Didier Casane

Preprints in BioRxiv and Research Square

Policarpo M., Laurenti P., Metcalfe C.J., Rétaux S. and Casane D. (2021) Genomic evidence that blind cavefishes are not wrecks of ancient life. BioRxiv
Rode J., Pelletier A., Fumey J., Rode S., Cabanat A.-L., Ouvrard A., Chaix B., White B., Harnden M., Xuan N.T., Vereshagin A. and Casane D. (2020) Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study. BioRxiv

Publications

75 – Policarpo M., Legendre L., Germon I., Lafargeas P., Espinasa L., Rétaux S. and Casane D. (2024) The nature and distribution of non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations. BMC Ecology and Evolution 24(1):41
74 – Policarpo M., Baldwin M., Casane D. and Salzburger W. (2024) Diversity and evolution of the vertebrate chemoreceptor gene repertoire. Nature communications 15:1421
73 – Rodríguez-Machado S., Ponce de León J.L., Germon I., Casane D. and García-Machado E. (2023) Phylogeography of Limia vittata (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids. Biological Journal of the Linnean Society 140(3): 459-470
72 – Hyacinthe C., Attia J., Schutz E., Lego L., Casane D. and Rétaux S. (2023) Acoustic signatures in Mexican cavefish populations inhabiting different caves. PLoS ONE 18(8):e0289574
71 – Legendre L., Rode J., Germon I., Pavie M., Quiviger C., Policarpo M., Leclercq J., Pere S., Fumey J., Hyacinthe C., Ornelas-Garcia P., Espinasa L., Retaux S. and Casane D. (2023) Genetic identification and reiterated captures suggests that the Astyanax mexicanus El Pachon cavefish population is closed and declining. Zoological Research 44(4): 701-711
70 – Syed A.S., Sharma K., Policarpo M., Ferrando S., Casane D. and Korsching S.I. (2023) Ancient and nonuniform loss of olfactory receptor expression renders the shark nose a de facto vomeronasal organ. Molecular Biology and Evolution 40(4):msad076
69 – Policarpo M., Bemis K.E., Laurenti P., Legendre L., Sandoz J.C., Rétaux S. and Casane D. (2022) Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes. BMC Biology 20:195
68 – Van Helden J., Butler C.D., Achaz G., Canard B., Casane D., Claverie J.-M., Colombo F., Courtier V., Ebright R.H., Graner F., Leitenberg M., Morand S., Petrovsky N., Segreto R., Decroly E., Halloy J. (2021) An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2. The Lancet 398(10309):1402–1404
67 – Policarpo M., Bemis K.E., Tyler J.C., Metcalfe C.J., Laurenti P., Sandoz J.C., Rétaux S. and Casane D. (2021) Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape. Molecular Biology and Evolution 38(9):3742–3753
66 – Sallard E., Halloy J., Casane D., Decroly E., van Helden J. (2021) Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review. Environmental Chemistry Letters published online Feb 4:1–17
65 – Policarpo M., Fumey J., Lafargeas P., Naquin D., Thermes C., Naville M., Dechaud C., Volff J.-N., Cabau C., Klopp C., Møller P.R., Bernatchez L., García-Machado E., Rétaux S. and Casane D. (2021) Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution 38(2):589–605
64 – Hernández D., Møller P.R., Casane D. and García-Machado E. (2020) A new species of the cave-fish genus Lucifuga (Ophidiiformes, Bythitidae), from eastern Cuba. ZooKeys 946:17-35
63 – García-Machado E., Ponce de Léon J.L., Gutiérrez-Costa M.A., Michel-Salzat A., Germon I. and Casane D. (2020) Phylogeographic evidence that the distribution of cryptic euryhaline species in the Cuban Gambusia punctata species group was shaped by the archipelago geological history. Molecular Phylogenetics and Evolution 144:106712
62 – Ulmo-Díaz G., Casane D., Bernatchez L., González-Díaz P., Apprill A., Castellanos-Gell J., Hernández-Fernández L. and García-Machado E. (2018) Genetic differentiation in the mountainous star coral Orbicella faveolata around Cuba. Coral Reefs 37(4):1217-1227
