The following list includes papers published by users from the Labex CEMeB and the ISE-M institute.

All these papers used at least one of our services or involved one person from our team (ISE-M / MBB Clusters and/or Web services). For any work using the computing platform and other “Bioinformatics Biodiversity Montpellier” services, thank you to include the following sentence in your publications: “[Replace_with_your_project_name] benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB, an ANR”Investissements d’avenir" program (ANR-10-LABX-04-01)."

 Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia
Alix Armero, Nicolas Berthet, and Jean-Christophe Avarre
doi: 10.3390/v13010133
 Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants.
Allio R., Nabholz B., Wanke S., Chomicki G., Pérez-Escobar O.A., Cotton A.M., Clamens A.-L., Kergoat G.J., Sperling F.A.H. & Condamine F.L. (2021) 
Nature Communications, 12, 354.
DOI: 10.1038/s41467-020-20507-3
 Island Songbirds as Windows into Evolution in Small Populations.
Leroy, Thibault, Marjolaine Rousselle, Marie-Ka Tilak, Aude E. Caizergues, Céline Scornavacca, María Recuerda, Jérôme Fuchs, et al.
Current Biology, janvier. 2021
DOI: 10.1016/j.cub.2020.12.040.
 Brown trout phylogenetics: a persistent mirage towards (too) many species.
Bruno Guinand, Münevver Oral & Christelle Tougard.
J Fish Biol. 2021;1-10
DOI: 10.1111/jfb.14686
 How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels.
Simon, A., Fraïsse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021).
Journal of Evolutionary Biology, 34, 208-223.
DOI: 10.1111/jeb.13709
Jay P*, Chouteau M*, Whibley A, Bastide H, Parrinello H, Llaurens V, Joron M
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms.
Nature Genetics. 2021
DOI: 10.1038/s41588-020-00771-1.
 Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.).
Krick M.V., Desmarais E., Samaras A., Guéret E., Dimitroglou A., Pavilidis M., Tsigenopoulos C., Guinand B.
BMC Genomics 22: 111. 2021
DOI: 10.1186/s12864-021-07420-9
 Sampling schemes and drift can bias admixture proportions inferred by structure
Ken S. Toyama, Pierre‐André Crochet, Raphaël Leblois
Molecular Ecology Resources 20: 1769-1785. 2020
DOI: 10.1111/1755-0998.13234
 New genomic resources for three exploited Mediterranean fishes
Katharina Fietz, Elena Trofimenko, Pierre-Edouard Guerin, Véronique Arnal, Montserrat Torres-Oliva, Stéphane Lobréaux, Angel Pérez-Ruzafa, Stéphanie Manel, Oscar Puebla
DOI: 10.1016/j.ygeno.2020.06.041
 Global determinants of freshwater and marine fish genetic diversity
Stéphanie Manel, Pierre-Edouard Guerin, David Mouillot, Simon Blanchet, Laure Velez, Camille Albouy & Loïc Pellissier
Nature Communications
DOI: 10.1038/s41467-020-14409-7
 Transcriptomic regulation of seasonal coat color change in hares
Mafalda S. Ferreira, Paulo C. Alves, Colin M. Callahan, Iwona Giska, Liliana Farelo, Hannes Jenny, L. Scott Mills, Klaus Hackländer, Jeffrey M. Good, José Melo‐Ferreira
Ecology and Evolution.
DOI: 10.1002/ece3.5956
 DynACof: A Process-Based Model to Study Growth, Yield and Ecosystem Services of Coffee Agroforestry Systems
Vezy Rémi, Guerric le Maire, Mathias Christina, Selena Georgiou, Pablo Imbach, Hugo G. Hidalgo, Eric J. Alfaro, et al.
Environmental Modelling & Software 124 (1 février 2020): 104609
DOI: 10.1016/j.envsoft.2019.104609
 Sex Chromosome Degeneration by Regulatory Evolution.
Lenormand T, F Fyon, E Sun, D Roze. 
Current Biology 30: 3001-3006 2020
DOI: 10.1016/j.cub.2020.05.052
Philip Agnew: 
 MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.
Allio, Rémi, Alex Schomaker-Bastos, Jonathan Romiguier, Francisco Prosdocimi, Benoit Nabholz, et Frédéric Delsuc.
Molecular Ecology Resources. 2020
DOI: 10.1111/1755-0998.13160
 Life tables shape genetic diversity in marine fishes.
Barry, P., Broquet, T., & Gagnaire, P. A.
bioRxiv 2020.
DOI: 10.1101/2020.12.18.423459
 On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo, 
Rabier C-E, Berry V., Glaszmann J.C., Pardi F., Scornavacca C.
under revision for Plos Computational Biology, available from biorxiv.
DOI: 10.1101/2020.10.07.329425
 Forest gains and losses in Southeast Asia over 27 years: the slow convergence towards reforestation. 
Paradis E.
Forest Policy and Economics 122: 102332. 2020
DOI: 10.1016/j.forpol.2020.102332
 Modelling transition in land cover highlights forest losses and gains in Southeast Asia.
Paradis E.
Biodiversity and Conservation 29: 2539–2551. 2020
DOI: 10.1007/s10531-020-01987-7
 The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse.
North HL, Caminade P, Severac D, Belkhir K, Smadja CM.
Philosophical Transactions of the Royal Society B: Biological Sciences 375(1806): 20190540. 2020
DOI: 10.1098/rstb.2019.0540
 An update on the distribution and diversification of <i>Rhabdomys</i> sp. (Muridae, Rodentia).
Ganem, G., Dufour, C. M. S., Avenant, N. L., Caminade, P., Eiseb, S. J., Tougard, C., & Pillay, N.
Journal of Vertebrate Biology, 69(2), 1-17. 2020
DOI: 10.25225/jvb.20013
 Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites
Macedo D., I. Caballero, M. Mateos, R. Leblois, S. McCay, L. A. Hurtado.
