, Genes|Genomes|Genetics Genes|Genomes|Genetics, vol.7, pp.1357-1363

R. J. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor et al.,

, Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database, pp.30-030, 2011.

E. Kopylova, L. Noé, and H. Touzet, SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, pp.3211-3217, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00748990

J. Krauss, P. Astrinides, H. G. Frohnhofer, B. Walderich, and C. Nusslein-volhard, transparent, a gene affecting stripe formation in Zebrafish, encodes the mitochondrial protein Mpv17 that is required for iridophore survival, Biol Open, vol.2, pp.703-710, 2013.

R. L. Lamason, M. Mohideen, J. R. Mest, A. C. Wong, H. L. Norton et al., SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans, Science, vol.310, pp.1782-1788, 2005.

S. Q. Le and O. Gascuel, An Improved General Amino Acid Replacement Matrix, Mol Biol Evol, vol.25, pp.1307-1320, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009.

J. A. Lister, B. M. Lane, A. Nguyen, and K. Lunney, Embryonic expression of zebrafish MiT family genes tfe3b, tfeb, and tfec, Dev Dyn, vol.240, p.2529, 2011.

G. Litsios, C. A. Sims, R. O. Wüest, P. B. Pearman, N. E. Zimmermann et al., Mutualism with sea anemones triggered the adaptive radiation of clownfishes, BMC Evol Biol, vol.12, p.212, 2012.

S. S. Lopes, X. Yang, J. Müller, T. J. Carney, A. R. Mcadow et al.,

, Leukocyte Tyrosine Kinase Functions in Pigment Cell Development (G Barsh, PLoS Genet, vol.4, p.1000026

T. Lorin, F. G. Brunet, V. Laudet, and J. Volff, Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates. G3 Genes|Genomes|Genetics: g3, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806995

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, 2014.

R. Mallarino, C. Henegar, M. Mirasierra, M. Manceau, C. Schradin et al., Developmental mechanisms of stripe patterns in rodents, Nature, vol.539, pp.518-523, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01392179

R. N. Mariscal, The symbiosis between tropical sea anemones and fishes: a review, The Galápagos: Proceedings of the Symposia of the Galápagos International Scientific Project, p.318, 1966.

T. A. Militz and S. Foale, The 'Nemo Effect': Perception and reality of Finding Nemo 's impact on marine aquarium fisheries, Fish Fish, vol.18, pp.596-606, 2017.

A. R. Moise, A. Isken, M. Domínguez, A. R. De-lera, V. Lintig et al., Specificity of Zebrafish Retinol Saturase: Formation of Alltrans -13,14-dihydroretinol and All-trans -7,8-dihydroretinol ?, Biochemistry, vol.46, pp.1811-1820, 2007.

C. M. Moraes-mn-de, L. Lima, . De, B. Ramos, and O. Poletini-m-de, Endothelin modulates the circadian expression of non-visual opsins, Gen Comp Endocrinol, vol.205, pp.279-286, 2014.

Y. Nagao, H. Takada, M. Miyadai, T. Adachi, R. Seki et al., Resolution of ray-finned fish phylogeny and timing of diversification, Proc Natl Acad Sci, vol.14, pp.13698-13703, 2012.

J. S. Nelson, T. C. Grande, and M. Wilson, How fish color their skin: A paradigm for development and evolution of adult patterns, BioEssays, vol.39, p.1600231, 2016.

E. Oancea, J. Vriens, S. Brauchi, J. Jun, I. Splawski et al., , 2009.

, TRPM1 Forms Ion Channels Associated with Melanin Content in Melanocytes. Sci Signal, vol.2, pp.21-21

D. M. Parichy and J. M. Turner, Temporal and cellular requirements for Fms signaling during zebrafish adult pigment pattern development, Development, vol.130, pp.817-850, 2003.

W. Pei, L. Xu, G. K. Varshney, B. Carrington, K. Bishop et al., Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases, Sci Rep, vol.6, p.29946, 2016.

L. M. San-jose and A. Roulin, Genomics of coloration in natural animal populations, Philos Trans R Soc B Biol Sci, vol.372, 2017.

M. E. Santos, L. Baldo, L. Gu, N. Boileau, Z. Musilova et al., , 2016.

, Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes, BMC Genomics, vol.17, p.712

E. Santos, I. Braasch, N. Boileau, B. S. Meyer, A. Bo et al., The evolution of cichlid fish egg-spots is linked with a cis-regulatory change, Nat Commun, 2014.

M. Schartl, L. Larue, M. Goda, M. W. Bosenberg, H. Hashimoto et al., What is a vertebrate pigment cell?, Pigment Cell Melanoma Res, vol.29, pp.8-14, 2016.

M. D. Shapiro, Z. Kronenberg, C. Li, E. T. Domyan, H. Pan et al., Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon, Science (80-), vol.339, pp.1063-1067, 2013.

F. Sievers and D. G. Higgins, Clustal omega, accurate alignment of very large numbers of sequences, Methods in Molecular Biology, vol.1079, pp.105-116, 2014.

A. P. Singh and C. Nüsslein-volhard, Zebrafish Stripes as a Model for Vertebrate Colour Pattern Formation, Curr Biol, vol.25, pp.81-92, 2015.

C. Soneson, M. I. Love, and M. D. Robinson, Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, vol.4, p.1521, 1000.

C. J. Starr, J. A. Kappler, D. K. Chan, R. Kollmar, and A. J. Hudspeth, From The Cover: Mutation of the zebrafish choroideremia gene encoding Rab escort protein 1 devastates hair cells, Proc Natl Acad Sci, vol.101, pp.2572-2577, 2004.

A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert et al., Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci, vol.102, pp.15545-15550, 2005.

K. M. Szymanski, D. Binns, R. Bartz, N. V. Grishin, W. Li et al., The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology, Proc Natl Acad Sci, vol.104, pp.20890-20895, 2007.

