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Publications

Journal Publications

2023

98. Teullet S., Tilak M.-K., Magdeleine A., Schaub R., Weyer N.M., Panaino W., Fuller A., Loughry W.J., Avenant N.L., de Thoisy B., Borrel G. & Delsuc F. (2023).

Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals.

mSystems 8: e00388-23. [pdf]

97. Heighton S.P.*, Allio R.*, Murienne J., Salmona J., Meng H., Scornavacca C., Bastos A.D.S., Njiokou F., Pietersen D., Tilak M.-K., Luo S.-J.*,  Delsuc F.* & Gaubert P.* (2023).

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals.

Molecular Biology and Evolution 40: msad190. [pdf]

96. Emerling C.A., Gibb G.C., Tilak M.-K., Hughes J.J., Kuch M., Duggan A.T., Poinar H.N., Nachman M.W. & Delsuc F. (2023).

Genomic data suggest parallel dental vestigialization within the xenarthran radiation.

Peer Community Journal 3: e75. [pdf]

95. Theissinger K.*, Fernandes C.*, Formenti G.*, Bista I., Berg P.R., Bleidorn C., Bombarely A., Crottini A., Gallo G.R, Godoy J.A., Jentoft S., Malukiewicz J., Mouton A., Oomen R.A., Paez S., Palsbøll P.J., Pampoulie C., Ruiz-Lopez M.J., Secomandi S., Svardal H., Theofanopoulou C., de Vries J., Waldvogel A.-M., Zhang G., Jarvis E.D., Bálint M., Ciofi C., Waterhouse R.M., Mazzoni C.J., Höglund J. & The European Reference Genome Atlas Consortium (including Delsuc F.) (2023).

How genomics can help biodiversity conservation.

Trends in Genetics 39: 545-559. [pdf]

2022

94. Meseguer A.S., Michel A., Fabre P.-H., Pérez-Escobar O.A., Chomicki G., Riina R., Antonelli A., Antoine P.-O., Delsuc F. & Condamine F.L. (2022).

Diversification dynamics in the Neotropics through time, clades and biogeographic regions. eLife 11: e74503. [pdf]

93. Ferreira-Cardoso S., Claude J., Goswami A., Delsuc F. & Hautier L. (2022).

Flexible conservatism in the skull modularity of convergently evolved myrmecophagous placental mammals.

BMC Ecology and Evolution 22: 87. [pdf]

92. Formenti G.*, Theissinger K.*, Fernandes C.*, Bista I., Bombarely A., Bleidorn C., Ciofi C., Crottini A., Godoy J.A., Höglund J., Malukiewicz J., Mouton A., Oomen R.A., Paez S., Palsbøll J.J., Pampoulie C., Ruiz-Lopez M.J., Svardal H., Theofanopoulou C., de Vries J., Waldvogel A.-M., Zhang G., Mazzoni C.J., Jarvis E.D., Bálint M. & The European Reference Genome Atlas consortium (including Delsuc F.) (2022).

The era of reference genomes in conservation genomics.

Trends in Ecology and Evolution 37: 197-202. [pdf]

2021

91. Emerling C.A., Springer M.S., Gatesy J., Jones Z., Hamilton D., Xia-Zhu D., Collin M.A. & Delsuc F. (2021).

Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals.

Open Research Europe 1: 75. [pdf]

90. Allio R., Tilak M.-K., Scornavacca C., Avenant N.L., Kitchener A.C., 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. [pdf]

2020

89. Le Verger K., Hautier L., Bardin J., Gerber S., Delsuc F. & Billet G. (2020).

Ontogenetic and static allometry in the skull and cranial units of nine-banded armadillos (Cingulata: Dasypodidae: Dasypus novemcinctus).

Biological Journal of the Linnean Society 131: 673-698. [pdf]

88. Ferreira-Cardoso S., Fabre P.-H., de Thoisy B., Delsuc F. & Hautier L. (2020).

3D models related to the publication: “Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals”.

MorphoMuseuM 6: e114. [pdf]

87. Ferreira-Cardoso S., Fabre P.-H., de Thoisy B., Delsuc F. & Hautier L. (2020).

Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals.

PeerJ 8: e9690. [pdf]

86. Meseguer A.S., Antoine P.-O., Fouquet A., Delsuc F. & Condamine F.L. (2020).

The role of the Neotropics as a source of world tetrapod biodiversity.

Global Ecology and Biogeography 29: 1565-1578. [pdf]

85. Allio R., Schomaker-Bastos A., Romiguier J., Prosdocimi F., Nabholz B. & Delsuc F. (2020).

MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.

Molecular Ecology Resources 20: 892-905. [pdf]

84. Ripple W.J, Wolf C., Newsome T.M., Barnard P., Moomaw W.R. & 11,258 scientist signatories from 153 countries (including Delsuc F.) (2020).

World scientists’ warning of a climate emergency.

