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 31 to 60 publications on 1098 in total

Small ruminants versus endogenous retroviruses: an evolutive showdown still in progress in the domestic goat genome

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

International congress on transposable elements .

Poster

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A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

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

DOI: 10.1101/2024.06.21.600049

Preprint

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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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Diversité et diversification des Pectobacteriaceae, une famille de bactéries phytopathogènes d’importance mondiale

Céline Brochier, Nicole Hugouvieux-Cotte-Pattat, Jean-Pierre Flandrois, Sylvie Reverchon, Jérôme Briolay

Cahiers Scientifiques de la Fondation Pierre Vérots . ( 10 ) : 19-29

Journal article

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ISMB/ECCB 2023 organization benefited from the strengths of the French bioinformatics community

Anna-Sophie Fiston-Lavier, Sandra Dérozier, Guy Perrière, Marie-France Sagot

Bioinformatics Advances . 4 ( 1 ) : vbae040

DOI: 10.1093/bioadv/vbae040

Journal article

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Bradyrhizobium hardenbergiae sp. nov., isolated from Hardenbergia violacea in Australia, represents a novel basal lineage of the B. elkanii supergroup

Bénédicte Lafay, Elina Coquery, Phil M. Oger

Preprint

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A Wright–Fisher graph model and the impact of directional selection on genetic variation

Ingemar Kaj, Carina Mugal, Rebekka Müller-Widmann

Theoretical Population Biology . 159 : 13-24

DOI: 10.1016/j.tpb.2024.07.004

Journal article

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Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam

Dinh Huong Thao, Tran Huu Dinh, Shigeki Mitsunaga, La Duc Duy, Nguyen Thanh Phuong, Nguyen Phuong Anh...

PLoS ONE . 19 ( 6 ) : e0304964

DOI: 10.1371/journal.pone.0304964

Journal article

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Complete mitochondrial genomes of patients from Thailand with cardiovascular diseases

Wipada Woravatin, Rattanasak Wongkomonched, Wichittra Tassaneeyakul, Mark Stoneking, Pattarapong Makarawate, Wibhu Kutanan

PLoS ONE . 19 ( 7 ) : e0307036

DOI: 10.1371/journal.pone.0307036

Journal article

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GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

Florian Bénitière, Laurent Duret, Anamaria Necsulea

NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064

DOI: 10.1093/nargab/lqae064

Journal article

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Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids

Jesper Boman, Anna Qvarnström, Carina Mugal

BMC Biology . 22 ( 1 ) : 124

DOI: 10.1186/s12915-024-01920-2

Journal article

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High prevalence of PRDM9-independent recombination hotspots in placental mammals

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

Proceedings of the National Academy of Sciences of the United States of America . 121 ( 23 ) : e2401973121

DOI: 10.1073/pnas.2401973121

Journal article

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LncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma

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

DOI: 10.1101/2021.03.03.433778

Preprint

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Persistent homology reveals strong phylogenetic signal in 3D protein structures

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

PNAS Nexus . 3 ( 4 ) : 158

DOI: 10.1093/pnasnexus/pgae158

Journal article

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The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Cesar A Fortes-Lima, Concetta Burgarella, Rickard Hammarén, Anders Eriksson, Mário Vicente, Cecile Jolly...

Nature . 625 ( 7995 ) : 540–547

DOI: 10.1038/s41586-023-06770-6

Journal article

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

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

DOI: 10.1101/2024.03.06.583651

Preprint

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The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome

Madeline Chase, Maurine Vilcot, Carina Mugal

Proceedings of the Royal Society B: Biological Sciences . 291 ( 2015 ) : 20232382

DOI: 10.1098/rspb.2023.2382

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 . : e17262

DOI: 10.1111/mec.17262

Journal article

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Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov

Nicole Hugouvieux-Cotte-Pattat, Jean-Pierre Flandrois, Jérôme Briolay, Sylvie Reverchon, Céline Brochier-Armanet

Systematic and Applied Microbiology . 47 ( 2-3 ) : 126497

DOI: 10.1016/j.syapm.2024.126497

Journal article

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MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Jérémy Tournayre, Valérie Polonais, Ivan Wawrzyniak, Reginald Florian Akossi, Nicolas Parisot, Emmanuelle Lerat...

International Journal of Molecular Sciences . 25 ( 2 ) : 880

DOI: 10.3390/ijms25020880

Journal article

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Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Florian Bénitière, Anamaria Necsulea, Laurent Duret

eLife . 13 : RP93629

DOI: 10.7554/eLife.93629.3

Journal article

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Imbalanced speciation pulses sustain the radiation of mammals

Ignacio Quintero, Nicolas Lartillot, Hélène Morlon

Science . 384 ( 6699 ) : 1007-1012

DOI: 10.1126/science.adj2793

Journal article

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Transposable element expression with variation in sex chromosome number: insights into a toxic Y effect on human longevity

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

Peer Community In Genomics .

DOI: 10.1101/2023.08.03.550779

Journal article

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MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, Sophie Abby

Peer Community Journal . 3 : e28

DOI: 10.24072/pcjournal.250

Journal article

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Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes

Charles Coluzzi, Martin Guillemet, Fanny Mazzamurro, Marie Touchon, Maxime Godfroid, Guillaume Achaz...

Molecular Biology and Evolution . 40 ( 10 ) : msad217

DOI: 10.1093/molbev/msad217

Journal article

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The evolution of GC-biased gene conversion by means of natural selection

Nicolas Lartillot, Julien Joseph, Augustin Clessin

ETEE'2023: Empiricism & Theory in Ecology and Evolution .

Conference paper

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Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Gilles Prilaux, Jeremy E. Martin, Romain Amiot...

International Journal of Osteoarchaeology . 33 ( 1 ) : 39-50

DOI: 10.1002/oa.3172

Journal article

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Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense

Ram Prasad Awal, Frank D Müller, Daniel Pfeiffer, Caroline L Monteil, Guy Perrière, Christopher T Lefèvre...

mBio . 14 ( 5 )

DOI: 10.1128/mbio.01649-23

Journal article

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