A. R. Wallace, The colours of animals and plants, Am Nat, vol.11, pp.713-728, 1877.

M. Watanabe, Gap Junction in the Teleost Fish Lineage: Duplicated Connexins May Contribute to Skin Pattern Formation and Body Shape Determination, Front Cell Dev Biol, vol.5, 2017.

B. Altincicek, J. L. Kovacs, and N. M. Gerardo, Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae, Biol Lett, vol.8, pp.253-257, 2012.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990.

M. Anisimova, M. Gil, J. Dufayard, C. Dessimoz, and O. Gascuel, Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes, Syst Biol, vol.60, pp.685-699, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00715506

J. T. Bagnara, J. D. Taylor, and M. E. Hadley, The dermal chromatophore unit, J Cell Biol, vol.38, pp.67-79, 1968.

B. Battelle, J. F. Ryan, K. E. Kempler, S. R. Saraf, C. E. Marten et al., Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata), 2016.

, Genome Biol Evol, vol.8, pp.1571-1589

C. Beimforde, K. Feldberg, S. Nylinder, J. Rikkinen, H. Tuovila et al., Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data, Mol Phylogenet Evol, vol.78, pp.386-398, 2014.

D. A. Benson, M. Cavanaugh, K. Clark, I. Karsch-mizrachi, D. J. Lipman et al., GenBank. Nucleic Acids Res, vol.41, pp.36-42, 2013.

C. Berthelot, F. Brunet, D. Chalopin, A. Juanchich, M. Bernard et al., The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates, Nat Commun, vol.5, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01193812

. Betancur-r-r, E. O. Wiley, G. Arratia, A. Acero, N. Bailly et al., Phylogenetic classification of bony fishes, BMC Evol Biol, vol.17, p.162, 2017.

D. Borek, M. Kozak, J. Pei, and M. Jaskolski, Crystal structure of active site mutant of antileukemic <scp>l</scp> -asparaginase reveals conserved zinc-binding site, FEBS J, vol.281, pp.4097-4111, 2014.

L. Boto, Horizontal gene transfer in the acquisition of novel traits by metazoans, Proc R Soc B Biol Sci, vol.281, 2014.

I. Braasch, F. Brunet, J. Volff, and M. Schartl, Pigmentation pathway evolution after whole-genome duplication in fish, Genome Biol Evol, vol.1, pp.479-493, 2009.

I. Braasch, A. R. Gehrke, J. J. Smith, K. Kawasaki, T. Manousaki et al., The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons, Nat Genet, vol.48, pp.427-437, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01595410

I. Braasch, J. N. Volff, and M. Schartl, The evolution of teleost pigmentation and the fish-specific genome duplication, J Fish Biol, vol.73, pp.1891-1918, 2008.

S. J. Braddy, Eurypterid palaeoecology: palaeobiological, ichnological and comparative evidence for a 'mass-moult-mate' hypothesis, Palaeogeogr Palaeoclimatol Palaeoecol, vol.172, pp.115-132, 2001.

M. Brameier, A. Krings, and R. M. Maccallum, NucPred Predicting nuclear localization of proteins, Bioinformatics, vol.23, pp.1159-1160, 2007.

K. A. Bratke and A. Mclysaght, Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach, BMC Evol Biol, vol.8, p.67, 2008.

C. Brenner, Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases, Biochemistry, vol.41, pp.9003-9017, 2002.

Y. Cai, C. N. Cronin, A. G. Engel, K. Ohno, L. B. Hersh et al., , 2004.

, Choline acetyltransferase structure reveals distribution of mutations that cause motor disorders, EMBO J, vol.23, pp.2047-2058

P. J. Casey, Protein lipidation in cell signaling, Science, vol.268, pp.221-226, 1995.

Y. Chang, S. Wang, S. Sekimoto, A. L. Aerts, C. Choi et al., , 2015.

, Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants, Genome Biol Evol, vol.7, pp.1590-1601

J. A. Chapman, E. F. Kirkness, O. Simakov, S. E. Hampson, T. Mitros et al., The dynamic genome of Hydra, Nature, vol.464, pp.592-596, 2010.

K. Chen, J. Miadlikowska, K. Molnár, A. E. Arnold, U. &apos;ren et al.,

, to Chaetothyriales, Eurotiales, and a new orderPhaeomoniellales, vol.85, pp.117-130

C. Cobbs, J. Heath, J. O. Stireman, and P. Abbot, Carotenoids in unexpected places: Gall midges, lateral gene transfer, and carotenoid biosynthesis in animals, Mol Phylogenet Evol, vol.68, pp.221-228, 2013.

M. A. Coelho, C. Gonçalves, J. P. Sampaio, and P. Gonçalves, Extensive Intra-Kingdom Horizontal Gene Transfer Converging on a Fungal Fructose Transporter Gene (J Heitman, PLoS Genet, vol.9, p.1003587, 2013.

T. La-cour, L. Kiemer, A. Mølgaard, R. Gupta, K. Skriver et al., , 2004.

, Analysis and prediction of leucine-rich nuclear export signals, Protein Eng Des Sel, vol.17, pp.527-536

A. Crisp, C. Boschetti, M. Perry, A. Tunnacliffe, and G. Micklem, , 2015.

D. Darriba, G. L. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, p.1164, 2011.

G. D. Edgecombe and D. A. Legg, Origins and early evolution of arthropods (A Smith, Palaeontology, vol.57, pp.457-468, 2014.

G. Eriani, J. Cavarelli, F. Martin, L. Ador, B. Rees et al., , 1995.

N. Fankhauser and P. Maser, Identification of GPI anchor attachment signals by a Kohonen self-organizing map, Bioinformatics, vol.21, p.1846, 2005.

