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

All these papers used at least one service or included one person from our team (ISE-M / MBB Clusters and/or Web services).

 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)
doi: 10.1111/mec.13765
 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.
doi: 10.1111/jzs.12152
 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 (in press)
doi: 10.1111/geb.12581
 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)
doi: 10.1093/bioinformatics/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
doi: 10.1101/094763
 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)
doi: 10.1111/gcb.13293
 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)
doi: 10.1093/gbe/evw214
 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)
doi: 10.1371/journal.pbio.2000618
 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)
doi: 10.1098/rsbl.2015.1073
 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)
doi: 10.1007/s10709-016-9915-0
 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)
doi: 10.1093/molbev/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)
doi: 10.1371/journal.pbio.2000234
 Incomplete lineage sorting in mammalian phylogenomics.
Scornavacca C. & Galtier N.
Systematic Biology (66(1) 112-120)
doi: 10.1093/sysbio/syw082
 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)
doi: 10.1111/jfb.13131
 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)
doi: 10.1111/mec.13854
 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)
doi:10.1038/srep34229
 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
doi: 10.1111/mec.13717
 Resampling : an improvement of importance sampling in varying population size models.
Merle, C., Leblois, R., Rousset, F., Pudlo, P.
Theor. Pop. Biol. in press. 
doi: 10.1016/j.tpb.2016.09.002
 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 in press.
doi: 10.1073/pnas.1607612113
 The evolution of mutual mate choice under direct benefits.
Courtiol, A., Étienne, L., Feron, R., Godelle, B., Rousset, F. (2016)
Am. Nat. in press.
 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
doi: 10.1111/mec.13486
 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.
doi: 10.1111/mec.13299
 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)
doi: 10.1093/molbev/msw033
 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.
doi: 10.1007/s12080-016-0299-7
 Adaptive protein evolution in animals and the effective population size hypothesis.
Galtier N. 2016.
PLoS Genetics 12:e1005774.
doi: 10.1371/journal.pgen.1005774
 Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels
Christelle Fraïsse, Khalid Belkhir, John J. Welch, Nicolas Bierne
Molecular Ecology (vol. 25, issue 1 Pages 269-286)
doi: 10.1111/mec.13299
 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).
doi:10.1186/s12862-015-0431-0
 Evolution of proteasome regulators in Eukaryotes.
Fort P., Kajava A.V., Delsuc F. & Coux O. (2015).
Genome Biology and Evolution 7: 1363-1379.
doi:10.1093/gbe/evv068
 Evolution of spatially structured host-parasite interactions.
Lion S. & Gandon S. (2015)
Journal of evolutionary biology. 28(1): 10-28.
doi: 10.1111/jeb.12551
 Gene expression, chromosome heterogeneity and the fast-X effect in mammals.
Nguyen L.-P., Galtier N. & Nabholz B. 2015.
Biology Letters 11:20150010.
doi: 10.1098/rsbl.2015.0010
 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.
doi: 10.1086/680009
 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.
doi: 10.1093/molbev/msv121
 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.
doi:10.1093/gbe/evv036
 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.
doi: 10.1101/gr.185488.114
 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.
doi: 10.1111/ele.12455
 Spatial structure, transmission modes and the evolution of viral exploitation strategies.
Berngruber T., Lion S. & Gandon S. (2015)
PLos Pathogens. 11(4): e1004810
doi: 10.1371/journal.ppat.1004810
 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.
doi: 10.1093/jmammal/gyv082
 Virulence evolution at the front line of spreading epidemics
Griette, Quentin and Raoul, Gaël and Gandon, Sylvain
Evolution (vol. 69 2810-2819)
doi: 10.1111/evo.12781
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
doi:10.1111/1755-0998.12334
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)
doi:10.1038/nature13685
 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)
doi: 10.1093/molbev/msu132
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.
doi: 10.1186/1471-2105-15-127
 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.
doi: 10.1093/gbe/evu277
 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.
doi: 10.1111/mec.12936
 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.
doi:10.1186/s13059-014-0549-1
 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.
doi: 10.1111/mec.12754
 Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species.
Hartfield M, Glemin S
Genetics (196 (1)) (2014): 281-293.
doi: 10.1534/genetics.113.158196
 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.
doi:10.1186/s13059-014-0542-8
 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.
doi: 10.1111/jeb.12356
 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.
doi: 10.1093/molbev/msu212
 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.
doi: 10.1111/jeb.12361
 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.
doi: 10.1111/jeb.12331
 Testing environmental and genetic effects in the presence of spatial autocorrelation.
Rousset F, Ferdy J-B
Ecography (37) (2014): 781-790.
doi: 10.1111/ecog.00566
 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.
doi: 10.1093/gbe/evu278
 Thrice better than once: quality control guidelines to validate new mitogenomes
Fidel Botero-Castro, Frédéric Delsuc, and Emmanuel J. P. Douzery
Mitochondrial DNA (2014)
doi:10.3109/19401736.2014.900666
 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.
doi: 10.1111/mec.12738
 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.
doi: 10.1126/science.1253451
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.
doi: 10.1371/journal.pgen.1003457
 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
doi: 10.1534/g3.112.005181
 Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation.
