- GC-biased segregation of noncoding polymorphisms in DrosophilaNicolas Galtier
UMR 5171, Genome, Populations, Interactions, Adaptation, CNRS, Universite Montpellier 2, IFREMER, 34095 Montpellier, France
Genetics 172:221-8. 2006..These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content...
- Mutation hot spots in mammalian mitochondrial DNANicolas Galtier
Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5171 Génome, Populations, Interactions, Adaptation, Universite Montpellier 2, 34095 Montpellier, France
Genome Res 16:215-22. 2006..It also gives hints about the proximal causes of mitochondrial site-specific hypermutability in humans...
- The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammalsBenoit Nabholz
Université Montpellier 2 CNRS UMR 5554 Institut des Sciences de l Evolution Place E Bataillon CC064, Montpellier, France
BMC Evol Biol 9:54. 2009..These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation...
- Detecting groups of coevolving positions in a molecule: a clustering approachJulien Dutheil
Institut des Sciences de l Evolution UM2 CNRS Université Montpellier 2 Place Eugéne Bataillon, CC064, 34 095 Montpellier Cedex 5, France
BMC Evol Biol 7:242. 2007....
- Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population geneticsJulien Dutheil
CNRS UMR 5171 Génome, Populations, Interactions, Adaptation GPIA, Universite Montpellier 2, France
BMC Bioinformatics 7:188. 2006..Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications...
- Markov-modulated Markov chains and the covarion process of molecular evolutionN Galtier
CNRS UMR 5171 GPIA, Université Montpellier 2 CC 63, Place E Bataillon, 34095 Montpellier, France
J Comput Biol 11:727-33. 2004..We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models...
- Recombination, GC-content and the human pseudoautosomal boundary paradoxNicolas Galtier
CNRS UMR 5171, Genome, Populations, Interactions, Adaptation, Université Montpellier 2 CC63, Place E Bataillon, 34095 Montpellier Cedex, France
Trends Genet 20:347-9. 2004..The paradox might be explained by the mirror histories of the pseudoautosomal boundary in the two species, and by the asymmetric nature of the forces driving GC-content evolution in mammalian genomes...
- Mouse biodiversity in the genomic eraN Galtier
UMR 5171 Genome, Populations, Interactions, Adaptation, Universite Montpellier 2, Montpellier, France
Cytogenet Genome Res 105:385-94. 2004....
- A model of horizontal gene transfer and the bacterial phylogeny problemNicolas Galtier
Institut des Sciences de l Evolution UM2 CNRS, Universite Montpellier 2, Montpellier, France
Syst Biol 56:633-42. 2007..Surprisingly, when applied to a bacterial and a eukaryotic multigene data set, this criterion rejects the HGT hypothesis for the former, but not the latter data set...
- Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sitesNicolas Galtier
CNRS UMR 5000, Genome, Populations, Interactions, Universite Montpellier 2, CC 63, Place E Bataillon, 34095 Montpellier, France
Syst Biol 53:38-46. 2004..In particular, nonindependence can lead to strongly supported wrong internal branches...
- Gene conversion drives GC content evolution in mammalian histonesNicolas Galtier
CNRS UMR 5000 Génome, Populations, Interactions, Université Montpellier 2 CC63, Place E Bataillon, 34095, Montpellier, France
Trends Genet 19:65-8. 2003..Thus, it seems that gene conversion is a biased process that tends to increase the DNA GC content, a conclusion that has implications for the evolution of isochores in vertebrates...
- Coevolution within and between genesN Galtier
Universite Montpellier 2, Montpellier, France
Genome Dyn 3:1-12. 2007..The reasons for this discrepancy are discussed...
- The intriguing evolutionary dynamics of plant mitochondrial DNANicolas Galtier
Universite Montpellier 2, CNRS UMR 5554 Institut des Sciences de l Evolution, Place E Bataillon CC64, 34095 Montpellier, France
BMC Biol 9:61. 2011..precisely characterized the role played by recombination and DNA repair in controlling mitochondrial variations in Arabidopsis thaliana, thus opening new perspectives on the long-term evolution of this intriguing genome...