R. D. Finn, P. Coggill, R. Y. Eberhardt, S. R. Eddy, J. Mistry et al.,

, The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res, vol.44, pp.279-285

D. A. Fitzpatrick, Horizontal gene transfer in fungi, FEMS Microbiol Lett, vol.329, pp.1-8, 2012.

R. Gazis, A. Kuo, R. Riley, K. Labutti, A. Lipzen et al., , 2015.

C. Gilbert and R. Cordaux, Viruses as vectors of horizontal transfer of genetic material in eukaryotes, Curr Opin Virol, vol.25, pp.16-22, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01586956

C. Gilbert, S. S. Hernandez, J. Flores-benabib, E. N. Smith, and C. Feschotte, , 2012.

, Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles, Mol Biol Evol, vol.29, pp.503-515

C. Gilbert, S. Schaack, I. I. Pace, . Jk, P. J. Brindley et al., A role for host-parasite interactions in the horizontal transfer of transposons across phyla, Nature, vol.464, pp.1347-1350, 2010.

M. Goda and R. Fujii, Blue Chromatophores in Two Species of Callionymid Fish, Zoolog Sci, vol.12, pp.811-813, 1995.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol Biol Evol, vol.27, pp.221-224, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

G. Gray and W. Fitch, Evolution of antibiotic resistance genes: the DNA, 1984.

I. V. Grigoriev, R. Nikitin, S. Haridas, A. Kuo, R. Ohm et al., , 2014.

, MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Res, vol.42, pp.699-704

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

K. Hansen, B. A. Perry, A. W. Dranginis, and D. H. Pfister, A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits, Mol Phylogenet Evol, vol.67, pp.311-335, 2013.

G. Von-heijne, The signal peptide, J Membr Biol, vol.115, pp.195-201, 1990.

S. Hongsanan, S. Maharachchikumbura, K. D. Hyde, M. C. Samarakoon, R. Jeewon et al., An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence, Fungal Divers, vol.84, pp.25-41, 2017.

M. A. Houck, Mites as Potential Horizontal Transfer Vectors of Eukaryotic Mobile Genes: Proctolaelaps regalis as a Model, pp.45-69, 1994.

J. Huang, Horizontal gene transfer in eukaryotes: The weak-link model, 2013.

V. Hustad and A. Miller, Phylogenetic placement of four genera within the Leotiomycetes (Ascomycota), North Am Fungi, vol.6, pp.1-13, 2011.

T. Igawa, M. Nozawa, D. G. Suzuki, J. D. Reimer, A. R. Morov et al., Evolutionary history of the extant amphioxus lineage with shallow-branching diversification, Sci Rep, vol.7, p.1157, 2017.

J. Inoue, Y. Sato, R. Sinclair, K. Tsukamoto, and M. Nishida, Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling, Proc Natl Acad Sci, vol.112, pp.14918-14923, 2015.

K. Inouye, K. Yamano, Y. Maeno, K. Nakajima, M. Matsuoka et al., Iridovirus Infection of Cultured Red Sea Bream, Pagrus major, Fish Pathol, vol.27, pp.19-27, 1992.

O. Jaillon, J. Aury, F. Brunet, J. Petit, N. Stange-thomann et al., Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol.431, pp.946-957, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427605

A. J. Jeram, Book-lungs in a Lower Carboniferous scorpion, Nature, vol.343, pp.360-361, 1990.

P. Jones, D. Binns, H. Chang, M. Fraser, W. Li et al., InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.30, pp.1236-1240, 2014.

E. Jones, S. Suetrong, J. Sakayaroj, A. H. Bahkali, A. et al., Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota, Fungal Divers, vol.73, pp.1-72, 2015.

L. Kall, A. Krogh, and E. Sonnhammer, Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server, Nucleic Acids Res, vol.35, pp.429-432, 2007.

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, vol.10, pp.845-858, 2015.

P. Kenrick, C. H. Wellman, H. Schneider, and G. D. Edgecombe, A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic, Philos Trans R Soc B Biol Sci, vol.367, pp.519-536, 2012.

T. Kimura, Y. Takehana, and K. Naruse, pnp4a Is the Causal Gene of the Medaka Iridophore Mutant guanineless, G3 Genes|Genomes|Genetics Genes|Genomes|Genetics, vol.7, pp.1357-1363, 2017.

S. P. Kishore, J. W. Stiller, and K. W. Deitsch, Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans, BMC Evol Biol, vol.13, p.37, 2013.

Y. Kodama, J. Mashima, T. Kosuge, E. Kaminuma, O. Ogasawara et al., DNA Data Bank of Japan: 30th anniversary, Nucleic Acids Res, vol.46, pp.30-35, 2018.

S. Kosugi, M. Hasebe, M. Tomita, and H. Yanagawa, Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc Natl Acad Sci, vol.106, pp.10171-10176, 2009.

J. Krauss, P. Astrinides, H. G. Frohnhofer, B. Walderich, and C. Nusslein-volhard, transparent, a gene affecting stripe formation in Zebrafish, encodes the mitochondrial protein Mpv17 that is required for iridophore survival, Biol Open, vol.2, pp.703-710, 2013.

A. Krogh, B. Larsson, G. Von-heijne, and E. L. Sonnhammer, , 2001.

S. Kumar, G. Stecher, M. Suleski, and S. B. Hedges, TimeTree: A Resource for Timelines, Timetrees, and Divergence Times, Mol Biol Evol, vol.34, p.1812, 2017.

J. Kurita and K. Nakajima, Megalocytiviruses. Viruses, vol.4, pp.521-538, 2012.

T. Kuriyama, K. Miyaji, M. Sugimoto, and M. Hasegawa, Ultrastructure of the Dermal Chromatophores in a Lizard (Scincidae: Plestiodon latiscutatus) with Conspicuous Body and Tail Coloration, Zoolog Sci, vol.23, pp.793-799, 2006.

E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al.,

A. Lapedriza, K. Petratou, and R. N. Kelsh, Neural Crest Cells and Pigmentation, Neural Crest Cells, pp.287-311, 2014.

S. Q. Le and O. Gascuel, An Improved General Amino Acid Replacement Matrix, Mol Biol Evol, vol.25, pp.1307-1320, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

P. L. Lebrun and . Koch, Acari Oribatei) Densité et structure de la population, Oikos, vol.20, p.34, 1969.

S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent et al., , 2016.

