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 61 to 90 publications on 136 in total

Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

Journal article

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Dating with transfers

Adrián Davín, Gergely J Szöllosi, Eric Tannier, Bastien Boussau, Vincent Daubin

Journées Ouvertes Biologie Informatique Mathématiques .

Conference paper

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SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

F. Pouyet, M. Bailly-Bechet, Dominique Mouchiroud, Laurent Guéguen

Genome Biology and Evolution . 8 : 2427-41

DOI: 10.1093/gbe/evw165

Journal article

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Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

Journal article

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Efficient gene tree correction guided by genome evolution

Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen...

PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)

DOI: 10.1371/journal.pone.0159559

Journal article

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Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

R. Schep, A. Necsulea, E. Rodriguez-Carballo, I. Guerreiro, G. Andrey, T.H. Nguyen Huynh...

Proceedings of the National Academy of Sciences of the United States of America . 113 ( 48 ) : e7720-e7729

DOI: 10.1073/pnas.1617141113

Journal article

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Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

Priscila Biller, Laurent Guéguen, Carole Knibbe, Eric Tannier

Genome Biology and Evolution . 8 ( 5 ) : 1427-1439

DOI: 10.1093/gbe/evw083

Journal article

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A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

L. Beccari, N. Yakushiji-Kaminatsui, J. M. Woltering, A. Necsulea, N. Lonfat, E. Rodriguez-Carballo...

Genes and Development . 30 : 1172-86

DOI: 10.1101/gad.281055.116

Journal article

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

S. Hohna, M. J. Landis, T. A. Heath, Bastien Boussau, Nicolas Lartillot, B. R. Moore...

Systematic Biology . 65 : 726-36

DOI: 10.1093/sysbio/syw021

Journal article

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Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree

S. Mirarab, M. Bayzid, B. Boussau, T. Warnow

Science . 350 ( 6257 ) : 171-171

DOI: 10.1126/science.aaa7719

Journal article

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The inference of gene trees with species trees

Gergely Szöllősi, Eric Tannier, Vincent Daubin, Bastien Boussau

Systematic Biology . 64 ( 1 ) : e42-e62

DOI: 10.1093/sysbio/syu048

Journal article

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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Md Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow

PLoS ONE . 10 ( 6 ) : e0129183

DOI: 10.1371/journal.pone.0129183

Journal article

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Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

Ruchi Chaudhary, Bastien Boussau, J. Gordon Burleigh, David Fernández-Baca

Systematic Biology . 64 ( 2 ) : 325-339

DOI: 10.1093/sysbio/syu128

Journal article

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Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

R. A. Wiberg, D. L. Halligan, R. W. Ness, A. Necsulea, H. Kaessmann, P. D. Keightley

Genome Biology and Evolution . 7 : 2432-44

DOI: 10.1093/gbe/evv155

Journal article

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Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen

BMC Bioinformatics . 16 ( Suppl 14 ) : S5

DOI: 10.1186/1471-2105-16-S14-S5

Journal article

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Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Arellano Davin, Eric Tannier, Vincent Daubin, Bastien Boussau

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)

DOI: 10.1098/rstb.2014.0335

Journal article

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Probabilistic Graphical Model Representation in Phylogenetics

S. Höhna, Ta. Heath, Bastien Boussau

Systematic Biology . 63 ( 5 ) : 753-771

DOI: 10.1093/sysbio/syu039

Journal article

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Whole-genome analyses resolve early branches in the tree of life of modern birds.

Erich Jarvis, Siavash Mirarab, Andre Aberer, Bo Li, Peter Houde, Cai Li...

Science . 346 ( 6215 ) : 1320-31

DOI: 10.1126/science.1253451

Journal article

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Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

Claudia C. Weber, Bastien Boussau, Jonathan Romiguier, Erich D. Jarvis, H. Ellegren

Genome Biology . 15 : 549

DOI: 10.1186/s13059-014-0549-1

Journal article

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau, Tandy Warnow

Science . 346 ( 6215 ) : 1250463

DOI: 10.1126/science.1250463

Journal article

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Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

Bastien Boussau, Z. Walton, Ja. Delgado, F. Collantes, L. Beani, Ij. Stewart...

PLoS ONE . 9 : e107709

DOI: 10.6084/m9.figshare.1040412

Journal article

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The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy

Biology Letters . 9 ( 5 ) : 20130608

DOI: 10.1098/rsbl.2013.0608

Journal article

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Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Cedric Chauve, Nadia El-Mabrouk, Laurent Gueguen, Magali Semeria, Eric Tannier

Models and Algorithms for Genome Evolution . 19 : 47-62

Book chapter

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Efficient Exploration of the Space of Reconciled Gene Trees.

Gergely J Szöllosi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier, Vincent Daubin

Systematic Biology . 62 ( 6 ) : 901-912

DOI: 10.1093/sysbio/syt054

Journal article

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

Journal article

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

Journal article

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Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

M. Soumillon, A. Necsulea, M. Weier, D. Brawand, X. Zhang, H. Gu...

Cell Reports . 3 ( 6 ) : 2179-2190

DOI: 10.1016/j.celrep.2013.05.031

Journal article

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A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

Journal article

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