Functional Evolutionary Genomics Group

Members

In the "Functional evolutionary genomics" team, one of our ovearching aims is understanding the genomic basis of phenotypic evolution. We are particularly interested in convergent phenotypic evolution events. We study a wide range of phenotypic traits, including morphological traits, sensory traits, physiological traits. Our aim is to identify the genomic changes that accompany phenotypic evolution. We also aim to characterize the evolutionary processes that underlie phenotypic changes, by searching for instances of lineage-specific positive selection or relaxation of purifying selection.

We study both protein-coding gene evolution and non-coding DNA evolution, in particular regulatory elements that control gene expression. We aim to develop new methods for this purpose, and rely on statistical inference, including deep learning.

Publications

Display of 91 to 120 publications on 136 in total

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

Philippe Julien, David Brawand, Magali Soumillon, Anamaria Necsulea, Angélica Liechti, Frédéric Schütz...

PLoS Biology . 10 ( 5 ) : e1001328

DOI: 10.1371/journal.pbio.1001328

Journal article

see the publication

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.

Gergely J Szöllosi, Bastien Boussau, Sophie S Abby, Eric Tannier, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 43 ) : 17513-17518

DOI: 10.1073/pnas.1202997109

Journal article

see the publication

Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

Jean Bérard, Laurent Guéguen

Systematic Biology . 61 ( 3 ) : 510-521

DOI: 10.1093/sysbio/sys024

Journal article

see the publication

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Jonathan Romiguier, Emeric Figuet, Nicolas Galtier, Emmanuel J.P. Douzery, Bastien Boussau, Julien y Dutheil...

PLoS ONE . 7 ( 3 ) : e33852

DOI: 10.1371/journal.pone.0033852

Journal article

see the publication

Efficient selection of branch-specific models of sequence evolution.

Julien y Dutheil, Nicolas Galtier, Jonathan Romiguier, Emmanuel J.P. Douzery, Vincent Ranwez, Bastien Boussau

Molecular Biology and Evolution . 29 ( 7 ) : 1861-1874

DOI: 10.1093/molbev/mss059

Journal article

see the publication

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

Jj. Fong, Jm. Brown, Mk. Fujita, Bastien Boussau

PLoS ONE . 7 : e48990

DOI: 10.1371/journal.pone.0048990

Journal article

see the publication

Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, Eric Tannier

Bioinformatics . 28 ( 18 ) : i382-i388

DOI: 10.1093/bioinformatics/bts374

Journal article

see the publication

The evolution of gene expression levels in mammalian organs

David Brawand, Magali Soumillon, Anamaria Necsulea, Philippe Julien, Gábor Csárdi, Patrick Harrigan...

Nature . 478 ( 7369 ) : 343-348

DOI: 10.1038/nature10532

Journal article

see the publication

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot...

Genome Biology and Evolution . 3 ( 3 ) : 762-781

DOI: 10.1093/gbe/evr070

Journal article

see the publication

Meiotic recombination favors the spreading of deleterious mutations in human populations

Anamaria Necsulea, L. Duret, Alexandra Popa, David N. Cooper, Peter Stentson, Dominique Mouchiroud...

Human Mutation . 32 ( 2 ) : 198-206

DOI: 10.1002/humu.21407

Journal article

see the publication

La notion d'espèce en écologie microbienne

T. Campillo, Malek Shams, Sally Burr, Martha Helena Ramírez-Bahena, Florent Lassalle, Franck Bertolla...

1er Colloque National d'Ecologie Scientifique .

Conference paper

see the publication

Toward an ecological concept for bacterial species in Agrobacterium

Tony Campillo, Florent Lassalle, M. Shams, Martha Helena Ramírez-Bahena, Jessica Baude, Celine Lavire...

12th International Conference on Plant Pathogenic Bacteria .

Conference paper

see the publication

Identification de fonctions « spécifiques d'espèce » impliquées dans l'individualisation en écovar de l’espèce G8 du complexe Agrobacterium tumefaciens

Florent Lassalle, Daniel Muller, Denis Costechareyre, David Chapulliot, Celine Lavire, Laurent Guéguen...

Journées des Microbiologistes de l'INRA .

Conference paper

see the publication

Computing the likelihood of sequence segmentation under Markov modelling

Laurent Guéguen

Preprint

see the publication

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

Journal article

see the publication

Genomes as documents of evolutionary history

Bastien Boussau, Vincent Daubin

Trends in Ecology & Evolution . 1192 : 1-9

Journal article

see the publication

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Ravi D. Barabote, Gary Xie, David H. Leu, Philippe Normand, Anamaria Necsulea, Vincent Daubin...

Genome Research . ( 19 ) : 1033-1043

DOI: 10.1101/gr.084848.108

Journal article

see the publication

Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea, M. Sémon, L. Duret, L.D. Hurst

Trends in Genetics . 25(12) : 519-522

Journal article

see the publication

The relationship between DNA replication and human genome organization.

Anamaria Necsulea, Claire Guillet, Jean-Charles Cadoret, Marie-Noëlle Prioleau, L. Duret

Molecular Biology and Evolution . 26 ( 4 ) : 729-741

DOI: 10.1093/molbev/msn303

Journal article

see the publication

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event ?

Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler...

BMC Evolutionary Biology . 8:336 : 1-19

DOI: 10.1186/1471-2148-8-336

Journal article

see the publication

Etude des patrons d`évolution asymétrique dans les séquences d`ADN

A. Necşulea

incollection . -- : 476-482

Journal article

see the publication

The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome

N. Mugnier, Laurent Guéguen, Cristina Vieira, C. Biémont

Gene . 411 : 87-93

Journal article

see the publication

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

Journal article

see the publication

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

Journal article

see the publication

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

J. Dutheil, Bastien Boussau

BMC Evolutionary Biology . 8:255 : 31-42

Journal article

see the publication

Etude des patrons d'évolution asymétrique dans les séquences d'ADN

Anamaria Necsulea

Thesis

see the publication