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2024
(58) Reboud EL, Nabholz B, Chevalier E, Lafon BJ, Tilak M, Mielke CGC, Cotton AM, Condamine FL. 2024 Nov 28. Clarifying the phylogeny and systematics of the recalcitrant tribe Leptocircini (Lepidoptera: Papilionidae) with whole‐genome data. Systematic Entomology.:syen.12661. doi:10.1111/syen.12661.
(57) Nabholz B, Puissant S, Defaut B. 2024. A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023. Zootaxa. 5481(1):146–150.
(56) Gabrielli M, Leroy T, Salmona J, Nabholz B, Milá B, Thébaud C. 2024. Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole‐genome sequencing. Molecular Ecology. 33(4):e17243. doi:10.1111/mec.17243.
(55) M. Barthe, L. Rancilhac, M. C. Arteaga, A. Feijó, M.-K. Tilak, F. Justy, W. J. Loughry, C. M. McDonough, B. de Thoisy, F. Catzeflis, G. Billet, L. Hautier, B. Nabholz and F. Delsuc, 2024. Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield. Systematic Biology.
2023
(54) Marino A, E. L. Reboud, E. Chevalier, M.-K. Tilak, J. Contreras-Garduño, B. Nabholz and F. L. Condamine, 2023. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 - Genes Genomes Genetics.
(53) Jérémie Février, Benoit Nabholz, Louis Ton. 2023. Synthèse des données et probabilité de détection de l’Arcyptère languedocienne, Arcyptera brevipennis vicheti (Brunner von Wattenwyl, 1861), en France (Orthoptera, Acrididae). Matériaux orthoptériques et entomocénotiques. Matériaux orthoptériques et entomocénotiques. 28 : 31-43
(52) Louis Ton, Didier Morin, Antoine Foucart, Jean-Michel Catil, Benoit Nabholz. 2023. Le Dectique verrucivore, Decticus verrucivorus (Linnaeus, 1758), en France continentale : étude morphologique et implications taxonomiques (Orthoptera : Tettigoniidae). Matériaux orthoptériques et entomocénotiques. Matériaux orthoptériques et entomocénotiques. 28 : 45-68
(51) Nabholz B. 2023. Incomplete lineage sorting explains the low performance of DNA barcoding in a radiation of four species of Western European grasshoppers (Orthoptera: Acrididae: Chorthippus). Biological Journal of the Linnean Society:blad106. [full text]
(50) Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. 2023. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. Journal of Evolutionary Biology 36:1226–1241.
(49) Pélissié M, Nabholz B, Labadessa R, Ancillotto L. 2023. Hidden in plain sight: unveiling the distributions of green-winged grasshoppers (Aiolopus spp.) with citizen-science data. Journal of Zoology 320:301–307.
(48) Reboud EL, Nabholz B, Chevalier E, Tilak M, Bito D, Condamine FL. 2023. Genomics, population divergence and historical demography of the world’s largest and endangered butterfly, the Queen Alexandra’s birdwing. Genome Biology and Evolution:evad040.
2022
(47) Barthe M, Doutrelant C, Covas R, Melo M, Illera JC, Tilak M-K, Colombier C, Leroy T, Loiseau C, Nabholz B. 2022. Evolution of immune genes in island birds: reduction in population sizes can explain island syndrome. Peer Community Journal [Internet] 2. Available from: https://peercommunityjournal.org/articles/10.24072/pcjournal.186/
(46) Leroy T, Nabholz B. 2022. Response to Kratochvíl and Rovatsos. Curr. Biol. 32:R30–R31.
2021
(45) Leroy T, Rousselle M, Tilak M-K, Caizergues AE, Scornavacca C, Recuerda M, Fuchs J, Illera JC, De Swardt DH, Blanco G, Milá B, Thébaud C, Nabholz B. 2021. Island songbirds as windows into evolution in small populations. Curr. Biol. 31:1303-1310.e4.
(44) Allio R, Tilak M-K, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. 2021. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. Elife 10:e63167.