PeerJ 7:e7780 2019
DOI: 10.7717/peerj.7780
 ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.
Paradis E. & Schliep K.
Bioinformatics 35: 526–528. 2019
DOI: 10.1093/bioinformatics/bty633
 Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution
Allio R., Scornavacca C., Nabholz B., Clamens A.-L., Sperling F.A.H. & Condamine F.L.
Systematic Biology, 69, 38-60.
 An annotated draft genome of the mountain hare (Lepus timidus)
Marques, J. P., F. A. Seixas, L. Farelo, C. M. Callahan, J. M. Good, W. I. Montgomery, N. Reid, P. C. Alves, P. Boursot, and J. Melo-Ferreira.
2019. Genome Biology and Evolution. 
 Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates
Debiais-Thibaud M, Simion P, Ventéo S, Muñoz D, Marcellini S, Mazan S, Haitina T
Mol Biol Evol. 2019 Oct 1;36(10):2265-2276
 Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels
Alexis Simon, Christine Arbiol, Einar Eg Nielsen, Jérôme Couteau, Rossana Sussarellu, Thierry Burgeot, Ismaël Bernard, Joop W. P. Coolen, Jean‐Baptiste Lamy, Stéphane Robert, Maria Skazina, Petr Strelkov, Henrique Queiroga, Ibon Cancio, John J. Welch, Frédérique Viard, Nicolas Bierne
Evolutionary Applications
 Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily
Courcelle M., Tilak M., Leite Y. L. R., Douzery E. J. P. & Fabre P.-H.
2019. Molecular Phylogenetics and Evolution 136 : 241-253
 Empathy and compassion toward other species decrease with evolutionary divergence time
Aurélien Miralles, Michel Raymond & Guillaume Lecointre
Scientific Reports 9, 19555 (2019)
 Introgression drives repeated evolution of winter coat color polymorphism in hares.
Giska, I., L. Farelo, J. Pimenta, F. A. Seixas, M. S. Ferreira, J. P. Marques, I. Miranda, J. Letty, H. Jenny, K. Hackländer, E. Magnussen, and J. Melo-Ferreira.
Proc Natl Acad Sci USA 116:201910471. (2019)
 Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range
Orianne Tournayre, Jean‐Baptiste Pons, Maxime Leuchtmann, Raphael Leblois, Sylvain Piry, Ondine Filippi‐Codaccioni, Anne Loiseau, Jeanne Duhayer, Inazio Garin, Fiona Mathews, Sébastien Puechmaille, Nathalie Charbonnel, Dominique Pontier
2019. Ecology and Evolution, Volume 9, Issue 21
 Limited genetic structure and demographic expansion of the Brassicogethes aeneus populations in France and in Europe
Amandine S Juhel, Corentin M Barbu, Muriel Valantin‐Morison, Bertrand Gauffre, Raphaël Leblois, Jérôme Olivares, Pierre Franck
Pest Management Science, Volume 75, Issue 3
 Cyprinid Herpesvirus 3 Evolves in vitro through an Assemblage of Haplotypes that Alternatively become Dominant or Under-Represented
Sandro Klafack, Anna-Sophie Fiston-Lavier, Sven M. Bergmann, Saliha Hammoumi, Lars Schröder, Walter Fuchs, Angela Lusiastuti, Pei-Yu Lee, Sarahi Vega Heredia, Master student consortium, Anne-Sophie Gosselin-Grenet, and Jean-Christophe Avarre
Viruses. 2019 Aug; 11(8): 754.
 Chemical fingerprints suggest direct familiarisation rather than phenotype matching during olfactory recognition in Australian sea lions (Neophoca cinerea)
Kaja Wierucka, Nicolas Barthes, RobertHarcourt, Benoist Schaal, Isabelle Charrier, Benjamin J.Pitcher
Journal of Experimental Marine Biology and Ecology, Volume 517, 2019, Pages 49-53, ISSN 0022-0981,
 Handedness heritability in industrialized and nonindustrialized societies
Winati Nurhayu, Sarah Nila, Kanthi Arum Widayati, Puji Rianti, Bambang Suryobroto, Michel Raymond
Heredity (2019)
 Why cooperation is not running away
Félix Geoffroy, Nicolas Baumard, Jean‐Baptiste André
2019. Journal of Evolutionary Biology
 Sponge digestive system diversity and evolution: filter feeding to carnivory
Nelly Godefroy, Emilie Le Goff, Camille Martinand-Mari, Khalid Belkhir, Jean Vacelet, Stephen Baghdiguian
Cell Tissue Res (2019) 377: 341.
 Modeling competition, niche, and coexistence between an invasive and a native species in a two‐species metapopulation
Maxime Dubart, Jelena H. Pantel, Jean‐Pierre Pointier, Philippe Jarne, Patrice David
Ecology, 2019 Jun;100(6):e02700
 Evolution of Gene Expression during a Transition from Environmental to Genetic Sex Determination
Cécile Molinier, Céline M O Reisser, Peter D Fields, Adeline Ségard, Yan Galimov, Christoph R Haag
Molecular Biology and Evolution, Volume 36, Issue 7, July 2019, Pages 1551–1564
 OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
Celine Scornavacca, Khalid Belkhir, Jimmy Lopez, Rémy Dernat, Frédéric Delsuc, Emmanuel J P Douzery, Vincent Ranwez.
Molecular Biology and Evolution, msz015,
 Chemical Profiles of Integumentary and Glandular Substrates in Australian Sea Lion Pups (Neophoca cinerea)
Kaja Wierucka, Nicolas Barthes, Benjamin J Pitcher, Benoist Schaal, Isabelle Charrier, Robert G Harcourt
Chemical Senses, Volume 44, Issue 3, March 2019, Pages 205–214
 Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
Florentine Riquet, Cathy Liautard‐Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero‐Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud‐Haond, Pierre‐Alexandre Gagnaire, Nicolas Bierne
Evolution (2019)
 The genomic impact of historical hybridization with massive mitochondrial DNA introgression.
