coleoptera: Scarabaeidae) and Nemopterella (Neuroptera: Nemopteridae)
(University of Pretoria, 2019-06) Sole, Catherine L.; Mansell, Mervyn W.; Scholtz, Clarke H.; Abdalla Mohammed, Ishtiag Hassan
Phylogenetic, taxonomic and biogeographic analyses were conducted to investigate the role of the paleoclimatic and geological oscillations on the diversification and evolutionary history of two disparate southern African insect genera: the dung beetle genus Macroderes Westwood, 1842 and the lacewing genus Afroptera Abdalla & Mansell, 2019. The taxonomic revision of Macroderes resulted in the description of seven new species: M. cederbergensis Abdalla & Deschodt, 2018, M. tortuosus Abdalla & Scholtz, 2018, M. gifboomi Abdalla & Scholtz, 2018, M. leipoldti Abdalla & Deschodt, 2018, M. oreatus Abdalla & Deschodt, 2018, M. porselinus Abdalla, 2018 and M. soleiana Abdalla & Deschodt, 2018. One species, Macroderes nitidus Harold, 1877 is redescribed and its lectotype designated. The diagnostic characters as well as an updated geographic distribution of each species are considered. An identification key to the species in the genus, photographs of habitus, internal sac sclerite, pronotum, pronotal punctures and elytra are also provided. The phylogenetic analyses, based on concatenated molecular and combined concatenated molecular and morphological datasets, suggest Macroderes as a monophyletic group within the Scarabaeinae with strong statistical support. Molecular dating estimation suggests that the genus emerged approximately 38.9 Mya. Rapid recent speciation occurred during the late Miocene and throughout the Plio-Pleistocene eras (5.0-0.1 Mya), which is ascribed to the effects of the paleoclimatic and geological oscillations during the late Mio-Pliocene and the recurrent warming and cooling of the Pleistocene. Taxonomic revisions of the genera Nemopterella Banks, 1910 and Nemia Navás, 1915 resulted in the split of Nemopterella into three: Nemopterella sensu stricto with type species Nemopteryx africana Leach, 1815 (= Nemopterella africana), Afroptera Abdalla & Mansell, 2019 with type species Nemopterella munroi Tjeder, 1967, and the monotypic genus Siccanda Abdalla & Mansell, 2019, with type species Nemopterella arenaria Tjeder, 1967. Eight new species are described in the genus Afroptera these are: A. acuta Abdalla & Mansell, 2019, A. alba Mansell & Abdalla, 2019, A. brinkmani Abdalla & Mansell, 2019, A. balli Abdalla & Mansell, 2019, A. cylindrata Abdalla & Mansell, 2019, A. folia Abdalla & Mansell, 2019, A. koranna Mansell & Abdalla, 2019 and A. maraisi Abdalla & Mansell, 2019. In addition, two new species are added to Nemopterella: N. kabas Mansell & Abdalla, 2019 and N. cedrus Mansell & Abdalla, 2019. Nemia remained unaffected by these changes. The phylogenetic analyses based on concatenated molecular and combined concatenated molecular and morphological datasets Afroptera resulted in well-supported phylogeny and two major clades were identified. The Divergence time estimates suggest that Afroptera originated in the early Eocene (53.9 Mya) but commenced diversification in the late Eocene 36.5 Mya. Most descendant species underwent rapid recent speciation during the late Mio-Pliocene and through the Pleistocene 4.6-0.2 Mya. Biogeographic analyses of Macroderes and Afroptera indicate that the genera have different spatiotemporal origins. The most common ancestor of Macroderes originated in the Cape Floristic Region or the Namaqualand-Namib Domain and the Cape Floristic Region (CFR) during the late Eocene 38.9 Mya and evolved in the Namaqualand-Namib Domain and CFR in the late mid-Miocene 14.5 Mya. By contrast, the most common ancestor of Afroptera is shown to have originated earlier, during the Early Eocene (53.9 Mya) in the Namaqualand-Namib Domain, the Cape Floristic Region and Namib Desert Eco-region and evolved in the Namaqualand-Namib Domain and Namib Desert Eco-region during late Eocene 36.5 Mya. Dispersal was found to be the most prominent ecological mechanism that led to the present-day distribution of extant species. The late Mio-Pliocene witnessed synchronised dispersal and vicariant events for both genera resulting in synchronised lineage splitting in many of their populations; indicating that the genera experienced the same paleoclimatic and geological processes driving speciation. The extant species of both genera appear to have evolved during the Pleistocene.
