Bioinformatics, Phylogeny and Evolutionary Genomics Group

Members

equipe_bpge_2021

Our group focuses on two main axes: phylogenomics (i.e. the inference of evolutionary history based on genomics data) and evolutionary genomics (understanding the molecular and population processes that drive genome evolution). We see genomes both as a subject of research (how do genomes evolve, why are they structured the way they are?), but also as a main source of empirical knowledge about the macroevolutionary patterns (what do they tell us about the history of life on Earth?), or about the phenotypes and life-history strategies of organisms. Our works heavily rely on methodological developments (bioinformatics, modeling and statistical inference).

Evolution of genome architecture and expression

Genomes are the result of a long-term evolutionary process, shaped by multiple evolutionary forces. Some genomic features are adaptive (i.e. are beneficial for the fitness of organisms), others result from non-adaptive processes (random drift and biased gene conversion - BGC) or are caused by conflicts between multiple levels of selection (e.g. meiotic drive or the spread of selfish genetic elements). We explore different aspects of genome architecture (base composition landscapes, genome structure and size, impact of transposable elements, …) or functioning (gene expression, lncRNAs, epigenetic landscapes, …), and try to disentangle the relative contribution of adaptive and non-adaptive processes to their evolution. For this purpose, we consider both the molecular mechanisms (mutation, repair, recombination) and the population processes (selection, drift, BGC, …) that shape genetic variation.

Phylogenomics

We are interested in reconstructing the history of life on Earth. This research unfolds along several axes. First, we develop phylogenomic databases of aligned genetic sequences (e.g. BIBI, RiboDB or HOGENOM). Second, we conduct methodological research on how to accurately reconstruct deep phylogenies, infer divergence times, reconstruct ancestral genetic sequences, gene repertoires and life-history traits. This methodological work is translated into publicly available software programs (e.g. SeaView, PhyloBayes, Coevol). Finally, we apply these approaches to several important problems, among which: reconstructing the phylogeny of animals, of archaea, or the global tree of life; using phylogenies and ancestral gene repertoires to investigate the evolution of complex systems and the emergence of molecular and cellular functions in the three domains of life; reconstructing ancestral genetic sequences, a research activity that has industrial and biotechnological applications.

Teaching and outreach

We teach at University Lyon 1 (Master Bioinfo@Lyon), INSA, ENS Lyon, we organize bioinformatics internships. We regularly give conferences on evolution (tree of life, human evolution, genetic diversity, …).
Prospective students and postdocs are invited to apply, as we often welcome visitors for internships or research projects.
 
Keywords: Molecular evolution and Population Genomics; Phylogenomics; Computational Genomics; Comparative genomics; Bioinformatics; Statistical inference.

Publications

Display of 1 to 30 publications on 813 in total

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

T. Latrille, N. Rodrigue, Nicolas Lartillot

DOI: 10.1101/2022.09.23.509132

Preprint

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The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn...

Trends in Ecology and Evolution . 37 ( 3 ) : 197-202

DOI: 10.1016/j.tree.2021.11.008

Journal article

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Population designations in biomedical research: limitations and perspectives

Caroline Gombault, Guillaume Grenet, Laure Ségurel, Laurent Duret, François Gueyffier, Pascal Cathébras...

HLA: Immune Response Genetics .

DOI: 10.1111/tan.14852

Journal article

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Modelling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure L. Segurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

DOI: 10.1101/2021.07.21.453231

Preprint

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Codiversification of gut microbiota with humans

Taichi Suzuki, J. Liam Fitzstevens, Victor Schmidt, Hagay Enav, Kelsey Huus, Mirabeau Mbong Ngwese...

Science . 377 ( 6612 ) : 1328-1332

DOI: 10.1126/science.abm7759

Journal article

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The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn...

Trends in Ecology & Evolution . 37 ( 3 ) : 197-202

DOI: 10.1016/j.tree.2021.11.008

Journal article

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The era of reference genomes in conservation genomics

Florian Maumus, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely...

Trends in Ecology & Evolution .

DOI: 10.1016/j.tree.2021.11.008

Journal article

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Protein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual mutations

Antonio Iorio, Céline Brochier-Armanet, Caroline Mas, Fabio Sterpone, Dominique Madern

Molecular Biology and Evolution . 39 ( 9 ) : msac186

DOI: 10.1093/molbev/msac186

Journal article

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

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An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac005

Journal article

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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Monique Aouad, Jean-Pierre Flandrois, Frédéric Jauffrit, Manolo Gouy, Simonetta Gribaldo, Celine Brochier-Armanet

BMC Ecology and Evolution . 22 ( 1 ) : 1-12

DOI: 10.1186/s12862-021-01952-0

Journal article

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Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Alexandre Laverré, Eric Tannier, Anamaria Necsulea

Genome Research . 32 ( 2 ) : 280-296

DOI: 10.1101/gr.275901.121

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The human gut microbiome and health inequities

Katherine Amato, Marie-Claire Arrieta, Meghan Azad, Michael Bailey, Josiane Broussard, Carlijn Bruggeling...

Proceedings of the National Academy of Sciences of the United States of America . 118 ( 25 ) : e2017947118

DOI: 10.1073/pnas.2017947118

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No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas

Shelly Masi, Frédéric Austerlitz, Chloé Chabaud, Sophie Lafosse, Nina Marchi, Myriam Georges...

Ecology and Evolution . 11 ( 12 ) : 7634-7646

DOI: 10.1002/ece3.7596

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Elevated rates of horizontal gene transfer in the industrialized human microbiome

Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean Kearney, Katya Moniz, Mary Noel...

Cell . 184 ( 8 ) : 2053-2067.e18

DOI: 10.1016/j.cell.2021.02.052

Journal article

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Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

Gaël Even, Ana Lokmer, Jules Rodrigues, Christophe Audebert, Eric Viscogliosi, Laure L. Segurel...

Frontiers in Cellular and Infection Microbiology . 11 : 533528

DOI: 10.3389/fcimb.2021.533528

Journal article

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The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Michel Lecocq, Mathieu Groussin, Manolo Gouy, Celine Brochier-Armanet

Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776

DOI: 10.1093/molbev/msaa312

Journal article

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DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13323

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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto...

Plos Biology . 19 ( 7 ) : e3001309

DOI: 10.1371/journal.pbio.3001309

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

Book chapter

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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti...

Molecular Biology and Evolution . : 1-44

DOI: 10.1093/molbev/msab146

Journal article

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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Jan Felix, Claire Siebert, Juila Novion Ducassou, Jérôme Nigou, Pierre Simon Garcia, Angélique Fraudeau...

Scientific Reports . 11 ( 1 ) : 972

DOI: 10.1038/s41598-020-79611-5

Journal article

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Natural Selection beyond Life? A Workshop Report

Sylvain Charlat, André Ariew, Pierrick Bourrat, María Ferreira Ruiz, Thomas Heams, Philippe Huneman...

Life . 11 ( 10 ) : 1051

DOI: 10.3390/life11101051

Journal article

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Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Thibault Latrille, Nicolas Lartillot

Theoretical Population Biology . 142 : 57-66

DOI: 10.1016/j.tpb.2021.09.005

Journal article

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Inferring Long-Term Effective Population Size with Mutation–Selection Models

Thibault Latrille, Vincent Lanore, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 10 ) : 4573-4587

DOI: 10.1093/molbev/msab160

Journal article

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