Seixas, F. A., P. Boursot, and J. Melo-Ferreira. 2018.
Genome Biology 19:91.
DOI: 10.1186/s13059-018-1471-8
 Measuring and modelling energy partitioning in canopies of varying complexity using MAESPA model.
Vezy, R., Christina, M., Roupsard, O., Nouvellon, Y., Duursma, R., Medlyn, B., Soma, M., Charbonnier, F., Blitz-Frayret, C., Stape, J.-L., Laclau, J.-P., de Melo Virginio Filho, E., Bonnefond, J.-M., Rapidel, B., Do, F.C., Rocheteau, A., Picart, D., Borgonovo, C., Loustau, D., & le Maire, G. 
Agricultural and Forest Meteorology, 253-254, 203-217 (2018)
 Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts
Leitwein M, Gagnaire PA, Desmarais E, Berrebi P, Guinand B
Mol Ecol. 2018 Sep;27(17):3466-3483.
 Evolution of dental tissue mineralization: an analysis of the jawed vertebrate SPARC and SPARC-L families.
Enault S, Muñoz D, Simion P, Ventéo S, Sire JY, Marcellini S, Debiais-Thibaud M.
BMC Evol Biol. 2018 Aug 30;18(1):127.
 Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius.
Pinharanda A., Rousselle M., Martin S.H., Hanly J.J., Davey J.W., Kumar S., Galtier N., Jiggins C.D. 2019.
Journal of Evolutionary Biology
 Influence of recombination and GC-biased gene conversion on the adaptive and non-adaptive substitution rate in mammals vs. birds.
Rousselle M., Laverré A., Figuet E., Nabholz B., Galtier N. 2019.
Molecular Biology and Evolution
 Illumina library preparation for sequencing the GC-rich fraction of heterogeneous genomic DNA.
Tilak M.K., Botero-Castro F., Galtier N., Nabholz B. 2018.
Genome Biology and Evolution 10: 161-622.
 Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations.
Rousset, F., Beeravolu C.R., Leblois R. (2018)
J. Soc. Française de Statistique
159 : 142-166.
 Confronting species aesthetics with ecological functions in coral reef fish
Anne-Sophie Tribot, Quentin Carabeux, Julie Deter, Thomas Claverie, Sébastien Villéger & Nicolas Mouquet
Scientific Reports, vol. 8
 Contrasting phyogeography of two Western Palaearctic fish parasites despite similar life cycles.
Perrot-Minnot M-J, Špakulova M, Wattier R, Kotlik P, Düsen S, Aydoğdu A, Tougard C (2018)
Journal of Biogeography, 45: 101-115.
 Salmo macrostigma (Teleostei, Salmonidae): nothing more than a brown trout (S. trutta) lineage?
Tougard C, Justy F, Guinand B, Douzery EJP, Berrebi P (2018)
Journal of Fish Biology, 93 : 302-310.
 MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
Vincent Ranwez, Emmanuel J P Douzery, Cédric Cambon, Nathalie Chantret, Frédéric Delsuc
Mol. Biol. Evol.  Vol 35, Issue 10, 1 October 2018, Pages 2582–2584
 Artificial barriers prevent genetic recovery of small isolated populations of a low mobility freshwater fish.
Coleman R., B. Gauffre, A. Pavlova, L. Beheregaray, J. Kearns, J. Lyon, M. Sasaki, R. Leblois, C. Sgro, P. Sunnucks.
Heredity. 2018 Jun;120(6):515-532
 Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
Yoann Anselmetti, Wandrille Duchemin, Éric Tannier, Cedric Chauve, et Sèverine Bérard.
BMC Genomics 2018 19(Suppl 2):96.
 A phylogenetic framework and timescale for comparative studies of Tunicates.
Delsuc F., Philippe H., Tsagkogeorga G., Simion P., Tilak M., Turon X., López-Legentil S., Piette J., Lemaire P. & Douzery E. J. P.
BMC Biology 16 : 39.
 Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion.
Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L.
Mol Biol Evol. 2018 May 1;35(5):1092-1103.
 Overestimation of the adaptive substitution rate in fluctuating populations.
Rousselle M, Mollion M, Nabholz B, Bataillon T, Galtier N.
Biol Lett. 2018 May;14(5). pii: 20180055.
 A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.
Simion P, Belkhir K, François C, Veyssier J, Rink JC, Manuel M, Philippe H, Telford MJ.
BMC Biol. 2018 Mar 5;16(1):28.
 The Scientific Filesystem (SCIF)
Sochat V.
GigaScience, giy023,
 Analysis of haplotype networks: the randomized minimum spanning tree method
Paradis E.
Methods in Ecology Evolution
 Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes.
Mollion M. Ehlers B.K., Figuet E., Santoni S., Lenormand T., Maurice S., Galtier N. & Bataillon T. 2017.
Genome Biology and Evolution 2018 Jan 1;10(1):239-248
Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats.
Wereszczuk A., R. Leblois, A. Zalewski1. 2017. BMC ecology 17 :46.
 Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan.
Aimé C., André, J.-B., Raymond, M. 2017. PLOS Computational Biology, 13:e1005631
 Evolutionary forces affecting synonymous variations in plant genomes.
Clement, Y., G. Sarah, Y. Holtz, F. Homa, S. Pointet, S. Contreras, B. Nabholz, F. Sabot, L. Saune, M. Ardisson, R. Bacilieri, G. Besnard, A. Berger, C. Cardi, F. De Bellis, O. Fouet, C. Jourda, B. Khadari, C. Lanaud, T. Leroy, D. Pot, C. Sauvage, N. Scarcelli, J. Tregear, Y. Vigouroux, N. Yahiaoui, M. Ruiz, S. Santoni, J. P. Labouisse, J. L. Pham, J. David, and S. Glémin.