, The Atlantic salmon genome provides insights into rediploidization, Nature, vol.533, pp.200-205

J. Lin, A. Mondal, R. Liu, and J. Hu, Minimalist ensemble algorithms for genome-wide protein localization prediction, BMC Bioinformatics, vol.13, 2012.

H. Liu, Y. Fu, D. Jiang, G. Li, J. Xie et al., Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes, J Virol, vol.84, pp.11876-11887, 2010.

T. Lorin, F. G. Brunet, V. Laudet, and J. Volff, Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates. G3 Genes|Genomes|Genetics: g3, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806995

A. Louis, N. Nguyen, M. Muffato, R. Crollius, and H. , Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics, Nucleic Acids Res, vol.43, pp.682-689, 2015.

A. Luo, H. Qiao, Y. Zhang, W. Shi, S. Y. Ho et al., Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets, BMC Evol Biol, vol.10, 2010.

L. Ma, H. C. Van-der-does, K. A. Borkovich, J. J. Coleman, M. Daboussi et al., Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, vol.464, pp.367-373, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00574227

L. Mallet, J. Becq, and P. Deschavanne, , 2010.

A. Marcionetti, V. Rossier, J. Bertrand, G. Litsios, and N. Salamin, First draft genome of an iconic clownfish species ( Amphiprion frenatus ), Mol Ecol Resour, 2018.

C. L. Mcgrath, J. Gout, P. Johri, T. G. Doak, and M. Lynch, Differential retention and divergent resolution of duplicate genes following wholegenome duplication, Genome Res, vol.24, pp.1665-1675, 2014.

E. M. Mellgren and S. L. Johnson, The evolution of morphological complexity in zebrafish stripes, Trends Genet, vol.18, pp.128-162, 2002.

A. Meyer and M. Schartl, Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions, Curr Opin Cell Biol, vol.11, pp.699-704, 1999.

J. Miadlikowska, F. Kauff, F. Högnabba, J. C. Oliver, K. Molnár et al., A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families, Mol Phylogenet Evol, vol.79, pp.132-168, 2014.

K. Michalska, A. Hernandez-santoyo, and M. Jaskolski, The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases, J Biol Chem, vol.283, pp.13388-13397, 2008.

N. A. Moran and T. Jarvik, Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids, Science (80-), vol.328, pp.624-627, 2010.

K. Nakajima and J. Kunita, Red sea bream iridoviral disease, Uirusu, vol.55, pp.115-140, 2005.

K. Nakajima and Y. Maeno, Pathogenicity of Red Sea Bream Iridovirus and Other Fish Iridoviruses to Red Sea Bream, Fish Pathol, vol.33, pp.143-144, 1998.

A. N. Nguyen-ba, A. Pogoutse, N. Provart, and A. M. Moses, NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction, BMC Bioinformatics, vol.10, p.202, 2009.

H. Nilsson-sköld, S. Aspengren, and M. Wallin, Rapid color change in fish and amphibians -function, regulation, and emerging applications, Pigment Cell Melanoma Res, vol.26, pp.29-38, 2013.

N. A. O&apos;leary, M. W. Wright, J. R. Brister, S. Ciufo, D. Haddad et al., Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, vol.44, pp.733-745, 2016.

S. Ohno, Evolution by gene duplication, 1970.

A. A. Ojanguren-affilastro, R. S. Adilardi, C. I. Mattoni, M. J. Ramírez, and F. S. Ceccarelli, Dated phylogenetic studies of the southernmost American buthids (Scorpiones; Buthidae), Mol Phylogenet Evol, vol.110, pp.39-49, 2017.

S. Oulion, S. Bertrand, M. R. Belgacem, L. Petillon, Y. Escriva et al., , 2012.

, Sequencing and Analysis of the Mediterranean Amphioxus (Branchiostoma lanceolatum) Transcriptome (V Laudet, PLoS One, vol.7, p.36554

D. M. Parichy, Evolution of danio pigment pattern development, Heredity (Edinb), vol.97, pp.200-210, 2006.

E. Park, D. Hwang, J. Lee, J. Song, T. Seo et al., Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record, Mol Phylogenet Evol, vol.62, pp.329-345, 2012.

J. Pasquier, I. Braasch, P. Batzel, C. Cabau, J. Montfort et al., Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome, J Exp Zool Part B Mol Dev Evol, vol.328, pp.709-721, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01788671

L. B. Patterson and D. M. Parichy, Interactions with Iridophores and the Tissue Environment Required for Patterning Melanophores and Xanthophores during Zebrafish Adult Pigment Stripe Formation (GS Barsh, PLoS Genet, vol.9, p.1003561, 2013.

T. N. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, vol.8, pp.785-786, 2011.

O. Piskurek and N. Okada, Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals, Proc Natl Acad Sci, vol.104, pp.12046-12051, 2007.

D. Posada, jModelTest: Phylogenetic Model Averaging, Mol Biol Evol, vol.25, pp.1253-1256, 2008.

M. Prieto and M. Wedin, Dating the Diversification of the Major Lineages of Ascomycota (Fungi) (S Ho, PLoS One, vol.8, p.65576, 2013.

J. C. Regier, J. W. Shultz, A. Zwick, A. Hussey, B. Ball et al., , 2010.

, Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences, Nature, vol.463, pp.1079-1083

U. L. Rosewich and H. C. Kistler, Role of Horizontal Gene Transfer in the Evolution of Fungi, Annu Rev Phytopathol, vol.38, pp.325-363, 2000.

M. Schartl, L. Larue, M. Goda, M. W. Bosenberg, H. Hashimoto et al., What is a vertebrate pigment cell?, Pigment Cell Melanoma Res, vol.29, pp.8-14, 2016.

