Bioinformatics, Phylogeny and Evolutionary Genomics Group

Members

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 1098 in total

Neanderthal adaptive introgression shaped LCT enhancer region diversity without linking to lactase persistence in East Asian populations

Xixian Ma, Yan Lu, Mark Stoneking, Shuhua Xu

Proceedings of the National Academy of Sciences of the United States of America . 122 ( 11 ) : e2404393122

DOI: 10.1073/pnas.2404393122

Journal article

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Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation

Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet

Molecular Biology and Evolution . 42 ( 2 )

DOI: 10.1093/molbev/msae271

Journal article

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Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny) .

Poster

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A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Mobile DNA . 16 ( 1 ) : 4

DOI: 10.1186/s13100-024-00337-6

Journal article

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Exploring the role of transposable elements to sex gap in longevity in Drosophila species

Miriam Merenciano, Sonia Janillon, Camille Mermet-Bouvier, Nelly Burlet, Valentina Rodriguez-Rada, Victor Ronget...

DOI: 10.1101/2025.01.22.634250

Preprint

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Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family

Sandrine Coquille, Caroline Simões Pereira, Jennifer Roche, Gianluca Santoni, Sylvain Engilberge, Céline Brochier-Armanet...

Molecular Biology and Evolution . 42 ( 1 )

DOI: 10.1093/molbev/msae265

Journal article

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PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids fish

Marie Raynaud, Paola Sanna, Julien Joseph, Julie A. J. Clément, Yukiko Imai, Jean-Jacques Lareyre...

PLoS Biology . 23 ( 1 ) : e3002950

DOI: 10.1101/2024.03.06.583651

Journal article

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The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, Aline Muyle...

Science . 387 ( 6734 ) : 630-636

DOI: 10.1126/science.adj7430

Journal article

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Out-of-Africa migration and clonal expansion of a recombinant Epstein-Barr virus drives frequent nasopharyngeal carcinoma in southern China

Xinyi Zhang, Yanhong Chen, Jingtong Liang, Yue Yang, Hui Chen, Zehui Chen...

National Science Review . 12

DOI: 10.1093/nsr/nwae438

Journal article

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Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction

Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon

Genome Biology and Evolution . 16

DOI: 10.1093/gbe/evae250

Journal article

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Divergence in expression of a singing-related neuro-plasticity gene in the brains of two Ficedula flycatchers and their hybrids

David Wheatcroft, Niclas Backström, Ludovic Dutoit, S Eryn Mcfarlane, Carina Mugal, Mi Wang...

G3 .

DOI: 10.1093/g3journal/jkae293

Journal article

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Evolution and functional relevance of non-coding elements in vertebrate genomes

Anamaria Necsulea

HDR

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From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps

Erik Gobbo, Nicolas Lartillot, Jack Hearn, Graham N Stone, Yoshihisa Abe, Christopher W Wheat...

Genome Biology and Evolution . 12 : 2060 - 2073

DOI: 10.1093/gbe/evaa204

Journal article

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Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements

Manuel Ares-Arroyo, Charles Coluzzi, Jorge A Moura de Sousa, Eduardo P C Rocha

PLoS Biology . 22 ( 8 ) : e3002796

DOI: 10.1371/journal.pbio.3002796

Journal article

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A type IVB secretion system contributes to the pathogenicity of Yersinia pseudotuberculosis strains responsible for the Far East scarlet-like fever

Marion Lemarignier, Cyril Savin, Ines Ruedas Torres, Anne Derbise, Charles Coluzzi, Julien Burlaud-Gaillard...

DOI: 10.1101/2024.06.14.598817

Preprint

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Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees

Maxime Godfroid, Charles Coluzzi, Amaury Lambert, Philippe Glaser, Eduardo P C Rocha, Guillaume Achaz

Methods in Ecology and Evolution . 15 ( 2 ) : 282 - 289

DOI: 10.1111/2041-210x.14190

Journal article

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Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis.

Nicolas Lartillot, Alice Genestier, Laurent Duret

RecomBern .

Conference paper

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The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation

D Madern, Frédéric Halgand, Chantal Houée-Levin, A-B Dufour, S Coquille, S Ansanay-Alex...

Molecular Biology and Evolution . : msae231

DOI: 10.1093/molbev/msae231

Journal article

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High prevalence of Prdm9-independent recombination hotspots in placental mammals

Laurent Duret, Julien Joseph, Djivan Prentout, Alexandre Laverré, Théo Tricou

Probabilistic Modeling in Genomics Conference : ProbGen 2024 .

Conference paper

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The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation

D Madern, Frédéric Halgand, Chantal Houée-Levin, A-B Dufour, S Coquille, S Ansanay-Alex...

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msae231

Journal article

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Prevalence of PRDM9-dependent vs PRDM9-independent recombination hotspots in animals

Laurent Duret

RecomBern .

Conference paper

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Meta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research

Anamaria Necsulea, Philippe Veber, Tuyana Boldanova, Charlotte Ky Ng, Stefan Wieland, Markus H Heim

DOI: 10.1101/2024.08.17.608405

Preprint

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The Inca child of the Quehuar volcano: Stable isotopes clue to geographic origin and seasonal diet, with putative seaweed consumption

Eve Poulallion, Violeta Galván, Verónica Seldes, María Fernanda Zigarán, Gabriela Recagno Browning, François Fourel...

Journal of Archaeological Science: Reports . 59 : 104784

DOI: 10.1016/j.jasrep.2024.104784

Journal article

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Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis

Mobile DNA . 15 ( 1 ) : 8

DOI: 10.1186/s13100-024-00317-w

Journal article

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The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations

Laure Ségurel, Thirumalai Selvi Ulaganathan, Sophie Mathieu, Mélanie Touvrey, Laurent Poulet, Sophie Drouillard...

DOI: 10.1101/2023.03.30.534863

Preprint

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Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

Marie Verneret, van Anthony Le, Thomas Faraut, Jocelyn Turpin, Emmanuelle Lerat

DOI: 10.1101/2024.09.25.614865

Preprint

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