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 1 to 30 publications on 136 in total

Search for photosynthesis-related protein sites through chloroplast phylogenomics

Pierre Gérenton, Philippe Veber, Vincent Lacroix, Bastien Boussau

ALPHY/AIEM 2025 .

Poster

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Convergent transcriptomic and genomic adaptation in xeric rodents

Chalopin Domitille, Rey Carine, Ganofsky Jeremy, Blin Juliana, Chevret Pascale, Mouginot Marion...

DOI: 10.1101/2024.10.02.616319

Preprint

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Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks

Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2024.06.17.599404

Preprint

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Simulations of Sequence Evolution: How (Un)realistic They Are and Why

Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau

Molecular Biology and Evolution . 41 ( 1 )

DOI: 10.1093/molbev/msad277

Journal article

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Evolution and functional relevance of non-coding elements in vertebrate genomes

Anamaria Necsulea

HDR

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

DOI: 10.1101/2023.05.27.542554

Preprint

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Meta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research

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

DOI: 10.1101/2024.08.17.608405

Preprint

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SAMD9L acts as an antiviral factor against HIV-1 and primate lentiviruses by restricting viral and cellular translation

Alexandre Legrand, Clara Dahoui, Clément de la Myre Mory, Kodie Noy, Laura Guiguettaz, Margaux Versapuech...

PLoS Biology . 22 ( 7 ) : e3002696

DOI: 10.1371/journal.pbio.3002696

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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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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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

Peer Community Journal . 4 ( e89 )

DOI: 10.24072/pcjournal.457

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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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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An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Adrián Davín, Ben Woodcroft, Rochelle Soo, Benoit Morel, Ranjani Murali, Dominik Schrempf...

DOI: 10.1101/2023.08.08.552427

Preprint

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Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

Journal article

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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

Journal article

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Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

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Calculs d’inférence dans les arbres phylogénétiques

Laurent Guéguen

Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202

DOI: 10.51926/ISTE.9069.ch7

Book chapter

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Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

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Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Rui Borges, Bastien Boussau, Sebastian Höhna, Ricardo Pereira, Carolin Kosiol

Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346

DOI: 10.1111/2041-210X.13980

Journal article

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Relative Time Constraints Improve Molecular Dating

Gergely Szöllõsi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

Systematic Biology . 71 ( 4 ) : 797-809

DOI: 10.1093/sysbio/syab084

Journal article

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

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Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

Marie Cariou, Léa Picard, Laurent Guéguen, Stéphanie Jacquet, Andrea Cimarelli, Oliver Fregoso...

Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )

DOI: 10.1073/pnas.2206610119

Journal article

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Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet...

Current Biology . 32 ( 10 ) : 2325-2333.e1-e6

DOI: 10.1016/j.cub.2022.04.014

Journal article

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