PLoS Genet 13:e1006799
 A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes
Bonnet, T., Leblois, R., Rousset, F., Crochet, P.-A. (2017)
Evolution 71: 2140–2158
 The summary likelihood method and its implementation in the Infusion package.
Rousset, F., Gouy, A., Martinez-Almoyna, C., Courtiol, A. (2017)
Mol. Ecol. Resources. 17 : 110–119.
 Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.
Chang PL, Kopania E, Keeble S, Sarver BAJ, Larson E, Orth A,Belkhir K, Boursot P, Bonhomme F, Good JM, Dean MD.
Mamm Genome. 2017 Oct;28(9-10):416-425.
Epub 2017 Aug 17.
 Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae).
Tougard C, Davila CRG, Romer U, Duponchelle F, Cerqueira F, Paradis E, Guinand B, Chavez CA, Salas V, Querouil S, Sirvas S, Renno JF (2017)
PLoS One 12 (9): e0182618.
 Positive selection drives sperm motility in the brittle star species complex Ophioderma longicauda.
Weber A.A., Abi-Rached L., Galtier N., Bernard A., Bouchez O., Montoya-Burgos J.I. & Chenuil A.  2017.
Molecular Ecology 26:3744-3759.
 Mapping and explaining wolf recolonization in France using dynamic occupancy models and opportunistic data.
Louvrier, J., C. Duchamp, V. Lauret, E. Marboutin, S. Cubaynes, R. Choquet, C. Miquel, O. Gimenez (2017).
Ecography. 40: 001-013
 Spatial memory shapes density dependence in population dynamics.
Riotte-Lambert, L., Benhamou, S., Bonenfant, C., & Chamaillé-Jammes, S. (2017).
Proc. R. Soc. B, 284:20171411
 New software tool 'CroCo' detects pervasive cross contamination in multi-species NGS data.
Paul Simion, Khalid Belkhir, Clémentine François, Julien Veyssier, Jochen C. Rink, Michaël Manuel, Hervé Philippe, Maximilian J. Telford.
BMC Biology
 Performance Evaluation of Container-based Virtualization for High Performance Computing Environments
Carlos Arango, Rémy Dernat, John Sanabria
arXiv preprint
 Designing oil palm architectural ideotypes for optimal light interception and carbon assimilation through a sensitivity analysis of leaf traits
Raphaël P A Perez, Jean Dauzat, Benoît Pallas, Julien Lamour, Philippe Verley, Jean-Pierre Caliman, Evelyne Costes, Robert Faivre
Annals of Botany, mcx161
 Toward a general tropical forest biomass prediction model from very high resolution optical satellite images
P.Ploton, N.Barbier, P.Couteron, C.M.Antin, N.Ayyappan, N.Balachandran, N.Barathan, J.-F.Bastin, G.Chuyong, G.Dauby, V.Droissart, J.-P.Gastellu-Etchegorry, N.G.Kamdem, D.Kenfack, M.Libalah, G.MofackII, S.T.Momo, S.Pargal, P.Petronelli, C.Proisy, M.Réjou-Méchain, B.Sonké, N.Texier, D.Thomas, P.Verley, D.Zebaze Dongmo, U.Berger, R.Pélissier
Remote Sensing of Environment, vol. 200, oct. 2017, p. 140-153
 Patterns of cross-contamination in a multi-species population genomic project: detection, quantification, impact, solutions.
Ballenghien M., Faivre N. & Galtier N. 2017.
BMC Biology 15:25.
 Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker.
Allio R., Donega S., Galtier N. & Nabholz B. 2017.
Molecular Biology and Evolution 34:2762-2772.
 Avian genomes revisited: hidden genes uncovered and the rates vs. traits paradox in birds.
Botero-Castro F., Figuet E., Tilak M., Nabholz B. & Galtier N. 2017.
Molecular Biology and Evolution 34:3123-3131.
 Lacking conservation genomics in giant Galápagos tortoises.
Loire E. & Galtier N. 2017.
bioRxiv, 101980. Recommended by Peer Community In Evolutionary Biology.
 Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.
Figuet E., Ballenghien M., Lartillot N. & Galtier N. 2017.
BioRxiv 139147. Recommended by Peer Community In Evolutionary Biology.
 Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.
Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C (2018)
Molecular Ecology
 The discovery of Halictivirus resolves the Sinaivirus phylogeny
Diane Bigot, Anne Dalmon, Bronwen Roy, Chunsheng Hou, Mich e le Germain, Manon Romary, Shuai Deng, Qingyun Diao, Lucy A. Weinert, James M. Cook, Elisabeth A. Herniou and Philippe Gayral
Bigot et al., Journal of General Virology
 Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow
Camille Christe, Kai N. Stölting, Margot Paris, Christelle Fraїsse, Nicolas Bierne, Christian Lexer
Molecular Ecology (Vol. 26, Issue 1, Jan 2017 pages 59-76)
 Did the Quaternary climatic fluctuations really influence the tempo and mode of diversification in European rodents?
Tougard C.
Journal of Zoological Systematics and Evolutionary Research, 55 : 46-56.
 Performance of partitioning functional beta diversity indices: influence of functional representation and partitioning methods
Loiseau N., Legras G., Gaertner J.C., Verley P., Chabanet P., Mérigot B.
Global Ecology and Biogeography
 Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.
Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca.
Bioinformatics. (2017 Jan 10. pii: btw778)
 A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in the Salmo genus and the impact of selection on linked neutral diversity
Maeva Leitwein, Bruno Guinand, Juliette Pouzadoux, Erick Desmarais, Patrick Berrebi, Pierre-Alexandre Gagnaire
G3 | G3 Genes | Genomes | Genetics
Black rat invasion of inland Sahel: insights from interviews and population genetics in South Western Niger.
Berthier K., M. Garba, R. Leblois, M. Navascues, C. Tatard, P. Gauthier, S Gagaré, S. Piry, A. Dalecky, A. Loiseau , G. Dobigny. 2016. Biological Journal of the Linean Society 119:748–765.
