Development and validation of a novel forensic STR multiplex assay for blue (Anthropoides paradiseus), wattled (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum).

The blue crane (Anthropoides paradiseus), wattled crane (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum) are species of concern as their populations are declining and they face several threats including habitat loss, disturbance and illegal trade. In South Africa, these species are bred in captivity for trade purposes which is permitted and regulated globally under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Legal sustainable trade through captive breeding of endangered wildlife species such as cranes has been promoted to counteract the illegal trade of individuals from the wild.

Hybridization in an isolated population of blesbok and red hartebeest.

Hybridization in antelope species has been widely reported in South African national parks and provincial reserves as well as on private land due to anthropogenic effects. In a closed management setting, hybridization may occur due to the crossbreeding of closely related species with unequal sex ratios, resulting in either sterile or fertile offspring. In this study, we used molecular techniques to evaluate the risk of anthropogenic hybridization between blesbok () and red hartebeest () in an isolated group that purposely included the two species with unequal sex ratios (one red hartebeest male and 19 male and female blesbok).

Identification of low levels of neutral and functional genetic diversity in South African bontebok ().

Bontebok () and blesbok () are classified as separate sub-species. The blesbok has a widespread distribution throughout South Africa and is listed as least concern by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Bontebok on the other hand is endemic within the Cape Floristic Region of the Western Cape in South Africa and has been listed as near-threatened species on the IUCN Red List of Threatened Species.

Methylation-based markers for the estimation of age in African cheetah, Acinonyx jubatus.

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 as their future fitness.

Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies.

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.

Dataset generated in a systematic review and meta-analysis of biological clocks as age estimation markers in animal ecology.

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 of 78 methylation studies and 108 telomere studies were included after rigorous screening.

Biological clocks as age estimation markers in animals: a systematic review and meta-analysis.

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 applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species.

PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses.

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, several published studies have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species.

Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics.

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 behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus).

We live in a world characterized 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 functions as apex predators; yet, they are quickly heading towards an uncertain future.

Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA.

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.

Monitoring compliance of CITES lion bone exports from South Africa.

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-sourced bones. South Africa is required under its obligations to CITES to employ mechanisms for monitoring and reporting trade, and to limit the potential for illegal trade and laundering of lion and other large felid bones.

Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus).

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 Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents.

Isolation and characterization of 30 STRs in Temminck's ground pangolin () and potential for cross amplification in other African species.

Temminck's ground pangolin () 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 bushmeat. In this study, we developed 30 species-specific short-tandem repeats (STRs) in Temminck's ground pangolin using next-generation sequencing.

Molecular genotyping and epidemiology of equine piroplasmids in South Africa.

Recently reported substantial genetic diversity within Theileria equi 18S rRNA gene sequences has led to the identification of five genotypes A, B, C, D, and E, complicating molecular and serological diagnosis. In addition, T. haneyi has lately been reported as a species closely related to the T.

Population genetic structure of the thick-tailed bushbaby () from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.

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. Currently, there is no population genetic data or study published on the species.

Molecular characterization in the toll-like receptor 9 gene of Cape Mountain Zebra (Equus zebra zebra) from three populations.

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 donkey breeds. Overall, we identified six single nucleotide polymorpHisms (SNPs).

Assessing introgressive hybridization in roan antelope (Hippotragus equinus): Lessons from South Africa.

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 Biological Diversity. The current study concerns roan antelope, the second largest antelope in Africa.

Lessons for conservation management: Monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra).

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.

Canine parvovirus detected from a serval (Leptailurus serval) in South Africa.

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 wild felids. This report documents the first known case of canine parvovirus-2b detected in unvaccinated serval (Leptailurus serval) from South Africa.

Occurrence and diversity of avian haemosporidia in Afrotropical landbirds.

Avian haemosporidian infections are widespread and can result in the decline of wild bird populations or in some cases contribute to extinction of species. We determined the prevalence and genetic diversity of avian haemosporidia in 93 samples from 22 landbird species from South Africa (N = 76) and West Africa (N = 17), of which six are intra-African migrants and one is a Palearctic migrant. The samples were analysed for the presence of avian haemosporidian DNA using real-time quantitative PCR (qPCR) and nested PCR assays targeting specific mitochondrial genes of these parasites.