Seasonal development and trapping of coryphodema tristis in eucalyptus nitens
(University of Pretoria, 2020-02) Hurley, Brett P.; Slippers, Bernard; kayla.noeth@gmail.com; Noeth, Kayla Philippa
Plantation forestry is a significant economic contributor in many countries around the world, accounting for approximately 0.9% of the global GDP according to a 2011 estimate. These exotic commodities are often at risk of being invaded by various pests and diseases, both native and exotic. In Brazil, for example, losses of up to US$6.5 million per annum have been estimated due to infestations of the Sirex wood wasp (Sirex noctilio, Hymenoptera: Siricidae). Management of these biological risks is crucial to curb significant economic losses; however, management strategies can often be complicated and require a thorough understanding of the target pest’s biology and ecology. In South Africa, one of the more important pests in plantation forests is the cossid moth (Coryphodema tristis, Lepidoptera: Cossidae). This wood-boring moth was previously described as a pest of quince and grapevines in the Western Cape region, but has recently been found to infest plantations of Eucalyptus nitens on the Mpumalanga Highveld. Despite its significant impact on E. nitens, few studies have investigated the biological and ecological characteristics of this pest, as well as aspects relating to its management, on this recent host. The aim of this study was to obtain a better understanding of the biological and ecological characteristics of C. tristis on E. nitens, and to use this knowledge to develop an effective management strategy. The dissertation contains three chapters. The literature review in the first chapter provides a summary of wood-boring Lepidoptera as pests in commercial forestry plantations. The review draws on general characteristics present in the groups discussed and includes information on their diversity and distribution, life cycle characteristics, host associations, diet and nutrition, pathways of invasion and early detection mechanisms. Eradication as a control strategy, as well as other management tactics such as biological, chemical and behavioural control, is also discussed. The aim of the first research chapter was to investigate the seasonal development and occurrence of C. tristis in association with E. nitens, on the Mpumalanga Highveld, and to compare these findings to those previously published for the Western Cape area on quince and vines. This was achieved through the regular felling of cossid infested E. nitens trees on the Mpumalanga Highveld over a 23-month period to investigate development of the immature stages, and through the trapping of C. tristis male adults to monitor the flight season(s). Since the previously recorded hosts and environment (quince and vines in the Western Cape) differ from the new host and environment (E. nitens on the Mpumalanga Highveld), differences in the life cycle of C. tristis between the two regions were expected. The broad objective of the second research chapter was to optimise the management of C. tristis using behavioural control tactics. Specifically, we investigated the influence of trapping density on moth captures, using pheromone-baited traps that have recently been used for an experimental mass trapping programme. Six different trap spacing treatments, ranging from 10 m to 60 m between traps, were investigated over a period of 23 months and the mean moth captures per trap and total estimated moth captures per hectare were compared between these treatments. It was expected that the lower trap densities would capture significantly more male moths than the higher trap densities, since inter-trap interference may occur at the higher trap densities. This was the first study to investigate the seasonal development and occurrence of C. tristis on E. nitens. These results, together with results from the trapping density study, will be useful to inform future management strategies for this pest. In addition, this study made an important contribution to the knowledge on economically significant wood-boring moths.
Evaluation of anthropogenic disturbance on African clawless otter (Aonyx capensis) physiological stress, behaviour, and population density using non-invasive methods
(University of Pretoria, 2019) Ganswindt, Andre; McIntyre, Trevor; u17297002@tuks.co.za; Majelantle, Tshepiso Lesedi
Land transformation for anthropogenic use is the leading cause of species declines globally, but some species are able to succeed in these environments. African clawless otters (Aonyx capensis) are the most widely distributed otter species in Africa and occur in a wide variety of habitats, including transformed landscapes. Thus, they are a good model species to investigate animal adaptions to anthropogenic environments. The aim of the study was to examine and compare the stress-related endocrine responses, population density, and behaviour of African clawless otters (ACOs) from a transformed area and natural areas using non-invasive techniques. An enzyme-immunoassay for measuring faecal glucocorticoid metabolite (fGCM) concentrations as a measure of stress in ACOs was established by comparing fGCM concentrations from a captive otter before and after a stress event caused by translocation to a different site. Thereafter, fresh faeces from ACO latrines were collected, and camera traps were set up at a transformed area (Millstream Farm) and two natural areas (Verloren Vallei Nature Reserve and Cobham Nature Reserve). Camera trap arrays, consisting of between 18 and 24 cameras, were placed on all three sites, recording otter presence for a total of 2439 camera days. From the five different enzyme-immunoassays (EIAs) tested, the cortisol and oxoaetiocholanolone (measuring 11,17 dioxoandrostanes) EIAs showed the highest response (74% and 48% increase, respectively) 30-, 24- hours after the stress event. For both EIAs, a desiccation experiment illustrated that alterations in fGCM concentrations after defecation is acceptable (≤ 16.2 %) for samples collected up to 3 hours postdefecation. Using the cortisol EIA for subsequent analyses, fGCM concentrations of animals from the transformed area (n = 20; mean (± SD): 0.468 (± 0.539) μg/g dry weight (DW)) were significantly higher (p = 0.019) than those from otters in the natural areas (n = 17; 0.242 (± 0.226) μg/g DW), with an overall difference of 220%. Using a random encounter model approach, the transformed area was estimated to have the highest density of ACOs (8.2 ± 2.3 km-2), whereas Verloren Vallei and Cobham Nature Reserve (natural areas) had estimated densities of 0.7 ± 0.2 km-2 and 2.1 ± 0.6 km-2, respectively. There was a significant difference (p = 0.007) between group sizes in the transformed area (detections = 112; group size range = 1 – 5) and natural areas (detections = 29; group size range = 1 – 3) and in otter activity time (p = 0.033, activity overlap = 66.5 ± 8.33 %) between Verloren Vallei and Millstream farm. With the newly established non-invasive method, this study demonstrates that ACOs show increased adrenocortical activity in a transformed environment. Conversely, the otters exhibit substantial behavioural plasticity to exploit the anthropogenic landscape. Transformed areas such as Millstream farm provide ACOs with suitable habitat and abundant food resources, evidently supporting higher than average otter population densities. Such densities likely exacerbate conflict with trout farm managers due to their perceived depredation impact on trout stocks. Further studies evaluating the potential causes of elevated fGCM concentrations and investigate approaches to reduce human-otter conflict will contribute to African clawless otter conservation.