C. L. Schoch, P. W. Crous, J. Z. Groenewald, and E. Boehm,

J. Gruyter, A class-wide phylogenetic assessment of Dothideomycetes, Stud Mycol, vol.64, pp.1-15, 2009.

C. L. Schoch, G. Sung, F. López-giráldez, J. P. Townsend, J. Miadlikowska et al., The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits, Syst Biol, vol.58, pp.224-239, 2009.

G. Schönknecht, A. Weber, and M. J. Lercher, , 2014.

M. Schwentner and T. Bosch, Revisiting the age, evolutionary history and species level diversity of the genus Hydra (Cnidaria: Hydrozoa), Mol Phylogenet Evol, vol.91, pp.41-55, 2015.

B. Séraphin, The HIT protein family: a new family of proteins present in prokaryotes, yeast and mammals, DNA Seq, vol.3, pp.177-186, 1992.

P. P. Sharma, C. M. Baker, J. G. Cosgrove, J. E. Johnson, J. T. Oberski et al., A revised dated phylogeny of scorpions: Phylogenomic support for ancient divergence of the temperate Gondwanan family Bothriuridae, Mol Phylogenet Evol, vol.122, pp.37-45, 2018.

F. Sievers and D. G. Higgins, Clustal omega, accurate alignment of very large numbers of sequences, Methods in Molecular Biology, vol.1079, pp.105-116, 2014.

D. N. Silva, S. Duplessis, P. Talhinhas, H. Azinheira, O. S. Paulo et al., Genomic Patterns of Positive Selection at the Origin of, PLoS One, vol.10, p.143959, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01269480

V. Solovyev, Statistical Approaches in Eukaryotic Gene Prediction, Handbook of Statistical Genetics, pp.97-159, 2008.

S. M. Soucy, J. Huang, and J. P. Gogarten, Horizontal gene transfer: building the web of life, Nat Rev Genet, vol.16, pp.472-482, 2015.

E. A. Sperling, D. Pisani, and K. J. Peterson, Molecular paleobiological insights into the origin of the Brachiopoda, Evol Dev, vol.13, pp.290-303, 2011.

M. J. Stanhope, A. Lupas, M. J. Italia, K. K. Koretke, C. Volker et al., , 2001.

S. Suetrong, C. L. Schoch, J. W. Spatafora, J. Kohlmeyer, B. Volkmannkohlmeyer et al., Molecular systematics of the marine Dothideomycetes, Stud Mycol, vol.64, pp.155-173, 2009.

Y. Sun, Y. Huang, X. Li, C. C. Baldwin, Z. Zhou et al., Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies, Gigascience, vol.5, p.18, 2016.

B. Sun, T. Li, J. Xiao, L. Jia, L. Liu et al., Horizontal functional gene transfer from bacteria to fishes, Sci Rep, vol.5, p.18676, 2015.

A. Szilágyi and J. Skolnick, Efficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures, J Mol Biol, vol.358, pp.922-933, 2006.

M. Vasse, H. Voglmayr, V. Mayer, C. Gueidan, M. Nepel et al., A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales), Proc R Soc B Biol Sci, vol.284, 2017.

M. Vidotto, A. Grapputo, E. Boscari, F. Barbisan, A. Coppe et al., Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon, BMC Genomics, vol.14, p.407, 2013.

H. Wang, Z. Xu, L. Gao, and B. Hao, A fungal phylogeny based on 82 complete genomes using the composition vector method, BMC Evol Biol, vol.9, p.195, 2009.

T. Williams, Natural invertebrate hosts of iridoviruses (Iridoviridae), Neotrop Entomol, vol.37, pp.615-647, 2008.

G. M. Wright and K. M. Mcburney, Changes in the ventral dermis and development of iridophores in the anadromous sea lamprey, Petromyzon marinus, during metamorphosis: an ultrastructural study, Histol Histopathol, vol.7, pp.237-50, 1992.

Y. Xie, Y. Zheng, H. Li, X. Luo, Z. He et al., GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites, Sci Rep, vol.6, p.28249, 2016.

F. Zapata, F. E. Goetz, S. A. Smith, M. Howison, S. Siebert et al., Phylogenomic Analyses Support Traditional Relationships within Cnidaria (RE Steele, PLoS One, vol.10, p.139068, 2015.

J. Zhang, Protein-length distributions for the three domains of life, Trends Genet, vol.16, pp.107-116, 2000.

L. Zhou and U. Kõljalg, A new species of Lenzitopsis (Thelephorales, Basidiomycota) and its phylogenetic placement, Mycoscience, vol.54, pp.87-92, 2013.

F. Zhou, Y. Xue, X. Yao, and Y. Xu, CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS), Bioinformatics, vol.22, pp.894-896, 2006.

, cette représentation permet de se rendre compte que de nombreux marqueurs d'iridophores ont un profil d'expression correspondant à une augmentation aux stades 5 et 6 par rapport au stade 4. De plus, aucun de ces gènes n'est représenté vers "le bas et le milieu de la branche gauche" du graphe (clusters gris, rose, jaune et cyan), correspondant aux gènes qui ont une expression croissante avant S4 puis décroissante après S4, Que la différence soit significative ou pas

, De même, les deux TR? ont une expression qui augmente entre les stades 4 et 6. Cela pourrait donc suggérer un contrôle des gènes de différentiation des iridophores par la voie des hormones thyroïdiennes. Cela reste évidemment à tester fonctionnellement, mais ce serait une première, à ma connaissance. En effet, jusqu'à présent, le rôle de ces hormones n'a été montré que dans la différentiation des mélanocytes et des xanthophores, On peut remarquer qu'un autre des gènes évoqués au-dessus a un profil d'expression faible jusqu'au stade 4 et en constante augmentation par la suite : TR-?, 2014.

, Autre point intéressant : sur la figure 12 est également représenté le profil d'expression de roshi-a. Celui-ci est, nous l'avons montré, un probable nouveau marqueur d'iridophores. Son expression est compatible avec une augmentation entre S4 et S5/S6, et va de fait dans le sens de ce qui est avancé au-dessus (Figure 12

, Les iridophores, chez le poisson-clown, se mettent en place massivement au cours de la métamorphose post-S4

, (même si, ensuite, leur expression semble réaugmenter après le stade 4), et ont un profil d'expression en "creux" plutôt qu'en exponentielle : gart, impdh1b, fhl2, roshi-a? Cela pourrait correspondre, de manière un peu équivalente à ce qui est observé chez le Poisson-zèbre, à la présence de deux populations d'iridophores : des iridophores larvaires, qui seraient présents précocement au cours du développement, mais diffus et sans former de bandes, et des iridophores adultes, se mettant en place en même temps que les bandes, On peut donc "s'étonner" de constater que de nombreux marqueurs d'iridophores sont exprimés de manière plus précoce, aux stades, vol.1, 2015.

R. J. Denver and K. E. Williamson, Identification of a thyroid hormone response element in the mouse Krüppel-like factor 9 gene to explain its postnatal expression in the brain, Endocrinology, vol.150, pp.3935-3943, 2009.

G. Holzer, M. Besson, A. Lambert, L. François, P. Barth et al., Fish larval recruitment to reefs is a thyroid hormone-mediated metamorphosis sensitive to the pesticide chlorpyrifos, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01633712

C. T. Kuo, S. Zhu, S. Younger, and J. Ly, Identification of E2/E3 Ubiquitinating Enzymes and Caspase Activity Regulating Drosophila Sensory Neuron Dendrite Pruning, Neuron, vol.51, pp.283-290, 2006.

P. Langfelder and S. Horvath, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, vol.9, p.559, 2008.

V. Laudet, The Origins and Evolution of Vertebrate Metamorphosis, Curr Biol, vol.21, pp.726-737, 2011.

Y. Liu, L. Fu, D. Chen, and S. S. Deeb, Identification of novel retinal target genes of thyroid hormone in the human WERI cells by expression microarray analysis, Vision Res, vol.47, pp.2314-2326, 2007.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, 2014.

, Genome Biol, vol.15, p.550

S. K. Mcmenamin, E. J. Bain, A. E. Mccann, L. B. Patterson, D. S. Eom et al., Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish, Science (80-), vol.345, issue.602, pp.1358-1361, 2014.

P. K. Reddy and T. J. Lam, Effect of thyroid hormones on morphogenesis and growth of larvae and fry of telescopic-eye black goldfish, Carassius auratus, Aquaculture, vol.107, pp.383-394, 1992.

J. Reimand, T. Arak, P. Adler, L. Kolberg, S. Reisberg et al., g:Profiler -a web server for functional interpretation of gene lists (2016 update), Nucleic Acids Res, vol.44, pp.83-89, 2016.

A. L. Scarman, J. D. Hooper, K. J. Boucaut, M. L. Sit, G. C. Webb et al., Organization and chromosomal localization of the murine Testisin gene encoding a serine protease temporally expressed during spermatogenesis, Eur J Biochem, vol.268, pp.1250-1258, 2001.

A. P. Singh and C. Nüsslein-volhard, Zebrafish Stripes as a Model for Vertebrate Colour Pattern Formation, Curr Biol, vol.25, pp.81-92, 2015.

L. Stachorski, V. Thangapandi, D. Reinhardt, and J. Klusmann, Characterization of oncogenes on chromosome 21 identified by shRNA-based viability screening, Mol Cell Pediatr, vol.1, p.20, 2014.

R. Suzuki and H. Shimodaira, Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.22, pp.1540-1542, 2006.

;. Au and . Panchy, Il y a donc rapidement une divergence des patrons d'expression entre les paralogues. Parmi une multitude de grandeurs, le niveau d'expression d'un gène est celle qui est la plus intimement corrélée à son taux d'évolution (Cherry, 2010). Ainsi, un gène fortement exprimé a une évolution plus contrainte qu'un gène faiblement exprimé, car l'impact phénotypique d'une modification du premier risque d'être plus important. Au cours de cette thèse, nous n'avons pas étudié de manière systématique ni les différences d'expression, ni de taux d'évolution, entre paralogues. Ces mesures pourraient être intéressantes à mener sur les familles de gènes de la pigmentation, -delà des taux de rétention : autres aspects susceptibles d'influer l'évolution des gènes de la pigmentation Au cours de cette thèse, j'ai envisagé les conséquences des duplications de génomes essentiellement sous l'angle de la rétention, vol.4, 2016.

. Ii, Évolution" de l'étude du répertoire pigmentaire et de la compréhension de la pigmentation chez les Vertébrés 1. Pourquoi il est important d'en apprendre plus sur la pigmentation des Vertébrés

. Cuthill, En évolution, elle permet en particulier de répondre à des questions fondamentales sur le processus adaptatif. Enfin, l'étude de la couleur de différentes populations d'espèces de mammifères polyphéniques (pelage brun en été et blanc en hiver), qui ont du mal à s'adapter au rythme du changement climatique actuel, 2017.

, Le répertoire pigmentaire s'enrichit constamment a. Études "omiques

. Hysi, Les Genome-Wide Association Studies permettent d'identifier de nouveaux candidats, de même que les études transcriptomiques, telle que celle ayant conduit à la mise en évidence du rôle de alx3 dans le patterning pigmentaire chez les rongeurs, 2016.

, Article de vulgarisation sur les cellules des crêtes neurales

, Intéressé par la biologie du développement et l'évolution des Vertébrés, je me suis naturellement orienté vers la rédaction d'un article traitant des cellules des crêtes neurales. Après des retours de Jean-Nicolas Volff sur une première version de l'article, j'ai proposé ce texte à Pascal Combemorel, éditeur du site institutionnel Planet-Vie ayant pour vocation de publier des articles pour les enseignants de SVT (https://planet-vie.ens.fr/). P. Combemorel m'a grandement aidé à le rendre plus accessible pour des enseignants du secondaire, après avoir appris que je voulais devenir enseignant, Frédéric Flamant et Marc Robinson-Rechavi m'ont tous deux suggéré d'écrire un article de vulgarisation en rapport avec ma thèse

, Je joins ici l'équivalent en format pdf du texte publié en ligne. Je tiens à remercier chaleureusement Pascal

A. C. Price, Pigments , Patterns , and Fish Behavior, Zebrafish, vol.5, pp.297-307, 2008.

L. B. Patterson, Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution, Nat. Commun, vol.5, p.5299, 2014.

A. Kodric-brown, Sexual Dichromatism and Temporary Color Changes in the Reproduction of Fishes, Am. Zool, vol.38, pp.70-81, 1998.