(43) Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens A-L, Kergoat GJ, Sperling FAH, Condamine FL. 2021. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat. Commun. 12:354.
2020
(42) R. Allio, A. Schomaker-Bastos, J. Romiguier, F. Prosdocimi, B. Nabholz and F. Delsuc, 2020. MitoFinder: efficient automated large-scale extraction 1 of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources.: in press. [Software]
(41) M. Gabrielli, B. Nabholz, T. Leroy, B. Milá and C. Thébaud, 2020. Within-island diversification in a passerine bird. Proceedings of the Royal Society B: Biological Sciences. 287: 20192999.
2019
(40) Rousselle M, Simion P, Tilak M-K, Figuet E, Nabholz B, Galtier N. 2019. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. bioRxiv, 643619, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. DOI:10.1101/643619
(39) Allio R, Scornavacca C, Nabholz B, Clamens A-L, Sperling FA, Condamine F. 2019. Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Systematic Biology, Volume 69, Issue 1, January 2020, Pages 38–60, https://doi.org/10.1093/sysbio/syz030
(38) Leroy T, Anselmetti A, Tilak MK, Bérard S, Csukonyi L, Gabrielli M, Scornavacca C, Milá B, Thébaud C and Nabholz B. A bird’s white-eye view on neo-sex chromosome evolution. 2019. Peer Community Journal 10.24072/pcjournal.70
2018
(36) Rousselle M, Mollion M, Nabholz B, Bataillon T, Galtier N. 2018. Overestimation of the adaptive substitution rate in fluctuating populations. Biol. Lett. 14:20180055.
(35) Condamine FL, Nabholz B, Clamens A-L, Dupuis JR, Sperling F a. H. Mitochondrial phylogenomics, the origin of swallowtail butterflies, and the impact of the number of clocks in Bayesian molecular dating. Syst. Entomol.: in press. [pdf]
(34) Tilak M-K, Botero-Castro F, Galtier N, Nabholz B. 2018. Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA. Genome Biology and Evolution 10:616–622.
2017
(33) Botero-Castro F, Figuet E, Tilak M-K, Nabholz B, Galtier N. 2017. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds. Molecular Biology and Evolution 34:3123–3131. [pdf]
(32) Allio R, Donega S, Galtier N and Nabholz B. 2017. Large variation in the ratio of mitochondrial to nuclear mutation rate across animals : implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Molecular Biology and Evolution. 34(11):2762–2772 [dataset][pdf]
(31) Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M ... Glémin S (with 32 co-authors). 2017 Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genetics 13 (5): e1006799 [link].
2016
(30) Rousselle M, Faivre N, Ballenghien M, Galtier N and Nabholz B. 2016. Hemizygosity enhances purifying selection: lack of fast-Z evolution in two satyrine butterflies. Genome Biology and Evolution 8: 3108-3119 [link]
(29) Nabholz B, Lanfear R and Fuchs J. 2016. Body mass-corrected molecular rate for bird mitochondrial DNA. Molecular Ecology 25:4438-4449. [pdf, dataset and methods] See also guidelines here.
