Browsing by Author "Bishop, Jacqueline"

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    Caracals as sentinels for metal exposure in a human-transformed landscape
    (2023) Parker, Kim; Bishop, Jacqueline; Leighton, Gabriella
    Urbanisation and associated anthropogenic activity release large quantities of metallic elements and metalloids into the environment. Due to their toxicity, environmental persistence and bioaccumulative nature, these chemical pollutants threaten wildlife and human health. As urbanisation increases and top predators are forced to utilise more urban spaces, they will likely be exposed to more toxic heavy metals and metalloids. As secondary and tertiary consumers, terrestrial carnivores may be at increased risk of metal exposure through biomagnification effects. Relatively little is known about this emerging threat to terrestrial carnivores persisting in human-transformed landscapes, especially in the Global South. To better understand the extent of this issue, I quantified the level of metallic element and metalloid exposure in a sentinel top predator, the caracal (Caracal caracal), inhabiting the rapidly-urbanising, primarily coastal metropole of the Greater City of Cape Town, South Africa. Whole blood samples (n = 67) from GPS-collared (n = 25) and opportunistically sampled (n = 31) individuals were collected. Using Redundancy Analysis (RDA) and mixed-effect models, I explored the relative influence of caracal demography, landscape use, and diet on levels of individual exposure to 11 metallic elements and metalloids: Aluminium (Al), Arsenic (As), Cadmium (Cd), Chromium (Cr), Cobalt (Co), Copper (Cu), Mercury (Hg), Manganese (Mn), Lead (Pb), Selenium (Se), and Zinc (Zn). Mean metal concentrations (including Al, Cd, Co, Cu, Hg, Mn, Pb, Se and Zn) were generally found to be below toxic thresholds, however, As and Cr are present at potentially sublethal levels in certain individuals. The results suggest that increased use of human-transformed landscapes in home ranges (particularly urban areas, roads, and vineyards) was significantly associated with increased caracal exposure to Al (P < 0.05), Co (P = 0.05) and Pb (P = 0.07). Home ranges closer to the coast (RDA, P < 0.05) and feeding within aquatic food webs (marine and wetland-adapted prey) were associated with higher blood levels of Hg (P < 0.05), Se (P < 0.01) and As (P < 0.05). Further, increased predation on seabirds and aquatic birds likely facilitates the transfer of metals from aquatic to terrestrial food webs. Overall, these findings highlight the importance of urbanisation and anthropogenic activity as major environmental sources of metal exposure in terrestrial wildlife, including more natural areas through long-distance transport of pollutants. Further, they contribute towards a growing global evidence base suggesting cities act as ecological traps for wildlife, threatening their long-term health and persistence in these landscapes. Therefore, it is crucial that cities work to reduce the large quantities of chemical pollutants released into their surrounding environment. In Cape Town, this effort could be focused on the urban edge, waste management, water treatments, roads and agricultural areas. Future research into a possible ecological trap for urban-adapted carnivores should focus on assessing metal exposure at different trophic levels and investigating the potential physiological responses of exposure in species. I argue that the caracal is a valuable sentinel for assessing metal exposure and should be used in tandem with other small and mediumsized carnivores and aquatic bird species in local and national pollutant monitoring programmes to mitigate further exposure and promote carnivore conservation in human landscapes. A charismatic species, with a well-established local platform of research and science communication, the caracal is centrally positioned to help promote greater public awareness and engagement in issues concerning environmental pollutant contamination and monitoring.
