Dear subscribers,

We are looking for an enthusiastic, motivated new student to join us for a fully funded PhD position at the Institute of Genomics, University of Tartu, Estonia this September. Below is the information.


Group: Estonian Biocentre/Institute of Genomics, Ancient DNA Research Group. 
Supervisor: Dr. Christiana Scheib; co-supervisor Dr. Kristiina Tambets.
 
Deadline: 
01.05.2021 (please get in touch by emailing [log in to unmask] as soon as possible before applying)
 
Salary:
1300 EUR/month net. The position is funded for 4 years. For a cost of living comparison see: numbeo. Students are allowed to work in Estonia during their studies as long as it does not interfere with their degree progression. 
 
Title: Tracking the history of human disease using ancient oral microbiome data.  
 
Project Description:
Food has long been a crucial component of human sociality and health. More and more, we are finding that there is a delicate balance between what we eat, the microbes that live within us and our general health and susceptibility to infectious disease. Ancient dental calculus, a calcified biofilm from teeth, is a valuable resource containing ancient microbial, host and dietary biomolecules; however, the methodologies used in analysing this complex data are still in the developmental stage and the full scope of how this data can be used to study human health has yet to be determined. This doctoral research project will generate whole-genome metagenomic libraries from ancient dental calculus samples and analyse this data in the context of ancient proteins and human (host) DNA to better understand how shifts in culture have affected human health.

The main objective of the project is to assess the impact of cultural differences on the quantitative and qualitative structure of the oral microbiome within sets of European populations. There are three main components: the Bronze Age transition, urban vs. rural and tobacco-use vs. non-use. The first component of the project will assess differences between the Neolithic and Bronze Age populations in Italy. The Bronze Age transition brought both demographic and cultural change as well as a shift in the prevalence of pathology in the archaeological record. This component will assess if these shifts in ancestry, diet, pathology and culture correlate with shifts in the oral microbiome as part of the ERC Advanced Grant, Making Ancestors: The Politics of Death in Prehistoric Europe. The second component will assess differences in oral microbiome between urban and rural populations in medieval Estonia as part of the interdisciplinary medieval Estonia project headed by Dr. Kristiina Tambets. The final component will compare oral microbiomes of pre-Tobacco populations in Western Europe with known smokers as part of the Tobacco Health and History project. You will collaborate with Dr. Sarah Inksip at the University of Leicester who has post-doctoral researchers generating novel metabolomic data identifying psychoactive substances (e.g. tobacco) and health markers for these populations. Both of these data sources will be combined with the host and pathogen (e.g. Mycobacterium tuberculosis) genomes to better understand the impact of the introduction of tobacco smoking on the health of European populations after 1492. There will be opportunities to travel for collaborative interaction and conferences. 

 
About us
The ancient DNA research group at the Estonian Biocentre, Institute of Genomics is a friendly, growing group focused on producing exemplary research in the fields of ancient human population genetics, pathogen genomics and the emerging field of ancient meta-genome/proteomics. The lab is headed by Dr. Scheib (Associate Professor of Ancient DNA) and includes Dr. Tambets (Associate Professor of Population Genetics), post-docs, PhD students, Master’s students and two laboratory technicians. You can check out our lab on Research Gate and the official UT website. 
 
Duties and responsibilities
The PhD student will be carrying out research activity in the field of ancient DNA including the generation of ancient metagenomic data from dental calculus samples, analysis of this data and writing publications.
 
Required qualifications
MSc or MA in archaeogenetics, bioinformatics, bioarchaeology, biological anthropology, genetics, molecular biology, computer programming or related subjects. If you have some knowledge and experience of: 1) working in a cleanroom/ancient DNA wet lab protocols and/or 2) bioinformatic analysis, this would be ideal but is not necessary. If you do not know how to code in Python 3, shell scripting, or R, you must be willing to learn as this project will be very analysis heavy. There are courses at the University of Tartu for programming and the lab has online resources we can provide in order for you to learn.  
 
Required language skills
English
 
Starting at 
01.09.2021 as earliest
 
Workload 
1,0
 
Additional information
Please contact Christiana Scheib: [log in to unmask] for information.
Why the University of Tartu?

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