Development of novel surveillance tools for rapid detection of citrus psyllids
(University of Pretoria, 2024) Weldon, Christopher W.; Kruger, Kerstin; Manrakhan, Aruna; dylanpullock@gmail.com; Pullock, Dylan Andrew
South Africa’s citrus industry is lucrative but its profitability is threatened by pest insects, either due to direct damage or via the transmission of pathogens causing disease that negatively impact citrus production. The citrus psyllids Diaphorina citri and Trioza erytreae are vectors for ‘Candidatus Liberibacter asiaticus’, the pathogen of one of the most devastating citrus diseases in the world known as Huanglongbing (HLB). Vector control is essential to minimise the disease’s spread. Huanglongbing and D. citri are not yet present in South Africa but have become established in parts of the African continent and are both spreading. My project attempted to improve the attractiveness and identification process of yellow sticky traps; a psyllid monitoring technique recommended in citrus orchards for T. erytreae. This was done to help prevent the introduction of HLB and D. citri, the invasive vector of its pathogen, to South Africa. To improve attractiveness, various plant semiochemical odour lures were tested using T. erytreae as model organism. For improvement of the identification process, an automated vision-based artificial intelligence (A.I.) driven system was developed and tested. The successful development and implementation of these tools has the potential for the speedy implementation of control measures to prevent the establishment or spread of the HLB pathogen and its insect vectors. Yellow sticky trap augmentation was done using eight plant semiochemicals, a commercially available D. citri lure, and hexane as a solvent control. All test attractants were dispensed from sealed polyethylene bulbs. Field cage trials were used to determine the most effective semiochemicals for further field tests. The field tests were done in a pesticide free lemon orchard using a randomised 5 × 6 grid. Temperature and humidity were recorded so that their effect on semiochemical release rate could be determined. Using gas chromatography-mass spectrometry, odorant composition and release rates were evaluated. None of the semiochemicals improved psyllid catch during the field cage or field trials, and weathering in the field did not affect the composition of odorants. However, temperature influenced odorant loss, and release rate from polyethylene bulbs decreased over time. Development and training of the automated psyllid identification system was done by setting out, then collecting 544 traps around South Africa, Mauritius, and Reunion. They then underwent manual processing where target psyllid groups were identified, and relevant traps photographed. Photographs were then annotated and uploaded onto Roboflow for data augmentation and training, validation, the testing of the A.I. models. Five models were developed using YOLOv8 with two models, YOLOv8s and YOLOv8m, showing promise as a workable means to speed up and improve the psyllid identification process. While semiochemicals did not improve psyllid captures in this study, they should not be ruled out to improve yellow sticky trap monitoring. Both YOLOv8 models, while promising, have limitations that need to be addressed. Further studies into yellow sticky trap augmentation should investigate blends of semiochemicals with overlapping attractiveness to citrus psyllids as well as the possibility of using pheromones as an alternative. For the A.I. models, increasing the number of images used during training could increase effectiveness and accuracy, though another option is to develop and test a tandem model system where the same input is fed into two separate models so that the outputs can be compared.
The effects of climate change on freshwater fauna in the lower Olifants River, South Africa
(University of Pretoria, 2024) Chimimba, Christian Timothy; Woodborne, Stephan; amanda.adlam@up.ac.za; Adlam, Amanda Laura
Freshwater rivers are under threat worldwide from anthropogenic disturbances including climate change. Climate change will increase air temperature and, consequently, water temperature in rivers. The survival of aquatic fauna is closely tethered to water temperature, therefore, the increase in water temperature will influence freshwater fauna at both population and community levels. The ecologically and economically important lower Olifants River, in the Kruger National Park (KNP), South Africa was investigated as it is already negatively affected by anthropogenic disturbances, with the aim of validating a statistical model to predict future water temperatures. The study validated a water temperature model for the Olifants River, with Nash Sutcliffe efficiency values of >0.9 for monthly and >0.75 for daily timesteps, indicating the robustness of this model. The model was further validated using the upper Klaserie River. This statistical model was then used to predict average water temperatures (WTavg) from projected air temperatures to predict monthly and daily WTavg under the Representative Concentration Pathway (RCP) 8.5 scenario using 16 General Circulation Models (GCMs) to 2100 CE. The results showed that monthly WTavg will increase by 3.7° C, and maximum WTavg will reach 33.6° C by 2100 CE. The daily results showed a similar increase of 3.9° C, with some extreme days reaching 42-44° C, and maximum WTavg will increase to 41.1° C by 2100 CE. These predictions were compared to the thermal tolerances of fauna present in the Olifants River to extrapolate which taxa may be vulnerable to the effects of climate change. The investigation used WTavg of 33.6° C and 41.1° C as the thresholds for chronic and acute heat stress, respectively. It was found that 12 fish species and 11 macroinvertebrate families will be susceptible to acute heat stress while five fish species and five macroinvertebrate families will be vulnerable to chronic heat stress. Although statistical modelling approaches are instrumental in modelling climate change as a driver of water flow and temperature over time, they do not extend beyond these parameters to address climate change impact-related questions on ecological functioning, such as trophic ecology. This study used stable isotope analysis (SIA) to extrapolate what the loss of these fish and macroinvertebrates could have on the trophic dynamics under the RCP 8.5 scenario. The results showed that the apex predator is vulnerable, along with other predators, algivores and insectivores. This will ultimately lead to top-down effects and over-proliferation of prey, plants, and algae. While this study is based on a single river, it represents a novel approach that combines: 1) a mechanistic approach of statistical modelling future water temperature; 2) the evaluation of thermal tolerances; and 3) the assessment of trophic cascades using SIA and applying them to evaluate faunal changes at both population and community levels in a river system. This study has implications at a global level on how climate change may affect not only freshwater water temperatures, fish, and macroinvertebrates, but also with ecological, economic, and human health implications in similarly data-deficient river systems globally.