 Thrice better than once: quality control guidelines to validate new mitogenomes
Botero-Castro F., Delsuc F. & Douzery E. J. P. Mitochondrial DNA 27 : 449-454
 A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate
Thomas Bataillon, Nicolas Galtier, Aurelien Bernard, Nicolai Cryer, Nicolas Faivre, Sylvain Santoni, Dany Severac, Teis N. Mikkelsen, Klaus S. Larsen, Claus Beier, Jesper G. Sørensen, Martin Holmstrup, and Bodil K. Ehlers
Global Change Biology (2016 Jul; 22(7): 2370-2379)
 Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies
Marjolaine Rousselle, Nicolas Faivre, Marion Ballenghien, Nicolas Galtier, Benoit Nabholz
Genome Biology and Evolution (Oct 2016, 3108-3119)
 The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications.
Assogba BS, Milesi P, Djogbénou LS, Berthomieu A, Makoundou P, Baba-Moussa LS, Fiston-Lavier AS, Belkhir K, Labbé P, Weill M.
PLoS Biol. (2016 Dec 5;14(12):e2000618)
 Predicting biotic interactions and their variability in a changing environment.
Kadowaki, K., Barbera, C. G., Godsoe, W., Delsuc, F., & Mouquet, N.
Biology letters (2016 May;12(5), pii: 20151073)
 Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci.
Nardelli, M., Ibáñez, E. A., Dobler, D., Justy, F., Delsuc, F., Abba, A. M., ... & Túnez, J. I.
Genetica (2016 Aug;144(4), 469-476)
 Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome.
Céline M.O. Reisser, Dominique Fasel, Evelin Hürlimann, Marinela Dukič, Cathy Haag-Liautard, Virginie Thuillier, Yan Galimov, Christoph R. Haag
Mol Biol Evol (2016 msw251)
 Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence
Camille Roux , Christelle Fraïsse, Jonathan Romiguier, Yoann Anciaux, Nicolas Galtier, Nicolas Bierne
PLoS Biology (Dec. 2016)
 Incomplete lineage sorting in mammalian phylogenomics.
Scornavacca C. & Galtier N.
Systematic Biology (66(1) 112-120)
 Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations
M. Leitwein, P.-A. Gagnaire, E. Desmarais, S. Guendouz, M. Rohmer, P. Berrebi, B. Guinand
Journal of Fish Biology (vol. 89 issue 6 dec 2016 : 2717-2734)
 Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species
Sarah Bouchemousse, Cathy Liautard-Haag, Nicolas Bierne, Frédérique Viard
Molecular Ecology (vol. 25 issue 21, Nov 2016 pages 5537-5542)
 Taxonomic and functional diversity increase the aesthetic value of coralligenous reefs
Anne-Sophie Tribot, Nicolas Mouquet, Sébastien Villéger, Michel Raymond, Fabrice Hoff, Pierre Boissery, Florian Holon & Julie Deter
Scientific Reports (vol. 6)
 Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect
S. L. Ament-Velásquez, E. Figuet, M. Ballenghien, E. E. Zattara, J. L. Norenburg, F. A. Fernández-Álvarez, J. Bierne, N. Bierne, N. Galtier
Molecular Ecology (25, 3356-3369) 14 July 2016
 Resampling : an improvement of importance sampling in varying population size models.
Merle, C., Leblois, R., Rousset, F., Pudlo, P.
Theor. Pop. Biol. 114 : 70-87.
 Pollen dispersal slows geographical range shift and accelerates ecological niche shift under climate change.
Aguilée, R., Raoul, G., Rousset, F., Ronce, O. (2016)
Proc. Natl. Acad. Sci. USA 113 : E5741–E5748.
 The evolution of mutual mate choice under direct benefits.
Courtiol, A., Étienne, L., Feron, R., Godelle, B., Rousset, F. (2016)
Am. Nat. 188 : 521-538.
 Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits
M. Szulkin,P.-A. Gagnaire,N. Bierne and A. Charmantier
Molecular Ecology (2016) 25, 542-558
 Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels.
Fraïsse, C., Belkhir, K., Welch, J. J., & Bierne, N. (2016).
Molecular Ecology, 25(1), 269-286.
 Life-history traits, protein evolution and the nearly-neutral theory in amniotes.
Figuet E., Nabholz B., Bonneau M., Mas Carrio E., Nadachowska-Brzyska K., Ellegren H. & Galtier N.
Molecular Biology and Evolution (2016 vol. 33 issue 6 1517-1527)
 ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony
Edwin Jacox, Cedric Chauve, Gergely J. Szollosi, Yann Ponty, Celine Scornavacca.
BIOINFORMATICS, under press.
 Trait selection during food web assembly: the roles of interactions and temperature
Isabelle Gounand, Sonia Kéfi, Nicolas Mouquet, Dominique Gravel
Theor Ecol (2016) 9: 417.
 Adaptive protein evolution in animals and the effective population size hypothesis.
Galtier N. 2016.
PLoS Genetics 12:e1005774.
 Ancestral gene synteny reconstruction improves extant species scaffolding,
Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Éric Tannier et Sèverine Bérard.
BMC Genomics 16(Suppl 10):S11
doi:10.1186/1471-2164-16-S10-S11, 2015. ISEM 2015-158
 Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta.
BMC Evolutionary Biology 15: 148.
Delsuc F., Gasse B. & Sire J.-Y. (2015).
 Evolution of proteasome regulators in Eukaryotes.
Fort P., Kajava A.V., Delsuc F. & Coux O. (2015).
Genome Biology and Evolution 7: 1363-1379.
 Evolution of spatially structured host-parasite interactions.
Lion S. & Gandon S. (2015)
Journal of evolutionary biology. 28(1): 10-28.
 Gene expression, chromosome heterogeneity and the fast-X effect in mammals.
Nguyen L.-P., Galtier N. & Nabholz B. 2015.
Biology Letters 11:20150010.
