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PhD thesis on archaeal phylogeny

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

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General information

Reference : UMR8079-DAVMOR-001
Workplace : ORSAY
Date of publication : Monday, September 09, 2019
Scientific Responsible name : David Moreira
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 December 2019
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

During the last decades, the use of molecular approaches, such as metabarcoding and metagenomics, has led to the discovery of a large diversity of archaea, some of which even defining new phyla. That is particularly the case for the lineages collectively classified within the supergroup DPANN. These archaea show a high evolutionary rate and their genomes appear to have lost many genes, two traits probably due to their presumed parasitic lifestyle. These characteristics make the phylogenetic analysis of these organisms very challenging and, as a result, their position in the tree of Archaea remains uncertain. Another consequence of this problem is the difficulty to infer the position of the root of the archaeal tree. In this project, the PhD student will take advantage of the availability of new genome sequences of DPANN archaea to carry out phylogenetic and comparative genomic analyses to 1) resolve the phylogenetic position of these archaea, 2) reconstruct the evolutionary history of their genomes (gene gains and losses), and 3) place the root of the archaeal tree.

# Activities #
- Assembly and annotation of new genome sequences of DPANN archaea
- Identification of conserved genes in archaea
- Phylogenetic and phylogenomic analyses (maximum likelihood, Bayesian inference, etc.)
- Comparative genomics analyses, inference of gene gains and looses in DPANN archaea, reconstruction of the ancestral gene content in different archaeal lineages.

# Skills #
The candidates must have an excellent level in bioinfomatics, including genome analysis for the assembly and annotation of new sequences and/or in phylogenetic and phylogenomic approaches.

Additional requirements:
- Good level in English (writing and speaking)
- Good oral and written communication skills
- Autonomy, organization skills

Work Context

The "Ecologie, Systématique et Evolution" (ESE) is a CNRS - University Paris-Sud - AgroParisTech institute, located in the University Paris-Sud campus in Orsay. This campus is 20 km south of Paris and well connected through commuter train.

The PhD student will work within the DEEM (Diversity, Ecology and Evolution of Microbes: team, which is interested in the study of the diversity of microorganisms and their evolution using molecular phylogeny and comparative genomic approaches. The PhD student will be co-supervised by David Moreira (, Purificación López-García ( and Laura Eme (

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