Development of CRISPR/Cas9 gene editing tools for the insect pest Gonipterus sp. n. 2
(University of Pretoria, 2024-03-21) Dittrich-Schröder, Gudrun; Slippers, Bernard; Doung, Tuan; Jade.ashmore13@gmail.com; Ashmore, Jade Sabrina
Literature review of insect sex determination pathway and CRISPR/Cas9 gene editing tool in application for genetic-based pest control methods. The de novo genome of Gonipterus sp. n. 2 was sequenced with long and short read sequencing, assembled and annotated using RNA sequencing data and Protein sequences from other Coleopteran species with published, assembled genomes. The expansion and contraction of gene families, with a focus on the cytochrome P450 detoxification gene, was assessed. A CRISPR/Cas9 transformation protocol for Gonipterus sp. n. 2 embryos with microinjection. The Tyrosine 3-monooxygenase (Pale) gene was targeted to assess the efficiency of the embryo transformations.
Assessing longitudinal profiles of glucocorticoid concentrations in the baleen of male and female southern right whales ( Eubalaena australis)
(University of Pretoria, 2024-07-08) Ganswindt, Andre; Vermeulen, Els; estefanpieterse1@gmail.com; Pieterse, Estefan
Marine mammals are subject to a variety of anthropogenic and natural stressors. However, it is still poorly understood how these stressors may affect physiological adaptations including affecting reproductive biology. Due to the association between glucocorticoids and the general health and wellbeing of animals, the monitoring of stress responses in mammals which trigger the production of glucocorticoids has grown in popularity in conservation studies. In the 1950s, the southern right whale (Eubalaena australis, hereafter SRWs) was given legal protection against whaling after which populations gradually increased again. Long-term annual arial surveys along the South African calving ground have, however, uncovered some drastic changes in the demographics of the South African population of SRWs, including a reduced reproductive rate and overall reduced body condition. In this regard, it would be important to gain a better understanding on the physiological responses of these whales to stressors as to gain an insight in the biological consequences of increased pressures on their environment. Therefore, this study aimed to look at longitudinal glucocorticoid (bGC) profiles in baleen plates of male and female SRWs and assess the relationship with reproductive hormones (androgens (bA) and progestogens (bP) respectively). A biological validation established a corticosterone assay's appropriateness for quantifying bGC metabolites in SRW baleen. Further results indicated a strong correlation between bGC and bP concentrations in females. Males ii with low levels of bA and bGC, and only a few brief moments of heightened bGC raised the questions of male sexual maturity and how they may respond to mating behaviours. The results of this study contribute to the understanding of SRW physiological responses to stressors and will aid in further research on the effects of anthropogenic pressures on their environment.
Cellular- and symbiont-mediated defenses in Bactrocera dorsalis (Hendel) and Ceratitis cosyra (Walker) against their native and introduced parasitoids
(University of Pretoria, 2024-07-08) Weldon, Christopher W.; Mohamed, Samira A.; Herren, Jeremy K.; u21832073@tuks.co.za; Gwokyalya, Rehemah
The use of parasitoids as pest biological control agents has been adopted globally. Nonetheless, the success of parasitoid-oriented biological control programs is dependent on the virulence of the parasitoid, a phenomenon that is influenced by several host (pest) and parasitoid-associated factors. Common among the host factors are host innate (i.e., cellular, and humoral) immune defences and host-associated bacterial symbionts. Host innate immunity, through regulating encapsulation and melanisation of the parasitoid egg, has been shown to influence host-parasitoid dynamics. Additionally, bacterial symbionts through immunomodulation, competition for nutrients, and releasing toxins, affect the development and fitness of the parasitoids. However, in the oriental fruit fly, Bactrocera dorsalis (Hendel) and the marula fruit fly, Ceratitis cosyra (Walker) (both Diptera: Tephritidae), common pests of fruticulture, the effect of host immunity on the outcome of their interaction with parasitoid wasps is unknown. Moreover, several B. dorsalis-associated symbionts are known to affect the development, reproduction, pesticide resistance, and susceptibility of this pest to entomopathogenic fungi. Nonetheless, the effect of larvae-associated gut symbionts on the outcome of the interaction between B. dorsalis and its associated parasitoid wasps is unknown. The egg-prepupal parasitoid, Fopius arisanus (Sonan) and the larval-pre-pupal parasitoid, Diachasmimorpha longicaudata (Ashmead) (both Hymenoptera: Braconidae) and are the most common parasitoid wasps used as biological control agents of B. dorsalis, globally. Additionally, since its invasion and detection in Africa, some native parasitoids, such as the larval-prepupal parasitoid, Psyttalia cosyrae (Wilkinson) (Hymenoptera: Braconidae) has been investigated as a potential biological control agent of this pest and its native counterpart, C. cosyra. Diachasmimorpha longicaudata and F. arisanus successfully develop in B. dorsalis and C. cosyra whereas P. cosyrae develops in C. cosyra but not in B. dorsalis. This is suggestive of possible differences in defence mechanisms of B. dorsalis and C. cosyra against these parasitoids, a phenomenon that could be attributed to host intrinsic factors e.g., cellular immunity and host-associated microbes that enable the pests to defend themselves against some parasitoids and not others. Moreover, the differences in wasp performance could be due to variations in parasitoid virulence. This thesis investigated the cellular immune responses of C. cosyra and B. dorsalis to parasitoids, the impact of parasitisation on B. dorsalis gut microbiota, as well as the effects of B. dorsalis-associated larval gut symbionts on parasitoid development and their consequences for parasitoid offspring fitness. To evaluate the role of cellular immune defences on the outcome of host-parasitoid interactions in B. dorsalis and C. cosyra, I investigated the melanotic encapsulation responses, total and differential hemocyte counts, hemocyte viability, and hemocyte spreading ability in the fruit flies after parasitisation by D. longicaudata and P. cosyrae. The adult fly emergence rate post-parasitisation was also recorded. I found stronger immune responses in B. dorsalis, mediated by a higher haemocyte load enabled this pest to mount effective melanotic-encapsulation responses against D. longicaudata and P. cosyrae than in C. cosyra. Furthermore, D. longicaudata