Glémin S, Ronfort J (2013)
Evolution 67 (1): 225-240.
doi: 10.1111/j.1558-5646.2012.01778.x
 Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics.
Robin Aguilée, David Claessen and Amaury Lambert
Evolution (2013) (67: 1291-1306)
doi:10.1111/evo.12008
 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.
doi: 10.1093/molbev/mst097
 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)
doi:10.1093/molbev/mst066
 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.
doi: 10.1093/gbe/evt081
 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.
doi: 10.1111/febs.12282
 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.
doi: 10.1186/1471-2164-14-86
 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.
doi: 10.1093/molbev/mss211
 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.
doi: 10.1093/molbev/mss238
 How does pollen versus seed dispersal affect niche evolution?
Aguilée R, Shaw FH, Rousset F, Shaw RG, Ronce O
Evolution 67: 792-805.
doi: 10.1111/j.1558-5646.2012.01816.x
 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.
doi: 10.1093/molbev/mst116
 Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion
Emmanuel Paradis
Mol Phylogenet Evol. 2013
doi: 10.1016/j.ympev.2013.02.008
 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.
doi: 10.1016/j.ympev.2013.07.003
 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.
doi: 10.1186/gb-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.
doi: 10.1093/gbe/evt083
 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.
doi: 10.1371/journal.pone.0073667
 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.
doi: 10.1111/jeb.12031
 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.
doi: 10.1098/rstb.2012.0088
 The rate of molecular adaptation in a changing environment.
Lourenco JM, Glémin S, Galtier N
Mol Biol Evol (2013) 30 (6): 1292-1301.
doi: 10.1093/molbev/mst026
 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.
doi: 10.1105/tpc.111.093674
 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.
doi: 10.1111/j.1755-0998.2012.03148.x
 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.
doi: 10.1186/1471-2105-15-127
 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.
doi: 10.1089/cmb.2011.0122
 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.
doi: 10.1016/j.ympev.2011.10.022
 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.
doi: 10.1093/molbev/mss059
 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.
doi: 10.1093/molbev/mss025
 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.
doi: 10.1016/j.chom.2012.01.007
 Extinction and fixation times with dominance and inbreeding.
Glémin S
Theor Popul Biol (2012) 81 (4): 310-316.
doi: 10.1016/j.tpb.2012.02.006
 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.
doi: 10.1371/journal.pone.0033852
 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.
doi: 10.1093/molbev/msr226
 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.
doi: 10.1111/j.1558-5646.2011.01558.x
Likelihood-based inferences under isolation by distance : two-dimensional habitats and confidence intervals.
Rousset, F., Leblois R.
Mol. Biol. Evol. (2012) 29 : 957-973.
doi: 10.1093/molbev/msr262
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
doi: 10.1111/j.1365-2745.2012.02023.x
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.
doi: 10.1016/j.crvi.2011.11.002
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
doi: 10.1186/1741-7007-10-65
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.
doi: 10.1186/1471-2148-12-103
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.
doi: 10.1093/gbe/evs054
Complexity, pleiotropy, and the fitness effect of mutations.
Lourenco J, Galtier N, Glemin S
Evolution (2011) (65 (6)): 1559-1571.
doi: 10.1111/j.1558-5646.2011.01237.x
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)
doi:10.1093/molbev/msr083
 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.
doi: 10.1093/molbev/msr104
 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.
doi: 10.1093/molbev/msr079
 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)
doi:10.1371/journal.pone.0022594
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.
doi:10.1016/j.meegid.2011.02.004
 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.
doi: 10.1186/1471-2148-11-181
 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.
doi:10.1007/s00239-010-9372-9
 Isolation by distance in a continuous population under stochastic demographic fluctuations.
Robledo-Arnuncio, J.J., Rousset, F.
J. Evol. Biol. (2010) 23: 53-71.
doi:10.1111/j.1420-9101.2009.01860.x
 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.
doi:10.1126/science.1194167
 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.
doi:10.1186/1471-2148-9-187
 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.
doi:10.1007/978-1-59745-251-9_6
 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.
PMID: 19154799
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.
doi:10.1016/j.tpb.2009.03.006
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.
PMID: 19284537
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.
doi:10.1186/1471-2164-10-534
Additional molecular support for the new chordate phylogeny.
Delsuc F., Tsagkogeorga G., Lartillot N. & Philippe H.
Genesis (2008) 46: 592-604.
doi:10.1002/dvg.20450
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.
doi:10.1073/pnas.0803785105
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.
doi:10.1186/1471-2148-7-241
Constraints on the origin and maintenance of genetic kin recognition.
Rousset, F., Roze, D.
Evolution (2007) 61: 2320-2330.
doi:10.1111/j.1558-5646.2007.00191.x
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.
PMID: 17893401
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.
doi:10.1093/molbev/msm201
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.
PMID: 17998254