Bioscience 70: 8-12. [pdf]

83. Song S.J.*, Sanders J.*, Delsuc F., Metcalf J.L., Amato K.R., Taylor M.W., Mazel F., Lutz H.L., Winker K., Graves G.R., Humphrey G., Gilbert J.A., Hackett S.J., White K.P., Skeen H.R., Kurtis S.M., Withrow J., Braile T., Miller M., McCracken K., Maley J., Blanto, J.M., McKenzie V.J. & Knight R. (2020).

Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats.

mBio 11: e02901-19. [pdf]

82. Ferreira-Cardoso S., Billet G., Gaubert P., Delsuc F. & Hautier L. (2020).

Skull shape variation in extant pangolins (Manidae, Pholidota): allometric patterns and systematic implications.

Zoological Journal of the Linnean Society 188: 255-275. [pdf]

2019

81. Santos, P.M. and 501 co-authors (including Delsuc F.) (2019).

Neotropical xenarthrans: a dataset of occurrence of xenarthran species in the Neotropics.

Ecology 100:e02663. [pdf]

80. Delsuc F., Kuch M., Gibb G.C., Karpinski E., Hackenberger D., Szpak P., Martínez J.G., Mead J.I., McDonald H.G., MacPhee R.D.E., Billet G., Hautier L. & Poinar H.N. (2019).

Ancient mitogenomes reveal the evolutionary history and biogeography of sloths.

Current Biology 29: 2031-2042. [pdf]

Associated Feature article by Michael Gross in Current Biology 

Associated Blog article by Brian Switek in Scientific American

79. Scornavacca C., Belkhir K., Lopez J., Dernat R., Delsuc F., Douzery E.J.P. & Ranwez V. (2019).

OrthoMaM v10: scaling-up orthologous coding sequence and exon alignments with more than one hundred mammalian genomes.

Molecular Biology and Evolution 36: 861-862. [pdf]

78. Ferreira-Cardoso S., Delsuc F. & Hautier L. (2019).

Evolutionary tinkering of the mandibular canal linked to convergent regression of teeth in placental mammals.

Current Biology 29: 468-475. [pdf]

77. Springer M.S., Emerling C.A., Gatesy J., Randall J., Collin M., Hecker N., Hiller M. & Delsuc F. (2019). Odontogenic Ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.

BMC Evolutionary Biology 19: 31. [pdf]

76. Delsuc F., Emerling C.A. & Nachman M.W. (2019).

Les chitinases, témoins de la radiation des mammifères placentaires.

Médecine/Sciences 35:12-15. [pdf]

2018

75. Ranwez V., Douzery E.J.P., Cambon C., Chantret N. & Delsuc F. (2018).

MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Molecular Biology and Evolution 35: 2582–2584. [pdf]

74. Botero-Castro F., Tilak M.-K., Justy F., Catzeflis F., Delsuc F. & Douzery E.J.P. (2018).

In cold blood: compositional bias and positive selection drive the high evolutionary rate of vampire bats mitochondrial genomes.

Genome Biology and Evolution 10: 2218–2239. [pdf]

73. Alié A.*, Hiebert L.S.*, Simion P.*, Scelzo M., Prünster M.M., Lotito S., Delsuc F., Douzery E.J.P., Dantec C., Lemaire P., Darras S., Kawamura K., Brown F.D. & Tiozzo S. (2018).

Convergent acquisition of nonembryonic development in styelid ascidians.

Molecular Biology and Evolution 35: 1728-1743. [pdf]

72. Emerling C.A., Delsuc F. & Nachman M.W. (2018).

Chitinase genes (CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals.

Science Advances 4: eaar6478. [pdf]

71. Delsuc F., Kuch M., Gibb G.C., Hughes J., Szpak P., Southon J., Enk J., Duggan A.T. & Poinar H.N. (2018).

Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data.

Proceedings of the Royal Society B 285: 20180214. [pdf]

70. Delsuc F.*, Philippe H.*, Tsagkogeorga G.*, Simion P., Tilak M.-K., Lopez-Legentil S., Turon X., Piette J., Lemaire P. & Douzery E.J.P. (2018).

A phylogenomic framework and timescale for comparative studies of tunicates.

BMC Biology 39:16. [pdf]

Commentary by Gonzalo Giribet in BMC Biology [pdf]

69. Teeling E.C., Vernes S., Davalos L.M., Ray D.A., Gilbert M.T.P., Myers E. & Bat1K Consortium (including Delsuc F.) (2018).

Bat biology, genomes, and the Bat1K project: to generate chromosome-level genomes for all living bat species.

Annual Review of Animal Biosciences 6: 23-46. [pdf]

68. Brozovic M.*, Dantec C.*, Dardaillon J.*, Dauga D.*, Faure E., Gineste M., Louis A., Naville M., Nitta K.R., Piette J., Reeves W., Scornavacca C., Simion P., Vincentelli R., Bellec M., Ben Aicha S., Fagotto M., Guéroult-Bellone M., Haeussler M., Jacox E., Lowe E. K., Mendez M., Roberge A., Stolfi A., Yokomori R., Brown C.T., Cambillau C., Christiaen L., Delsuc F., Douzery E.J.P., Dumollard R., Kusakabe T., Nakai K., Nishida H., Satou Y., Swalla B., Veeman M., Volff J.-N. & Lemaire P. (2018).

ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Nucleic Acids Research 46: D718-D725. [pdf]

2017

67. Thompson L.R., Sanders J.G., McDonald D., Amir A., Ladau J., Locey K.J., Prill R.J., Tripathi A., Gibbons S.M., Ackermann G., Navas-Molina J.A., Janssen S., Kopylova E., Vázquez-Baeza Y., González A., Morton J.T., Mirarab S., Xu Z.Z., Jiang L., Haroon M.F., Kanbar J., Zhu Q., Song S.J., Kosciolek T., Bokulich N.A., Lefler J., Brislawn C.J., Humphrey G.C., Owens S.M., Hampton-Marcell J., Berg-Lyons D., McKenzie V., Fierer N., Fuhrman J.A., Clauset A., Stevens R.L., Shade A., Pollard K.S., Goodwin K.D., Jansson J.K., Gilbert J.A., Knight R. & The Earth Microbiome Project Consortium (including Delsuc F.)(2017).

A communal catalogue reveals Earth’s multiscale microbial diversity.

Nature 551: 457-463. [pdf]

 

Associated News & Views by Jeroen Raes in Nature

66. McKenzie V.J., Song S.J., Delsuc F., Prest T.L., Oliverio A.M., Korpita T.M., Alexiev A., Amato K.R., Metcalf J.L., Kowalewski M., Avenant N.L., Link A., Di Fiore A., Seguin-Orlando A., Feh C., Orlando L., Mendelson J.R., Sanders J. & Knight R. (2017).

The effects of captivity on the mammalian gut microbiome.

Integrative and Comparative Biology 57: 690-704. [pdf]

65. Irisarri I., Baurain D., Brinkmann H., Delsuc F., Sire J.-Y., Kupfer A., Petersen J., Jarek M., Meyer A., Vences M. & Philippe H. (2017).

Phylotranscriptomic consolidation of the jawed vertebrate timetree.

Nature Ecology and Evolution 1: 1370-1378. [pdf]

64. Hautier L., Billet G., de Thoisy B. & Delsuc F. (2017).

Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus).

PeerJ 5: e3650. [pdf]

63. Billet G., Hautier L., de Thoisy B. & Delsuc F. (2017).

The hidden anatomy of paranasal sinuses reveals geographically distinct morphotypes in the nine-banded armadillo (Dasypus novemcinctus).

PeerJ 5: e3593. [pdf]

62. Simion P.*, Philippe H.*, Baurain D., Jager M., Richter D., Di Franco A., Roure B., Satoh N., Quéinnec E., Ereskowsky A., Lapébie P., Corre E., Delsuc F., King N., Wörheide G. & Manuel M. (2017).

A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals.

Current Biology 27: 958-967. [pdf]

 

Associated dispatch by D. Timothy J. Littlewood in Current Biology 

61. Philippe H., De Vienne D.M., Ranwez V., Roure B., Baurain D. & Delsuc F. (2017).

Pitfalls in supermatrix phylogenomics.

European Journal of Taxonomy 283: 1-25. [pdf]  

60. Le Gall L., Delsuc F., Hourdez S., Lecointre G. & Rasplus J.-Y. (2017).

Towards the DNA library of life.

European Journal of Taxonomy 266: 1-9. [pdf]

2016

59. Malicorne S., Vernochet C., Cornelis G., Mulot B., Delsuc F., Heidmann O., Heidmann T. & Dupressoir A. (2016).

Genome-wide screening of retroviral envelope genes in the nine-banded armadillo (Dasypus novemcinctus, Xenarthra) reveals an unfixed chimeric endogenous betaretrovirus using the ASCT2 receptor.

Journal of Virology 90: 8132-8149. [pdf]  

58. Nardelli M., Ibanez E.A., Dobler D., Justy F., Delsuc F., Abba A.M., Cassini M.H. & Tunez J.I. (2016).

Genetic differentiation in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microstatellite loci.

Genetica 144: 469-476. [pdf]

57. Kadowaki K., Barbera C.G., Godsoe W. Delsuc F. & Mouquet N. (2016).

Predicting biotic interactions and their variability in a changing environment.

Biology Letters 12: 20151073. [pdf]  

56. Delsuc F., Gibb G.C., Kuch M., Billet G., Hautier L., Southon J., Rouillard J.-M., Fernicola J.C.,Vizcaíno S.F., McPhee R.D.M & Poinar H.N. (2016).

The phylogenetic affinities of the extinct glyptodonts.

Current Biology 24: R155-R156. [pdf]

 

Associated CNRS press release (in french
Associated University of McMaster press release (in english

55. Gibb G.C., Condamine F.L., Kuch M., Enk J., Moraes-Barros N., Superina M., Poinar H.N. & Delsuc F. (2016).

Shotgun mitogenomics provides a reference phylogenetic framework and timescale for living xenarthrans.

