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 1098 in total

Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium

Helit Cohen, Claire Hoede, Felix Scharte, Charles Coluzzi, Emiliano Cohen, Inna Shomer...

PLoS Pathogens . 18 ( 4 ) : 35 p.

DOI: 10.1371/journal.ppat.1010425

Journal article

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ICEscreen

Hélène Chiapello, Charles Coluzzi, Nathalie N. Leblond-Bourget, Thomas Lacroix, Julie Lao, Gérard Guédon

Software

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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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Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan)

Leonardo Arias, Nicholas Q Emlen, Sietze Norder, Nora Julmi, Magdalena Lemus Serrano, Thiago Chacon...

Interface Focus . 13

DOI: 10.1098/rsfs.2022.0056

Journal article

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Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago

Jae Joseph Russell B Rodriguez, John Meldwin D Cuales, Michael James B Herrera, Louward Allen M Zubiri, Richard N. Muallil, Altan I. Ishmael...

Frontiers in Genetics . 13 : 901515

DOI: 10.3389/fgene.2022.901515

Journal article

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The transmission of human mitochondrial DNA in four‐generation pedigrees

Qi Liu, Muhammad Faaras Iqbal, Tahir Yaqub, Sehrish Firyal, Yiqiang Zhao, Mark Stoneking...

Human Mutation . 43 : 1259-1267

DOI: 10.1002/humu.24390

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

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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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

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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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

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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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