was more efficient than P. cosyrae at suppressing host-immune defences, especially by reducing hemocyte spreading and the proportion of viable hemocytes in both host fruit flies. This was corroborated by the low encapsulation rates of this parasitoid and the consequential higher number of emerging D. longicaudata adults compared to P. cosyrae. These results reveal that D. longicaudata is a more efficient parasitoid wasp and can be used as a biological control agent of C. cosyra and B. dorsalis. Using next generation amplicon sequencing, parasitoid-mediated perturbations on the B. dorsalis gut microbiota were investigated in response to parasitisation by D. longicaudata and the native counterpart, P. cosyrae. My results showed that, parasitisation shaped the composition, abundance, and diversity of the bacterial and fungal communities of B. dorsalis. Parasitisation by P. cosyrae had no effect on the gut microbial diversity of B. dorsalis larvae. On the other hand, D. longicaudata induced dysbiosis in the guts of B. dorsalis larvae and increased the abundance of pathogenic bacteria genera such as Stenotrophomonas, Serratia and MorganelIa. Diversity and abundance of the fungi community of B. dorsalis were negatively affected by parasitisation by both parasitoid species. Furthermore, I investigated the impact of some B. dorsalis gut symbionts on the acceptability of B. dorsalis (axenic, symbiotic, or the bacteria mono-associated lines) by parasitoids, adult parasitoid emergence, and the fitness of parasitoid offsprings. I found that Lactococcus lactis, a common gut symbiont of this pest, increased the number of F. arisanus and D. longicaudata emerging from B. dorsalis. This bacterium also increased the fitness of the F1 parasitoid offspring. In contrast, Providencia alcalifaciens, reduced the proportion of emerging parasitoid wasps but increased F1 wasp fitness parameters such as size and fecundity. The findings of my thesis contribute to our understanding of the underlying physiological factors influencing parasitoid performance and their implications for the management of the frugivorous pest, B. dorsalis. This thesis has also identified a candidate symbiont, L. lactis that can be incorporated as a probiotic during mass rearing of the potent parasitoids, D. longicaudata and F. arisanus. This could potentially increase the number and fitness of the mass-reared parasitoids hence contributing to the development of a sustainable biological control programme against B. dorsalis.
The role of termites in South African savanna ecology
(University of Pretoria, 2023-07-08) Robertson, Mark P.; Parr, Catherine Lucy; Eggleton, Paul; Katherine.bunney@gmail.com; Bunney, Katherine
Termites are ecosystem engineers that influence savannas through the process of decomposition and bioturbation (movement of soil by biota). Firstly, decomposition is the process by which dead plant biomass is recycled and made available again for uptake by other plants. Using a novel large-scale termite suppression experiment, I quantify, for the first time, the relative contribution of microbes, termites, and other invertebrates to the decomposition of wood (native and non-native), dung, and grass in a mesic savanna. I found that termites were responsible for two thirds of the mass loss from dry wood and a third of the mass loss from fresh native wood, dry dung, and dry grass. Microbes were wholly responsible for the difference as there was no evidence of other invertebrates contributing to decomposition, even with fresh wood. Global decomposition studies have demonstrated that decomposition is primarily temperature-driven with rainfall playing a secondary role, although to date, all global decomposition studies have used a single substrate to measure decomposition meaning differences with substrate type may be missed. Here I explored the decomposition of wood, dung and grass along a rainfall gradient (380–650 mm/year) at three savanna sites in South Africa. As the three sites experience a similar temperature range, I effectively controlled for temperature allowing us to explore the effect of rainfall in isolation. I used decomposition bags - with and without termite access - and measured mass loss after set time intervals. I predicted that the absolute decomposition of all three substrates would increase along the rainfall gradient. This assumption held for dung and grass, but I found the reverse for wood. My study highlights the importance of considering multiple substrates as decomposition patterns and dominant agents can vary. I suggest that termites should be recognised alongside microbes and fire as the primary agents of wood, grass, and dry dung turnover in global carbon models. Secondly, through the process of bioturbation, termites profoundly affect soil turnover rates and modify the patterns of water and chemical flux in soils. Termites build two kinds of above-ground biogenic structures: mounds and sheeting. Sheeting is constructed to protect foraging termites against desiccation and predation while they consume the organic material. The characteristics and dynamics of soil sheeting are not yet well understood. In terms of quantity, I found there were approximately two tonnes of soil sheeting per hectare present across both the soil surface and the trees of my mesic savanna (650 mm p.a.) at each survey time. Both horizontal and vertical sheeting soils were significantly enriched in nitrogen relative to the matrix soils. In savannas, primary productivity is strongly limited by nitrogen. These nutrient differences likely give rise to the creation of small nutrient rich patches, on a finer scale than those created by termite mounds, with important consequences for savanna spatial dynamics. Finally, I present the first rigorous and directly measured combined carbon stock and net primary productivity (NPP) dataset from a southern African savanna. This study serves to provide larger system ecological context in which to place termite functioning. My findings serve to highlight the extreme spatial and temporal (annual and inter-annual) heterogeneity present in savannas. In addition, my results are suggestive that greater termite activity gives rise to greater grass production but owing to the small sample size this result needs rigorous testing. I contextualised my biomass and NPP findings within both the published African GEM sites and the other African savanna studies that were assessed using a biomass dynamics approach. The results of this study highlight the need for a greater number of plots per site and greater within plot replication, particularly below-ground, within these plots in future savanna GEM studies. Quantifications such as this are urgently needed to enable ecologists to rigorously evaluate the potential of savannas as carbon sinks.
