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 1110 in total

Epigenetic Clock Analysis of Sex Chromosome Aneuploidies

Joshua Zhang, Jordan Teoli, Benjamin Rey, Cristina Vieira, Jean‐françois Lemaitre, Ingrid Plotton...

Aging Cell .

DOI: 10.1111/acel.70243

Journal article

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Plant sex-determining genes and the genetics of the evolution towards dioecy

Gabriel a B Marais, Catarina Branco, Margarida Rocheta, Mathilde Dufay, Jeanne Tonnabel

Journal of Experimental Botany . 76 ( 14 ) : 3896-3911

DOI: 10.1093/jxb/eraf224

Journal article

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Origin and evolution of Inhibitors of apoptosis (IAPs) in early metazoans

Mélanie Ribeiro Lopes, Nicolas Parisot, Sergio Peignier, François Renoz, Patrice Baa-Puyoulet, Emmanuelle Jousselin...

EVOLYON 2025 .

Poster

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Specific expansion and diversification of Inhibitors of APoptosis (IAPs) support symbiont maintenance and morph-specific regulation in aphids

Mélanie Ribeiro Lopes, Nicolas Parisot, Karen Gaget, Sergio Peignier, Emmanuelle Jousselin, Hubert Charles...

XII International Symposium on Aphids (ISA) .

Conference paper

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The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range

Charles Coluzzi, Eduardo Rocha

Molecular Biology and Evolution . 42 ( 3 ) : msaf060

DOI: 10.1093/molbev/msaf060

Journal article

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Comment les espèces s’adaptent génétiquement à leur environnement ? Sélection positive, balancée, et microbiote intestinal

Laure Ségurel

HDR

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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 Loiodice, Laurent Poulet, Sophie Drouillard...

PLoS ONE . 20 : e0329457

DOI: 10.1371/journal.pone.0329457

Journal article

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Multi-proteins similarity-based sampling to select representative genomes from large databases

Rémi-Vinh Coudert, Jean-Philippe Charrier, Frédéric Jauffrit, Jean-Pierre Flandrois, Céline Brochier-Armanet

BMC Bioinformatics . 26 ( 1 ) : 121

DOI: 10.1186/s12859-025-06095-3

Journal article

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An XY chromosome system in Laurus azorica, an endemic dioecious laurel from the Azores

Catarina Branco, Guilherme Roxo, Isaline Chapoix, Ruben M C Rego, Hugo Tessarotto, Sylvain Santoni...

Journal of Evolutionary Biology . 38 ( 7 ) : 1008-1015

DOI: 10.1093/jeb/voaf032

Journal article

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Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies

Vincent Mérel, Théo Tricou, Nelly Burlet, Annabelle Haudry

Molecular Biology and Evolution . 42 ( 6 )

DOI: 10.1093/molbev/msaf111

Journal article

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Human population history on the North Coast of peru from Y chromosomes and mitogenomes

Lea Lorene Huber, Epifanía Arango-Isaza, José R Sandoval, Matthias Urban, Paolo Francalacci, Carla Calò...

Scientific Reports . 15 : 27362

DOI: 10.1038/s41598-025-08241-6

Journal article

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Transposable element expression is associated with sex chromosome number in humans

Jordan Teoli, Miriam Merenciano, Marie Fablet, Anamaria Necsulea, Daniel Siqueira-De-Oliveira, Alessandro Brandulas-Cammarata...

PLoS Genetics . 21 ( 6 ) : e1011668

DOI: 10.1371/journal.pgen.1011668

Journal article

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14C dating of tsunami deposits in arid environments: How challenging can it be? The example of La Graciosa, Canary Islands

Raphaël Paris, Franck Lavigne, Christine Hatté, Juan Francisco Betancort, Jean-Pierre Flandrois, Arnauld Vinçon-Laugier...

Marine Geology . 488 : 107607

DOI: 10.1016/j.margeo.2025.107607

Journal article

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Origin and evolution of Inhibitors of apoptosis (IAP) in early metazoans

Mélanie Ribeiro Lopes, Nicolas Parisot, Sergio Peignier, François Renoz, Patrice Baa-Puyoulet, Hubert Charles...

Conférences Jacques-Monod .

Poster

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Cushion plants in the Alps are swarming with invertebrate life

Keyvan Dumas, Gabriel Marais, Samuel Paitreault, Jean-Noël Avrillier, Alexy Rosa, Mickaël Hedde...

Alpine Botany .

DOI: 10.1007/s00035-025-00335-1

Journal article

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An ancient regulatory variant of ACSF3 influences the coevolution of increased human height and basal metabolic rate via metabolic homeostasis

Yufeng Zhang, Jie Wang, Chuanyou Yi, Yue Su, Zi Yin, Shuxian Zhang...

Cell Genomics . 5 : 100855

DOI: 10.1016/j.xgen.2025.100855

Journal article

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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

Peer Community Journal . 5 : e63

DOI: 10.24072/pcjournal.570

Journal article

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Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers

Tianyi Wang, Melinda A Yang, Zhonghua Zhu, Minmin Ma, Han Shi, Leo Speidel...

Science . 388

DOI: 10.1126/science.adq9792

Journal article

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Maternal genetic origin of Chao Lay coastal maritime populations from Thailand

Wibhu Kutanan, Wipada Woravatin, Metawee Srikummool, Chatmongkon Suwannapoom, Alexander Hübner, Jatupol Kampuansai...

BMC Biology . 23

DOI: 10.1186/s12915-025-02252-5

Journal article

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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: 10.1371/journal.pbio.3002950

Journal article

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Variation in the fitness impact of translationally optimal codons among animals

Florian Bénitière, Tristan Lefébure, Laurent Duret

Genome Research . 35 ( 3 ) : 446-458

DOI: 10.1101/gr.279837.124

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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Evidence that genetic drift not adaptation drives fast‐Z and large‐Z effects in Ficedula flycatchers

Madeline Chase, Maurine Vilcot, Carina Mugal

Molecular Ecology . 34 ( 18 ) : e17262

DOI: 10.1111/mec.17262

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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