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Proposition for a Ph-D (M/W) Modélisation du polymorphisme en phylogénie

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Français - Anglais

Date Limite Candidature : vendredi 2 juillet 2021

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General information

Reference : UMR5558-NATARB-018
Workplace : VILLEURBANNE
Date of publication : Friday, June 11, 2021
Scientific Responsible name : Laurent Gueguen
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Context
Batantivir project aims at the evolutive study of adaptation of immunity genes
in bats.
Bats (Chiroptera) are one of the most diverse and widespread mammalian
order. They host many viruses, including high-pro le zoonoses (rabies, Nipah,
Ebola Marburg loviruses, SARS coronavirus) and viruses close to primate
pathogens (poxvirus, Hepatitis B Virus). During bat evolution, lineage-speci c
adaptation may have occurred as a response to pathogen selective pressure,
differentially shaping the innate immune repertoire in bat species. However,
most of the evolutionary history and mechanism of bat antiviral immunity is
still unknown.
This study involves phylogenetic methods. But, since bats genes are highly
polymorphic, there is a crucial need to incorporate polymorphism in those phy-
logenetic analyses.
If polymorphism dynamics is at the core of population genetics theory, those
approches focus at the time-scale of a single species, and do not explicitly extend
to inter-species scale. On the other hand, in phylogeny analysis, substitutions
are assumed instantaneous, which has an influence on the inference of selection.
Typically, on polymorphic sites, mutations are considered as substitutions, and
selection is underestimated.
Project
The aim of this PhD is to fi ll the gap between phylogenetics and population
genetics, and provide a multi-scale approach for the estimation of selection that
incorporates intra- and inter-speci c data.
This work will be based on the theoretical work of Carina Mugal, which
provides analytic solutions between the estimation of selection in phylogenetic
approaches and population genetics theory, from the distribution of polymor-
phism.
The approach would be to compute the transition probabilities between
allelic distributions. This work involves also to study the dynamics of speciation
(starting with the simplest models of speciation, with no gene
ow).
These models will be implemented in Bio++ libraries, which are a set of
C++ libraries dedicated to bioinformatics, phylogenetics, molecular evolution,
and population genetics, and in which a vast amount of models and modeling
hypotheses are already explored and implemented (heterogeneity in time and
sites, mixture of models, hidden Markov chains, etc.).
Finally, owing to these tools the student will manage to analyse the evolutive
dynamics of bats genes studied by our collaborators of Batantivir project.
Requirements
The candidate has a good knowledge of molecular evolution, and solid
bases in modelling. She/he is familiar with bioinformatics, population genetcs
& phylogenetic concepts. Last, she/he is autonomous in C++ programming.
Keywords
phylogeny, evolution, bioinformatics, genomics, models.
References

Work Context

The selected candidate will work in the Biometry and Evolutionary Biology laboratory (LBBE), which offers a highly
stimulating scienti c environment, located in Lyon.
The PhD student will be supervised by Laurent Gueguen (University of Lyon 1) - laurent.gueguen@univ-lyon1.fr and Carina Mugal (University of Uppsala Sweden) - carina.mugal@ebc.uu.se

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