Factors influencing the efficacy of biological control of Gonipterus sp. n. 2 by Anaphes nitens
(University of Pretoria, 2024-06) Hurley, Brett P.; Schröder, Michelle; Slippers, Bernard; harmen148982@live.nl; Barten, Harm
The Eucalyptus snout beetle, Gonipterus sp. n. 2 (Coleoptera: Curculionidae), native to Australia, is a major pest in South African Eucalyptus plantations. In 1926 the egg parasitoid Anaphes nitens Girault (Hymenoptera: Mymaridae) was imported from Australia into South Africa, and after its release it became an example of the success of classical biological control. However, recent outbreaks of the beetle have raised questions about the efficacy of biocontrol by this natural enemy. In this thesis the prevailing hypotheses in the literature for the failure of biocontrol of Gonipterus sp. n. 2 by A. nitens were summarized in a review. Elevation, climate, host plant susceptibility, genetic variation, and population dynamics were found to be involved in biocontrol success. The effects of elevation and climate were further studied in a data analysis with field data collected in KwaZulu-Natal between 2010 and 2015. Severity of beetle attacks was found to increase with elevation as expected from previous studies, but unexpectedly this was not accompanied by a decrease in parasitism. Few clear relationships with weather variables were found, the most direct relationship being the negative relationship of parasitism with potential evapotranspiration (PET). To test whether this biocontrol system could be enhanced by addition of intraspecific variation to the parasitoid population, a new A. nitens population was imported from Queensland, Australia, from an area climatically better matched to the current Eucalyptus growing areas in South Africa. Reproductive compatibility of the newly imported Australian and existing South African A. nitens populations was ensured by performing controlled crosses. Subsequently a population genetics study was performed using 15 newly developed microsatellite markers with populations from the native range in Australia and introduced populations from South Africa, Portugal, Brazil, and West Australia. Overall, genetic diversity was high, and population structure was present. The introduced populations formed separate genetic clusters, while the native Australian population was composed of a mix of these clusters. Interestingly, the A. nitens population from the Western Cape province in South Africa formed a separate genetic cluster from the other South African populations and grouped more closely with the sampled native Australian population. Next, a field release was performed in two Eucalyptus plantations in KwaZulu-Natal. The microsatellite marker set was further used to determine establishment of the newly released A. nitens population by comparing pre- and post-release samples collected at the release sites. Signs of establishment were found in the form of unique Australian alleles being present in two post-release samples, and by post-release individuals being assigned to the Australian population by a DAPC clustering method. Ultimately more studies such as whole genome sequencing are needed to unambiguously establish whether those individuals were true descendants of the newly released A. nitens population. In conclusion, this study provides an overview of the factors involved in biocontrol of Gonipterus sp. n. 2 by A. nitens and gives new insights into how they might be responsible for failing biocontrol. Furthermore, a first attempt was made to use population genetic techniques to enhance biocontrol of an important Eucalyptus pest.
Initial steps for developing large-scale rearing and processing of black soldier flies, Hermetia illucens L., in a start-up bioconversion facility
(University of Pretoria, 2024-01-30) Weldon, Christopher W.; nina.jparry@gmail.com; Parry, Nina Jennifer
The aim of this project was to establish large-scale rearing and processing methods for Hermetia illucens L. larvae reared on organic waste streams for use in animal feed. This work builds on existing knowledge of the effects of organic waste streams as larval substrates, and waste mixing to optimise larval development on substrates with variable nutrient content. The experiments were conducted at an industrial scale using thousands of larvae fed many kilograms of feed, rather than at a lab scale (hundreds of larvae fed grams of feed) in a newly established bioconversion facility that was still optimising its processes. As such, the results are more applicable to large-scale, commercial bioconversion operations. The results also provide insights into the processing methods and safety of insects reared on organic waste as animal feed supplements, and provide some guidance on the optimal substrate composition for improved performance of larvae, bioconversion and waste reduction. Following an in depth literature review (Chapter 1), four different experiments were conducted. For all experiments, freshly hatched H. illucens neonates were collected from an established colony held at Aegis Environmental Bioconversion Facility, Centurion, South Africa. Preconsumer fruit and vegetable waste was sourced from a local fresh produce market and poultry manure was sourced from a local chicken layer hen farm. The first three experiments were conducted with 12 kg of waste and 90 mg (approximately 6000) neonates in large plastic meat trays. All trays were held at 28 ± 0.5°C with 65% relative humidity. Measurements of the larvae were taken to determine the development time, size, biomass production, survival, bioconversion, efficiency of conversion of digested feed, and waste reduction, collectively referred to as larval performance. The first experiment (Chapter 2) focused on the nutritional differences between larvae and prepupae (harvested at 15 and 20 days, respectively) that had been fed fruit and vegetable waste. Prepupae had slightly higher fiber content than larvae, and no other nutritional differences were found. Larvae had higher total biomass and higher survival rates. Based on the results of this experiment, larvae should be harvested in preference to prepupae to maximise waste reduction and biomass production. However, harvesting a mixture of larvae and prepupae should not impact the nutritional quality of the final product due to the minimal nutritional differences between the two stages. The second experiment (Chapter 3) investigated the effects of three different drying methods on the nutritional composition and microbiological contamination present in H. illucens larvae. A sample of 280 g of 15-day old larvae, fed on fruit and vegetable waste and euthanized using boiling water, was used. There were no nutritional or microbiological differences between hot air, oven or microwave drying. A cost benefit analysis of each drying method was completed, and it was determined that hot air drying, followed by oven drying were the most cost-effective while microwave drying was