Antoinette Kotze

University of the Free State | ufs · Department of Genetics

The Diederik cuckoo, Chrysococcyx caprius, is a small Afrotropical bird in the family Cuculidae. It is taxonomically related to 13 other species within the genus Chrysococcyx and is migratory in sub‐Saharan Africa. It has a unique breeding behaviour of being a brood parasite: Breeding pairs lay their eggs in the nests of a host species and hatchlin...

The Southern Ground-hornbill (SGH) (Bucorvus leadbeateri) is considered an umbrella species for biodiversity conservation in savannah biomes since they require large territories and significant protection measures that help to conserve a wide range of biodiversity with similar savanna and grassland requirements. Declines of the species are attribut...

Age is a key demographic in conservation where age classes show differences in important population metrics such as morbidity and mortality. Several traits, including reproductive potential, also show senescence with ageing. Thus, the ability to estimate age of individuals in a population is critical in understanding the current structure as well a...

The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS...

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across insti...

Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evid...

Age is key factor in animal ecology as it can be used to assign animals to important age classes, ranging from immature young to reproductive adults and eventual old age and fragility. Different groups contribute to different aspects that need to be considered when modeling current and future population dynamics as part of continued conservation ef...

The dataset comprises a comprehensive systematic review and meta-analysis exploring the utility of biological clocks as age estimation markers in the context of animal ecology. The systematic review adhered to PRISMA guidelines and employed optimized Boolean search strings to retrieve relevant studies from Scopus and Dimensions databases. A total o...

Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been a...

South Africa has a large captive lion (Panthera leo) sector, but detailed knowledge on the origin of individuals and any potential genetic value to conservation targets is lacking. In 2021, the South African government committed to closing the sector and have since appointed a Ministerial Lion Task Team (2022) to initiate this process. Some have su...

Pickersgill’s Reed Frog ( Hyperolius pickersgilli ) is an Endangered (IUCN, 2016) species, endemic to South Africa and restricted to the KwaZulu-Natal coastal region. The species occurs in fragmented patches of Indian Ocean Coastalbelt Wetland, a Critically Endangered habitat type threatened by urbanisation, agriculture, mining, and forestry. We us...

The Magellan mussel Aulacomya atra is a bivalve mollusc found along parts of the South African and Namibian coastline. Its numbers were low historically compared with other indigenous species but have decreased further since the 1970s owing to habitat invasion by Mediterranean mussels Mytilus galloprovincialis. We studied sequences of the mitochond...

Evolutionary processes happen gradually over time and are, thus, considered time dependent. In addition, several evolutionary processes are either adaptations to local habitats or changing habitats, otherwise restricted thereby. Since evolutionary processes driving speciation take place within the landscape of environmental and temporal bounds, sev...

Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual be...

Evolutionary processes such as speciation happens gradually over time making such processes time-dependant. Many studies conducted over the past two decades have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species in most lineages of the tree of life, including fish, amphibians, repti...

In South Africa, cheetahs (Acinonyx jubatus) occur as a relictual, unmanaged population of ‘free‐roamers’, a managed metapopulation across fenced reserves, and in various captive facilities. To ensure that the Cheetah Metapopulation Project (CMP) is not at risk of losing overall genetic variation to drift or inbreeding, we propose various intervent...

Chronological age is a key factor in animal ecology, as many biological traits appear and change over time. Such traits include development, age of reproductive maturity, reproductive success, future reproductive potential, and mortality. Several molecular methods have emerged as potential vehicle for biological age determination. The aim of this e...

We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock‐on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem...

Throughout history, identifying life on earth included organisms such as plants. Species are going extinct at an alarming rate, faster than they can be described. This adds to the responsibility of scientists to protect species and the environments they live in. If policymakers do not know what to protect, how are they going to know where to protec...

The Nubian ibex ( Capra nubiana ) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species wi...

The E.Z.N.A. Blood DNA Mini Kit provides an easy and rapid method for the isolation of genomic DNA for consistent PCR and Southern analysis. Up to 250 μL fresh, frozen, or anticoagulated whole blood can be readily processed at one time. The E.Z.N.A. Blood DNA Mini Kit can also be used for the preparation of genomic DNA from buffy coat, serum, plasm...

This protocol follows up on "PCR Amplification of Clock genes withEmeraldAmp® GT PCR Master Mix in Avian species" and is intended to provide the next steps used in the sanger sequencing of the produced amplicons. This protocol uses ABI BigDye reagents (but suitable alternatives exist). The same primers used to produce the PCR products, of the respe...

This PCR protocol is used to amplify Clock and Adcyap1 gene regions in avian species which have previously shown polymorphisms, such as poly-Q runs, that correlated to migration phenology. It was tested and optimized in Woodlands kingfisher (Halcyon senegalensis) and Diederik cuckoos (Chrysococcyx caprius). The primers were designed based on those...

Pangolins are the most trafficked mammal in the world, and all eight species are listed under CITES Appendix I. DNA-based wildlife forensic techniques are recognized as an important component of investigating a pangolin seizure. In particular, determining the species of pangolin in a seizure will 1) confirm the presence of pangolin to establish the...

The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of popu...

From 2008 to 2018, South Africa permitted the export of captive-bred African lion (Panthera leo) skeletons to Southeast Asia under CITES Appendix II. Legal exports rose from approximately 50 individuals in 2008 to a maximum of 1,771 skeletons in 2016, and has led to ongoing concerns over possible laundering of non-lion, multiple-source and wild-sou...

Several standard descriptions of the avian male and female reproductive tract have been reported, including effects of age, stage of reproductive maturity and gonadal hormone concentrations. Limited information on penguin reproductive biology and a lack of information on the African penguin (Spheniscus demersus) necessitated a detailed description...

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered...

The Cape mountain zebra (Equus zebra zebra) has recovered from near extinction over more than eight decades. While their numbers have increased, populations remain isolated with low genetic diversity. With more than 75 new populations being founded and more than 4800 extant animals, conservation management strategies are being implemented to mitiga...

Tigers are killed to supply a demand for many wildlife products despite a ban on commercial international trade. As populations decrease, products from substitute species (i.e. lions and leopards) have been fraudulently sold as tiger. DNA forensic techniques are needed to definitively identify tiger in order to secure prosecutions although this is...

The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging env...

Computer-assisted semen analysis (CASA) is an automated and objective method of evaluating structural (e.g. morphology) and functional sperm parameters (e.g. motility and hyperactivation). Sperm hyperactivation is essential for successful fertilization and is thus an important aspect in determining the fertility potential of a male. In the current...

The taxonomy and number of Cercopithecus monkey radiation events in southern Africa are still debated. To date, genetic studies have largely been limited to single specimens per taxon and a scattered geographical distribution. A recent study focusing on South African Cercopithecus monkeys showed that populations can be divided into three distinct g...

Reintroduction to, or reinforcement of, threatened wild populations are commonly used conservation strategies. Reintroductions of the Southern Ground-hornbill Bucorvus leadbeateri have been tested as a potential conservation tool for this vulnerable species since 1995. Forty-two individuals have been reintroduced under varying management strategies...

Temminck’s ground pangolin (Smutsia temminckii) is one of four species of pangolin, endemic to Africa. Two of the African pangolin species are listed as vulnerable and two are listed as endangered on the International Union for Conservation of Nature Red List of Threatened Species due to their ongoing exploitation for traditional medicine and bushm...

Cheetahs (Acinonyx jubatus) are majestic carnivores and the fastest land animals; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-interactions and illegal trafficking, there are only approximately 7,100 individuals remaining in the wild. Cheetahs used to roam large parts of Africa, and Western and Southe...

Fragmented wildlife populations are challenged by limited gene flow that can lead to significant inbreeding. The lion (Panthera leo) population in South Africa’s Hluhluwe-iMfolozi Park (HiP) started from a small founder population of one adult male (1958), one adult female, followed by two lionesses and three cubs (two females and one male; 1965; u...

Poaching of South African wildlife is considered a threat to biodiversity. In the absence of diagnostic morphometric traits, DNA barcoding is considered as a method of choice for species identification. Here, we report on forensic case work involving the illegal hunting of antelope species. Three forensic cases which included confiscated material w...

This study aimed to address the lack of information on quantitative semen and sperm characteristics of free-ranging African elephants. Nineteen ejaculates were collected from 12 elephant bulls by means of electroejaculation in spring (Season 1, end of dry season, n = 7) and in autumn (Season 2, end of rainy season, n = 12). While most elephant cows...

The aim of this study was to characterise and compare phenotypic characteristics of South African unimproved indigenous and Tankwa goats. Phenotypic characteristics of 44 South African unimproved indigenous and 41 Tankwa goats were assessed. The qualitative characteristics were assessed through visual appraisal. Quantitative characteristics such as...

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. C...

Toll-like receptors (TLR) are a family of proteins that signal activation of the innate immune response through the recognition of a variety of pathogen molecular compounds. Here, we characterized the complete TLR9 gene in Cape mountain zebra (Equus zebra zebra) from three populations in South Africa and compared sequences to a variety of horse and...

Biological diversity is being lost at unprecedented rates, with genetic admixture and introgression presenting major threats to biodiversity. Our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Bi...

The Cape mountain zebra (Equus zebra zebra) is a subspecies of mountain zebra endemic to South Africa. The Cape mountain zebra experienced near extinction in the early 1900’s and their numbers have since recovered to more than 4,800 individuals. However, there are still threats to their long-term persistence. A previous study reported that Cape mou...

Wildlife ranching including the hunting, collection, sales and husbandry of wild animals in captivity, is practised worldwide and is advocated as an approach towards the conservation of wild species. While many authors have explored the biological impacts of intensive wild population management, primarily with respect to disease transmission (espec...

Birdstrikes to aircrafts are increasing on an annual basis and pose significant aviation safety risks. Identification of the birds involved is key to developing mitigation strategies. Often the only information available to make identifications are feather and/or tissue samples. Relying on feathers alone to identify the bird species requires specia...

Otters are flagship species for pristine habitats and their southernmost distribution in Africa includes two species; Aonyx capensis and Hydrictis maculicollis. Here, we present novel full mitochondrial genomes of these otter species. The comparable mitogenomes consist of 36 genes including 13 protein-coding genes, 2 ribosomal RNAs, and 22 tRNAs in...

Translocation of animals in fragmented habitats is an important means of dispersal and gene flow, however, the movement of animals has led to the spread of various diseases globally and wildlife are often the reservoirs of these diseases. Currently, Cape mountain zebra are translocated within South Africa as a management method for augmentation of...

Canine parvovirus first emerged in domestic dogs (Canis familiaris), most likely as a variant of the feline panleucopaenia virus. Relatively recently, canine parvovirus-2a and canine parvovirus-2b infections have been identified in both symptomatic and asymptomatic domestic cats, while canine parvovirus infections have also been demonstrated in wil...

The Endangered Pickersgill’s Reed Frog (Hyperolius pickersgilli) is endemic to South Africa and restricted to the KwaZulu-Natal (KZN) coast. The natural habitat of H. pickersgilli is limited to fragmented patches of coastal reed-bed wetland, the majority of which continues to undergo transformation and degradation caused by urbanisation, agricultur...

Biological diversity is being lost at unprecedented rates, with admixture and introgression presenting major threats to species' conservation. To this end, our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Co...

Promoting forensic science in wildlife law enforcement is critical to combatting the illegal trade in pangolins. An understanding of poaching, illegal trade routes, verification of species, identification of protected species in traditional medicines and illegal smuggling of pangolins necessitated the development of capacity to conduct forensic ana...

The aim of the study was to characterize and compare seminal plasma constituents of unimproved indigenous and Tankwa goats. In this study, unimproved indigenous (11) and Tankwa (11) goats were used. Their average age was 3 ± 0.8 years and average bodyweights were 35.5 ± 2.1 kg and 59.8 ± 1.9 kg, respectively. Semen samples were collected with an el...

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR)...

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR)...

The blue wildebeest (Connochaetes taurinus) is distributed throughout southern and east Africa while the black wildebeest (Connochaetes gnou) is endemic to South Africa and was driven to near extinction in the early 1900s due to hunting pressure and disease outbreaks. Extensive translocation of both species throughout South Africa is threatening th...

Introgressive hybridization poses a threat to the genetic integrity of black wildebeest (Connochaetes gnou) and blue wildebeest (Connochaetes taurinus) populations in South Africa. Black wildebeest is endemic to South Africa and was driven to near extinction in the early 1900s due to habitat destruction, hunting pressure and disease outbreaks. Blue...

Pangolins are elusive and threatened mammals, considered the most widely traded mammals on Earth supplying local African and Asian traditional medicine markets. African pangolins are sourced as bushmeat and perceived to cure diverse ailments when body parts are used in traditional medicine practices. Currently, there is no documentation on cultural...

A rapid allelic discrimination real-time polymerase chain reaction (qPCR) assay has been developed for the confirmation of lion (Panthera leo) or tiger (P. tigris) DNA. The method includes a low cost allele specific PCR assay designed for each SNP variant where the genotype is determined by incorporation and subsequent fluorescence of FAM or HEX fo...

Canine distemper virus (CDV) causes a severe contagious disease in a broad range of hosts. This is the first study to genetically characterise CDV strains from four different wildlife species in South Africa. The phylogenetic diversity of CDV is examined, using the haemagglutinin gene. The South African wildlife CDV isolates showed a high degree of...