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    The characterization of MHC Class II genes of the Nile crocodile (Crocodylus niloticus) : an investigation of mechanisms that shape genetic diversity in natural populations
    (2008) Badenhorst, Lourie; O'Ryan, Colleen; Bishop, Jacqueline
    Genes within the Major Histocompatibility Complex (MHC) of vertebrates code for proteins that are involved in antigen recognition and activation of the adaptive immune response. The hallmark of the MHC is the extremely high levels of polymorphism found at loci. A diverse array of mechanisms have been proposed to explain the generation and maintenance of diversity at MHC loci, including the processes of gene conversion, genetic drift and selection; in the presence of many pathogens balancing selection is thought to be the dominant mechanism by which selection operates. Amino acid substitutions within the peptide-binding region (PBR) of MHC genes further supports the hypothesis that positive selection enhances amino acid diversity in the PBR, such that natural selection will favour PBR diversity in natural populations. This study investigated mechanisms that shape genetic diversity of MHC class II genes in a natural population of the Nile crocodile, Crocodylus niloticus. Using PCR-cloning-sequencing methodology, allelic diversity at MHC Class II genes was investigated and provides evidence for at least two Class II 13 gene families in the Nile crocodile. The Crni-OAB family is homologous to classical Class II vertebrate genes; high levels of both allelic and amino acid diversity characterise this gene family and a strong signal of balancing selection acts to maintain functional diversity. The second family, Crni-OBB, most likely represents a non-classical Class II locus in crocodiles and was characterized by reduced levels of diversity. Analysis suggests that Crni-OBB loci have evolved in a divergent manner to those of the Crni-OAB as balancing selection was not detected within the putative PBR. Results from this study suggest that duplication followed by a recombination event has most likely led to the formation of two distinct crocodilian Class II 13 gene families. Secondly, the relative contributions of balancing selection and random genetic drift in the evolution of extant MHC diversity are examined in a natural population of the Nile crocodile. Temporal variation in allele frequencies for MHC and microsatellite loci was assessed in four successive cohorts of crocodiles from the Okavango Delta, Botswana. Results from this study suggest that a combination of short-term neutral forces such as random genetic drift, together with longer-term selection influence variation at Class II loci in the Okavango Nile crocodile. Loci within the MHC of the Nile crocodile appear to be evolving within a dynamic framework of selection, random genetic drift and recombination. This study is the first of its kind to investigate the respective influence of demography and selection on allele frequencies in a natural population of crocodilians.
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    Characterization of the intraspecific variation within the nickel (Ni) hyperaccumulator species Senecio coronatus (Asteraceae): a preliminary analysis of genetic population structure and shoot proteome expression
    (2013) Wolf, Michael; Ingle, Robert; Bishop, Jacqueline; Muasya, Muthama
    Heavy metal (HM) accumulator plants possess the ability to actively hyperaccumulate and detoxify exceptionally high concentrations of metals in their aboveground tissues, without exhibiting any apparent signs of toxicity. Despite nickel (Ni) hyperaccumulator plants representing the largest percentage of known metal accumulator taxa (over 75%), the underlying genetic and molecular basis of Ni accumulation remains unclear. A prominent difficulty in understanding Ni hyperaccumulation has been the severe lack of intraspecific variation in the trait. Hence, the study of a single species exhibiting a significant degree of variation is highly desirable. as it avoids the use of inter-species comparative studies mostly utilized to date. The Ni hyperaccumulator Senecio coronatus (Asteraceae) has been reported to contain a significant degree of phenotypic plasticity with respect to the amount accumulated and subsequent cellular distribution of Ni. This apparent intraspecific variation means that S. coronatus may represent a useful system in which to study Ni hyperaccumulation. No population genetics study has been carried out to date on this species, and the evolutionary relationships between hyper and non- accumulator populations were unknown. Here, results are presented from a genetic analysis of 15 naturally occurring S. coronatus populations. Analysis of molecular variance (AMOVA) and phylogenetic analysis (based on non-coding nuclear and plastid markers) suggest that Ni accumulation may have evolved twice within S. coronatus, as hyperaccumulator plants from site Kaapsehoop, cluster with non-accumulating serpentine populations and demonstrate distinct genetic differentiation from other accumulator populations. Four populations were selected for a preliminary comparative shoot proteome analysis by means of two-dimensional SDS-polyacrylamide gel electrophoresis (2D SDS-PAGE) to identify proteins potentially involved in Ni hyperaccumulation. This analysis identified nine chloroplastic proteins involved in plant energy production and metabolism as overexpressed in hyperaccumulator plants from Agnus Mine and Kaapsehoop, compared to hypertolerant non-accumulator and non-serpentine plants from Galaxy Mine and Pullen Farm, respectively. However, no difference in photosynthetic efficiency, as determined by chlorophyll fluorescence measurements, was detected between these populations.
