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PhD student (M/F) to work on ancient microbial phylogenomics with a CNRS-UCPH funded fellowship at the Microbial Paleogenomics Unit of Institut Pasteur

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : mercredi 6 juillet 2022

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General information

Reference : UMR2000-MARVIC-001
Workplace : PARIS 15
Date of publication : Wednesday, June 15, 2022
Scientific Responsible name : Nicolas RASCOVAN
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Project title:
Predicting ancient human populations movements using phylogenomics of ancient commensal microbes

Candidate profile:
Our lab is 100% computational. Thus, the candidate for this project should have from good to strong background in bioinformatics. A background in at least some of the following areas will be also needed: microbial genomics, metagenomics, phylogenetics, human populations genetics, statistics, mathematics. Candidates should be willing to constantly read, learn and integrate concepts from different fields, to cooperate with others and to promote a friendly, healthy and altruistic work environment.

Work Context

Scientific context:
Humans and microbes have closely interacted throughout the evolutionary history of our species. Some of the microbial species that form part of the human microbiome can be found in populations from all continents, time periods and ecosystems. Moreover, different works have shown evidence that the genomes of certain core microbial species, and even the metagenome of the human microbiota, could be used to trace back migrations of individuals and populations. However, to date, no one has systematically investigated at which extent, how far in time and how precisely these migrations could be inferred from microbial DNA.

Goals:
The ultimate goal of this project is to develop new methodological and statistical approaches to estimate migration patterns of ancient human populations (e.g., timings, directions), by using microbial genomes as a proxy. To do so, we will combine ancient and modern genomic data from humans and their oral microbial species, both retrieved from the same individuals, with samples spanning over thousands of years and vast geographic regions. Assuming that ancient human populations diverged from each other together with at least some of their associated microbes, our hypothesis is that these microbes will likely contain phylogenetic signatures reflecting the migration histories of their host populations. If so, phylogenomic and molecular clock analyses of such species could be used to estimate the divergence times and spread directions between ancient human populations.

Work environment:
The Microbial Paleogenomics Unit at Institut Pasteur investigates how human microbes emerged, spread and changed at the genomic level over the course of human history, and uses this information to better understand the complexity of modern infectious diseases and human microbiomes. We do so by combining ancient DNA (using ancient human remains as sources of DNA), deep sequencing, genomics and metagenomics, phylogenetics, bioinformatics approaches. We closely interact with historians and archaeologist to properly contextualize our results. The lab is placed at the Institut Pasteur campus in Paris, which is a highly dynamic and international environment, with research groups working in a wide diversity of life science topics.

Constraints and risks

Risks and constraints:
- The student will spend most if not all of his time woking in a computer
- Long sitting hours in front of a screen in therefore expected
- Recurrent trips between Paris and Copenhagen are also planned

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