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 past, but the lack of well-preserved human remains renders skeletal pathology rather limiting in terms
of determining the impact of pathogens on our ancestors. Accordingly, and with the aim to explore the use of alternative sources of insight into the past, Dr Riaan Rifkin, a Senior Postdoctoral Fellow at the Centre for Microbial Ecology and Genomics (CMEG), recently initiated a pioneering research project aimed at identifying human pathogens in ancient (archaeological) sediments.
Dr Rifkin addresses two largely unanswered questions concerning the evolutionary history of
our species in southern Africa: First, what is the so- called ‘Pleistocene disease baseline’? And, second, in which ways did diseases have an impact on human evolution? Innovative molecular analytical techniques
have been successfully applied to the emerging field of ancient pathogen DNA (apDNA) and have contributed significantly to current understandings of prehistoric disease origins. And although the recovery of ancient sedimentary DNA (sedaDNA) has been reported in European and North American contexts, no ancient DNA has yet been recovered from African sediments.
How does one extract molecular information
from ancient sediments? First, sediment samples are obtained from South African caves, such as Wonderwerk and Bushman Rock, where evidence of human occupation spans the Holocene and Pleistocene epochs. Samples are taken according to strict contamination-prevention protocols, as the inclusion of any modern DNA will severely limit the ability to detect the highly fragmented ancient DNA molecules. Following sample acquisition, the sealed and frozen tubes are sent to a state-of-the- art laboratory for DNA extraction and analyses. While ancient human pathogens have indeed been recovered from these sediments, stringent bioinformatic analyses are currently applied to confirm, unequivocally, the incidence of these microbes and sediments.
Given the multidisciplinary nature of bio- archaeological research, Dr Rifkin works in collaboration with Professor Don Cowan and
Dr Jean-Baptiste Ramond (CMEG), and with Professor Anders Hansen at the Centre for GeoGenetics in Copenhagen. This contribution,
and the latent significance of ancient biomolecular research, cannot be underestimated. History has taught us that disease is potentially the most effective eradicator of our species – and that past epidemics are much more than just ancient history. They are also significant drivers of human genetic diversity and natural selection.
Obtaining sediment samples from Wonderwerk caves.
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Wonderwerk caves – Riaan Rifkin

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