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Items: 38

1.

Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds.

Rousselle M, Laverré A, Figuet E, Nabholz B, Galtier N.

Mol Biol Evol. 2019 Mar 1;36(3):458-471. doi: 10.1093/molbev/msy243.

2.

Overestimation of the adaptive substitution rate in fluctuating populations.

Rousselle M, Mollion M, Nabholz B, Bataillon T, Galtier N.

Biol Lett. 2018 May;14(5). pii: 20180055. doi: 10.1098/rsbl.2018.0055.

3.

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

Tilak MK, Botero-Castro F, Galtier N, Nabholz B.

Genome Biol Evol. 2018 Feb 1;10(2):616-622. doi: 10.1093/gbe/evy022.

4.
5.

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

Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N.

Mol Biol Evol. 2017 Dec 1;34(12):3123-3131. doi: 10.1093/molbev/msx236.

PMID:
28962031
6.

Evolutionary forces affecting synonymous variations in plant genomes.

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S.

PLoS Genet. 2017 May 22;13(5):e1006799. doi: 10.1371/journal.pgen.1006799. eCollection 2017 May.

7.

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

Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B.

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

8.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M.

Mol Ecol Resour. 2017 May;17(3):565-580. doi: 10.1111/1755-0998.12587. Epub 2016 Aug 29.

PMID:
27487989
9.

Body mass-corrected molecular rate for bird mitochondrial DNA.

Nabholz B, Lanfear R, Fuchs J.

Mol Ecol. 2016 Sep;25(18):4438-49. doi: 10.1111/mec.13780. Epub 2016 Sep 6.

PMID:
27483387
10.

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.

Mol Biol Evol. 2016 Jun;33(6):1517-27. doi: 10.1093/molbev/msw033. Epub 2016 Mar 4.

PMID:
26944704
11.

Phylogenomic analyses data of the avian phylogenomics project.

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, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.

12.

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

Nguyen LP, Galtier N, Nabholz B.

Biol Lett. 2015 Feb;11(2):20150010. doi: 10.1098/rsbl.2015.0010.

13.
14.

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

Clément Y, Fustier MA, Nabholz B, Glémin S.

Genome Biol Evol. 2014 Dec 19;7(1):336-48. doi: 10.1093/gbe/evu278.

15.

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, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

16.

Comparative population genomics in animals uncovers the determinants of genetic diversity.

Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AA, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N.

Nature. 2014 Nov 13;515(7526):261-3. doi: 10.1038/nature13685. Epub 2014 Aug 20.

17.

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, Ghesquière A, Santoni S, David J, Glémin S.

Mol Ecol. 2014 May;23(9):2210-27. doi: 10.1111/mec.12738. Epub 2014 Apr 18.

PMID:
24684265
18.

Population genomics of the endangered giant Galápagos tortoise.

Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N.

Genome Biol. 2013 Dec 16;14(12):R136. doi: 10.1186/gb-2013-14-12-r136.

20.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Guéguen 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, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.

PMID:
23699471
21.

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 Apr;9(4):e1003457. doi: 10.1371/journal.pgen.1003457. Epub 2013 Apr 11.

22.

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 Feb 8;14:86. doi: 10.1186/1471-2164-14-86.

23.

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 Feb;30(2):272-84. doi: 10.1093/molbev/mss238. Epub 2012 Oct 15.

PMID:
23071102
24.

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

Künstner A, Nabholz B, Ellegren H.

Genome Biol Evol. 2011;3:1381-9. doi: 10.1093/gbe/evr112. Epub 2011 Oct 31.

25.

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

Nygren K, Strandberg R, Wallberg A, Nabholz B, Gustafsson T, García D, Cano J, Guarro J, Johannesson H.

Mol Phylogenet Evol. 2011 Jun;59(3):649-63. doi: 10.1016/j.ympev.2011.03.023. Epub 2011 Mar 23.

PMID:
21439389
26.

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

Nabholz B, Künstner A, Wang R, Jarvis ED, Ellegren H.

Mol Biol Evol. 2011 Aug;28(8):2197-210. doi: 10.1093/molbev/msr047. Epub 2011 Apr 4.

27.

Evolutionary constraint in flanking regions of avian genes.

Künstner A, Nabholz B, Ellegren H.

Mol Biol Evol. 2011 Sep;28(9):2481-9. doi: 10.1093/molbev/msr066. Epub 2011 Apr 4.

PMID:
21393603
28.

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

Nabholz B, Jarvis ED, Ellegren H.

Mol Phylogenet Evol. 2010 Oct;57(1):466-70. doi: 10.1016/j.ympev.2010.06.009. Epub 2010 Jun 25.

PMID:
20601014
29.

Molecular evolution of genes in avian genomes.

Nam K, Mugal C, Nabholz B, Schielzeth H, Wolf JB, Backström N, Künstner A, Balakrishnan CN, Heger A, Ponting CP, Clayton DF, Ellegren H.

Genome Biol. 2010;11(6):R68. doi: 10.1186/gb-2010-11-6-r68. Epub 2010 Jun 23.

30.

The genome of a songbird.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.

Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.

31.

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

Jobson RW, Nabholz B, Galtier N.

Mol Biol Evol. 2010 Apr;27(4):840-7. doi: 10.1093/molbev/msp293. Epub 2009 Dec 2.

PMID:
19955481
32.

Mitochondrial DNA as a marker of molecular diversity: a reappraisal.

Galtier N, Nabholz B, Glémin S, Hurst GD.

Mol Ecol. 2009 Nov;18(22):4541-50. doi: 10.1111/j.1365-294X.2009.04380.x. Epub 2009 Oct 9. Review.

PMID:
19821901
33.

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

Galtier N, Jobson RW, Nabholz B, Glémin S, Blier PU.

Biol Lett. 2009 Jun 23;5(3):413-6. doi: 10.1098/rsbl.2008.0662. Epub 2009 Mar 4.

34.

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. doi: 10.1186/1471-2148-9-54.

35.

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. doi: 10.1016/j.mito.2008.11.006. Epub 2008 Dec 24.

PMID:
19154799
36.

Determination of mitochondrial genetic diversity in mammals.

Nabholz B, Mauffrey JF, Bazin E, Galtier N, Glemin S.

Genetics. 2008 Jan;178(1):351-61. doi: 10.1534/genetics.107.073346.

37.

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
38.

[The sympathetic trunk and its branches to the abdominal and pelvic viscera in the gerbil (Meriones unguiculatus)].

Nabholz B, Frewein J.

Zentralbl Veterinarmed C. 1976 Nov;5(4):342-53. German. No abstract available.

PMID:
1015062

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