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Ancient pathogen identification in anthropogenic sediments from Bushman Rock Shelter

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CaseHeader

Status: 

HeritageAuthority(s): 

Case Type: 

ProposalDescription: 

Ancient pathogen identification in anthropogenic sediments from Bushman Rock Shelter

Expanded_Motivation: 

This proposal forms part of a project which aims to cultivate the currently undeveloped southern African ancient DNA (aDNA) research niche and includes the establishment of a local aDNA analytical facility at the Department of Genetics, University of Pretoria. Sedimentary samples will be subjected to DNA extraction protocols and analysed to ascertain the ancient pathogenic (bacterial, viral and fungal) composition of the anthropogenic sediments. The samples derive from Later Stone Age (LSA) levels at Bushman Rock Shelter, Limpopo Province, dated to between c. 10,000 and 15,000 years ago This proposal forms part of a project which aims to cultivate the currently undeveloped southern African ancient DNA (aDNA) research niche and includes the establishment of a local aDNA analytical facility at the Department of Genetics, University of Pretoria. Sedimentary samples will be subjected to DNA extraction protocols and analysed to ascertain the ancient pathogenic (bacterial, viral and fungal) composition of the anthropogenic sediments. The samples derive from Later Stone Age (LSA) levels at Bushman Rock Shelter, Limpopo Province, dated to between c. 10,000 and 15,000 years ago. A prevailing view of the origins of modern human diseases is that most arose following the advent of animal domestication and urbanisation that occurred during the Neolithic Period, c. 12 000 years ago (ka). Consequently, the search for the origins of diseases has focussed primarily on domestic animals and environments outside Africa. Many of these tropical infections are however likely to have played a significant role in the human evolutionary process for much lengthier periods of time. Results derived from the previous analyses of sedaDNA samples derived from BRS confirms the feasibility of this study. Given the small sample size, the submitted research manuscript was however deemed inadequate for publication. The addition of 11 sediment samples to the study will result in a total sample set of 15 samples, plus two control samples, i.e. BRS18 from M3b (as an MSA control) and BRS1 from M4d (as a modern surface control).

ApplicationDate: 

Friday, May 18, 2018 - 09:00

CaseID: 

12484

OtherReferences: 

ContactPerson
Phillip Hine

ReferenceList: 

Citation
Houldcroft, C.J., Pimenoff, V.N., Rifkin, R.F., Underdown, S. In press. The role of aDNA in understanding the co-evolutionary patterns of human sexually transmitted infections. Genome Biology. 2. Rifkin, R.F., Potgieter, M., Ramond, J-B., Cowan, D.A. 2017. Ancient oncogenesis, infection and human evolution. Evolutionary Applications doi: 10.1111/eva.12497. 3. Houldcroft, C., Ramond, J.-B., Rifkin, R.F., Underdown, S. 2017. Migrating microbes: What pathogens can tell us about population movements and human evolution. Annals of Human Biology doi: 10.1080/03014460. 2017. 1325515.
AdditionalDocuments
  1. PDF icon Table indicating samples to be exported to Copenhagen for sedaDNA analyses.
 
 

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