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    Evaluation of the elephant immunocontraception program at Hluhluwe-iMfolozi Park, South Africa
    (2023) Fagan, Emma; Bishop, Jacqueline
    Managing African savannah elephant (Loxodonta africana) overpopulation in enclosed reserves is currently a major issue in southern Africa due to the potential negative impact of high elephant density on biodiversity. Immunocontraception of elephants has been proven to be an effective method of population control on small reserves with populations of less than 250 individuals, but there is uncertainty regarding its application in larger populations. South Africa's Hluhluwe-iMfolozi Park (HiP), with over 700 elephants, started a porcine zona pellucida (pZP) immunocontraception program in 2014 with the aim of reducing the population growth rate from 7.7% (2014-2016) to between 2 and 3%, but the program has not yet been formally assessed. In this study, I aimed to (1) evaluate the effectiveness of the 8-year program at the park, by measuring its effect on the population growth rate, and (2) explore potential factors affecting contraception efficacy. The proportion of infants within breeding herds was used to estimate growth rate. The proportion was determined using on-the- ground observations of breeding herds collected during six weeks of fieldwork in October and November 2022 and compared to previous years. The infant proportion in breeding herds and population growth rate were estimated as 0.156 and 7.16% respectively, only slightly less than the 2016 values of 0.167 and 7.7%. A critical assessment suggests that the key reasons for reduced contraception efficacy are consistency of individuals being contracepted and population coverage of breeding-age females. Approximately 75% of all reproductive-age females in the park are associated with collared herds (GPS collars are used to help locate herds for darting), but herd size variation due to fission-fusion social dynamics limited the role of collars in improving efficacy. An average 14% of reproductive-age females were missed each year due to failure to locate some collared herds. Despite high annual coverage of females in any one year, the estimated probability of a reproductive-age female being darted consistently (every year) between 2018 and 2022 was estimated at only 0.355 due to multiplied probability effects. Records also suggest that HiP has been significantly under- darting every year, except for 2022, due to inaccurate darting targets. That this program has not reduced the growth rate as planned suggests that the use of porcine zona pellucida (pZP) immunocontraception in larger elephant populations may be limited by important practical aspects of implementing and maintaining the number of contracepted females. Further research is required to assess its potential at the scale of populations such as HiP's elephants, which currently totals an estimated 1100 individuals. Given the management goals of the program, HiP will need to consider whether to continue the program with adjustments to improve efficacy or explore other options to manage overpopulation, especially in the short term. Keywords: Loxodonta africana, immunocontraception, porcine zona pellucida, overpopulation
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    Life on the edge: exploring the effects of urbanisation on the foraging ecology and ecotoxicology of caracals
    (2021) Leighton, Gabriella Ruth Michaela; Bishop, Jacqueline; Serieys, Laurel; O'riain, Justin
    The continuing loss of natural habitat to a broad range of human activities is one of the main drivers of biodiversity decline worldwide and a defining feature of the Anthropocene. However, some opportunistic, generalist species may benefit from transformed landscapes through, for example, the absence of apex predators or access to human-subsidised food resources. These benefits may thus offset the higher mortality and health risks typically associated with human-dominated landscapes. To understand the cost-benefit trade-offs of life on the urban edge, I investigated the foraging ecology and ecotoxicology of a highly adaptable medium-sized carnivore, the caracal (Caracal caracal), utilising both natural and transformed landscapes around the rapidly growing city of Cape Town, South Africa. Through a combination of scat analysis (n = 654 scats) and prey remains located at 677 GPS clusters, I quantified dietary resource use of 26 collared individuals, as well as opportunistically sampled caracals. Using a range of gut transit times, I estimated whether scat at cluster sites was from the same or an earlier feeding event, thereby increasing the overall detection of individual-specific feeding events by > 50%. While most feeding