expensive and unprofitable. If there is no effect on the nutritional or microbiological content of H. illucens larvae, the best drying method is the one that is most cost effective and time efficient. The third experiment (Chapter 4) investigated the performance of larvae fed varying mixes of fruit and vegetable waste and poultry manure, and it was determined that larvae performed best on fruit and vegetable waste only but tolerated up to 60% fruit and vegetable waste mixed with 40% poultry manure before the performance of the larvae was severely reduced. In terms of using poultry manure as a substrate for H. illucens larvae, it should be added only in low quantities, up to 40% total wet mass of the substrate. The final experiment (Chapter 5) used large, specifically designed metal trays with 60 kg of waste and 450 mg (approximately 30 000) neonates. The effect of poultry manure inclusion, from 5 to 40%, with fruit and vegetable waste was assessed and temperature and pH of the trays were recorded throughout development of the larvae. There was no effect of mixing poultry manure with fruit and vegetable waste at different inclusion percentages on any measure of larval performance. However, temperature and pH of the substrate were key factors in development, survival and waste reduction potential of H. illucens larvae. This study showed that a substrate temperature of 28°C, an initial substrate pH of 6.3, and a final pH of around 9.6 is ideal for larval performance and waste reduction when larvae are fed a mixture of fruit and vegetable waste with a small portion of poultry manure. Comparing the results between Chapter 4 and Chapter 5, specifically trays that contained 40% poultry manure, larvae performed better overall in medium-sized trays, although individual larval masses were similar between both tray types. This study indicates that medium-sized experiments do not scale up in a predictable manner, making it more difficult for knowledge gained from especially small-scale experiments to be applicable to large-scale applications. Comparing the results from the larger and medium-sized trays, the use of medium-sized trays would be recommended in a facility over the use of larger trays that are more exposed to the ambient air. In Chapter 6, an overall discussion of each experiment, implications of the results, limitations experienced, future directions and a final conclusion are presented. This work has added to and expanded on the scientific knowledge that is now available about H. illucens larvae and their use in bioconversion. This work builds on the current knowledge base of organic waste streams, and mixing of waste streams, with variable nutrient content and the experiments were conducted at an industrial scale, in a bioconversion facility, rather than a lab-scale study. As such, the results are more applicable to large-scale, commercial bioconversion operations and will provide some guidance on future large-scale rearing and processing experiments and application of that knowledge in industry. There are several very complex interactions that occur during larval rearing; including substrate conditions like nutrients, microbes, moisture, pH and temperature, the ambient temperature and rates of substrate evaporation, larval density and age, and size and shape of the tray. Future work should consider these complex interactions to untangle and understand these complex interactions. Doing so will provide industry with recommendations for future best practices
Molecular epidemiology of African swine fever genotype I and II viruses: insights from genome sequencing
(University of Pretoria, 2024-05) Bastos, Armanda D.S.; Heath, Livio Edward; Van Schalkwyk, Antoinette; rivalani85@gmail.com; Mthombeni, Rivalani Forget
African swine fever (ASF), a haemorrhagic disease of domestic pigs caused by ASF virus (ASFV) was confined to Africa until 1957. Since then, two other excursions have occurred, in 1960 and in 2007. The first was a genotype I virus introduction to the Iberian Peninsula in 1957 and the second a genotype II virus introduction to Georgia in 2007. Both excursions were associated with a range expansion within and outside Africa, which in the absence of vaccination and treatments options had significant impact to the pork industry globally. Eradication of genotype I from mainland Europe took almost four decades to achieve, and the genotype II pandemic is ongoing. The origin of the latter virus introduction could not be determined despite the availability of gene sequence data for viruses causing outbreaks in Mozambique and two Indian Ocean islands (Mauritius and Madagascar) in the decade prior to the 2007 introduction to the Caucasus. In this study, next generation sequencing (NGS) technologies were used to generate complete genome sequences for eight genotype II viruses from eight Southern African Development Community (SADC) countries spanning a 26-year period (1993-2019). In addition to identifying the Mozambique/2005 as the most likely origin of Georgia 2007/1, the data permitted assessment of the diversity and phylogenomic relatedness of genotype II ASFVs from Africa. The identification of an atypical pre-2007 genotype II virus from Zambia (1993) warranted comprehensive analysis of this strain, which, based on genome sequencing, was shown to contain features of both genotypes (I and II) under study. In addition, eight genotype I strains, representative of three discrete outbreak clusters (2016-2019) were selected for NGS. The generation of sixteen genome sequences, with equal representation for each of the ASFV genotypes (I and II), allowed for identification of single nucleotide polymorphisms (SNPs), deletions in multigene family (MGF) genes and variation on tandem repeat sequences that are useful for distinguishing between genotype II viruses grouping within the six clades (I-IV) identified in this study, underscoring the value of a whole genome sequencing approach. In contrast, the genome data generated for virus’s representative of three genotype I sub-clusters, recovered the same clusters that were discernible based on partial p72 gene sequences and the central variable region (CVR). The high levels of variation and recovery of three sub-clusters (Ia, Ib and Ic) despite a short field presence (2016-2019) suggests independent transboundary introductions. In conclusion, the study has provided insight in the most likely origin of Georgia 2007/1 virus and confirmed high levels of intra-genotypic diversity for genotype II viruses of African origin. The findings also highlighted that the genotype II virus from Zambia may represent a naturally occurring recombinant based on the observed similarities between the 1993 Lusaka isolate and genotype I viruses. By generating reference genome sequences for genotype I and II viruses from the SADC region, this study contributes to global efforts to expand ASF genome databases to include genotypes and geographical regions that are under-represented.