61 – Fumey J., Hinaux H., Noirot C., Thermes C., Rétaux S. and Casane D. (2018) Evidence of late Pleistocene origin of Astyanax mexicanus cavefish. BMC Evolutionary Biology 18(1):43
60 – García-Machado E., Ulmo-Díaz G., Castellanos-Gell J. and Casane D. (2018) Patterns of population connectivity in marine organisms around Cuba. Bulletin of Marine Science 94(2):193-211
59 – Rodríguez-Machado S., Ponce de León J.L., Casane D. and García-Machado E. (2017) Morphology and genetics reveal the occurrence of Girardinus falcatus (Eigenmann, 1903) (Cyprinodontiformes, Poeciliidae) in eastern Cuba. Check List 13(6):1059-1065
58 – Ulmo-Díaz G., Castellanos-Gell J., Ponce de León J.L., Casane D., Hurtado A. and García-Machado E. (2016) Evidence of very low genetic diversity of Cuban gar (Atractosteus tristoechus). Revista Investigaciones Marinas 36(1):16-23
57 – Castellanos-Gell J., Robainas-Barcia A., Pina-Amargós F., Chevalier-Monteagudo P., Metcalfe C., Franco Molina W., Casane D. and García-Machado E. (2016) Genetic diversity of reef fishes around Cuba: A multi-species assessment. Marine Biology 163:165
56 – Casane D. and Rétaux S. (2016) Evolutionary genetics of the cavefish Astyanax mexicanus. Advances in Genetics 95:117-159
55 – Hernández D., Casane D., Chevalier-Monteagudo P., Bernatchez L. and García-Machado E. (2016) Go West: A one way stepping-stone dispersion model for the cavefish Lucifuga dentata in western Cuba. PLoS ONE 11(4):e0153545
54 – Shone V., Oulion S., Casane D., Laurenti P. and Graham A. (2016) Mode of reduction in the number of pharyngeal segments within the sarcopterygians. Zoological Letters 2:6
53 – Debiais-Thibaud M., Chiori R., Enault S., Oulion S., Germon I., Martinand-Mari C., Casane D. and Borday-Birraux V. (2015) Tooth and scale morphogenesis in shark: an alternative process to the mammalian enamel knot system. BMC Evolutionary Biology 15(1):292
52 – Naville M., Chalopin D., Casane D., Laurenti P. and Volff J.-N. (2015) The coelacanth: can a “living fossil” have active transposable elements in its genome? Mobile Genetic Elements 5(4):55-59
51 – Hinaux H., Blin M., Fumey J., Legendre L., Heuzé A., Casane D. and Rétaux S. (2015) Lens defects in Astyanax mexicanus cavefish: evolution of crystallins and a role for alphaA-crystallin. Developmental Neurobiology 75(5):505–521
50 – Ponce de León J.L., León-Finalé G., Rodríguez-Silva R., Metcalfe C.J., Hernández D., Casane D. and Garcia-Machado E. (2014) Phylogeography of Cuban Rivulus: evidence for allopatric speciation and secondary dispersal across a marine barrier. Molecular Phylogenetics and Evolution 79:404-414
49 – Metcalfe C.J. and Casane D. (2014) Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements. Mobile DNA 5:19
48 – Rétaux S. and Casane D. (2013) Evolution of development in the darkness of caves: Adaptation, drift or both? EvoDevo 4(1):26
47 – Debiais-Thibaud M., Metcalfe C.J., Pollack J., Germon I., Ekker M., Depew M., Laurenti P., Borday-Birraux V. and Casane D. (2013) Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates. PLoS ONE 8(6):e68182
46 – Pradel A., Didier D., Casane D., Tafforeau P. and Maisey J.G. (2013) Holocephalan embryo provides new information on the evolution of the glossopharyngeal nerve, metotic fissure and parachordal plate in gnathostomes. PLoS ONE 8(6):e66988
45 – Metcalfe C.J. and Casane D. (2013) Accommodating the load: The transposable element content of very large genomes. Mobile Genetic Elements 3(2):e24775