Molecular Biology and Evolution 33: 621-642. [pdf]   

54. Brozovic M.*, Martin C.*, Dantec C.*, Dauga D.*, Mendez M., Simion P., Percher M., Laporte B., Scornavacca C., Di Gregorio A., Fujiwara S., Gineste M., Lowe E.K., Piette J., Racciopi C., Ristoratore F., Sasakura Y., Takatori N., Brown T.C., Delsuc F., Douzery E.J.P., Gissi C., McDougall A., Nishida H., Sawada H., Swalla B.J., Yasuo H. & Lemaire P. (2016).

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.

Nuclear Acids Research 44: D808-D818. [pdf]   

53. Botero-Castro F., Delsuc F. & Douzery E.J.P. (2016).

Thrice better than once: quality control guidelines for reporting new mitogenomes.

Mitochondrial DNA 27: 449-454. [pdf]

2015

52. Abba A.M., Cassini G.H., Valverde G., Tilak M.-K., Vizcaíno S.F., Superina M. & Delsuc F. (2015).
Systematics of hairy armadillos and the taxonomic status of the Andean hairy armadillo (Chaetophractus nationi).
Journal of Mammalogy 96: 673-689.
[pdf]   

51. Delsuc F., Gasse B. & Sire J.-Y. (2015).
Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta.
BMC Evolutionary Biology 15: 148.
[pdf]   

50. Fort P., Kajava A.V., Delsuc F. & Coux O. (2015).
Evolution of proteasome regulation in Eukaryotes.
Genome Biology and Evolution 7: 1363-1379. 
[pdf]   

49. Delsuc F. & Tilak M.-K. (2015).
Naked but not hairless: The pitfalls of analyses of molecular adaptation based on few genome sequence comparisons.
Genome Biology and Evolution 7: 768-774. 
[pdf]   

48. Tilak M.-K.*, Justy F.*, Debiais-Thibaud M., Botero-Castro F., Delsuc F. & Douzery E.J.P. (2015).
A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes.
Conservation Genetics Resources 7: 37-40. 
[pdf]

2014

47. Douzery E.J.P., Scornavacca C., Romiguier J., Belkhir K., Galtier N., Delsuc F. & Ranwez V.(2014).
OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.
Molecular Biology and Evolution 31: 1923-1928. 
[
pdf]   

 

46. Malé P.-J.G., Bardon L., Besnard G., Coissac E., Delsuc F., Engel J., Lhuillier E., Scotti-Saintagne C., Tinaut A. & Chave J. (2014).
Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree.
Molecular Ecology Resources 14: 966-975. 
[
pdf] [Dryad]

45. Delsuc F., Metcalf J.L., Wegener Parfrey L., Song S.J., Gonzalez A & Knight R. (2014).
Convergence of gut microbiomes in myrmecophagous mammals.
Molecular Ecology 23: 1301-1317. 
[
pdf] [Dryad]  

 

Associated INEE-CNRS prospective article (in french)

 

2013

44. Botero-Castro F., Tilak M.-K., Justy F., Catzeflis F., Delsuc F. & Douzery E.J.P. (2013).
Next-generation sequencing and phylogenetic signal of mitogenomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).
Molecular Phylogenetics and Evolution 69: 728-739. 
[pdf]  

 

43. Romiguier J., Ranwez V., Delsuc F., Galtier N. & Douzery E.J.P. (2013).
Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals.
Molecular Biology and Evolution 30: 2134-2144.
[pdf]    

 

Commentary by Emma Teeling & Blair Hedges in Molecular Biology and Evolution 

 

42. Rubinstein N.D., Feldstein T., Shenkar N., Botero-Castro F., Griggio F., Mastrototaro F., Delsuc F.,  Douzery E.J.P., Gissi C. & Huchon D. (2013).
Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.
Genome Biology and Evolution 5: 1185-1199.
[pdf] [Dryad]     
 

41. Nagy G.N., Marton L., Kramos B., Olah J., Révész A., Vékey K., Delsuc F., Hunyadi-Gulyas E., Medzihradszky K.F., Lavigne M., Vial H., Cerdan R., Vértessy B.G. (2013).
Evolutionary and mechanistic insights into substrate and product accomodation of CTP:phospocholine cytidylyltransferase from Plasmodium falciparum.
FEBS Journal 280: 3132-3148. 
[pdf]
 

2012

40. Chiari Y., Cahais V., Galtier N. & Delsuc F. (2012).
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).
BMC Biology 10: 65. 
[pdf] [Dryad]

 

Commentary by S. Blair Hedges in BMC Biology
 

39. Pointer M.A., Kamilar J.M., Warmuth V., Chester S.G.B., Delsuc F., Mundy N.I., Asher R.J. & Bradley B.B. (2012).
RUNX2 tandem repeats and the evolution of facial length in placental mammals.
BMC Evolutionary Biology 12: 103. 
[pdf] [Dryad]
 

38. Lartillot N. & Delsuc F. (2012).
Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model.
Evolution 66: 1773-1787. 
[pdf] [Dryad]
 

37. Laguette N.*, Rahm N.*, Sobhian B., Chable-Bessia C., Münch J., Snoeck J., Sauter D., Switzer W.M., Heneine W., Kirchhoff F., Delsuc F.*, Telenti A.* & Benkirane M.* (2012).
Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein.
Cell Host & Microbe 11: 205-217. 
[pdf]
 