Environmental and physiological correlates of response by three fruit fly (Diptera: Tephritidae) species to commercial lures
(University of Pretoria, 2024-01) Weldon, Christopher W.; Malod, Kevin; u17228132@tuks.co.za; Pogue, Tania
Traps are important tools for managing economically damaging pest fruit flies (Diptera: Tephritidae). Trap captures help fruit and vegetable producers to monitor fruit fly populations and shape their pest management action thresholds. However, biotic, and abiotic factors influence how fruit flies respond to attractive stimuli used in traps. Physiological changes within a fly can change its resource orientated behaviours. In a similar manner, environmental changes can limit or encourage insect activity that governs this behavioural response. Consequently, baited traps only catch subsets of the population under certain weather conditions. Understanding how fruit fly lure responses change is important for improving interpretation of trap captures with direct benefits for fruit fly monitoring and management programmes. In this dissertation, I aimed to test how fruit fly physiology, the environment, and lure weathering impact lure response. I assessed the response of three economically important fruit fly species to several commercial fruit fly lures. To do this I released known numbers of flies in field cages, which enabled unambiguous measurement of the relative response of species to lures under the experimental conditions. The response of Ceratitis capitata (Wiedemann) was tested for BioLure, E.G.O PheroLure and trimedlure. The response of C. cosyra (Walker) was tested for BioLure and E.G.O PheroLure, while the response of Bactrocera dorsalis (Hendel) was measured for BioLure and methyl eugenol. For each species and lure combination, response by a group of flies (n=25) was determined in a semi-field setting in relation to sex, diet (protein deprived and protein rich), and age (two-, 10-, and 20-days post emergence). The effect of nutrient reserves (protein, lipid, and carbohydrate content), and body weight on lure response was also quantified using colorimetric biochemical assays adapted from van Hendel’s method. The environmental effects of temperature (°C), relative humidity (%RH), and light intensity (lux) on lure response were also measured. Additionally, the effects of temperature and relative humidity on the weathering of the lures BioLure, E.G.O PheroLure, methyl eugenol and Capilure (trimedlure mixed with extenders) was evaluated in a field setting. The. The weight of each lure was measured at daily intervals for 30 days to determine weight loss of each lure product in relation to daily mean temperature and relative humidity. Additionally, I tested the effect that semiochemical pre-release feeding, diet (protein rich and iii protein deprived), and age (four-, 10-, and 20-days post emergence) had on the response of B. dorsalis males (n=20) to methyl eugenol baited traps in a field cage setting. Semiochemicals were fed to flies 48 hours prior to field cage testing, with methyl eugenol, eugenol, or no semiochemicals (control) being tested. Semiochemicals were mixed into the relevant diet treatment food at a concentration of 1.5%. I further assessed the effects that body weight and total body nutrient composition (protein, lipid, and carbohydrate content) had on the response of B. dorsalis to methyl eugenol. Body nutrient composition data was obtained with the revisited van Hendel’s method which uses colorimetric biochemical assays. The effect that temperature (°C), relative humidity (%RH), and light intensity (lux) had on the response of B. dorsalis to methyl eugenol lures was also measured. Overall, the effect of fly physiology and the environment on response is specific to the species and lure tested. Despite BioLure being considered a female biased lure there was no consistent bias towards female captures. Only in C. capitata were protein deprived females more likely to respond to BioLure. Irrespective of species, access to dietary protein decreased the response to BioLure baited traps. This suggests that abundant natural sources of protein may decrease the accuracy of fruit fly monitoring that relies on BioLure as the main attractant. Age affected the response of flies to male lures. Immature C. capitata and C. cosyra responded more strongly to E.G.O PheroLure and trimedlure. However, immature B. dorsalis were the least responsive to the male lure methyl eugenol. I found that the effects of temperature on response are largely lure and species specific. The response of B. dorsalis increased at warmer temperatures irrespective of the lure tested. Similarly, the response of flies to male lures increased with temperature. However, I observed that the response of C. capitata and C. cosyra to BioLure is not affected by temperature. Warmer temperatures resulted in greater lure weight loss for all tested lures, but this occurred to varying degrees. Combining the results of lure volatilisation and fly response, I identified that the increased response of C. capitata males to trimedlure at warmer temperatures is mostly driven by increased fly activity. Whereas increased response of C. capitata and B. dorsalis to E.G.O PheroLure and methyl eugenol, respectively, at warmer temperatures coincides with greater release rates of the lures. These results show that monitoring conducted when temperatures are cooler is likely to underestimate fruit fly populations. Feeding on either methyl eugenol or eugenol reduces the response of B. dorsalis males to methyl eugenol baited traps by similar amounts. Access to dietary protein had little effect iv onthe reduced response by males to methyl eugenol when fed semiochemicals. This suggests that feeding semiochemicals to B. dorsalis males may facilitate the simultaneous application of the sterile insect technique and the male annihilation technique. Furthermore, this shows that protein supplementation will not counteract the methyl eugenol response suppression induced by pre-release semiochemical feeding. These results also show that eugenol is a promising alternative to methyl eugenol to achieve the required reduction in response to methyl eugenol. Overall, this dissertation highlights that fly physiology and the environment significantly impact the response of fruit flies to commercially used lures. Specifically, access to natural sources of protein may decrease the accuracy of trap surveys that rely on BioLure. The minimal response of flies occurring at temperatures below 12 °C indicates that trapping surveys deployed below this will largely misrepresent population sizes and are likely to miss incipient fruit fly incursions. It is thus crucial to integrate fruit fly physiology and environmental variables into fruit fly monitoring and survey programmes to increase their accuracy. My results further indicate that eugenol is an effective and safe semiochemical that can be used in joint MAT-SIT programmes. I also observed that protein supplementation and semiochemical pre-release feeding can occur simultaneously in MAT-SIT programmes without increasing the response of B. dorsalis to methyl eugenol. Overall, this dissertation highlights the complex nature of tephritid lure response and the value that quantifying and integrating these effects into monitoring and control programmes can have on fruit fly management.

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