P. O. Dunn, Natural and sexual selection act on different axes of variation in avian plumage color, Sci. Adv, vol.1, p.5, 2015.

J. A. Tobias, The evolution of female ornaments and weaponry: social selection, sexual selection and ecological competition, Philos. Trans. R. Soc. B Biol. Sci, vol.367, pp.2274-2293, 2012.

M. E. Protas and N. H. Patel, Evolution of coloration patterns, Annu. Rev. Cell Dev. Biol, vol.24, pp.425-446, 2008.

R. Mallarino, Developmental mechanisms of stripe patterns in rodents, Nature, vol.539, pp.518-523, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01392179

N. Gompel, Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila, Nature, vol.433, pp.481-487, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00310898

A. E. Hof, The industrial melanism mutation in British peppered moths is a transposable element, Nature, vol.534, pp.102-105, 2016.

M. E. Santos, The evolution of cichlid fish egg-spots is linked with a cis-regulatory change, Nat. Commun, vol.5, p.11, 2014.

H. E. Hoekstra, Genetics, development and evolution of adaptive pigmentation in vertebrates, Heredity (Edinb), vol.97, pp.222-234, 2006.

L. Arnoult, Emergence and diversification of fly pigmentation through evolution of a gene regulatory module, Science, vol.339, pp.1423-1429, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00862170

G. Streisinger, Production of clones of homozygous diploid zebra fish (Brachydanio rerio), Nature, vol.291, pp.293-296, 1981.

M. L. Lamoreux, Pigment pattern formation in the medaka embryo, Pigment Cell Res, vol.18, pp.64-73, 2005.

A. P. Singh, Proliferation, dispersal and patterned aggregation of iridophores in the skin prefigure striped colouration of zebrafish, Nat. Cell Biol, vol.16, pp.607-621, 2014.

M. Goda, Rapid integumental color changes due to novel iridophores in the chameleon sand tilefish Hoplolatilus chlupatyi, Pigment Cell Melanoma Res, vol.30, pp.368-371, 2017.

M. F. Wucherer and N. K. Michiels, A fluorescent chromatophore changes the level of fluorescence in a reef fish, PLoS One, vol.7, p.18, 2012.

R. L. Lamason, SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Science (80-. ), vol.310, pp.1782-1786, 2005.

T. Lorin, Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806995

V. B. Baliga and C. J. Law, Cleaners among wrasses: Phylogenetics and evolutionary patterns of cleaning behavior within Labridae, Mol. Phylogenet. Evol, vol.94, pp.424-435, 2016.

P. F. Cowman and D. R. Bellwood, Coral reefs as drivers of cladogenesis: Expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots, J. Evol. Biol, vol.24, pp.2543-2562, 2011.

B. Frédérich, Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae), 2013.

, Am. Nat, vol.181, pp.94-113

B. Frédérich, Body shape convergence driven by small size optimum in marine angelfishes, Biol. Lett, vol.13, 2017.

F. Santini, A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes), Mol. Phylogenet. Evol, vol.66, pp.153-160, 2013.

F. Santini, A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes), Mol. Phylogenet. Evol, vol.69, pp.165-176, 2013.

R. Betancur-r, Phylogenetic classification of bony fishes, BMC Evol. Biol, vol.17, p.162, 2017.

G. Bernardi, Species boundaries, populations and colour morphs in the coral reef three-spot damselfish (Dascyllus trimaculatus) species complex, Proc. R. Soc. B Biol. Sci, vol.269, pp.599-605, 2002.

B. W. Bowen, Phylogeography of two Atlantic squirrelfishes (family Holocentridae): Exploring links between pelagic larval duration and population connectivity, Marine Biology, pp.899-913, 2006.

N. J. Marshall, Communication and camouflage with the same "bright" colours in reef fishes, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.355, pp.1243-1248, 2000.

J. A. Endler, Natural Selection on Color Patterns in Poecilia reticulata, Evolution (N. Y), vol.34, pp.76-91, 1980.

S. P. Mcrobert and J. Bradner, The influence of body coloration on shoaling preferences in fish, Anim. Behav, vol.56, pp.611-615, 1998.

W. N. Mcfarland, The influence of light on the twilight migrations of grunts, Environ. Biol. Fishes, vol.4, pp.9-22, 1979.

J. L. Kelley, Spots and stripes: ecology and colour pattern evolution in butterflyfishes, Proc. Biol. Sci, vol.280, 2013.

M. Stevens, The role of eyespots as anti-predator mechanisms, principally demonstrated in the Lepidoptera, Biological Reviews of the Cambridge Philosophical Society, vol.80, pp.573-588, 2005.

M. Gagliano, On the spot: The absence of predators reveals eyespot plasticity in a marine fish, Behav. Ecol, vol.19, pp.733-739, 2008.

M. Gagliano and M. Depczynski, Spot the Difference: Mimicry in a Coral Reef Fish, PLoS One, vol.8, p.37, 2013.

G. W. Barlow, The Attitude of Fish Eye-Lines in Relation to Body Shape and to Stripes and Bars, Copeia, vol.1972, p.4, 1972.

K. Kjernsmo, Adaptive constellations of protective marks: Eyespots, eye stripes and diversion of attacks by fish, Anim. Behav, vol.111, pp.189-195, 2016.

S. A. Price, Phylogenetic insights into the history and diversification of fishes on reefs, Coral Reefs, vol.34, pp.997-1009, 2015.