News and Views article by Vicente Planelles in Cell Host & Microbe 
Perspective article by Schaller et al. in Science

 

36. Hassanin A., Delsuc F., Ropiquet A., Hammer C., Janssen van Vuuren B., Matthee C., Ruiz-Garcia M., Catzeflis F., Areskoug V., Nguyen T.T. & Couloux A. (2012).
Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes.
Comptes Rendus Biologies 335: 32-50. 
[pdf]
 

35. Delsuc F., Superina M., Tilak M.-K., Douzery E.J.P. & Hassanin A. (2012).
Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos.
Molecular Phylogenetics and Evolution 62: 673-680. 
[pdf] [Dryad]

34. Fort P.*, Albertini A.*, Van-Hua A., Berthomieu A., Roche S., Delsuc F., Pasteur N., Capy P., Gaudin Y. & Weill M. (2012).
Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality.
Molecular Biology and Evolution 29: 367-379. 
[pdf]
 

2011

33. Atyame C.M., Delsuc F., Pasteur N., Weill M. & Duron 0. (2011).
Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.
Molecular Biology and Evolution 28: 2761-2772. 
[pdf]    

32. Ranwez V., Harispe S., Delsuc F. & Douzery E.J.P. (2011).
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
PLoS One 6: e22594. 
[pdf]  

31. Dsouli N., Delsuc F., Michaux J., De Stordeur E., Couloux A., Veuille M. & Duvallet G. (2011).
Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae).
Infection, Genetics and Evolution 11: 663-670.
 [pdf] [Dryad]     
 

2010

30. Denoeud F., Henriet S., Mungpakdee S., Aury J.-M., Da Silva C., Brinkmann H., Mikhaleva J., Olsen L.C., Jubin C., Cañestro C., Bouquet J.-M., Danks G., Poulain J., Campsteijn C., Adamski M., Cross I., Yadetie F., Muffato M., Louis A., Butcher S., Tsagkogeorga G., Singh S., Jensen M.F., Huynh Cong E., Eikeseth-Otteraa H., Noel B., Anthouard V., Porcel-Setterblad B., Kachouri-Lafond R., Nishino A., Ugolini M., Chourrout P., Nishida H., Aasland R., Huzurbazar S., Westhof E., Delsuc F., Lehrach H., Reinhardt R., Weissenbach J., Roy S.W., Artiguenave F., Postlethwait J.H., Manak J.R., Thompson E.M., Jaillon O., Du Pasquier L., Boudinot P., Liberles D.A., Volff J.-N., Philippe H., Lenhard B., Roest Crollius H., Wincker P. & Chourrout D. (2010).
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

Science 330: 1381-1385. [pdf] [Dryad]

29. Tsagkogeorga G., Turon X., Galtier N., Douzery E.J.P. & Delsuc F. (2010).
Accelerated evolutionary rate of housekeeping genes in tunicates.
Journal of  Molecular Evolution 71: 153-167. 
[pdf] [Dryad]
 

2009

28. Singh T. R.*, Tsagkogeorga G.*, Delsuc F., Blanquart S., Shenkar N., Loya Y., Douzery E.J.P. &Huchon D. (2009).
Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.
BMC Genomics 10: 534. 
[pdf] [Dryad]    
 

27. Tsagkogeorga G., Turon X., Hopcroft R.R., Tilak M.-K., Feldstein T., Shenkar N., Loya Y., Huchon D., Douzery E.J.P. & Delsuc F. (2009).
An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.
BMC Evolutionary Biology 9: 187.
[pdf] [Dryad]

26. Ranwez V., Clairon N., Delsuc F., Pourali S., Auberval N., Diser S. & Berry V.  (2009).
PhyloExplorer: a web server to validate, explore and query phylogenetic trees.
BMC Evolutionary Biology 9: 108. 
[pdf]     

 

25. Loughry W.J., Truman R.W., McDonough C.M., Tilak M.-K., Garnier S. & Delsuc F. (2009).
Is leprosy spreading among nine-banded armadillos in the southeastern United States?
Journal of Wildlife Diseases 45: 144-152. 
[pdf]

2008

24. Delsuc F., Tsagkogeorga G., Lartillot N. & Philippe H. (2008).
Additional molecular support for the new chordate phylogeny.
Genesis 46: 592-604. 
[pdf] [Dryad]

 

23. Pantalacci S., Chaumot A., Benoît G., Sadier A., Delsuc F., Douzery E.J.P. & Laudet V. (2008).
Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.
Molecular Biology and Evolution 25: 912-928. 
[pdf]

2007

22. Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M.-K. & Douzery E.J.P. (2007).
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics.
BMC Evolutionary Biology 7: 241. 
[pdf]

21. Möller-Krull M.*, Delsuc F.*, Churakov G., Marker C., Superina M., Brosius J., Douzery E.J.P. & Schmitz J. (2007).
Retroposed elements and their flanking regions resolved the evolutionary history of xenarthran mammals (armadillos, anteaters and sloths).
Molecular Biology and Evolution 24: 2573-2582. 
[pdf] [Dryad]
 

