Mitochondrial DNA variation and geographic population structure in the yellow mongoose (Cynictic penicillata)

Geographic population structure was determined for Cynictis penicillata, a carnivore species endemic to southern Africa. Restriction fragment length polymorphisms (RFLPs) were analyzed for 50 specimens from 21 localities. The 18 restriction endonucleases used in this analysis revealed 13 haplotypes. Low sequence divergence values separate most of these maternal lineages. With the exception of two haplotypes (E and F) which are distributed over a broad geographic range, most lineages are geographically localized. It is postulated that this is the result of a recent population bottleneck followed by a rapid range expansion. Polymerase Chain Reaction (PCR) amplification of a 600 bp fragment from the 5' end of the Cynictis mitochondrial DNA control region revealed the presence of a length polymorphism. Direct nucleotide sequencing of five yellow mongoose specimens revealed the length polymorphism to be due to a direct repeat of 81 bp in the larger fragment.Dissertation (MSc (Zoology))--University of Pretoria, 1995.Zoology and EntomologyMSc (Zoology)Unrestricte

Molecular evidence for hybridization in the aquatic plant Limosella on sub-Antarctic Marion Island

DNA sequence data have become a crucial tool in assessing the relationship between morphological variation and genetic and taxonomic groups, including in the Antarctic biota. Morphologically distinct populations of submersed aquatic vascular plants were observed on sub-Antarctic Marion Island, potentially representing the two species of such plants listed in the island's flora, Limosella australis R.Br. (Scrophulariaceae) and Ranunculus moseleyi Hook.f. (Ranunculaceae). To confirm their taxonomic identity, we sequenced a nuclear locus (internal transcribed spacer; ITS) and two plastid loci (trnL-trnF, rps16) from three specimens collected on Marion Island and compared the sequences with those in public sequence databases. For all three loci, sequences from the Marion Island specimens were nearly identical despite morphological dissimilarity, and phylogenetic analyses resolved them to a position in Limosella. In phylogenetic trees and comparisons of species-specific sequence polymorphisms, the Marion Island specimens were closest to a clade comprising Limosella aquatica L., L. curdieana F.Muell. and L. major Diels for ITS and closest to L. australis for the plastid loci. Cytonuclear discordance suggests a history of hybridization or introgression, which may have consequences for morphological variability and ecological adaptation.The National Research Foundationhttp://journals.cambridge.org/action/displayJournal?jid=ANSam2022Plant Production and Soil Scienc

COVID-19 and the academe in South Africa: Not business as usual

The famous R.E.M. song laments ‘It’s the end of the world as we know it, I had some time alone, I feel fine…’. Many South Africans would agree that COVID-19 signals the end of the world (or business) as we know it, and through the lockdown we have certainly had some time alone. But contrary to the lyrics, all may not be fine, especially for South Africa’s scientific community. The novel coronavirus SARS-CoV-2 has impacted every economic and social sector1 across the globe, including higher education in South Africa. Every student and staff member at a higher education institution will have been affected in some way and to varying degrees; not one person will emerge from this unscathed. It is impossible to predict every short- and long-term impact of the COVID-19 pandemic, but we will experience the aftershocks for a long time to come. Here we discuss some of these impacts, ranging from undergraduate level to large research projects, and we offer suggestions on how to mitigate some of the damage.Geograph

Local and regional scale genetic variation in the Cape dune mole-rat, Bathyergus suillus

The distribution of genetic variation is determined through the interaction of life history, morphology and habitat specificity of a species in conjunction with landscape structure. While numerous studies have investigated this interplay of factors in species inhabiting aquatic, riverine, terrestrial, arboreal and saxicolous systems, the fossorial system has remained largely unexplored. In this study we attempt to elucidate the impacts of a subterranean lifestyle coupled with a heterogeneous landscape on genetic partitioning by using a subterranean mammal species, the Cape dune mole-rat (Bathyergus suillus), as our model. Bathyergus suillus is one of a few mammal species endemic to the Cape Floristic Region (CFR) of the Western Cape of South Africa. Its distribution is fragmented by rivers and mountains; both geographic phenomena that may act as geographical barriers to gene-flow. Using two mitochondrial fragments (cytochrome b and control region) as well as nine microsatellite loci, we determined the phylogeographic structure and gene-flow patterns at two different spatial scales (local and regional). Furthermore, we investigated genetic differentiation between populations and applied Bayesian clustering and assignment approaches to our data. Nearly every population formed a genetically unique entity with significant genetic structure evident across geographic barriers such as rivers (Berg, Verlorenvlei, Breede and Gourits Rivers), mountains (Piketberg and Hottentots Holland Mountains) and with geographic distance at both spatial scales. Surprisingly, B. suillus was found to be paraphyletic with respect to its sister species, B. janetta–a result largely overlooked by previous studies on these taxa. A systematic revision of the genus Bathyergus is therefore necessary. This study provides a valuable insight into how the biology, life-history and habitat specificity of animals inhabiting a fossorial system may act in concert with the structure of the surrounding landscape to influence genetic distinctiveness and ultimately speciation.A Centre for Invasion Biology stipend to BJVV.http://www.plosone.orgam201

