Benoit Nabholz

Benoit Nabholz

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Benoit Nabholz

Benoit Nabholz

Publications by authors named "Benoit Nabholz"

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36Publications

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Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution.

Syst Biol 2019 May 7. Epub 2019 May 7.

Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France.

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http://dx.doi.org/10.1093/sysbio/syz030DOI Listing
May 2019

Overestimation of the adaptive substitution rate in fluctuating populations.

Biol Lett 2018 05;14(5)

UMR-5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France.

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http://dx.doi.org/10.1098/rsbl.2018.0055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6012701PMC
May 2018

Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA.

Genome Biol Evol 2018 02;10(2):616-622

Institut des Sciences de l'Evolution, ISEM, Université de Montellier, CNRS, IRD, EPHE, France.

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http://dx.doi.org/10.1093/gbe/evy022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808798PMC
February 2018

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds.

Mol Biol Evol 2017 Dec;34(12):3123-3131

Institut des Sciences de l'Evolution, UMR5554, Universitè de Montpellier, CNRS, IRD, EPHE, Montpellier, 34095, France.

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http://dx.doi.org/10.1093/molbev/msx236DOI Listing
December 2017

Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies.

Genome Biol Evol 2016 10 23;8(10):3108-3119. Epub 2016 Oct 23.

UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France.

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http://dx.doi.org/10.1093/gbe/evw214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174731PMC
October 2016

Body mass-corrected molecular rate for bird mitochondrial DNA.

Mol Ecol 2016 09 6;25(18):4438-49. Epub 2016 Sep 6.

Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205 CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Université, 57 rue Cuvier, CP5175005, Paris, France.

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http://dx.doi.org/10.1111/mec.13780DOI Listing
September 2016

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes.

Mol Biol Evol 2016 06 4;33(6):1517-27. Epub 2016 Mar 4.

UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France

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http://dx.doi.org/10.1093/molbev/msw033DOI Listing
June 2016

Gene expression, chromosome heterogeneity and the fast-X effect in mammals.

Biol Lett 2015 Feb;11(2):20150010

Institut des Sciences de l'Evolution, CC64, Université Montpellier II, Place Eugène Bataillon, Montpellier cedex 5 34095, France

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http://dx.doi.org/10.1098/rsbl.2015.0010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4360113PMC
February 2015

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

The bimodal distribution of genic GC content is ancestral to monocot species.

Genome Biol Evol 2014 Dec 19;7(1):336-48. Epub 2014 Dec 19.

Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier, France.

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http://dx.doi.org/10.1093/gbe/evu278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316631PMC
December 2014

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).

Mol Ecol 2014 May 18;23(9):2210-27. Epub 2014 Apr 18.

Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France; UMR AGAP 1334, Montpellier SupAgro, Montpellier, France.

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http://dx.doi.org/10.1111/mec.12738DOI Listing
May 2014

High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.

Mol Biol Evol 2013 Feb 15;30(2):272-84. Epub 2012 Oct 15.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/mss238DOI Listing
February 2013

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination.

BMC Genomics 2013 Feb 8;14:86. Epub 2013 Feb 8.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1186/1471-2164-14-86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600008PMC
February 2013

Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection.

Genome Biol Evol 2011 31;3:1381-9. Epub 2011 Oct 31.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/gbe/evr112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242499PMC
April 2012

Evolutionary constraint in flanking regions of avian genes.

Mol Biol Evol 2011 Sep 4;28(9):2481-9. Epub 2011 Apr 4.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msr066DOI Listing
September 2011

Dynamic evolution of base composition: causes and consequences in avian phylogenomics.

Mol Biol Evol 2011 Aug 4;28(8):2197-210. Epub 2011 Apr 4.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msr047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144382PMC
August 2011

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi.

Mol Phylogenet Evol 2011 Jun 23;59(3):649-63. Epub 2011 Mar 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18 D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.ympev.2011.03.023DOI Listing
June 2011

Molecular evolution of genes in avian genomes.

Genome Biol 2010 23;11(6):R68. Epub 2010 Jun 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, S-752 36, Sweden.

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http://dx.doi.org/10.1186/gb-2010-11-6-r68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911116PMC
November 2010

Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

Mol Phylogenet Evol 2010 Oct 25;57(1):466-70. Epub 2010 Jun 25.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.ympev.2010.06.009DOI Listing
October 2010

An evolutionary genome scan for longevity-related natural selection in mammals.

Mol Biol Evol 2010 Apr 2;27(4):840-7. Epub 2009 Dec 2.

Institut des Sciences de l'Evolution, CNRS UMR 5554, Université Montpellier 2, Montpellier, France.

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http://dx.doi.org/10.1093/molbev/msp293DOI Listing
April 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution.

Biol Lett 2009 Jun 4;5(3):413-6. Epub 2009 Mar 4.

Institut des Sciences de l'Evolution, CNRS UMR 5554, Université Montpellier 2, Place E. Bataillon, 34095 Montpellier, France.

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http://dx.doi.org/10.1098/rsbl.2008.0662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679905PMC
June 2009

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals.

BMC Evol Biol 2009 Mar 10;9:54. Epub 2009 Mar 10.

Université Montpellier 2 CNRS UMR 5554 - Institut des Sciences de l'Evolution Place E. Bataillon - CC064, Montpellier, France.

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http://dx.doi.org/10.1186/1471-2148-9-54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660308PMC
March 2009

Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds.

Mitochondrion 2009 Feb 24;9(1):51-7. Epub 2008 Dec 24.

Institut des Sciences de l'Evolution, Université Montpellier 2 - CNRS UMR 5554, Place E. Bataillon, 34095 Montpellier, France.

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http://dx.doi.org/10.1016/j.mito.2008.11.006DOI Listing
February 2009

Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis.

Mol Biol Evol 2008 Jan 12;25(1):120-30. Epub 2007 Nov 12.

Institut des Sciences de l'Evolution-CC64, Centre National de la Recherche Scientifique-Université Montpellier 2, Montpellier, France.

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http://dx.doi.org/10.1093/molbev/msm248DOI Listing
January 2008

Determination of mitochondrial genetic diversity in mammals.

Genetics 2008 Jan;178(1):351-61

CNRS UMR 5554-Institut des Sciences de l'Evolution, Montpellier, France.

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http://dx.doi.org/10.1534/genetics.107.073346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206084PMC
January 2008