44 – Compagnucci C., Debiais-Thibaud M., Coolen M., Fish J., Griffin J., Bertocchini F. Minoux M., Rijli F.M., Borday-Birraux V., Casane D., Mazan S. and Depew M.J. (2013) Pattern and Polarity in the Development and Evolution of the Gnathostome Jaw: Both Conservation and Heterotopy in the Branchial Arches of the Shark, Scyliorhinus canicula. Developmental Biology 377(2):428-448
43 – Da Lage J.-L., Binder M., Hua-Van A., Janeček Š. and Casane D. (2013) Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes. BMC Evolutionary Biology 13:40
42 – Casane D. and Laurenti P. (2013) Why coelacanths are not « living fossils ». BioEssays 35(4):332-338
41 – Hinaux H., Poulain J., Da Silva C., Noirot C., Jeffery W.R., Casane D. and Rétaux S. (2013) De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes. PLoS ONE 8(1):e53553
40 – Metcalfe C.J., Filée J., Germon I., Joss J.M.P. and Casane D. (2012) Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements. Molecular Biology and Evolution 29(11):3529-3539
39 – Castellanos-Gell J., Robainas-Barcia A., Casane D., Chevalier-Monteagudo P., Pina-Amargós F. and García-Machado E. (2012) The surgeonfish, Acanthurus bahianus, has crossed the Amazon – Orinoco outflow barrier. Marine Biology 159(7):1561-1565
38 – Griffiths A.M., Jacoby D.M.P., Casane D., McHugh M., Genner M.J. and Sims D.W. (2012) First analysis of multiple paternity in an oviparous shark species, the small-spotted catshark (Scyliorhinus canicula L.). Journal of Heredity 103(2):166-173
37 – Debiais-Thibaud M., Oulion S., Bourrat F., Laurenti P., Casane D. and Borday-Birraux V. (2011) The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology 11(1):307
36 – Griffiths A.M., Casane D., McHugh M., Wearmouth V.J., Sims D.W. and Genner M.J. (2011) Characterisation of polymorphic microsatellite loci in the small-spotted catshark (Scyliorhinus canicula L.). Conservation Genetics Resources 3(4):705-709
35 – García-Machado E., Hernández D., García-Debrás A., Chevalier-Monteagudo P., Metcalfe C.J., Bernatchez L. and Casane D. (2011) Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: Evidence for cryptic allopatric diversity. Molecular Phylogenetics and Evolution 61(2):470-483
34 – Oulion S., Borday-Birraux V., Debiais-Thibaud M., Mazan S., Laurenti P. and Casane D. (2011) Evolution of repeated structures along the body axis of jawed vertebrates, insights from the Scyliorhinus canicula Hox code. Evolution and Development 13(3):247-259
33 – Kano S., Xiao J.-H., Osório J., Ekker M., Hadzhiev Y., Müller F., Casane D., Magdelenat G. and Rétaux S. (2010) Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs. PLoS ONE 5(10):e13332
32 – Oulion S., Debiais-Thibaud M., d’Aubenton-Carafa Y., Thermes C., Da Silva C., Bernard-Samain S., Gavory F., Wincker P., Mazan S. and Casane D. (2010) Evolution of Hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome. Molecular Biology and Evolution 27(12):2829-2838
31 – Lara A., Ponce de León J.L., Rodríguez R., Casane D., Côté G., Bernatchez L. and García-Machado E. (2010) DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Molecular Ecology resources 10(3):421-430
30 – Moreno P., Alvarez M., Lopez L., Moratorio G., Casane D., Castells M., Castro S., Cristina J. and Colina R. (2009) Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient. Virology Journal 6:203
29 – Bon C., Caudy N., de Dieuleveult M., Fosse P., Philippe M., Maksud F., Beraud-Colomb E., Bouzaid E., Kefi R., Laugier C., Rousseau B., Casane D., van der Plicht J. and Elalouf J.M. (2008) Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet. Proceedings of the National Academy of Science USA 105(45):17447-17452
28 – Debiais-Thibaud M., Germon I., Laurenti P., Casane D. and Borday-Birraux V. (2008) Low divergence in Dlx gene expression between dentitions of the medaka (Oryzias latipes) versus high level of expression shuffling in osteichtyans. Evolution and Development 10(4):464-476
