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Project #17011
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#17011 : A pipeline to detect correlated evolution on phylogenetic trees
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Name of Applicant : Eduardo Rocha
Date of application : 10-06-2021
Unit : Microbial Evolutionary Genomics
Location : FJ-6
Phone : 3353
@ Mail : erocha@pasteur.fr

Project context and summary :

Correlated evolution is the process by which the evolution of a trait (e.g., a genetic mutation) influences the evolution of other traits. Notably, when genetic mutations evolve together, the fitness effect resulting from the combination can be more or less important than the sum of the independent fitness effects. The disposition of mutations on a phylogenetic tree reflects to some extent the relationships that may exist between different mutations. One example is the evolution of co-occurrent mutations, i.e., mutations that evolve on the same branch of the phylogenetic tree. In other words, one mutation cannot evolve without the other. We developed recently two tools to infer the correlation between evolutionary events mapped on a phylogenetic tree. Notably, our tools were able to retrieve the correlation between residues in contact in the ribosomal RNA three-dimensional structure. We further assemble our tools in a pipeline with a graphical interface to share the tool to as many relevant scientists that would implement the detection of correlated evolution in their projects. Examples of applications are the dynamics of gene gains and losses, the correlation between amino acid residues that are in interaction within the same protein or the evolution of compensatory mutations following the evolution of antibiotic resistance in bacteria.


Related team publications :
Behdenna A, Pothier J, Abby SS, Lambert A, Achaz G. 2016. Testing for Independence between Evolutionary Processes. Syst Biol. 65:812–823. doi: 10.1093/sysbio/syw004.
Behdenna A et al. 2021. A minimal yet flexible likelihood framework to assess correlated evolution. bioRxiv. 2020.09.04.282954. doi: 10.1101/2020.09.04.282954.
Patiño-Navarrete, R., Rosinski-Chupin, I., Cabanel, N. et al. Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli. Genome Med 12, 10 (2020). https://doi.org/10.1186/s13073-019-0699-6
Service Delivery
Project Manager : fabien.mareuil@pasteur.fr
Project Type : Medium
Status : In Progress


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