events occurred within 200 m of the urban edge of Cape Town, I found that caracals have flexible diets that largely comprise medium- to small-sized wild prey (60%), followed by human-associated species (27%), and introduced or domestic species (13%). Using a subset of the feeding and resting events (n = 326 prey remains, n = 384 scat, n = 177 resting sites) that were associated with known individuals (n = 17), I then investigated caracal resource selection using both anthropogenic and environmental factors. Additionally, I examined the behaviour of caracal at feeding clusters to determine if they respond to spatial and temporal risks associated with anthropogenic factors. I found divergent resource selection patterns based on the level of exposure to urbanisation: caracals living in the urban-dominated region of the Peninsula (n = 14; 548 feeding events) select for the urban edge, while caracals in the wildland-dominated region (n = 3; 162 feeding events) strongly avoid it. I argue that in the more urbanised region, caracals forage on or close to the urban edge because this is where the remaining low-lying wildland habitat is most productive and attractive. Consequently, caracals in heavily transformed areas, which might otherwise tend to avoid human disturbance, have habituated to human presence but reduce their risk of detection by remaining cryptic, prolonging handling time, and maintaining high feeding site fidelity where cover is available. To quantify the consequences of peri-urban foraging, I use an ecotoxicological approach to assess environmental contamination and its potential effects on caracals. It is widely reported that persistent organic pollutants (POPs), including organochlorines (OCs) such as PCBs and DDT and its metabolites, are extremely toxic, causing adverse effects on wildlife and human health. I tested blood and adipose tissues of caracals, with different diets utilising a range of natural and transformed landscapes, for exposure to commonly detected OCs. Despite restrictions on their use, I found extensive OC burdens, with 100% of adipose samples exposed to both DDT and PCBs, and 100% and 83% of blood samples exposed to DDT and PCBs respectively. Caracals using areas with a higher density of people and electrical transformers, and those using areas close to informal settlements, had higher exposure to OCs. Additionally, the use of vineyards and wetlands and a diet with a greater proportion of higher trophic level or exotic prey correlated with a higher risk of exposure to OC pollutants. Full blood analyses revealed that exposure levels to OCs were also associated with higher counts of infection-fighting cells, suggesting these compounds may affect the immune response of individuals. With time, these detrimental effects may have population-level repercussions through impacts on reproductive success and fitness. Together these findings reveal that while caracals and other medium-sized adaptable carnivores may persist within or adjacent to human transformed habitats, they still prefer natural habitat and pay a significant cost for foraging on prey species that have been contaminated by pollutants associated with urban and rural land uses. Urban edges may thus be an ecotoxicological trap, threatening the health and long-term persistence of caracals and other wildlife in this and other biodiversity hotspots. Reducing environmental contamination and limiting habitat loss to urban sprawl would benefit wildlife living on the transformed edges but requires significant improvements to both the legislation governing pollutants and the spatial planning of cities.
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    Phylogeny and phylogeography of the Chacma Baboon (Papio ursinus): the role of landscape in shaping contemporary genetic structure in the southern African baboon
    (2011) Sithaldeen, Riashna; Ackermann, Rebecca Rogers; Bishop, Jacqueline
    This thesis contributes to our understanding of the role of climate and landscape change in structuring diversity within chacma baboons (Papio ursinus). The data set comprises molecular sequences from two mitochondrial DNA markers: the Brown region and the hypervariable D-loop. DNA was extracted from faecal samples of 261 free living chacma baboons across southern Africa. Phylogenetic and phylogeographic techniques, including coalescent modeling, were used to examine past and present population dynamics of chacma baboon populations. Bayesian tree constructions provide a timeline of diversification for the sample. Although the ecological drivers of ongoing differentiation remain unclear, it was shown that population contractions and expansions have also played a significant role in driving regional genetic structure within the species.