- Mitochondrial DNA as a marker of molecular diversity: a reappraisalN Galtier
Institut des Sciences de l Evolution, Universite Montpellier 2, C N R S UMR 5554, Place E Bataillon, CC 64, 34195 Montpellier, France
Mol Ecol 18:4541-50. 2009..We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome...
- Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolutionNicolas Galtier
Institut des Sciences de l Evolution, CNRS UMR 5554, Universite Montpellier 2, Place E Bataillon, 34095 Montpellier, France
Biol Lett 5:413-6. 2009..We suggest that natural selection could act to reduce the (somatic) mtDNA mutation rate in long-lived species, in agreement with the mitochondrial theory of ageing...
- Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolutionNicolas Galtier
CNRS UMR 5554 Institut des Sciences de l Evolution, Université Montpellier 2 CC64, Place E Bataillon, 34095 Montpellier Cedex, France
Trends Genet 23:273-7. 2007..We argue that these regions, far from contributing to human adaptation, might represent the Achilles' heel of our genome...
- Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birdsNicolas Galtier
Institut des Sciences de l Evolution, Université Montpellier 2 CNRS UMR 5554, Place E Bataillon, 34095 Montpellier, France
Mitochondrion 9:51-7. 2009..This is because his interpretation invokes adaptation as the single evolutionary force at work, disregarding the effects of mutation, genetic drift, and purifying selection...
- Dealing with incongruence in phylogenomic analysesNicolas Galtier
CNRS UMR 5554, Institut des Sciences de l Evolution, Universite Montpellier 2, CC64, Place E Bataillon, 34095 Montpellier, France
Philos Trans R Soc Lond B Biol Sci 363:4023-9. 2008..We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals...
- Maximum-likelihood phylogenetic analysis under a covarion-like modelN Galtier
Centre National de la Recherche Scientifique UMR 5000 Génome, Populations, Interactions, Universite Montpellier 2, Montpellier, France
Mol Biol Evol 18:866-73. 2001..This theoretical effort should be useful for the study of protein adaptation, which presumably proceeds in a typical covarion-like manner...
- A new method for locating changes in a tree reveals distinct nucleotide polymorphism vs. divergence patterns in mouse mitochondrial control regionN Galtier
CNRS UMR Génome, Populations, Interactions, Universite Montpellier 2, Montpellier, France
J Mol Evol 50:224-31. 2000..Distinct change patterns were found at the polymorphism (within species) and divergence (between species) levels, rejecting the hypothesis of a neutral evolution of base composition in mitochondrial DNA...
- Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale feroxE Guldner
CNRS UMR 5000 Génome, Populations, Interactions, Universite Montpellier, Montpellier, France
J Evol Biol 17:48-54. 2004..This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis...
- Population genomics of eusocial insects: the costs of a vertebrate-like effective population sizeJ Romiguier
Institut des Sciences de l Evolution de Montpellier, Universite Montpellier 2, CNRS UMR 5554, Montpellier, France
J Evol Biol 27:593-603. 2014....
- Genomic evidence for large, long-lived ancestors to placental mammalsJ Romiguier
CNRS, Universite Montpellier 2, UMR 5554, ISEM, Montpellier, France
Mol Biol Evol 30:5-13. 2013..Our results imply that long-lived mammals existed in the Cretaceous era and were the most successful in evolution, opening new perspectives about the conditions for survival to the Cretaceous-Tertiary crisis...
- The evolutionary fate of recently duplicated retrogenes in miceP Gayral
CNRS UMR Génome, Populations, Interactions, Adaptation, Universite Montpellier, Montpellier, France
J Evol Biol 20:617-26. 2007..Purifying selection prevents them from acquiring a negative role until they are lost or silenced. This period of unnecessary redundancy could in rare cases give the time for new functions to evolve...
- Recombination explains isochores in mammalian genomesJuan Ignacio Montoya-Burgos
CNRS UMR 5000 Génome, Populations, Interactions, Université Montpellier 2 CC63, Place E Bataillon, 34095 Montpellier Cedex, France
Trends Genet 19:128-30. 2003..These results strongly suggest that recombination is the primary determinant of the isochore organization of mammalian genomes...
- Population size does not influence mitochondrial genetic diversity in animalsEric Bazin
CNRS UMR 5171 Génome, Populations, Interactions, Adaptation Université Montpellier 2 34095 Montpellier Cedex 5, France
Science 312:570-2. 2006..The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies...
- Comparative population genomics in animals uncovers the determinants of genetic diversityJ Romiguier
1 UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre National de la Recherche Scientifique, Place E Bataillon, 34095 Montpellier, France 2 Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
Nature 515:261-3. 2014..Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies. ..
- The determinants of the molecular substitution process in turtlesJ M Lourenço
Institut des Sciences de l Evolution, Universite Montpellier 2, Montpellier Cedex, France
J Evol Biol 26:38-50. 2013..These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms...
- Detecting bottlenecks and selective sweeps from DNA sequence polymorphismN Galtier
Institute of Cell, Animal and Population Biology, University of Edinburgh, United Kingdom
Genetics 155:981-7. 2000..An application to sequence data from an African population of Drosophila melanogaster shows that the bottleneck hypothesis is unlikely and that one or several selective sweeps probably occurred in the recent history of this population...
- A model-based approach for detecting coevolving positions in a moleculeJulien Dutheil
CNRS UMR 5171 Laboratoire Génome, Populations, Interactions, Adaptation, Universite Montpellier II, Montpellier Cedex, France
Mol Biol Evol 22:1919-28. 2005..More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs...
- Accelerated evolutionary rate of housekeeping genes in tunicatesGeorgia Tsagkogeorga
Université Montpellier 2 and CNRS, Institut des Sciences de l Evolution UMR 5554, CC064, Place Eugene Bataillon, 34095, Montpellier Cedex 05, France
J Mol Evol 71:153-67. 2010....
- Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizesJonathan Romiguier
Universite Montpellier 2, CNRS UMR 5554 Institut des Sciences de l Evolution, 34095 Montpellier, France
Genome Res 20:1001-9. 2010..We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model...
- GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primatesNicolas Galtier
Universite Montpellier 2, CNRS UMR 5554, Institut des Sciences de l Evolution, Place E Bataillon, CC64, 34095 Montpellier, France
Trends Genet 25:1-5. 2009..This demonstrates that gBGC has substantially (negatively) impacted the evolutionary trajectory of human proteins by promoting the fixation of deleterious AT-->GC mutations...
- Determination of mitochondrial genetic diversity in mammalsBenoit Nabholz
CNRS UMR 5554 Institut des Sciences de l Evolution, Montpellier, France
Genetics 178:351-61. 2008..They suggest that, even in the absence of selection, mtDNA genetic diversity is essentially unpredictable, knowing species biology, and probably uncorrelated to species abundance...
- Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesisBenoit Nabholz
Institut des Sciences de l Evolution CC64, Centre National de la Recherche Scientifique Université Montpellier 2, Montpellier, France
Mol Biol Evol 25:120-30. 2008..We propose that natural selection tends to decrease the mitochondrial mutation rate in long-lived species, in agreement with the mitochondrial theory of aging...
- Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosisEmilie Guldner
CNRS UMR 5171 Génome, Populations, Interactions, Adaptation, Universite Montpellier, 2 CC63, Place E Bataillon, 34095 Montpellier, France
J Mol Evol 59:416-25. 2004....
- Polymorphix: a sequence polymorphism databaseEric Bazin
Laboratoire Génome Populations Interactions Adaptation, Unité Mixte de Recherche No 5171 UMR UM2 IFREMER CNRS, Université de Montpellier 2, 34095 Montpellier Cedex 5, France
Nucleic Acids Res 33:D481-4. 2005..Polymorphix contains sequences from the nuclear, mitochondrial and chloroplastic genomes of every eukaryote species represented in EMBL. It can be accessed by a web interface (http://pbil.univ-lyon1.fr/polymorphix/query.php)...
- An evolutionary genome scan for longevity-related natural selection in mammalsRichard W Jobson
Institut des Sciences de l Evolution, CNRS UMR 5554, Universite Montpellier 2, Montpellier, France
Mol Biol Evol 27:840-7. 2010..In this study, we uncovered the way natural selection has completed this task during mammalian evolution. Cellular membrane and extracellular collagen composition, not genome integrity, have apparently been the optimized features...
