N Galtier

Summary

Country: France

Publications

  1. pmc GC-biased segregation of noncoding polymorphisms in Drosophila
    Nicolas Galtier
    UMR 5171, Genome, Populations, Interactions, Adaptation, CNRS, Universite Montpellier 2, IFREMER, 34095 Montpellier, France
    Genetics 172:221-8. 2006
  2. pmc Mutation hot spots in mammalian mitochondrial DNA
    Nicolas 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
  3. pmc The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals
    Benoit 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
  4. pmc Detecting groups of coevolving positions in a molecule: a clustering approach
    Julien 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
  5. pmc Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    Julien Dutheil
    CNRS UMR 5171 Génome, Populations, Interactions, Adaptation GPIA, Universite Montpellier 2, France
    BMC Bioinformatics 7:188. 2006
  6. ncbi request reprint Gene conversion drives GC content evolution in mammalian histones
    Nicolas Galtier
    CNRS UMR 5000 Génome, Populations, Interactions, Université Montpellier 2 CC63, Place E Bataillon, 34095, Montpellier, France
    Trends Genet 19:65-8. 2003
  7. doi request reprint Mitochondrial DNA as a marker of molecular diversity: a reappraisal
    N 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
  8. pmc Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution
    Nicolas 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
  9. ncbi request reprint Markov-modulated Markov chains and the covarion process of molecular evolution
    N Galtier
    CNRS UMR 5171 GPIA, Université Montpellier 2 CC 63, Place E Bataillon, 34095 Montpellier, France
    J Comput Biol 11:727-33. 2004
  10. ncbi request reprint Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds
    Nicolas Galtier
    Institut des Sciences de l Evolution, Université Montpellier 2 CNRS UMR 5554, Place E Bataillon, 34095 Montpellier, France
    Mitochondrion 9:51-7. 2009

Collaborators

Detail Information

Publications49

  1. pmc GC-biased segregation of noncoding polymorphisms in Drosophila
    Nicolas 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...
  2. pmc Mutation hot spots in mammalian mitochondrial DNA
    Nicolas 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...
  3. pmc The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals
    Benoit 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...
  4. pmc Detecting groups of coevolving positions in a molecule: a clustering approach
    Julien 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
    ....
  5. pmc Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    Julien 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...
  6. ncbi request reprint Gene conversion drives GC content evolution in mammalian histones
    Nicolas 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...
  7. doi request reprint Mitochondrial DNA as a marker of molecular diversity: a reappraisal
    N 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...
  8. pmc Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution
    Nicolas 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...
  9. ncbi request reprint Markov-modulated Markov chains and the covarion process of molecular evolution
    N 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...
  10. ncbi request reprint Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds
    Nicolas 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...
  11. ncbi request reprint Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution
    Nicolas 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...
  12. ncbi request reprint A model of horizontal gene transfer and the bacterial phylogeny problem
    Nicolas 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...
  13. pmc Dealing with incongruence in phylogenomic analyses
    Nicolas 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...
  14. ncbi request reprint Recombination, GC-content and the human pseudoautosomal boundary paradox
    Nicolas 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...
  15. ncbi request reprint Mouse biodiversity in the genomic era
    N Galtier
    UMR 5171 Genome, Populations, Interactions, Adaptation, Universite Montpellier 2, Montpellier, France
    Cytogenet Genome Res 105:385-94. 2004
    ....
  16. pmc The intriguing evolutionary dynamics of plant mitochondrial DNA
    Nicolas 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...
  17. ncbi request reprint Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites
    Nicolas 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...
  18. doi request reprint Coevolution within and between genes
    N Galtier
    Universite Montpellier 2, Montpellier, France
    Genome Dyn 3:1-12. 2007
    ..The reasons for this discrepancy are discussed...
  19. ncbi request reprint Maximum-likelihood phylogenetic analysis under a covarion-like model
    N 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...
  20. ncbi request reprint A new method for locating changes in a tree reveals distinct nucleotide polymorphism vs. divergence patterns in mouse mitochondrial control region
    N 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...
  21. ncbi request reprint Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale ferox
    E 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...
  22. doi request reprint Genomic evidence for large, long-lived ancestors to placental mammals
    J 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...
  23. ncbi request reprint The evolutionary fate of recently duplicated retrogenes in mice
    P 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...
  24. ncbi request reprint Recombination explains isochores in mammalian genomes
    Juan 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...
  25. ncbi request reprint Population size does not influence mitochondrial genetic diversity in animals
    Eric 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...
  26. doi request reprint The determinants of the molecular substitution process in turtles
    J 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...
  27. pmc Detecting bottlenecks and selective sweeps from DNA sequence polymorphism
    N 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...
  28. doi request reprint GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
    Nicolas 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...
  29. doi request reprint Accelerated evolutionary rate of housekeeping genes in tunicates
    Georgia 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
    ....
  30. pmc Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes
    Jonathan 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...
  31. doi request reprint An evolutionary genome scan for longevity-related natural selection in mammals
    Richard 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...
  32. ncbi request reprint Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosis
    Emilie 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
    ....
  33. ncbi request reprint Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis
    Benoit 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...
  34. pmc Determination of mitochondrial genetic diversity in mammals
    Benoit 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...
  35. ncbi request reprint A model-based approach for detecting coevolving positions in a molecule
    Julien 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...
  36. pmc Polymorphix: a sequence polymorphism database
    Eric 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)...
  37. doi request reprint Reference-free transcriptome assembly in non-model animals from next-generation sequencing data
    V 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...
  38. doi request reprint Biased gene conversion and the evolution of mammalian genomic landscapes
    Laurent 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...
  39. ncbi request reprint BAOBAB: a Java editor for large phylogenetic trees
    J Dutheil
    CNRS UMR 5000 Génome, Populations, Interactions, Université Montpellier 2 CC 63, Place E Bataillon, France
    Bioinformatics 18:892-3. 2002
    ....
  40. doi request reprint 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...
  41. ncbi request reprint Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals
    E 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...
  42. ncbi request reprint The influence of demography, population structure and selection on molecular diversity in the selfing freshwater snail Biomphalaria pfeifferi
    Bernard 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...
  43. doi request reprint Apparent longevity-related adaptation of mitochondrial amino acid content is due to nucleotide compositional shifts
    Richard 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...
  44. pmc A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes
    Tal 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...
  45. pmc Vanishing GC-rich isochores in mammalian genomes
    Laurent 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...
  46. ncbi request reprint BAGE genes generated by juxtacentromeric reshuffling in the Hominidae lineage are under selective pressure
    Myriam 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...
  47. ncbi request reprint Sex chromosomes: how X-Y recombination stops
    Gabriel Marais
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
    Curr Biol 13:R641-3. 2003
  48. ncbi request reprint The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny
    Elise 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...
  49. ncbi request reprint A new perspective on isochore evolution
    Laurent 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...