20. Delsuc F., Superina M., Ferraris G., Tilak M.-K. & Douzery E.J.P. (2007).
Molecular evidence for hybridization between the two living species of South-American ratites: potential conservation implications.
Conservation Genetics 8: 503-507. 
[pdf]

    

19. Slack K.E., Delsuc F., McLenachan P.A., Arnason U. & Penny D. (2007).
Resolving the root of the avian mitogenomic tree by breaking up long branches.
Molecular Phylogenetics and Evolution 42: 1-13. 
[pdf]

2006

18. Chourrout D., Delsuc F., Chourrout P., Edvardsen R.B., Rentzsch F., Renfer E., Jensen M.F., Zhu B., de Jong P., Steele R.E. & Technau U. (2006).
Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements.
Nature 442: 684-687. 
[pdf] [Dryad]

 

Developmental Biology Select article by Priya Prakash Budde in Cell 

17. Jeffroy O., Brinkmann H., Delsuc F. & Philippe H. (2006).

Phylogenomics: the beginning of incongruence?
Trends in Genetics 22: 225-231. 
[pdf]  

16. Delsuc F., Brinkmann H., Chourrout D. & Philippe H. (2006).
Tunicates and not cephalochordates are the closest living relatives of vertebrates.
Nature 439: 965-968. 
[pdf] [Dryad]

 

News and Views article by Henry Gee in Nature  
News and Views article by Peter Holland in Heredity 

News article by Stéphanie Belaud in Le Journal du CNRS (in french
Hot Paper in Phylogeny article by Jonathan Scheff in The Scientist

2005

15. Philippe H., Brinkmann H., Zhou Y., Rodrigue N. & Delsuc F. (2005).
Heterotachy and long-branch attraction in phylogenetics.
BMC Evolutionary Biology 5: 50. 
[pdf]

 

14. Philippe H., Delsuc F., Brinkmann H. & Lartillot N. (2005).
Phylogenomics.
Annual Review of Ecology, Evolution and Systematics 36: 541-562. 
[pdf]

 

13. Delsuc F., Brinkmann H. & Philippe H. (2005).
Phylogenomics and the reconstruction of the tree of life.
Nature Reviews Genetics 6: 361-375. 
[pdf]

 

12. Holland B.R., Delsuc F. & Moulton V. (2005).
Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods.
Systematic Biology 54: 1-11. 
[pdf]

 

11. Knapp M., Stöckler K., Havell D., Delsuc F., Sebastiani F. & Lockhart P.J. (2005).
Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (southern beech).
PLoS Biology 3: e14. 
[pdf]

Read the associated synopsis in PLoS Biology

2004

10. Douzery E.J.P., Snell E.A., Bapteste E., Delsuc F. & Philippe H. (2004).
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
Proceedings of the National Academy of Sciences of the USA 101: 15386-15391.
[pdf] [Dryad]


Commentary by Cranston & Rannala in Heredity

 

09. Phillips M.J., Delsuc F. & Penny D. (2004).
Genome-scale phylogeny and the detection of systematic biases.
Molecular Biology and Evolution 21: 1455-1458. 
[pdf] 

 

08. Delsuc F., Vizcaíno S.F. & Douzery E.J.P. (2004).
Influence of Tertiary paleoenvironnemental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.
BMC Evolutionary Biology 4: 11. 
[pdf] [Dryad]

2003

07. Delsuc F., Phillips M.J. & Penny D. (2003).
Comment on "Hexapod origins: monophyletic or paraphyletic?".
Science 301: 1482d. 
[pdf] 

 

06. Douzery E.J.P., Delsuc F., Stanhope M.J. & Huchon D. (2003).
Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals, and incompatibility among fossil calibrations.
Journal of Molecular Evolution 57: S201-S213.
[pdf] [Dryad]  

05. Delsuc F., Stanhope M.J. & Douzery E.J.P. (2003).
Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes.
Molecular Phylogenetics and Evolution 28: 261-275.
[pdf] [Dryad]  
 

04. Douady C.J., Delsuc F., Boucher Y., Doolittle W.F. & Douzery E.J.P. (2003).
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.
Molecular Biology and Evolution 20: 248-254. 
[pdf]

2002

03. Delsuc F., Scally M., Madsen O., Stanhope M.J., de Jong W.W., Catzeflis F.M., Springer M.S. & Douzery E.J.P. (2002).
Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting.
Molecular Biology and Evolution 19: 1656-1671. 
[pdf] [Dryad]
 

2001

02. Delsuc F., Catzeflis F.M., Stanhope M.J. & Douzery E.J.P. (2001).
The evolution of armadillos, anteaters, and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua.
Proceedings of the Royal Society of London, Biological Sciences 268: 1605-1615. 
[pdf]
 

1999

01. Huchon D.*, Delsuc F.*, Catzeflis F.M. & Douzery E.J.P. (1999). *Equal contribution.
Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra).
Molecular Ecology 8: 1743-1748. 
[pdf]
 

Books
PhylogenoBook_Cover_Final.png

2020

01. Scornavacca C., Delsuc F. & Galtier N. (2020).

Phylogenetics in the genomic era.