 How memory-based movement leads to nonterritorial spatial segregation.
Riotte-Lambert, L., Benhamou, S., and S Chamaillé-Jammes. 2015.
The American Naturalist. 185:E103-E116.
 Molecular evolution of freshwater snails with contrasting mating systems.
Burgarella C., Gayral P., Ballenghien M. Bernard A., David P., Jarne P., Correa A., Hurtrez-Boussès S., Escobar J., Galtier N. & Glémin S. 2015.
Molecular Biology and Evolution 32:2403-2416.
 Naked but not hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons.
Delsuc F. & Tilak M.-K. (2015).
Genome Biology and Evolution 7: 768-774.
 Quantification of GC-biased gene conversion in the human genome.
Glémin S., Arndt P.F., Messer P.W., Petrov D., Galtier N. & Duret L.
Genome Research 25:1215-1228.
 Spatial structure, host heterogeneity and parasite virulence: implications for vaccine-driven evolution.
Zurita-Gutiérrez Y. H. & Lion S. (2015)
Ecology Letters. 18(8): 779-789.
 Spatial structure, transmission modes and the evolution of viral exploitation strategies.
Berngruber T., Lion S. & Gandon S. (2015)
PLos Pathogens. 11(4): e1004810
 Systematics of hairy armadillos and the taxonomic status of the Andean hairy armadillo (Chaetophractus nationi).
Abba A.M., Cassini G.H., Valverde G., Tilak M.-K., Vizcaíno S.F., Superina M. & Delsuc F. (2015). Journal of Mammalogy 96: 673-689.
 Virulence evolution at the front line of spreading epidemics
Griette, Quentin and Raoul, Gaël and Gandon, Sylvain
Evolution (vol. 69 2810-2819)
Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat.
Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor ME, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A.
Mol Ecol Resour. 2014
Online software
 Comparative population genomics in animals uncovers the determinants of genetic diversity
J. Romiguier, P. Gayral, M. Ballenghien, A. Bernard, V. Cahais, A. Chenuil, Y. Chiari, R. Dernat, L. Duret, N. Faivre, E. Loire, J. M. Lourenco, B. Nabholz, C. Roux, G. Tsagkogeorga, A. A.-T. Weber, L. A. Weinert, K. Belkhir, N. Bierne, S. Glémin & N. Galtier
Nature (2014)
 OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals
Emmanuel J. P. Douzery, Celine Scornavacca, Jonathan Romiguier, Khalid Belkhir, Nicolas Galtier, Frédéric Delsuc and Vincent Ranwez
Mol Biol Evol (31 (7))(2014)
See the website/DB
 A practical approximation algorithm for solving massive instances of hybridization number for binary and non binary trees.
Iersel LV, Kelk S, Lekic N, Scornavacca C
BMC Bioinformatics (2014) 15: 127.
 Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates.
Figuet E, Ballenghien M, Romiguier J, Galtier N.
Genome Biol Evol (27 (5))(2014): 240-250.
 Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.
Vignaud TM, Mourier J, Maynard JA, Leblois R, Spaet J, Clua E, Neglia V, Planes S
Mol Ecol (23 (21)) (2014): 5193-5207.
 Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H
Genome biology (15 (12)) (2014): 549.
 Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline.
Vignaud TM, Maynard JA, Leblois R, Meekan MG, Vazquez-Juarez R, Ramirez-Macias D, Pierce SJ, Rowat D, Berumen ML, Beeravolu C, Baksay S, Planes S
Mol Ecol (23 (10)) (2014): 2590-2601.
 Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species.
Hartfield M, Glemin S
Genetics (196 (1)) (2014): 281-293.
 Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection.
Weber CC, Nabholz B, Romiguier J, Ellegren H
Genome biology (15 (12)) (2014): 542.
 Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms.
Glemin S, Muyle A
J Evol Biol (27 (7)) (2014): 1386-1399.
 Maximum likelihood inference of population size contractions from microsatellite data.
Leblois R, Pudlo P, Néron J, Bertaux F, Beeravolu CR, Vitalis R, Rousset F
Mol Biol Evol (31) (2014): 2805-2823.
 Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals.
Figuet E, Romiguier J, Dutheil JY, Galtier N
J Evol Biol (27 (5)) (2014): 899-910.
 Population genomics of eusocial insects: the costs of a vertebrate-like effective population size.
Romiguier J, Lourenco J, Gayral P, Faivre N, Weinert LA, Ravel S, Ballenghien M, Cahais V, Bernard A, Loire E, Keller L, Galtier N
J Evol Biol (27 (3)) (2014): 593-603.
 Testing environmental and genetic effects in the presence of spatial autocorrelation.
Rousset F, Ferdy J-B
Ecography (37) (2014): 781-790.
 The Bimodal Distribution of Genic GC Content Is Ancestral to Monocot Species.
Clement Y, Fustier MA, Nabholz B, Glemin S
Genome Biol Evol (7 (1))(2014): 336-348.
 Thrice better than once: quality control guidelines to validate new mitogenomes
Fidel Botero-Castro, Frédéric Delsuc, and Emmanuel J. P. Douzery
Mitochondrial DNA (2014)
 Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).
Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquiere A, Santoni S, David J, Glémin S
Mol Ecol (23 (9))(2014): 2210-2227.
 Whole-genome analyses resolve early branches in the tree of life of modern birds.
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F et al.
Science (346 (6215)) (2014): 1320-1331.
Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.
Gayral P, Melo-Ferreira J, Glémin S, Bierne N, Carneiro M, Nabholz B, Lourenco JM, Alves PC, Ballenghien M,
Faivre N, Belkhir K, Cahais V, Loire E, Bernard A, Galtier N
PLoS Genet (2013) 9 (4): e1003457.
 A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction
Estelle Harrang, Sylvie Lapègue, Benjamin Morga and Nicolas Bierne
G3 February 1, 2013
 Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation.