27 – Jaszczyszyn Y., Haeussler M., Heuzé A., Debiais-Thibaud M., Casane D., Bourrat F., and Joly J.S. (2007) Comparison of the expression of medaka (Oryzias latipes) pitx genes with other vertebrates show high conservation and a case of functional shuffling in the pituitary. Gene 406(1-2):42-50
26 – Debiais-Thibaud M., Borday-Birraux V., Germon I., Bourrat F., Metcalfe C.J., Casane D. and Laurenti P. (2007) Development of oral and pharyngeal teeth in the medaka (Oryzias latipes): comparison of morphology and expression of eve1 gene. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308(6):693-708
25 – Da Lage J.-L., Danchin E.G. and Casane D. (2007) Where do animal alpha-amylases come from? An interkingdom trip. FEBS Letters 581(21):3927-3935
24 – Moreno M.P., Casane D., López L. and Cristina J. (2006) Evidence of recombination in quasispecies populations of an Hepatitis C Virus patient undergoing anti-viral therapy. Virology Journal 3(1):87
23 – Deyts C., Casane D., Vernier P., Bourrat F. and Joly J.S. (2006) Morphological and gene expression similarities suggest that the ascidian neural gland may be osmoregulatory and homologous to vertebrate peri-ventricular organs. European Journal of Neuroscience 24(8):2299-2308
22 – Snell E.A., Brooke N.M., Taylor W.R., Casane D., Philippe H. and Holland P.W. (2006) An unusual choanoflagellate protein released by Hedgehog autocatalytic processing. Proceedings of the Royal Society of London, Series B 273:401-407
21 – Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W. and Casane D. (2004) Phylogenomics of eukaryotes: the impact of missing data on large alignments. Molecular Biology and Evolution 21(9):1740-1752
20 – Colina R., Casane D., Vasquez S., García-Aguirre L., Chunga A., Romero H., Khan B. and Cristina J. (2004) Evidence of intratypic recombination in natural populations of hepatitis C virus. Journal of general virology 85:31-37
19 – Gribaldo S., Casane D., Lopez P. and Philippe H. (2003) Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Molecular Biology and Evolution 20(11):1754-1759
18 – Philippe H., Casane D., Gribaldo S., Lopez P. and Meunier J. (2003) Heterotachy and functional shift in protein evolution. IUBMB Life 55(4-5):257-265
17 – Costa-Mattioli M., Ferré V., Casane D., Perez-Bercoff R., Coste-Burel M., Imbert-Marcille B.M., Andre E.C., Bressollette-Bodin C., Billaudel S. and Cristina J. (2003) Evidence of recombination in natural populations of hepatitis A virus. Virology 311(1):51-59
16 – Avaron F., Thaëron-Antono C., Beck C.W., Borday-Birraux V., Géraudie J., Casane D. and Laurenti P. (2003) Comparison of even-skipped related gene expression pattern in vertebrates shows an association between expression domain loss and modification of selective constraints on sequences. Evolution and Development 5(2):145-156
15 – Casane D. and Gueride M. (2002) Evolution of mitochondrial tandem repeats heteroplasmy in cultured rabbit cells. Current Genetics 42(1):66-72
14 – Lopez P., Casane D. and Philippe H. (2002) Heterotachy, an important process of protein evolution. Molecular Biology and Evolution 19(1):1-7
13 – Costa-Mattioli M., Cristina J., Romero H., Perez-Bercof R., Casane D., Colina R., Garcia L., Vega I., Glikman G., Romanosky V., Nicand E., Gassin M., Billaudel S. and Ferre V. (2002) Molecular evolution of hepatitis A virus: a new classification based on the complete VP1 protein. Journal of virology 76(18):9516-9525
12 – Delgado S., Casane D., Bonnaud L., Laurin M., Sire J.-Y. and Girondot M. (2001) Molecular evidence for Precambrian origin of amelogenin, the major protein of Vertebrate enamel. Molecular Biology and Evolution 18(12):2146-2153