No Commercial Publisher, Authors Open Access Book, 563 pages. [pdf] 

Book Chapters
101-secrets-adn.jpg
MethodsMolBiol2.jpg

2021

11. Ranwez V., Chantret N., Delsuc F. (2021).

Aligning Protein-Coding Nucleotide Sequences with MACSE.

In "Methods in Molecular Biology Vol. 2231: Multiple Sequence Alignment. Humana, New York, NY. [pdf]

2020

10. Delsuc F. & Ranwez V. (2020).

Accurate alignment of (meta)barcoding datasets using MACSE.

In "Phylogenetics in the Genomic Era" edited by C. Scornavacca, F. Delsuc, N. Galtier, No Commercial Publisher, Authors Open Access Book, pp. 2.3:1-2.3:31. [pdf]

09. Simion P., Delsuc F. & Philippe H. (2020).

To what extent current limits of phylogenomics can be overcome?

In "Phylogenetics in the Genomic Era" edited par C. Scornavacca, F. Delsuc, N. Galtier, No Commercial Publisher, Authors Open Access Book, pp. 2.1:1-2.1:34. [pdf]

2019

08. Delsuc F. & Thompson L.R. (2019).

Chapitre 23 : Un inventaire de la diversité microbienne de la Terre.

Pp 92-95. Dans 101 Secrets du Vivant: l’ADN des écosystèmes sous la direction de D. Faure, D. Joly & S. Salamitou. CNRS Editions, Paris, France. 

2016

07. Pompanon F., Samadi S., Debruyne R., Delsuc F., Lavergne S., Pante E., Puillandre N., Rasplus J.-Y. & Taberlet P. (2016). 
Chapitre 6 : Caractériser la biodiversité.
Pp. 77-87. Dans La Génomique Environnementale : La Révolution du Séquençage à Haut Débit sous la direction de
D. Faure & D. Joly. ISTE Editions, London, UK.
 

2015

06. Delsuc F., Dedeine F. & Vandenkoornhuyse P. (2015). 
Focus: Dis moi ton microbiote et je te dirai ce que tu manges.
Pp. 108-109. Dans Empreinte du vivant : l'ADN de l'environnement édité par D. Joly, D. Faure & S. Salamitou. Le Cherche Midi, Paris, France.

 

2010

05. Raymond M., Godelle B., Alizon S., Bourguet D., Caillau D., Couvet D., David J., David P. Debussche M., Delsuc F., Douzery E.J.P., Machon N., Pascal R., Robert A., Ronfort J., Sarrazin F., Schoenaeur M., Tenaillon O., Theodorou K. & Thompson J. (2010). 
Chapitre 19 : Applications de la biologie évolutive.
Pp. 749-788. Dans Biologie Evolutive édité par F. Thomas, T. Lefèvre & M. Raymond. De Boek Université, Bruxelles, Belgique.

 

04. Douzery E.JP., Blanquart S., Criscuolo A., Delsuc F., Douady C., Lartillot N., Philippe H. & Ranwez V.  (2010). 
Chapitre 6 : Phylogénie moléculaire.
Pp. 183-244. Dans Biologie Evolutive édité par F. Thomas, T. Lefèvre & M. Raymond. De Boek Université, Bruxelles, Belgique.

2009

03. Guindon S., Delsuc F., Dufayard J.-F. & Gascuel O. (2009).
Estimating maximum likelihood phylogenies with PhyML. 
Chapter 6. Pp. 113-137. In Methods in Molecular Biology Vol. 537: Bioinformatics for DNA sequence Analysis edited by D. Posada. Humana Press, Totowa, NJ. 
[pdf]

02. Delsuc F. & Douzery E.J.P. (2009).
Armadillos, anteaters and sloths (Xenarthra).
Chapter 72. Pp. 475-478. In The Timetree of Life edited by S.B. Hedges & S. Kumar. Oxford University Press, London, UK. 
[pdf]

2008

01. Delsuc F. & Douzery E.J.P. (2008).
Recent advances and future prospects in xenarthran molecular phylogenetics.
Pp. 11-23. In The Biology of the Xenarthra edited by S.F. Vizcaíno & W.J. Loughry. University Press of Florida, Gainesville, FL. 
[pdf]

Book review by Bruce J. Shockey in Journal of Mammalian Evolution

Other Publications
Couverture_Especes_Dossier_Neotropiques.

