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 391 to 420 publications on 1098 in total

Ancient west Eurasian ancestry in southern and eastern Africa

Joseph Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking...

Proceedings of the National Academy of Sciences of the United States of America . 111 ( 7 ) : 2632-2637

DOI: 10.1073/pnas.1313787111

Journal article

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Unraveling the complex maternal history of southern African Khoisan populations

Chiara Barbieri, Tom Güldemann, Linda Gerlach, Falko Berthold, Hirosi Nakagawa, Sununguko Mpoloka...

American Journal of Physical Anthropology . 153 ( 3 ) : 435-448

DOI: 10.1002/ajpa.22441

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New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa

Enrico Macholdt, Montgomery Slatkin, Brigitte Pakendorf, Mark Stoneking

American Journal of Physical Anthropology . 156 ( 4 ) : 661-664

DOI: 10.1002/ajpa.22675

Journal article

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Migration and Interaction in a Contact Zone: mtDNA Variation among Bantu-Speakers in Southern Africa

Chiara Barbieri, Mário Vicente, Sandra Oliveira, Koen Bostoen, Jorge Rocha, Mark Stoneking...

PLoS ONE . 9 ( 6 ) : e99117

DOI: 10.1371/journal.pone.0099117

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A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Takeshi Kawakami, Linnéa Smeds, Niclas Backström, Arild Husby, Anna Qvarnström, Carina Mugal...

Molecular Ecology . 23 ( 16 ) : 4035-4058

DOI: 10.1111/mec.12810

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Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Carina Mugal, Jochen B.W. Wolf, Ingemar Kaj

Molecular Biology and Evolution . 31 ( 1 ) : 212-231

DOI: 10.1093/molbev/mst192

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Preserving immune diversity through ancient inheritance and admixture

Laure L. Segurel, Lluis Quintana-Murci

Current Opinion in Immunology . 30 : 79-84

DOI: 10.1016/j.coi.2014.08.002

Journal article

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TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception

Amir Kermany, Laure L. Segurel, Tiffany Oliver, Molly Przeworski

Bioinformatics . 30 ( 14 ) : 2035-2042

DOI: 10.1093/bioinformatics/btu159

Journal article

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Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

Carla Aimé, Paul Verdu, Laure L. Segurel, Begoña Martinez-Cruz, Tatyana Hegay, Evelyne Heyer...

European Journal of Human Genetics . 22 ( 10 ) : 1201-1207

DOI: 10.1038/ejhg.2014.2

Journal article

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A call for benchmarking transposable element annotation methods.

Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte...

Mobile DNA . 6 : 13

DOI: 10.1186/s13100-015-0044-6

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Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells

Sophie Blanc, Florence Ruggiero, Anne-Marie Birot, Hervé Acloque, Didier Decimo, Emmanuelle Lerat...

PLoS ONE . 9 ( 3 ) : e92039

DOI: 10.1371/journal.pone.0092039

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The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Franck Picard, Jean-Charles Cadoret, Benjamin Audit, Alain Arneodo, Adriana A. Alberti, Christophe Battail...

PLoS Genetics . 10 ( 5 ) : e1004282

DOI: 10.1371/journal.pgen.1004282

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The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Y Lesecque, S. S. Glemin, N. Lartillot, D. Mouchiroud, L. Duret

PLoS Genetics . 10 : e1004790

DOI: 10.1371/journal.pgen.1004790

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Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome

E. M. Kvikstad, L. Duret

Molecular Biology and Evolution . 31 : 23-36

DOI: 10.1093/molbev/mst185

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Diet of ancient Egyptians inferred from stable isotope systematics

Alexandra Touzeau, Romain Amiot, Janne Blichert-Toft, Jean-Pierre Flandrois, François Fourel, Vincent Grossi...

Journal of Archaeological Science . 46 : 114-124

DOI: 10.1016/j.jas.2014.03.005

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MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.

Jean-Pierre Flandrois, Gérard Lina, Oana Dumitrescu

BMC Bioinformatics . 15 ( 1 ) : 107

DOI: 10.1186/1471-2105-15-107

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Mycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis

D. Pin, V. Guerin-Faublee, V. Garreau, F. Breysse, Oana Dumitrescu, Jean-Pierre Flandrois...

Emerging Infectious Diseases . 20 : 2111-4

DOI: 10.3201/eid2012.140184

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Promiscuous Nickel Import in Human Pathogens: Structure, Thermodynamics, and Evolution of Extracytoplasmic Nickel-Binding Proteins

Hugo Lebrette, Céline Brochier-Armanet, Barbara Zambelli, Hilde de Reuse, Elise Borezée-Durant, Stéfano Ciurli...

Structure . 22 ( 10 ) : 1421-1432

DOI: 10.1016/j.str.2014.07.012

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Protein SYCP2 Is an Ancient Component of the Metazoan Synaptonemal Complex

J. Fraune, M. Alsheimer, J. Redolfi, Céline Brochier-Armanet, R. Benavente

Cytogenetic and genome research . 144 : 299-305

DOI: 10.1159/000381080

Journal article

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Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family

R. Zallot, Céline Brochier-Armanet, K. W. Gaston, F. Forouhar, P. A. Limbach, J. F. Hunt...

ACS Chemical Biology . 9 ( 8 ) : 1812-1825

DOI: 10.1021/cb500278k

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Ail and PagC-Related Proteins in the Entomopathogenic Bacteria of Photorhabdus Genus

Annabelle Mouammine, Anne Lanois, Sylvie Pages, Bénédicte Lafay, Virginie Molle, Marc Canova...

PLoS ONE . 9 ( 10 ) : e110060

DOI: 10.1371/journal.pone.0110060

Journal article

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Contribution of graphs to the analysis of bacterial genome architecture

Olivier Poirion, Bénédicte Lafay

BioNetVisA workshop, ECCB'14, the 13th European Conference on Computational Biology .

Conference paper

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Structuration of the bacterial replicon space

Olivier Poirion, Bénédicte Lafay

ECCB'14 . CD

Conference paper

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Chromosome formation in bacteria

Olivier Poirion, Bénédicte Lafay

EMBO Conference "Microbiology after the genomics revolution : Genomes 2014" .

Conference paper

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Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

Johan Panek, Hicham El Alaoui, Anne Mone, Serge Urbach, Edith Demettre, Catherine Texier...

PLoS ONE . 9 ( 6 ) : e100791

DOI: 10.1371/journal.pone.0100791

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Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.

Nicolas Parisot, Adrian Pelin, Cyrielle Gasc, Valérie Polonais, Abdel Belkorchia, Johan Panek...

Genome Biology and Evolution . 6 ( 9 ) : 2289-300

DOI: 10.1093/gbe/evu178

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