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05 June 2018 Photo Supplied
Digging up truth South Africa was way different to what you thought
Archaeological excavations in the Wonderwerk Cave, north of Kuruman in the Northern Cape.

Research fellow Dr Lloyd Rossouw from the Department of Plant Sciences at the University of the Free State (UFS) recently published an article in the Nature Ecology and Evolution journal with Dr Michaela Ecker from the University of Toronto as lead author, and Dr James Brink, research fellow at the UFS Centre for Environmental Management. The findings described in “The palaeoecological context of the Oldowan-Acheulean in southern Africa” provides the first extensive paleoenvironmental sequence for the interior of southern Africa by applying a combination of methods for environmental reconstruction at Wonderwerk Cave, which have yielded multiple evidence of early human occupation dating back almost two million years ago.

Where water once was
The Wonderwerk Cave is found north of the Kuruman hills (situated in Northern Cape) a 140m long tube with a low ceiling. The surroundings are harsh. Semi-arid conditions allow for the survival of only hardy bushes, trees, and grasses. But during the Early Pleistocene, stepping out of the Wonderwerk Cave you would have been greeted by a completely different site, the researchers found. Using carbon and oxygen stable isotope analysis on the teeth of herbivores (Dr Ecker), fossil faunal abundance (Dr Brink), as well as the analysis of microscopic plant silica remains (phytoliths) excavated from fossil soils inside the cave (Dr Rossouw), the results show that ancient environments in the central interior of southern Africa were significantly wetter and housed a plant community unlike any other in the modern African savanna. 

What difference does it make?
While East African research shows increasing aridity and the spread of summer-rainfall grasslands more than a million years ago, the results from this study indicate an interesting twist. During the same period, shifts in rainfall seasonality allowed for alternating summer and winter-rainfall grass occurrences coupled with prolonged wetlands, that remained major components of Early Pleistocene (more or less the period between one and two million years ago) environments in the central interior of southern Africa. That means our human ancestors were also living and evolving in environments other than the generally accepted open, arid grassland model.

News Archive

Newly operational sequencing unit in genomics at UFS
2016-09-09

Description: Next Generation Sequencing  Tags: Next Generation Sequencing

Dr Martin Nyaga and his research assistant,
Tshidiso Mogotsi in the Next Generation
Sequencing Laboratory.
Photo: Charl Devenish

The Next Generation Sequencing (NGS) unit at the UFS was established as an interdisciplinary facility under the Directorate for Research Development, Faculty of Health Sciences and Faculty of Natural and Agricultural Sciences.

The aim of the NGS facility is to aid internal and external investigators undertaking studies on Deoxyribonucleic acid (DNA) sequencing, assembly and bioinformatics approaches using the more advanced Illumina MiSeq NGS platform.

The NGS unit became operational in 2016 and is managed by Dr Martin Nyaga and administered through the office of the Dean, Faculty of Health Sciences, under the leadership of Prof Gert Van Zyl. Dr Nyaga has vast experience in microbial genomics, having done his PhD in Molecular Virology.

He has worked and collaborated with globally recognised centres of excellence in Prokaryotic and Eukaryotic genomics, namely the J. Craig Venter Institute and the Laboratory of Viral Metagenomics, Rega Institute, among others.

The unit has undertaken several projects and successfully generated data on bacterial, viral and human genomes. Currently, work is ongoing on bacterial and fungal metagenomics studies through 16S rRNA sequencing.

In addition, the unit is also working on plasmid/insert sequencing and whole genome sequencing of animal and human rotaviruses. The unit has capacity to undertake other kinds of panels like the HLA, Pan-cancer and Tumor 15 sequencing, among others.

Several investigators from the UFS including but not limited to Prof Felicity Burt, Prof Wijnand Swart, Dr Frans O’Neil, Dr Trudi O'Neill, Dr Charlotte Boucher, Dr Marieka Gryzenhout and Dr Kamaldeen Baba are actively in collaboration with the NGS unit.

The unit has also invested in other specialised equipment such as the M220 Focused-ultrasonicator (Covaris), 2100 Bioanalyzer system (Agilent) and the real-time PCR cycler, the Rotor-Gene Q (Qiagen), which both the UFS and external investigators can use for their research.

Investigators working on molecular and related studies are encouraged to engage with Dr Nyaga on how they would like to approach their genomics projects at the UFS NGS unit. 

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