11 – Borday V., Thaeron C., Avaron F., Brulfert A., Casane D., Laurenti P. and Geraudie J. (2001) evx1 transcription in bony fin rays segment boundaries leads to a reiterated pattern during zebrafish fin development and regeneration. Developmental Dynamics 220(2):91-98
10 – Dufour C., Casane D., Denton D., Wickings J., Corvol P. and Jeunemaitre X. (2000) Human-Chimpanzee DNA sequence variation in the four major genes of the renin angiotensin system. Genomics 69:14-26
9 – Thaeron C., Avaron F., Casane D., Borday V., Thisse B., Thisse C., Boulekbache H. and Laurenti P. (2000) Zebrafish evx1 is dynamically expressed during embryogenesis in subsets of interneurones, posterior gut and urogenital system. Mechanisms of Development 99:167-172
8 – Casane D., Boissinot S., Chang B.H.-J., Shimmin L. and Li W.H. (1997) Mutation Pattern Variation among regions of the primate genome. Journal of Molecular Evolution 45:216-226
7 – Casane D., Dennebouy N., De Rochambeau H., Mounolou J.-C. and Monnerot M. (1997) Non-neutral evolution of tandem repeats in the mitochondrial DNA control region of logomorphs. Molecular Biology and Evolution 14(8):779-789
6 – Hardy C., Callou C., Vigne J.-D., Casane D., Dennebouy N., Mounolou J.-C. and Monnerot M. (1995) Rabbit mitochondrial DNA diversity from prehistoric to modern times. Journal of Molecular Evolution 40:227-237
5 – Monnerot M., Vigne J.-D., Biju-Duval C., Casane D., Callou C., Hardy C., Mougel F., Soriguer R., Dennebouy N. and Mounolou J.-C. (1994) Rabbit and Man: Genetic and Historic approach. Genetics Selection and Evolution 26(1):167-182
4 – Casane D., Dennebouy N., De Rochambeau H., Mounolou J.-C. and Monnerot M. (1994) Genetic analysis of systematic mitochondrial heteroplasmy in rabbits. Genetics 138:471-480
3 – Monnerot M., Casane D., Hardy C. and Vigne J.-D. (1994) Evolution of Oryctolagus: relationships within the Lagomorpha system and access to populations with ancient DNA. Polish Ecological Studies 20(3-4):543-551
2 – Hardy C., Casane D., Vigne J.-D., Callou C., Dennebouy N., Mounolou J.-C. and Monnerot M. (1994) Ancient DNA from Bronze Age bones of European rabbit (Oryctolagus cuniculus). Experientia 50:254-270
1 – Hardy C., Vigne J.-D., Casane D., Dennebouy N., Mounolou J.-C. and Monnerot M. (1994) Origin of European rabbit (Oryctolagus cuniculus) in a Mediterranean Island: Zooarchaeology and ancient DNA examination. Journal of Evolutionary Biology 7:217-226

Popular science

9 – Sallard E., Halloy J., Casane D., van Helden J. and Decroly E. (2020) Retrouver les origines du SARS-COV-2 dans les phylogénies de coronavirus. Médecine/Sciences 36(8-9):783-796
8 – Casane D., Policarpo M. and Laurenti P. (2019) Pourquoi le taux de mutation n’est-il jamais égal à zéro ? Médecine/Sciences 35(3):245-251
7 – Casane D. and Laurenti P. (2016) Le cas CRISPR, mutations « ready-made » et évolution lamarckienne d’un système immunitaire adaptatif. Médecine/Sciences 32(6-7):640-645
6 – Casane D., Fumey J. and Laurenti P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Médecine/Sciences 31(6-7):680-686
5 – Casane D. and Laurenti P. (2014) Syllogomanie moléculaire : l’ADN non codant enrichit le jeu des possibles. Médecine/Sciences 30(12):1177-1183
4 – Casane D. and Laurenti P. (2014) Une toute nouvelle tête pour l’ancêtre des vertébrés à mâchoires. Médecine/Sciences 30(1):38-40
3 – Casane D. and Laurenti P. (2012) Penser la biologie dans un cadre phylogénétique : l’exemple de l’évolution des vertébrés. Médecine/Sciences 28(12):1121-1127
2 – Oulion S., Laurenti P. and Casane D. (2012) Organisation des gènes Hox : l’étude de vertébrés non-modèles mène à un nouveau paradigme. Médecine/Sciences 28(4):10-13
1 – Lopez P., Casane D. and Philippe H. (2002) Phylogénie et évolution moléculaires. Médecine/Sciences 18:767-774