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 91 to 120 publications on 1073 in total

The social lives of isolates (and small language families): the case of the Northwest Amazon

Rik van Gijn, Sietze Norder, Leonardo Arias, Nicholas Q Emlen, Matheus C B C Azevedo, Allison Caine...

Interface Focus . 13 ( 1 ) : 20220054

DOI: 10.1098/rsfs.2022.0054

Journal article

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Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition

Dang Liu, Benjamin M Peter, Wulf Schiefenhövel, Manfred Kayser, Mark Stoneking

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac165

Journal article

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Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Sandra Oliveira, Kathrin Nägele, Selina Carlhoff, Irina Pugach, Toetik Koesbardiati, Alexander Hübner...

Nature Ecology & Evolution . 6 : 1024 - 1034

DOI: 10.1038/s41559-022-01775-2

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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Rebekka Müller, Ingemar Kaj, Carina Mugal

Genome Biology and Evolution . 14 ( 5 )

DOI: 10.1093/gbe/evac058

Journal article

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Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science . 147 : 105676

DOI: 10.1016/j.jas.2022.105676

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Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Archaeological and Anthropological Sciences . 14 ( 4 ) : 61

DOI: 10.1007/s12520-022-01534-1

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Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure Ségurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

eLife . 11

DOI: 10.7554/eLife.73767

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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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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

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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

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Labile sex expression in angiosperm species with sex chromosomes

Jos Käfer, Marcos Méndez, Sylvain Mousset

Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 )

DOI: 10.1098/rstb.2021.0216

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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

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Sex‐related differences in aging rate are associated with sex chromosome system in amphibians

Hugo Cayuela, Jean-François Lemaître Lemaître, Jean‐paul Léna, Victor Ronget, Iñigo Martínez‐solano, Erin Muths...

Evolution - International Journal of Organic Evolution . 76 ( 2 ) : 346-356

DOI: 10.1111/evo.14410

Journal article

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Sex chromosomes, sex ratios and sex gaps in longevity in plants

Gabriel Marais, Jean-François Lemaître Lemaître

Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 )

DOI: 10.1098/rstb.2021.0219

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A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants

Jos Käfer, Adam Bewick, Amélie Andres‐robin, Garance Lapetoule, Alex Harkess, José Caïus...

New Phytologist . 233 : 1636-1642

DOI: 10.1111/nph.17662

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Exploring correlations in genetic and cultural variation across language families in northeast Asia

Hiromi Matsumae, Peter Ranacher, Patrick Savage, Damián Blasi, Thomas Currie, Kae Koganebuchi...

Science Advances . 7 ( 34 )

DOI: 10.1126/sciadv.abd9223

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Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn

Song Guo, Shuyun Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S Moreno...

BMC Genomics . 22 : 286

DOI: 10.1186/s12864-021-07542-0

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Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Wibhu Kutanan, Dang Liu, Jatupol Kampuansai, Metawee Srikummool, Suparat Srithawong, Rasmi Shoocongdej...

Molecular Biology and Evolution . 38 ( 8 ) : 3459 - 3477

DOI: 10.1093/molbev/msab124

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Genomic insights into population history and biological adaptation in Oceania

Jeremy Choin, Javier Mendoza-Revilla, Lara R Arauna, Sebastian Cuadros-Espinoza, Olivier Cassar, Maximilian Larena...

Nature . 592 ( 7855 ) : 583-589

DOI: 10.1038/s41586-021-03236-5

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The genomic prehistory of peoples speaking Khoisan languages

Brigitte Pakendorf, Mark Stoneking

Human Molecular Genetics . 30 ( 2 ) : R49-R55

DOI: 10.1093/hmg/ddaa221

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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs

Madeline Chase, Hans Ellegren, Carina Mugal

Evolution - International Journal of Organic Evolution . 75 ( 9 ) : 2179-2196

DOI: 10.1111/evo.14234

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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes

Jesper Boman, Carina Mugal, Niclas Backström

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab064

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Les isotopes de l'hydrogène contenus dans les tissus osseux et dentaires de populations archéologiques et leurs usages comme proxys paléoclimatiques et paléoalimentaires

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, Fourel François...

27e édition de la Réunion des Sciences de la Terre .

Conference paper

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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

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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

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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

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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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