PhD position in ancient (Pathogen) genomics

Applications are invited for a joint three-year Ph.D.fellowship in the field of southern African archaeology and ancient DNA, to be hosted by the Centre for Microbial Ecology and Genomics (University of Pretoria, South Africa), and in collaboration with scientists based at the Institute of Genomics (University of Tartu, Estonia), the Department of Molecular Genetics and Microbiology (Pontificia Universidad Católica de Chile) and the Department of Laboratory Medicine(Karolinska Institutet, Sweden)

Project:
The Ph.D.position will be funded by the Oppenheimer Endowed Fellowship in Molecular Archaeology, and hosted by the Universities of Pretoria (South Africa). The successful candidate will analyse shotgunmetagenomic datasetsgenerated from the sequencing of sedimentary and other ancient samples derived from renowned South African archaeological contexts,spanning the Holocene and Late Pleistocene epochs. In general terms, the candidate will explore whether molecular (sedaDNA) analyses could provide insight into ancient African human ecology. More specifically, the candidate will aim to detect traces ancient human bacterial and viral pathogens,and explorethe evolutionary history of infectious diseases in prehistoric southern Africa.In addition, the candidate will endeavour to identify unique genomic signatures of prehistoric hunter-gatherer populations.

Candidate:
The ideal candidate will demonstrate abilities to work both independently and in a team environment,and strong expertise in the molecular tools used in next-generation sequencing and population genomics. The candidate should have strong background in molecular biology, particularly in molecular methods for generating large-scale sequence and SNPdatasets, and be familiar with basic concepts in computational science and optionally, with Bash or other programming languages such as R, Perl and or Python. Experience in the analysis of ancient DNA and/or Next-Generation Sequencing will be considered positively,but is not mandatory.

Tasks:
Key tasks of the Ph.D.candidate will comprise:
1.Generate and analyse genome-wide ancient DNA datasets for samples from South African archaeological contexts,
2.Complete a Ph.D.thesis,comprising at least two of peer-reviewed scientific articles based on the research performed,
3.Gain international research experience through a research visit to the Institute of Genomics (University of Tartu, Estonia)and through various fieldwork and sampling activities,
4.Gain important teaching experience teaching graduate and undergraduate students, and
5.Disseminate the research results to a broader public through conference presentations and public talks

The position will remain funded for three academic years, at ZAR 120,000.00 per annum, excluding research expenses, pending satisfactory bi-annual progress evaluations and reports.

Criteria:
1. The candidate must be a Southern African Development Community (SADC)citizen,
2.An M.Sc.degree related to the subject area of the project, preferably in bioinformatics, but not excluding biology, genetics, evolutionary genomics and ancient DNA analysis,
3.Previous peer-reviewed scientific publications,
4.Superior spoken and written English language skills, and
5.A proven ability to work both as part of a group and independently

Terms:
The employment as Ph.D.fellow is full-time and for three years, commencing as soon as possible. It is conditioned upon the applicant ́s successful enrolment as a Ph.D. student at the Department of Biochemistry, Genetics and Microbiology (Faculty of Natural and Agricultural Sciences, University of Pretoria).

Application:
Expressions of interest must be submitted electronically to riaanrifkin@gmail.com.Please include the following: 1.A Curriculum Vitae (with publication record, if any).2.A Letter of Motivation of no longer than two pages.3.Contact details of two professional references.Our review of submitted expressions of interest will continue until the position is filled. The appointment is expected to commence in mid-to late-2022,or soon thereafter.