Glémin S, Ronfort J (2013)
Evolution 67 (1): 225-240.
 Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics.
Robin Aguilée, David Claessen and Amaury Lambert
Evolution (2013) (67: 1291-1306)
 Bio++: efficient extensible libraries and tools for computational molecular evolution.
Gueguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V,
Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L et al. (2013)
Mol Biol Evol 30 (8): 1745-1750.
 Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species
Camille Roux, Georgia Tsagkogeorga, Nicolas Bierne and Nicolas Galtier
Molecular Biology and Evolution (2013)
 Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.
Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, Griggio F, Mastrototaro F, Delsuc F, Douzery EJ, Gissi C, Huchon D
Genome Biol Evol (2013) 5 (6): 1185-1199.
 Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum.
Nagy GN, Marton L, Kramos B, Olah J, Revesz A, Vekey K, Delsuc F, Hunyadi-Gulyas E, Medzihradszky KF,
Lavigne M, Vial H, Cerdan R, Vertessy BG
Febs J 280 (2013) (13): 3132-3148.
 Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination.
Mugal CF, Nabholz B, Ellegren H
BMC genomics (2013) 14: 86.
 Genomic evidence for large, long-lived ancestors to placental mammals.
Romiguier J, Ranwez V, Douzery EJ, Galtier N
Mol Biol Evol 30 (2013) (1): 5-13.
 High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.
Nabholz B, Ellegren H, Wolf JB
Mol Biol Evol (2013) 30 (2): 272-284.
 How does pollen versus seed dispersal affect niche evolution?
Aguilée R, Shaw FH, Rousset F, Shaw RG, Ronce O
Evolution 67: 792-805.
 Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals.
Romiguier J, Ranwez V, Delsuc F, Galtier N, Douzery EJ
Mol Biol Evol 30 (2013) (9): 2134-2144.
 Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion
Emmanuel Paradis
Mol Phylogenet Evol. 2013
 Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).
Botero-Castro F, Tilak MK, Justy F, Catzeflis F, Delsuc F, Douzery EJ
Mol Phylogenet Evol (2013) 69 (3): 728-739.
 Population genomics of the endangered giant Galapagos tortoise.
Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenco JM, Galtier N
Genome biology (2013) 14 (12): R136.
 Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds.
Nabholz B, Uwimana N, Lartillot N
Genome Biol Evol (2013) 5 (7): 1273-1290.
 Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods.
Nguyen T-H, Ranwez V, Berry V, Scornavacca C
PLoS One 8 (2013) (10): e73667.
 The determinants of the molecular substitution process in turtles.
Lourenco JM, Glémin S, Chiari Y, Galtier N
J Evol Biol (2013) (26 (1)): 38-50.
 The probability of evolutionary rescue: towards a quantitative comparison between theory and evolution experiments.
Martin G, Aguilée R, Ramsayer J, Kaltz O, Ronce O
Philos T Roy Soc B (2013) 368: 20120088.
 The rate of molecular adaptation in a changing environment.
Lourenco JM, Glémin S, Galtier N
Mol Biol Evol (2013) 30 (6): 1292-1301.
 Patterns and evolution of nucleotide landscapes in seed plants.
Serres-Giardi L, Belkhir K, David J, Glémin S
Plant Cell (2012) 24 (4): 1379-1397.
 Reference-free transcriptome assembly in non-model animals from next-generation sequencing data.
Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N
Molecular ecology resources (2012) 12 (5): 834-845.
 A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number.
Iersel Lv, Kelk S, Lekic N, Scornavacca C
WABI LNBI (2012) 7534: 430-440.
 Coalescent-based DNA barcoding: multilocus analysis and robustness.
David O, Laredo C, Leblois R, Schaeffer B, Vergne N (2012)
J Comput Biol 19 (3): 271-278.
 Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea.
Lourenco JM, Claude J, Galtier N, Chiari Y
Mol Phylogenet Evol (2012) 62 (1): 496-507.
 Efficient selection of branch-specific models of sequence evolution.
Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B (2012)
Mol Biol Evol 29 (7): 1861-1874.
 Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome.
Carneiro M, Albert FW, Melo-Ferreira J, Galtier N, Gayral P, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Ferrand N
Mol Biol Evol (2012) 29 (7): 1837-1849.
 Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein.
Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Munch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F, Delsuc F, Telenti A, Benkirane M
Cell Host Microbe (2012) 11 (2): 205-217.
 Extinction and fixation times with dominance and inbreeding.
Glémin S
Theor Popul Biol (2012) 81 (4): 310-316.
 Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.
Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V
PLoS One (2012) 7 (3): e33852.
 Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution and potential functionality.
Fort P., Albertini A., Van-Hua A., Berthomieu A., Roche S., Delsuc F., Pasteur N., Capy P., Gaudin Y. & Weill M.
Molecular Biology and Evolution (2012). 29 (1): 381-390.
 Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model.
Lartillot N, Delsuc F
Evolution (2012) 66 (6): 1773-1787.
Likelihood-based inferences under isolation by distance : two-dimensional habitats and confidence intervals.
Rousset, F., Leblois R.
Mol. Biol. Evol. (2012) 29 : 957-973.
Optimal resource allocation in a serotinous non-resprouting plant species under different fire regimes
Jeanne Tonnabel, Tom J.M. Van Dooren, Jeremy Midgley, Patsy Haccou, Agnès Mignot, Ophélie Ronce and Isabelle Olivieri
Journal of Ecology Volume 100, Issue 6, pages 1464-1474, November 2012
Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes.
Hassanin A, Delsuc F, Ropiquet A, Hammer C, Jansen van Vuuren B, Matthee C, Ruiz-Garcia M, Catzeflis F, Areskoug V, Nguyen TT, Couloux A
C R Biol (2012) 335 (1): 32-50.
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
Ylenia Chiari, Vincent Cahais, Nicolas Galtier and Frédéric Delsuc.
BMC Biology 2012 (2012) 10: 65
RUNX2 tandem repeats and the evolution of facial length in placental mammals.