2022

13. Delsuc F. (2022).
Making sense of vertebrate sirtuin genes.
PCI Evolutionary Biology 100151. 
[pdf]

2020

12. Fabre P.-H., Delsuc F., Münch P. (2020).
Les insulaires des Antilles.
Espèces 35:42-48. 
[pdf]
 

2015

11. Delsuc F. (2015).
Flawed evidence for convergent evolution of the circadian CLOCK gene in mole-rats.
BioRxiv doi: http://dx.doi.org/10.1101/022004. 
[pdf]

 

2011

10. Theulier Saint-Germain S., Beaumes V., Lallement J.-C. & Delsuc F. (2011).
Quand l'évolution se prête au jeu...
La Lettre de l'OCIM 136: 14-20. 
[pdf]
 

2010

09. Douzery E.J.P. & Delsuc F. (2010).
Les horloges de l'évolution.
Pour La Science 397: 102-107. 
[pdf]

2007

08. Pantalacci S., Chaumot A., Delsuc F., Sadier A., Douzery E.J.P. & Laudet V. (2007).
Evolution of the EDA pathway in vertebrates: a step towards tooth "Evo-Devo studies".
European Cells and Materials 14 suppl. 2: 118 [Meeting-Abstract]. 
[
pdf]

07. Delsuc F., Superina M., Tilak M.-K., Douzery E.J.P. & Hassanin A. (2007).
Advances in molecular and phylogenetic studies of Xenarthra.
Journal of Morphology 268: 1066 [ICVM8-Abstract].
 [pdf]

2006

06. Delsuc F., Baurain D. & Philippe H. (2006).
Origine des Vertébrés : la tunique fait-elle le moine ? [Vertebrate origin: does the tunic make the man?]
Médecine/Sciences 22: 688-690. 
[pdf]

2005

05. Douzery E.J.P., Delsuc F. & Philippe H. (2005).
Les datations moléculaires à l’heure de la génomique. [Molecular dating in the genomic era.]
Médecine/Sciences 22: 374-380. 
[pdf]

2004

04. Delsuc F. & Douzery E.J.P. (2004).
Les méthodes probabilistes en phylogénie moléculaire. (2) L’approche Bayésienne.
Biosystema : « Avenir et pertinence des méthodes d’analyses en phylogénie moléculaire »22: 75-86. 
[pdf]

03. Delsuc F. & Douzery E.J.P. (2004).
Les méthodes probabilistes en phylogénie moléculaire. (1) Les modèles d’évolution des séquences et le maximum de vraisemblance.
Biosystema : « Avenir et pertinence des méthodes d’analyses en phylogénie moléculaire »22: 59-74.
 [pdf]

2003

02. Delsuc F. (2003).
Army ants trapped by their evolutionary history.
PLoS Biology 1: e37. 
[pdf]  

 

01. Delsuc F., Mauffrey J.-F. & Douzery E.J.P. (2003).
Une nouvelle classification des Mammifères.
Pour La Science 303: 62-66. 
[pdf]

Theses
Theses

04. Delsuc F. (2016).

Phylogénomique : la reconstruction phylogénétique et ses applications à l'ère de la génomique.

Mémoire d'Habilitation à Diriger des Recherches, Université de Montpellier. [HDR Thesis]

03. Delsuc F. (2002).

Phylogénie moléculaire des Xénarthres (tatous, fourmiliers et paresseux) : application des méthodes probabilistes à la reconstruction de leur histoire évolutive au sein des Mammifères placentaires.

Thèse de Doctorat, Université Montpellier 2. [PhD Thesis]

02. Delsuc F. (1999).
Apports des phylogénies mitochondriales et nucléaires à la systématique et à la biogéographie des tatous, fourmiliers et paresseux (Mammalia, Xenarthra).
Mémoire de DEA Biologie de l'Evolution et Ecologie, Université Montpellier 2. [Master Thesis]

01. Delsuc F. (1998).
Etude de la région de contrôle de l’ADN mitochondrial du tatou à neuf bandes (Dasypus novemcinctus) : confirmation d’une perte de polymorphisme lors de la colonisation de l’Amérique du Nord.
Mémoire de Maîtrise Biologie des Populations et Ecosystèmes, Université Montpellier 2.  

Reviewing Activities

Reviewer for the following Journals and Agencies [number of manuscripts/projects]:

Journals

Molecular Biology and Evolution [12]

Systematic Biology [10]
Molecular Phylogenetics and Evolution [8]
BMC Evolutionary Biology [6]
European Journal of Taxonomy
 [4]

Nature [2]
Science Advances [2]

Current Biology [2]
Nuclear Acids Research [2]
Biology Letters
 [2]

Mammalia [2]

Molecular Ecology [1]

PLoS Genetics [1]
Genome Biology [1]
Genome Biology and Evolution [1]

Proceedings of the Royal Society of London Biological Sciences [1]
Philosophical Transactions of the Royal Society of London Biological Sciences
 [1]Heredity [1]

Environnemental Microbiology [1]

Zoologica Scripta [1]

Journal of Molecular Evolution [1]

Systematics and Biodiversity [1]
BMC Genetics [1]
PLoS One [1]
Chromosome Research [1]
Genomics [1]

GigaScience [1]
Comparative and Functional Genomics [1]
Edentata [1]
Senckenbergiana Biologica [1]
Zootaxa [1]

Research Agencies

Belgian National Science Foundation (FNRS) [15]
Center for the Study of Amazonian Biodiversity (CEBA) [4]

European Research Council (ERC) [2]

US National Science Foundation (NSF) [2]
French National Research Agency (ANR) [1]
French Foundation for Biodiversity Research (FRB) [1]
German Research Foundation (DFG) [1]
Swiss National Science Foundation (SNSF) [1]
Natural Sciences and Engineering Research Council of Canada (NSERC) [1]

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