Benoit Nabholz

Summary

Country: France

Publications

  1. 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
  2. doi request reprint High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 30:272-84. 2013
  3. pmc Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection
    Axel Künstner
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Genome Biol Evol 3:1381-9. 2011
  4. doi request reprint Evolutionary constraint in flanking regions of avian genes
    Axel Künstner
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 28:2481-9. 2011
  5. pmc Dynamic evolution of base composition: causes and consequences in avian phylogenomics
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 28:2197-210. 2011
  6. 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
  7. 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
  8. pmc Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination
    Carina F Mugal
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36, Uppsala, Sweden
    BMC Genomics 14:86. 2013
  9. doi request reprint Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Phylogenet Evol 57:466-70. 2010
  10. 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

Detail Information

Publications14

  1. 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...
  2. doi request reprint High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 30:272-84. 2013
    ..Our results not only reaffirm the link between gene expression and protein evolution but also open new questions about the functional role of expression level variation between mitochondrial genes...
  3. pmc Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection
    Axel Künstner
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Genome Biol Evol 3:1381-9. 2011
    ..We show by simulations that the rate of false positives in the detection of positively selected genes and sites increases several-fold at the levels of constraint at 4-fold degenerate sites found in this study...
  4. doi request reprint Evolutionary constraint in flanking regions of avian genes
    Axel Künstner
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 28:2481-9. 2011
    ..This study broadens the insights into gene flanking sequence evolution by adding new findings from a vertebrate lineage other than mammals...
  5. pmc Dynamic evolution of base composition: causes and consequences in avian phylogenomics
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Biol Evol 28:2197-210. 2011
    ..This study illustrates the potential of next-generation sequencing for phylogenomic studies but also the pitfalls when using genome-wide data with heterogeneous base composition...
  6. 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...
  7. 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...
  8. pmc Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination
    Carina F Mugal
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36, Uppsala, Sweden
    BMC Genomics 14:86. 2013
    ..Moreover, recombination might itself be mutagenic and thereby assert a direct effect on diversity levels...
  9. doi request reprint Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny
    Benoit Nabholz
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Mol Phylogenet Evol 57:466-70. 2010
    ..This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes...
  10. 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...
  11. pmc Molecular evolution of genes in avian genomes
    Kiwoong Nam
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, Uppsala, S 752 36, Sweden
    Genome Biol 11:R68. 2010
    ....
  12. ncbi request reprint Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima)
    Benoit Nabholz
    Institut des Sciences de l Evolution Montpellier, UMR CNRS UM2 5554, University Montpellier II, Montpellier, France UMR AGAP 1334, Montpellier SupAgro, Montpellier, France
    Mol Ecol 23:2210-27. 2014
    ..This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits...
  13. pmc Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap
    Philippe Gayral
    Universite Montpellier 2, CNRS UMR 5554, Institut des Sciences de l Evolution de Montpellier, Montpellier, France
    PLoS Genet 9:e1003457. 2013
    ..This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity...
  14. doi request reprint A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi
    Kristiina Nygren
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyv 18 D, SE 752 36 Uppsala, Sweden
    Mol Phylogenet Evol 59:649-63. 2011
    ..The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration...