A5017877088- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Forensic Anthropology and Bioarchaeology Studies
- Forensic and Genetic Research
- Paleopathology and ancient diseases
- Wildlife Ecology and Conservation
- Archaeology and ancient environmental studies
- Historical and Cultural Archaeology Studies
- Pleistocene-Era Hominins and Archaeology
- Insect and Arachnid Ecology and Behavior
- Primate Behavior and Ecology
- Chemical Synthesis and Analysis
- Radioactive contamination and transfer
- Particle physics theoretical and experimental studies
- Livestock Farming and Management
- Atmospheric and Environmental Gas Dynamics
- Identification and Quantification in Food
- Carbon Dioxide Capture Technologies
- Historical and Archaeological Studies
- Species Distribution and Climate Change
- Marine and environmental studies
- Chromosomal and Genetic Variations
University of Pretoria
2017-2025
University of Copenhagen
2023-2025
Ecofys (Netherlands)
2000
ABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data gain deeper insights into the phylogeography, evolutionary history biology non‐model species. While Cape buffalo ( Syncerus caffer ) been well‐studied across its range with traditional genetic markers over last 25 years, are building on this knowledge by generating whole genome, population‐level sets improve understanding composition Using publicly available...
The iconic Cape buffalo has experienced several documented population declines in recent history. These have been largely attributed to the late 19th century rinderpest pandemic. However, effect of pandemic on their genetic diversity remains contentious, and other factors that potentially affected this include environmental changes during Pleistocene, range expansions human activity. Motivated by this, we present analyses whole genome sequencing data from 59 individuals across assess...
Enzymatic removal of uracil bases from ancient DNA fragments. "Antarctic Thermolabile Uracil glycosylase (UDG) catalyzes the excision a base, forming an abasic (apyrimidinic) site while leaving phosphodiester backbone intact. The lyase activity Endonuclease III breaks at 3´and 5´ sides site. In addition to generating different 3´-terminus than USER Enzyme (a 3´-phospho-α, β-unsaturated aldehyde versus 3´phosphate left by Enzyme,NEB #M5505), II (NEB #M5508) can also be completely heat...
Ancient DNA Extraction Protocol (spin column-based) This protocol outlines the procedure for extracting ancient from bone or tooth powder using Monarch spin columns. The final extract volume will be 35 µL. Based on: column is based on Dabney et al. 2013 (DOI:10.1073/pnas.1314445110) modified binding buffer Allentoft 2015 extraction (DOI: 10.1038/nature14507) initially written up by Michael V. Westbury 20-08-2018. Annotations added Andrea A. Cabrera and Alba Rey-Iglesia 08-11-2019....
This protocol describes the preparation and hybridization of P5 P7 adapter-splint complexes for Santa Cruz Reaction library construction. Following this produces 12µM hybridized SCR build. is based on: Kapp, J. D., Green, R. E., & Shapiro, B. (2021). A Fast Efficient Single-stranded Genomic Library Preparation Method Optimized Ancient DNA. Journal Heredity, 112(3), 241-249. https://doi.org/10.1093/jhered/esab012 Always cite original paper (Kapp et al. 2021) when using protocol, in...
Abstract Genomes retain records of demographic changes and evolutionary forces that shape species populations. Remnant populations African buffalo ( Syncerus caffer ) in South Africa, with varied histories, provide an opportunity to investigate signatures left their genomes by past events, both recent ancient. Here, we produce 40 low coverage (7.14×) genome sequences Cape S. c. from four protected areas Africa. Genome-wide heterozygosity was the highest for any mammal which these data are...
Low genomic diversity is generally indicative of small population size and considered detrimental by decreasing long-term adaptability.
Abstract The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information available the set large. High levels relatedness or inbreeding can influence genotype frequencies thus genetic evaluation, as well accurate inference hidden structure. Identification also important in breeding programmes, to inform decisions about pairs translocations. We present Friends Family, a Windows executable program with graphical...
Wildlife ranching, although not considered a conventional conservation system, provides sustainable model for wildlife utilization and could be source of valuable genetic material. However, increased fragmentation intensive management may threaten the evolutionary potential value species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist populations with variety histories practices. We compared diversity national parks to private ranches found that, except Addo...
Abstract Many recent contributions have made a compelling case that genetic diversity is not adequately reflected in international frameworks and policies, as well local governmental processes implementing such frameworks. Using digital sequence information (DSI) other publicly available data supported to assess diversity, toward formulation of practical actions for long‐term conservation biodiversity, with the particular goal maintaining ecological evolutionary processes. Given inclusion...
Abstract Globally, levels of human–wildlife conflict are increasing as a direct consequence the expansion people into natural areas resulting in competition with wildlife for food and other resources. By being forced increasingly smaller pockets suitable habitat, many animal species at risk becoming susceptible to loss genetic diversity, inbreeding depression associated inability adapt environmental changes. Predators often lethally controlled due their threat livestock. such jackals (black...
Abstract Circular structures made from woolly mammoth bones are found across Ukraine and west Russia, yet the origin of remains uncertain. We present ten new radiocarbon dates largest circular structure at Kostenki 11-Ia, identifying two mandibles ∼200-1,200 years older than other dated materials site, suggesting skeletal material long-dead individuals was scavenged used in site construction. Biomolecular sexing 30 showed a predominance females, mammoths primarily herds. identify six...
Abstract The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data gain deeper insights into the phylogeography, evolutionary history, biology non-model species. While Cape buffalo ( Syncerus caffer ) been well-studied across its range with traditional genetic markers over last 25 years, are building on this knowledge by generating whole genome, population-level sets improve understanding composition history Using publicly...
In this study, we report the novel, complete mitochondrial genomes of two dwarf African antelope species: Raphicerus melanotis (Cape grysbok) and R. sharpei (Sharpe's grysbok). The circular mitogenomes were 16,384 16,392 base pairs in length, respectively, each contained expected 37 genes typically found mammalian mitogenomes. maximum-likelihood phylogenetic analysis placed as sister lineage to campestris, known steenbok, which is only other member genus, with 83% bootstrap support,...