(28) Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N et al. (29 co-authors). 2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Ressources 17: 565–580 [pdf]
(27) Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H and Galtier N. 2016. Life-history traits, protein evolution and the nearly-neutral theory in amniotes. Molecular Biology and Evolution: 33 (6): 1517-1527 [pdf]
2015
(26) Nguyen LP, Galtier N and Nabholz B. 2015. Gene expression, chromosome heterogeneity and the fast-X effect in mammals. Biology Letters 11: 20150010. [pdf, link, dataset]
(25) Clément, Y, Fustier MA, Nabholz B and Glémin S. 2015. The bimodal distribution of genic GC-content is ancestral to Monocots species. Genome Biology and Evolution 7: 336-348 [link]
(24) Jarvis E, Mirarab S, Aberer AJ, Bo Li, Houde P, Cai Li, Ho SYW, Faircloth BC, Nabholz B, Howard JT et al. (105 co-authors). 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds Science 346 (6215): 1320-1331 [pdf]
(23) Weber C, Nabholz B, Romiguier J, and Ellegren H. 2014. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biology 15 (12): 542. [link]
(22) 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 A, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N. 2014. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515 (7526): 261 [pdf]
(21) Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. 2014. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima). Molecular Ecology 23 (9): 2210-2227. [pdf, link, dataset, software]
2013
(20) Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM and Galtier N. 2013. Population genomics of the endangered giant Galapagos tortoise. Genome Biology 14:R136. [link]
(19) Nabholz B*, Uwimana N* and Lartillot N. 2013. Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino-acid replacement in mitochondrial genomes of mammals and birds Genome Biology and Evolution 5 (7:) 1273-1290. *These authors contributed equally to this work [link]
(18) Guéguen L et al. (18 co-authors) 2013. Bio++: Efficient, Extensible Libraries and Tools for Computational Molecular Evolution. Molecular Biology and Evolution 30 (8), 1745-1750. [pdf]
(17) 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 and Galtier N. 2013. Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap. PLoS Genet 9 (4): e1003457. [link]
(16) Mugal CF, Nabholz B, Ellegren H. 2013. Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics 14:86. [pdf]
(15) Nabholz B, Ellegren H and Wolf JBW. 2013. High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes. Molecular Biology and Evolution 30(2):272–284 [pdf]
2011
(14) Künstner A, Nabholz B and Ellegren H. 2011. Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection. Genome Biology and Evolution 3 1381-1389. [pdf]
(13) Nygren K, Strandberg R, Wallberg A, Nabholz B, Gustafsson T, García D, Cano J, Guarro J and Johannesson H. 2011. A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi. Molecular Phylogenetics and Evolution 59: 649-663. [pdf]
(12) Künstner A, Nabholz B and Ellegren H. 2011. Evolutionary constraint in flanking regions of avian genes. Molecular Biology and Evolution 28: 2481-2489. [pdf]
(11) Nabholz B, A Künstner A, R Wang R, Jarvis E and Ellegren H. 2011. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Molecular Biology and Evolution 28: 2197-2210. [pdf]
2010
(10) Kiwoong N, Mugal C,Nabholz B, Schielzeth H, Wolf JWB, Backström N, Künstner A, Balakrishnan CN, Heger A, Ponting CP, Clayton DF and Ellegren H. 2010. Molecular evolution of genes in avian genomes. Genome biology 11 (6), R68. (web link).
(9) Nabholz B, Erich DJ and H Ellegren H. 2010. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Molecular Phylogenetics and Evolution 57 :466-70. (dataset)
(8) Warren W C et al (with 74 co-authors). 2010. The genome of a songbird. Nature 464: 757-762.
(7) Jobson R W, B Nabholz and N Galtier. 2010. An evolutionary genome scan for longevity- related natural selection in mammals. Molecular Biology and Evolution 27: 840-847.
2009
(6) Galtier N, R W Jobson, B Nabholz, S Glémin and P U Blier. 2009. Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biology Letters 23: 413-416. Recommended article by F-1000 biology
(5) Nabholz B, S Glémin and N Galtier. 2009. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC evolutionary biology 9:54.
(4) Galtier N, P U Blier and B Nabholz. 2009. Inverse relationship between evolutionary rate of mitochondrial proteins and longevity in mammals and birds. Mitochondrion 9: 51-57.
(3) Galtier N, B Nabholz, S Glémin and GD Hurst. 2009. Mitochondrial DNA as markers of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-50.
2008
(2) Nabholz B, S Glémin and N Galtier. 2008. Strong Variations of Mitochondrial Mutation Rate across Mammals the Longevity Hypothesis. Molecular Biology and Evolution 25:120-130. A must read article by F-1000 biology (http://f1000.com/prime/1097599). Elected as MBE citation classic in 2013. (dryad link)
(1) Nabholz B, J Mauffrey, E Bazin, N Galtier, and S Glémin. 2008. Determination of Mitochondrial genetic diversity in Mammals. Genetics 178: 351 – 361. (dataset)
See the link at the bottom of the page to download my Ph.D Thesis (in French).
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