The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana

Spinicaudatan clam shrimp are a widespread and diverse group of branchiopod crustaceans, yet few mitochondrial genomes have been published for this taxonomic group. Here, we present the mitogenome of Leptestheria brevirostris from a rock pool ecosystem in Botswana. Massively parallel sequencing of a single specimen facilitated the reconstruction of the species’ 15,579 bp circularized mitogenome. The reconstructed phylogenetic tree confirms that L. brevirostris forms a monophyletic group with other diplostracan branchiopods, and that these are the sister taxon to Notostraca. The mitogenome reconstructed here is the first to be reported from a leptestherid clam shrimp

Characterization of 14 polymorphic microsatellite loci developed for an Afrotherian species endemic to southern Africa, Elephantulus myurus (Macroscelidea : Macroscelididae)

Fourteen microsatellite loci were developed for the eastern rock sengi, Elephantulus myurus Thomas & Schwann, 1906 by incorporating genetic diversity from across its range in South Africa. Sengis are small mammals belonging to the order Macroscelidea, which comprises 19 species, all of which are endemic to Africa. The loci were amplified in 66 individuals from six localities. An average of 10.5 alleles per locus were identified, with observed and expected heterozygosity values ranging from 0.081 – 0.909 and 0.484 – 0.885, respectively. We also investigated cross-species amplification within the family and found variation in amplification success for five different species. The preliminary results from these amplification efforts could aid further studies into aspects of species diversity and biology. The markers described here represent the first set of variable nuclear markers for the genus Elephantulus, and, together with a set of 8 recently developed markers for Rhynchocyon petersi, Bocage 1880, the first markers for the Order Macroscelidea.National Research Foundation of South Africa (BvV), the University of Johannesburg and the DST-NRF SARChi Chair of Behavioural Ecology and Physiology (NCB). Electrophoresis of microsatellite markers was done at the Analytical Facility based at Stellenbosch University.http://link.springer.com/journal/133552018-02-27hb2016Zoology and Entomolog

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is dis- tributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among spe- cies of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil cali- bration points to estimate a molecular timescale for carnivorans. According to our diver- gence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloi- dea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feli- formia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial diver- gences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene

Exploring South Africa’s southern frontier: A 20-year vision for polar research through the South African National Antarctic Programme

Antarctica, the sub-Antarctic islands and surrounding Southern Ocean are regarded as one of the planet’s last remaining wildernesses, ‘insulated from threat by [their] remoteness and protection under the Antarctic Treaty System’1 . Antarctica encompasses some of the coldest, windiest and driest habitats on earth. Within the Southern Ocean, sub-Antarctic islands are found between the Sub-Antarctic Front to the north and the Polar Front to the south. Lying in a transition zone between warmer subtropical and cooler Antarctic waters, these islands are important sentinels from which to study climate change.2 A growing body of evidence3,4 now suggests that climatically driven changes in the latitudinal boundaries of these two fronts define the islands’ short- and long-term atmospheric and oceanic circulation patterns. Consequently, sub-Antarctic islands and their associated terrestrial and marine ecosystems offer ideal natural laboratories for studying ecosystem response to change.5 For example, a recent study6 indicates that the shift in the geographical position of the oceanic fronts has disrupted inshore marine ecosystems, with a possible impact on top predators. Importantly, biotic responses are variable as indicated by different population trends of these top predators.7,8 When studied collectively, these variations in species’ demographic patterns point to complex spatial and temporal changes within the broader sub-Antarctic ecosystem, and invite further examination of the interplay between extrinsic and intrinsic drivers

Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today

Molecular phylogeny of duiker antelope (Mammalia : Cephalophini)

Please read the abstract in the section 00front of this documentThesis (PhD (Zoology))--University of Pretoria, 2007.Zoology and Entomologyunrestricte