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    Scale and impact of the illegal leopard skin trade for traditional use in southern Africa
    (2020) Naude, Vincent Norman; Bishop, Jacqueline; Balme, Guy A; O'riain, Mannus
    While leopards (Panthera pardus) currently occupy the most extensive geographic range of all large felids, they are also suffering the highest rate of current range loss amongst large terrestrial carnivores. This is primarily because most leopards still range outside of formally protected areas where they are exposed to the full suite of anthropogenic threats affecting carnivores including habitat loss, prey depletion, conflict with humans, and commercial harvest for body parts. The extensive use of leopard derivatives among traditional healers, royalty, and culturo-religious groups poses a known but poorly understood threat to leopards. Sociopolitical sensitivities surrounding cultural identity and the illegality of much of this use have impeded an objective assessment of both the drivers and impacts of this threat. Through a multi-disciplinary approach, this thesis describes the drivers of illegal leopard skin trade among a significant portion of traditional users in South Africa, quantifies the extent of this trade across the southern African region and assesses its impact on local leopard populations. Together these findings seek to address the lack of conservation- and policy-relevant data regarding the impact and scale of the trade for traditional use in South Africa. Followers of the recently established ‘Shembe' Church, with its estimated membership of over four million in South Africa, represent the foremost culturo-religious users of illegal leopard skins in the world. Following the introduction of a faux skin alternative, I used longitudinal surveys to explore the drivers of authentic skin desirability and possession amongst faux skin recipients. While demand for authentic skins decreased, and faux alternatives were generally considered satisfactory, 27% still expressed a desire for an authentic skin, and 15% had acquired one in the three years since receiving their faux skin. Both desiring and having obtained an authentic skin were best explained by improved economic status and the perceived weakness of law enforcement. The combined demand of all Shembe followers cannot be sustained by the estimated extant leopard population of South Africa, and it is predicted that traders must be sourcing leopards from surrounding range states to meet local demands. To investigate this, I created a genetic reference database of leopards across southern Africa (1,452 individuals) and using DNA-based assignment tests, inferred the geographic origins of illegally traded skins sourced within southern Africa. Smoothed continuous assignment techniques revealed leopard source ‘hotspots' in southwestern Zimbabwe, southern Mozambique and along the eastern borders of South Africa confirming suspicions that the illegal leopard skin trade for traditional use in South Africa is transnational. A similar distribution of leopard source populations was identified from leopard parts obtained in traditional wildlife markets and a large-scale confiscation from a single trader. Together, this suggests the regional trade in leopard parts has been syndicated with predictable harvesting and trade routes into the South African consumer market. Genotyping across all trade samples (237 individuals) revealed a clear bias towards males despite reported sex-ratios being female-biased for natural free-ranging populations. To understand the ecological cost of this sex-biased exploitation of leopards, I compared the spatial, genetic, and demographic data of two South African leopard populations with markedly different histories of anthropogenic mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation showed that extensive historical exploitation, linked to Shembe and other traditional trade, has reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry. The resultant kinclustering in males is comparable to that of females in the well-protected reserve and has promoted localised inbreeding. Together these results demonstrate novel evidence linking significant ecological consequences to an underestimated, transnational, and syndicated illegal leopard skin trade driven by demand for traditional and religious use in South Africa. These findings are translatable to all leopard populations threatened by exploitation and emphasise the importance of long-term monitoring of leopard populations within protected areas and improving management interventions to mitigate these effects. Interventions such as anti-poaching can be focussed on the ‘hotspots' identified in this study while protected area management should prioritise the maintenance of dispersal corridors to promote in situ recovery of exploited populations. Lastly, demand reduction strategies such as the continued provisioning of suitable alternatives, together with improved education and increased enforcement, are essential to addressing the growing culturo-religious demand for leopard products contributing to the illegal harvest and trade in this iconic large predator. Success will depend on finding the balance between an improved transnational policy which effectively conserves wild leopard populations and maintaining respect for cultural practices