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 151 to 180 publications on 1005 in total

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Nicolas Lartillot

Phylogenetics in the Genomic Era . : 1.5:1--1.5:16

Book chapter

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An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa

Djivan Prentout, Olga Razumova, Benedicte Rhone, Hélène Badouin, Hélène Henri, Cong Feng...

Genome Research . 30 ( 2 ) : 164-172

DOI: 10.1101/gr.251207.119

Journal article

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The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Hélène E Badouin, Amandine Velt, François Gindraud, Timothée Flutre, Vincent Dumas, Sonia Vautrin...

Genome Biology . 21 ( 1 ) : 223

DOI: 10.1186/s13059-020-02131-y

Journal article

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An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat

Genes . 11 ( 9 ) : 1046

DOI: 10.3390/genes11091046

Journal article

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A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

Stefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova...

Journal of Clinical Microbiology . 58 ( 6 ) : 1128

DOI: 10.1128/JCM.00060-20

Journal article

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Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System

Cécile Fruchard, Hélène E Badouin, David Latrasse, Ravi S Devani, Aline Muyle, Bénédicte Rhoné...

Genes . 11 ( 7 ) : 787

DOI: 10.3390/genes11070787

Journal article

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From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria

Keren-Khadmy Noa, Natalie Zeytuni, Nitzan Kutnowski, Guy Perriere, Caroline Monteil, Raz Zarivachid

PLoS ONE . 15 ( 4 ) : e0231839

DOI: 10.1371/journal.pone.0231839

Journal article

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Isotopic systematics point to wild origin of mummified birds in Ancient Egypt

Marie Linglin, Romain Amiot, Pascale Richardin, Stéphanie Porcier, Ingrid Antheaume, Didier Berthet...

Scientific Reports . 10 ( 1 )

DOI: 10.1038/s41598-020-72326-7

Journal article

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The Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France

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

Journal of Archaeological Science: Reports . 34 : 102595

DOI: 10.1016/j.jasrep.2020.102595

Journal article

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Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzzati, Mélissa Mary...

eLife . 9

DOI: 10.7554/eLife.54795

Journal article

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Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)

Nicole Hugouvieux-Cotte-Pattat, Celine Brochier-Armanet, Jean-Pierre Flandrois, Sylvie Reverchon

International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514

DOI: 10.1099/ijsem.0.004306

Journal article

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δ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?

Christophe Lécuyer, Antonio Sanchez Marco, Alejandro Lomoschitz, Juan-Francisco Betancort, François Fourel, Romain Amiot...

Journal of African Earth Sciences . 162 : 103702

DOI: 10.1016/j.jafrearsci.2019.103702

Journal article

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Phylogenomics and Genome Annotation

Anamaria Necsulea

Phylogenetics in the Genomic Era . : 4.1:1--4.1:26

Book chapter

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Bedrock radioactivity influences the rate and spectrum of mutation

Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny-Dupré, David Eme, Arnaud Bellec...

eLife . 9 : e56830

DOI: 10.7554/eLife.56830

Journal article

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Key role of chromosomal mobile genetic elements transferred by conjugation in the dissemination of antimicrobial resistance in S. suis

Virginie Libante, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk...

4th International Workshop on Streptococcus suis .

Conference paper

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Development of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions

Nicolas Parisot, Agnès Vallier, Justin Maire, Mariana G. Ferrarini, Benjamin Gillet, Sandrine Hughes...

Auvergne Rhône-Alpes Regional Workshop on Microbiome .

Poster

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Archaic mitochondrial DNA inserts in modern day nuclear genomes

Robert Bücking, Murray Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo, Mark Stoneking

BMC Genomics . 20 ( 1 ) : 1017

DOI: 10.1186/s12864-019-6392-8

Journal article

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Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations

Wibhu Kutanan, Jatupol Kampuansai, Metawee Srikummool, Andrea Brunelli, Silvia Ghirotto, Leonardo Arias...

Molecular Biology and Evolution . 36 : 1490 - 1506

DOI: 10.1093/molbev/msz083

Journal article

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Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome

Alexander Hübner, Manja Wachsmuth, Roland Schröder, Mingkun Li, Anna Maria Eis-Hübinger, Burkhard Madea...

Scientific Reports . 9 : 11219

DOI: 10.1038/s41598-019-47570-1

Journal article

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The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast

Chiara Barbieri, Rodrigo Barquera, Leonardo Arias, José R Sandoval, Oscar Acosta, Camilo Zurita...

Molecular Biology and Evolution . 36 ( 12 ) : 2698 - 2713

DOI: 10.1093/molbev/msz174

Journal article

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WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Lilit Nersisyan, Maria Nikoghosyan, Laurent C Francioli, Androniki Menelaou, Sara L Pulit, Clara C Elbers...

Scientific Reports . 9 : 18758

DOI: 10.1038/s41598-019-55109-7

Journal article

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Multiple Deeply Divergent Denisovan Ancestries in Papuans

Guy Jacobs, Georgi Hudjashov, Lauri Saag, Pradiptajati Kusuma, Chelzie Darusallam, Daniel Lawson...

Cell .

DOI: 10.1016/j.cell.2019.02.035

Journal article

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Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia

Nicolas Brucato, Verónica Fernandes, Pradiptajati Kusuma, Viktor Černý, Connie Mulligan, Pedro Soares...

Genome Biology and Evolution . 11 ( 3 ) : 748-758

DOI: 10.1093/gbe/evz028

Journal article

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The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Sandra Oliveira, Alexander Hübner, Anne-Maria Fehn, Teresa Aço, Fernanda Lages, Brigitte Pakendorf...

European Journal of Human Genetics . 27 ( 3 ) : 475-483

DOI: 10.1038/s41431-018-0304-2

Journal article

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Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels

Ana Lokmer, Amandine Cian, Alain Froment, Nausicaa Gantois, Eric Viscogliosi, Magali Chabé...

PLoS ONE . 14 ( 2 ) : e0211139

DOI: 10.1371/journal.pone.0211139

Journal article

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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

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Article 22. Crise du stockage: conserver les molécules d'ADN ou les données informatiques de l'ADN ?

Dominique D. Joly, Guy Perriere

101 Secrets de l'ADN. CNRS Editions, Paris, pp 90-91 . : 90-91

Book chapter

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Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Jean-Pierre Flandrois, Céline Brochier-Armanet, Jérôme Briolay, Danis Abrouk, Guillaume P Schwob, Philippe Normand...

Research in Microbiology . 170 ( 6-7 ) : 280-287

DOI: 10.1016/j.resmic.2019.06.005

Journal article

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Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA

Eaazhisai Kandiah, Diego Carriel, Pierre Simon Garcia, Jan Felix, Manuel Banzhaf, George Kritikos...

Structure .

DOI: 10.1016/j.str.2019.10.003

Journal article

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