- Reference-free transcriptome assembly in non-model animals from next-generation sequencing dataV Cahais
CNRS UMR 5554, Institut des Sciences de l Evolution de Montpellier, Universite Montpellier 2, Place E Bataillon, 34095 Montpellier, France
Mol Ecol Resour 12:834-45. 2012..A Galaxy pipeline implementing our best-performing assembling strategy is provided...
- Biased gene conversion and the evolution of mammalian genomic landscapesLaurent Duret
Universite de Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F 69622, Villeurbanne, France
Annu Rev Genomics Hum Genet 10:285-311. 2009..Here we review the recent evidence for a GC-biased gene conversion process in mammals, and its consequences for genomic landscapes, molecular evolution, and human functional genomics...
- Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effectS L Ament-Velásquez
Institute of Evolutionary Sciences, University Montpellier, CNRS, IRD, EPHE, Place Eugene Bataillon, 34095, Montpellier, France
Mol Ecol 25:3356-69. 2016..This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context. ..
- BAOBAB: a Java editor for large phylogenetic treesJ Dutheil
CNRS UMR 5000 Génome, Populations, Interactions, Université Montpellier 2 CC 63, Place E Bataillon, France
Bioinformatics 18:892-3. 2002....
- Comment on "Human-specific gain of function in a developmental enhancer"Laurent Duret
Universite de Lyon, Universite Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F 69622, Villeurbanne, France
Science 323:714; author reply 714. 2009..The reported human-specific gain of function is likely due to the accumulation of deleterious mutations driven by BGC, not positive selection...
- Mitochondrial DNA as a tool for reconstructing past life-history traits in mammalsE Figuet
UMR 5554, ISEM, CNRS, Universite Montpellier 2, Montpellier, France
J Evol Biol 27:899-910. 2014..This finding is in accordance with Cope's rule and the fossil record but could not be recovered via continuous character evolution methods...
- The influence of demography, population structure and selection on molecular diversity in the selfing freshwater snail Biomphalaria pfeifferiBernard Angers
Centre d Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, Montpellier, France
Genet Res 81:193-204. 2003..This highlights the fact that the interfering influences of population structure, demography and selection on molecular variation are not easily distinguished...
- Apparent longevity-related adaptation of mitochondrial amino acid content is due to nucleotide compositional shiftsRichard W Jobson
Institut des Sciences de l Evolution, CNRS UMR 5554, Universite Montpellier 2, Place E Bataillon, 34095 Montpellier, France
Mitochondrion 10:540-7. 2010..These results are strongly suggestive of mutational bias, or less efficient purifying selection, as the primary driver of whole proteome shifts in amino acid composition...
- BAGE genes generated by juxtacentromeric reshuffling in the Hominidae lineage are under selective pressureMyriam Ruault
Institut de Genetique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396 Montpellier, France
Genomics 81:391-9. 2003..Our data strongly suggest that BAGE proteins have a function and that juxtacentromeric regions, whose plasticity is now largely proved, are not a simple junkyard of gene fragments, but may be the birth site of novel genes...
- Sex chromosomes: how X-Y recombination stopsGabriel Marais
Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
Curr Biol 13:R641-3. 2003
- A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomesTal Pupko
The Institute of Statistical Mathematics, 4 6 7 Minami Azabu Minato ku, Tokyo 106 8569, Japan
Proc Biol Sci 269:1313-6. 2002..e. highly constrained) in primates, and some show the opposite pattern. Our results indicate that the mitochondrial genome of primates reached a new peak of the adaptive landscape through positive selection...
- The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogenyElise M S Belle
Centre for the Study of Evolution School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
J Mol Evol 58:653-60. 2004..These results are of interest because they confirm the recently suggested disappearance of GC-rich isochores in some mammalian genomes, and more importantly, they suggest that this disappearance started very early in mammalian evolution...
- A new perspective on isochore evolutionLaurent Duret
CNRS UMR 5558, BBE, Université C Bernard Lyon 1, France
Gene 385:71-4. 2006..In this article we review the existing support for these two hypotheses, and discuss how they can be combined to provide a new perspective on isochore evolution...
- Vanishing GC-rich isochores in mammalian genomesLaurent Duret
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558 Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
Genetics 162:1837-47. 2002..We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals...