A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa.
The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
- Book Chapter
- 10.1079/9781789245868.0016
- Dec 17, 2020
The research presented in this chapter determines the value that tourists on safari in protected areas in South Africa attach to elephant sightings and the relative importance of the elephant sighting compared with the other species in the Big Five. The study also determines whether tourists take the increased poaching of elephants - also in South Africa - into account when revealing their choice. Using information from five surveys conducted at different parks in South Africa from 2011 to 2013 and again in 2019, the elephant was found to be the fourth preferred species in the Big Five. The exception is Addo Elephant National Park, where the elephants are the second most preferred species. To determine the value that tourists attached to a sighting, contingent valuation was used. Although approximately a quarter to a third of respondents indicated positive amounts for a sighting across the years, the mean willingness to pay (WTP) reflects the scarcity of the species. The elephant is relatively abundant in all the parks and, in many instances, much easier to spot than the leopard or lion. It is therefore not surprising that the mean valuation of a sighting is much lower than that of the leopard and lion throughout all the years. Although tougher economic conditions in the country also influence WTP, it was found that tourists to South Africa's National Parks do not yet take the increased poaching of elephants into account when revealing their choice, nor in their valuation.
- Book Chapter
- 10.1079/9781789245868.0191
- Dec 2, 2020
<title>Abstract</title> The research presented in this chapter determines the value that tourists on safari in protected areas in South Africa attach to elephant sightings and the relative importance of the elephant sighting compared with the other species in the Big Five. The study also determines whether tourists take the increased poaching of elephants - also in South Africa - into account when revealing their choice. Using information from five surveys conducted at different parks in South Africa from 2011 to 2013 and again in 2019, the elephant was found to be the fourth preferred species in the Big Five. The exception is Addo Elephant National Park, where the elephants are the second most preferred species. To determine the value that tourists attached to a sighting, contingent valuation was used. Although approximately a quarter to a third of respondents indicated positive amounts for a sighting across the years, the mean willingness to pay (WTP) reflects the scarcity of the species. The elephant is relatively abundant in all the parks and, in many instances, much easier to spot than the leopard or lion. It is therefore not surprising that the mean valuation of a sighting is much lower than that of the leopard and lion throughout all the years. Although tougher economic conditions in the country also influence WTP, it was found that tourists to South Africa's National Parks do not yet take the increased poaching of elephants into account when revealing their choice, nor in their valuation.
- Research Article
- 10.1371/journal.pntd.0013754
- Dec 11, 2025
- PLOS Neglected Tropical Diseases
Brucellosis is a globally significant zoonotic disease, yet its ecology in wildlife remains poorly understood. In this study, we investigated the circulation of Brucella spp. in a wide range of wild mammals from multiple protected areas in South Africa. Organ and serum samples from 722 animals representing 23 species were analyzed employing a conservative diagnostic strategy, combining serology (rose bengal test confirmed by indirect ELISA) and four PCR-based assays in series, to maximize specificity and interpretative solidity. Molecular detection revealed Brucella spp. DNA in several atypical host species, including plains zebra, hippopotamus, African elephant, giraffe, warthog, cheetah, and African wild dog, expanding the known host range. In Greater Kruger National Park, African buffalo exhibited high seroprevalence (24/106; 23%, CI: 15–32%) and even higher molecular prevalence (29/57; 51%, CI: 37–64%), supporting their role as a primary wildlife reservoir for B. abortus in the region. One B. abortus isolate cultured from the spleen of a zebra and characterized by multiloci variable number of tandem repeat analysis (MLVA) showed genetic relatedness to South African buffalo and South American cattle strains. Co-infections with B. abortus and B. melitensis were identified in 17 animals across seven species. Notably, B. melitensis was detected in species (elephant, hippopotamus, zebra) not typically associated with small ruminants, suggesting complex interspecies transmission dynamics. Our findings underscore the limitations of serological testing and highligts the value of molecular diagnostics in understanding the epidemiology of Brucella spp. in South Africa. The detection of B. abortus and/or B. melitensis DNA in a range of wildlife species, including carnivores and megaherbivores, emphasises the need for integrated One Health surveillance approaches to enhance understanding of the disease’s life cycle and transmission dynamics.
- Research Article
18
- 10.1016/j.actao.2012.02.007
- Mar 15, 2012
- Acta Oecologica
Changes of population trends and mortality patterns in response to the reintroduction of large predators: The case study of African ungulates
- Research Article
36
- 10.3957/0379-4369-37.2.189
- Oct 1, 2007
- South African Journal of Wildlife Research
The views of visitors to national parks provide an important source of information to guide park planners and managers. A visitor questionnaire study was conducted in 2004 and 2005 in the Addo Elephant National Park, South Africa. A profile of the respondents, as well as records of their views on a number of park-related conservation and management issues, and of their observations of large and charismatic species (the ‘Big Five’) was compiled. The study clearly showed that national parks are important destinations for an African wildlife experience, along with other natural attractions that they have to offer. It also highlighted the scope for further visitor education, specifically aimed at improving the quality of their visits to the park. The relationship between elephant (Loxodonta africana) density and level of viewing success by visitors requires further investigation. Since the reintroduction of large predators, especially lion (Panthera leo), in the early 2000s, the daytime sighting rate of buffalo (Syncerus caffer) by visitors has increased markedly. Ongoing surveys, to monitor and expand on some of the aspects addressed in this study, are considered necessary in order to assist park staff to achieve conservation and management goals.
- Research Article
28
- 10.1038/s41598-021-83823-8
- Feb 25, 2021
- Scientific Reports
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
- Research Article
16
- 10.1007/s13364-011-0033-1
- Oct 1, 2011
- Acta Theriologica
We tested the widely accepted hypothesis that spotted hyaenas (Crocuta crocuta) are non-selective in their diet. The prey preference of spotted hyaena was studied in the Addo Elephant National Park (AENP), South Africa. Diet (frequency of occurrence of prey items in the diet) was quantified through the analysis of 55 scats, and compared with available prey. A combination of large- and medium-sized mammals (buffalo (Syncerus caffer), red hartebeest (Alcelaphus buselaphus) and common duiker (Sylvicapra grimmia) were the most preferred prey items. The most abundant species, warthog (Phacochoerus africanus) and kudu (Tragelaphus strepsiceros), were ignored and avoided, respectively. These results show that the assumption that hyaena prey on the most abundant available prey species may be overly simplistic. Predation patterns, such as the ones observed in AENP, may have important ramifications for less common species that are selected by hyaena in small enclosed reserves.
- Research Article
129
- 10.1016/s0006-3207(01)00056-8
- Sep 21, 2001
- Biological Conservation
Protecting plants from elephants: botanical reserve scenarios within the Addo Elephant National Park, South Africa
- Research Article
73
- 10.1016/j.landusepol.2013.05.016
- Jun 20, 2013
- Land Use Policy
Land claims and the pursuit of co-management on four protected areas in South Africa
- Research Article
6
- 10.1016/j.jag.2024.104064
- Jul 30, 2024
- International Journal of Applied Earth Observation and Geoinformation
Assessment of the effectiveness of coarse resolution fire products in monitoring long-term changes in fire regime within protected areas in South Africa
- Research Article
77
- 10.1007/s00267-007-9034-x
- Nov 13, 2007
- Environmental Management
Comanagement has recently become the most popular approach for reconciling land claims and biodiversity conservation in South Africa and beyond. Following the resolution of land claims on protected areas in South Africa, comanagement arrangements have been created between the relevant conservation authorities and the land claimant communities who are legally awarded tenure rights to the land. However, it is doubtful that these partnerships constitute success for the former land claimants. Using the case of a "resolved" land claim in Mkambati Nature Reserve, Eastern Cape Province, as well as insights from comanagement literature, this paper identifies and discusses three key possible reasons for the unimpressive performance of comanagement in reconciling land restitution and conservation. The first one is the origins of the comanagement idea in the conservation of high value natural resources (e.g., fisheries, forestry), rather than in or including concerns for resource rights. The second reason is the neglect of key conditions for successful comanagement, as discussed in the comanagement literature. The final reason is the ambiguity in settlement agreements, including the use of terminology and concepts that reinforce unequal power relationships, with the state emerging as the powerful partner. This paper concludes that, unless there is a serious reassessment of the comanagement idea as a way of reconciling land reform and conservation, and a possible review of settlement agreements that have relied on comanagement, both the integrity of the "successful land claimant's rights" and that of conservation remain under threat.
- Research Article
88
- 10.2989/025776197784160884
- Jun 1, 1997
- South African Journal of Marine Science
In the face of ever-increasing requests for the proclamation of Marine Protected Areas (MPAs) in South Africa, there is a need to develop an objective protocol for their evaluation. To achieve this, a methodology is described for which the acronym (Criteria and Objectives for Marine Protected ARea Evaluation) is coined. COMPARE also allows existing MPAs to be evaluated in terms of their efficacy, and can assess the effects of changes to either legislation or management of existing MPAs. As a first step, 14 objectives are defined that may be met by MPAs. These fall into three categories: biodiversity protection, fisheries management and human utilization. A series of criteria were then proposed which can be used selectively to quantify the degree to which MPAs meet these objectives. Each of the objectives is scored against the appropriate criteria in a semi-quantitative manner that allows areas to be compared, either overall or in terms of specific objectives. Simply by comparing the degree to wh...
- Research Article
10
- 10.1371/journal.pone.0236717
- Aug 14, 2020
- PLOS ONE
Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.
- Research Article
4
- 10.1371/journal.pone.0236717.r006
- Aug 14, 2020
- PLoS ONE
Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.
- Research Article
9
- 10.1080/15627020.2001.11657109
- Apr 1, 2001
- African Zoology
Population extinction evaluations, based on the model developed by Dennis et al. (1991) that did not take density dependence into account and that were based on census data, suggest that many of the herbivore species in Addo Elephant National Park (AENP) are vulnerable to local extinction. As a result of low abundance, grysbok and bushpig populations are likely to become extinct within the next ten years. Species such as the common duiker, eland, buffalo, ostrich and bushbuck are likely to go extinct within the next 60 years, whereas populations such as the black rhino, kudu and red hartebeest appear less vulnerable and display an insignificant probability of local extinction. This conclusion was supported by the absence of discernible density-dependence effects in all but one of the species included in the analyses. In addition, population variance parameters (F2 of herbivore species from AENP, were larger than those recorded from the Kruger National Park and various elephant populations from South Africa. These data suggest that strict adherence to the management objectives, by managing for increasing mega-herbivore populations (elephant, black rhino) in AENP may have been responsible for increasing the risk of local extinction of other herbivore populations. Consequently, should the objectives of AENP be amended to incorporate broader biodiversity objectives, the recent extension of AENP, which increased habitat heterogeneity in the Park, may prove timely.