Pointer MA, Kamilar JM, Warmuth V, Chester SG, Delsuc F, Mundy NI, Asher RJ, Bradley BJ
BMC Evol Biol (2012) 12: 103.
The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis.
Tsagkogeorga G, Cahais V, Galtier N
Genome Biol Evol (2012) 4 (8): 740-749.
Complexity, pleiotropy, and the fitness effect of mutations.
Lourenco J, Galtier N, Glemin S
Evolution (2011) (65 (6)): 1559-1571.
Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.
Atyame C.M., Delsuc F., Pasteur N., Weill M. & Duron O.
Molecular Biology and Evolution (2011)
 GC-biased gene conversion and selection affect GC content in the Oryza genus (rice).
Muyle A, Serres-Giardi L, Ressayre A, Escobar J, Glémin S
Mol Biol Evol (2011) (28 (9)): 2695-2706.
 GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes.
Escobar JS, Glémin S, Galtier N
Mol Biol Evol (2011) (28 (9)): 2561-2575.
 MACSE: Multiple Alignment of Coding Sequences accounting for frameshifts and stop codons.
Ranwez V., Harispe S., Delsuc F. & Douzery E.J.P.
PLoS One (2011)
Online software
 Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae).
Dsouli N., Delsuc F., Michaux J.R., De Stordeur E., Couloux A., Veuille M. & Duvallet G.
Infection, Genetics and Evolution (2011) (11): 663-670.
 Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).
Escobar JS, Scornavacca C, Cenci A, Guilhaumon C, Santoni S, Douzery EJ, Ranwez V, Glemin S, David J
BMC Evol Biol (2011) (11 (1)): 181.
 Accelerated evolutionary rate of housekeeping genes in tunicates.
Tsagkogeorga G., Turon X., Galtier N., Douzery E.J.P. & Delsuc F.
Journal of Molecular Evolution (2010) 71: 153-167.
 Isolation by distance in a continuous population under stochastic demographic fluctuations.
Robledo-Arnuncio, J.J., Rousset, F.
J. Evol. Biol. (2010) 23: 53-71.
 Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.
Denoeud F., Henriet S., Mungpakdee S., Aury J.-M., Da Silva C.,
Brinkmann H., Mikhaleva J., Olsen L.C., Jubin C., Cañestro C., Bouquet
J.-M., Danks G., Poulain J., Campsteijn C., Adamski M., Cross I.,
Yadetie F., Muffato M., Louis A., Butcher S., Tsagkogeorga G., Singh S.,
Jensen M.F., Huynh Cong E., Eikeseth-Otteraa H., Noel B., Anthouard V.,
Porcel-Setterblad B., Kachouri-Lafond R., Nishino A., Ugolini M.,
Chourrout P., Nishida H., Aasland R., Huzurbazar S., Westhof E., Delsuc
F., Lehrach H., Reinhardt R., Weissenbach J., Roy S.W., Artiguenave F.,
Postlethwait J.H., Manak J.R., Thompson E.M., Jaillon O., Du Pasquier
L., Boudinot P., Liberles D.A., Volff J.-N., Philippe H., Lenhard B.,
Roest Crollius H., Wincker P. & Chourrout D.
Science (2010) 330: 1381-1385.
 An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.
Tsagkogeorga G., Turon X., Hopcroft R.R., Tilak M.-K., Feldstein T.,
Shenkar N., Loya Y., Huchon D., Douzery E.J.P. & Delsuc F.
BMC Evolutionary Biology (2009) 9: 187.
 Estimating maximum likelihood phylogenies with PhyML.
Guindon S., Delsuc F., Dufayard J.-F. & Gascuel O. (2009).
Methods in Molecular Biology, vol. 537: Bioinformatics for DNA Sequence Analysis
édité par D. Posada, pp. 113-137, Humana Press Inc., Totowa, NJ.
 Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds.
Galtier N, Blier PU, Nabholz B.
Mitochondrion. 2009 Feb;9(1):51-7. Epub 2008 Dec 24.
 Perturbation expansions of multilocus fixation probabilities for frequency-dependent selection with applications to the Hill-Robertson effect and to the joint evolution of helping and punishment.
Lehmann, L., Rousset, F.
Theor. Pop. Biol. (2009) 76: 35-51.
 The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals.
Nabholz B, Glémin S, Galtier N.
BMC Evol Biol. 2009 Mar 10;9:54.
Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.
Singh T.R, Tsagkogeorga G., Delsuc F., Blanquart S., Shenkar N., Loya
Y., Douzery E.J.P. & Huchon D. (2009).
BMC Genomics 10: 534.
Additional molecular support for the new chordate phylogeny.
Delsuc F., Tsagkogeorga G., Lartillot N. & Philippe H.
Genesis (2008) 46: 592-604.
Selection and gene flow on a diminishing cline of melanic peppered moths.
Saccheri, I., Rousset, F., Watts, P., Brakefield, P., Cook, L.
Proc. Natl. Acad. Sci. USA (2008) 105: 16212-16217.
 OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics.
Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M.-K. & Douzery E.J.P.
BMC Evolutionary Biology (2007) 7: 241.
 Constraints on the origin and maintenance of genetic kin recognition.
Rousset, F., Roze, D.
Evolution (2007) 61: 2320-2330.
 Likelihood and approximate likelihood analyses of genetic structure in a linear habitat: performance and robustness to model mis-specification.
Rousset, F., Leblois, R.
Mol. Biol. Evol. (2007) 24: 2730-2745.
 Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters and sloths).
Möller-Krull M.*, Delsuc F.*, Churakov G., Marker C., Superina M., Brosius J., Douzery E.J.P. & Schmitz J.
Molecular Biology and Evolution (2007) 24: 2573-2582.
 Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis.
Nabholz B, Glémin S, Galtier N.
Mol Biol Evol. 2008 Jan;25(1):120-30. Epub 2007 Nov 12.