D. R. Robertson, Who Resembles Whom? Mimetic and Coincidental Look-Alikes among Tropical Reef Fishes, PLoS One, vol.8, p.41, 2013.

E. Moland, Ecology and evolution of mimicry in coral reef fishes, Oceanogr. Mar. Biol. an Annu. Rev, 2005.

J. E. Randall, A review of mimicry in marine fishes, Zoological Studies, pp.299-328, 2005.

C. P. Klingenberg, Morphological Integration and Developmental Modularity, Annu. Rev. Ecol. Evol. Syst, vol.39, pp.115-132, 2008.

M. Hirata, Pigment cell organization in the hypodermis of zebrafish, Dev. Dyn, vol.227, pp.497-503, 2003.

L. B. Patterson and D. M. Parichy, Interactions with Iridophores and the Tissue Environment Required for Patterning Melanophores and Xanthophores during Zebrafish Adult Pigment Stripe Formation, PLoS Genet, vol.9, pp.1-14, 2013.

F. J. Van-eeden, Genetic analysis of fin formation in the zebrafish, Danio rerio, Development, vol.123, pp.255-262, 1996.

P. Mahalwar, Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish, Science, vol.345, pp.1362-1366, 2014.

S. L. Johnson, Mitfa is required at multiple stages of melanocyte differentiation but not to establish the melanocyte stem cell, Dev. Biol, vol.350, pp.405-413, 2011.

S. K. Mcmenamin, Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish, Science, vol.345, pp.1358-61, 2014.

H. G. Frohnhöfer, Iridophores and their interactions with other chromatophores are required for stripe formation in zebrafish, Development, vol.140, pp.2997-3007, 2013.

A. Nakamasu, Interactions between zebrafish pigment cells responsible for the generation of Turing patterns, Pnas, vol.106, pp.8429-8434, 2009.

D. M. Parichy and J. M. Turner, Zebrafish puma mutant decouples pigment pattern and somatic metamorphosis, Dev. Biol, vol.256, pp.242-257, 2003.

S. Kondo and R. Asai, A reaction diffusion wave on the skin of the marine angelfish Pomacanthus, Nature, vol.376, pp.765-768, 1995.

V. Svetic, Sdf1a patterns zebrafish melanophores and links the somite and melanophore pattern defects in choker mutants, Development, vol.134, pp.1011-1022, 2007.

M. Goda, Integumental reddish-violet coloration owing to novel dichromatic chromatophores in the teleost fish, Pseudochromis diadema, Pigment Cell Melanoma Res, vol.24, pp.614-617, 2011.

M. Goda, Novel dichromatic chromatophores in the integument of the mandarin fish Synchiropus splendidus, Biol. Bull, vol.224, pp.14-17, 2013.

R. A. Barrio, Modeling the skin pattern of fishes, Phys. Rev. E -Stat. Nonlinear, Soft Matter Phys, vol.79, p.58, 2009.

S. Kondo and T. Miura, Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation, Science, vol.329, pp.1616-1620, 2010.

F. Cortesi, From crypsis to mimicry: changes in colour and the configuration of the visual system during ontogenetic habitat transitions in a coral reef fish, J. Exp. Biol, vol.219, pp.2545-2558, 2016.

L. Wang, In silico comparative transcriptome analysis of two color morphs of the common coral trout (Plectropomus leopardus), PLoS One, vol.10, p.61, 2015.

F. Cortesi, Phenotypic plasticity confers multiple fitness benefits to a mimic, Curr. Biol, vol.25, pp.949-954, 2015.

V. Messmer, Genetic and ecological characterisation of colour dimorphism in a coral reef fish, Environ. Biol. Fishes, vol.74, pp.175-183, 2005.

O. Puebla, Colour pattern as a single trait driving speciation in Hypoplectrus coral reef fishes?, Proc. R. Soc. B Biol. Sci, vol.274, pp.1265-1271, 2007.

B. G. Holt, Searching for speciation genes: Molecular evidence for selection associated with colour morphotypes in the caribbean reef fish genus hypoplectrus, PLoS One, vol.6, p.65, 2011.

O. Puebla, Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp, Serranidae). Mol. Ecol, vol.23, pp.5291-5303, 2014.

S. Picq, Population genomics of local adaptation versus speciation in coral reef fishes, Hypoplectrus spp, Serranidae). Ecol. Evol, vol.6, pp.2109-2124, 2016.

S. Jeong, Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution, Cell, vol.125, pp.1387-1399, 2006.

M. R. Servedio, Magic traits in speciation: "magic" but not rare?, Trends in Ecology and Evolution, vol.26, pp.389-397, 2011.

Y. Wakamatsu, The see-through medaka: A fish model that is transparent throughout life, Proc. Natl. Acad. Sci, vol.98, pp.10046-10050, 2001.

N. K. Michiels, Red fluorescence in reef fish: A novel signalling mechanism?, BMC Ecol, vol.8, p.71, 2008.

M. Goda and R. Fujii, Blue Chromatophores in Two Species of Callionymid Fish, Zoolog. Sci, vol.12, pp.811-813, 1995.

E. Ban, The signaling pathway in photoresponses that may be mediated by visual pigments in erythrophores of Nile tilapia, Pigment Cell Res, vol.18, pp.360-369, 2005.

D. C. Bennett and M. L. Lamoreux, The Color Loci of Mice -A Genetic Century, Pigment Cell Res, vol.16, pp.333-344, 2003.

M. Schartl, What is a vertebrate pigment cell?, Pigment Cell Melanoma Res, vol.29, pp.8-14, 2016.

L. M. San-jose and A. Roulin, Genomics of coloration in natural animal populations, Philos. Trans. R. Soc. B Biol. Sci, vol.372, 2017.

J. A. Lister, nacre encodes a zebrafish microphthalmia-related protein that regulates neural-crest-derived pigment cell fate, Development, vol.126, pp.3757-67, 1999.

L. Cal, BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of DorsalVentral Pigment Asymmetry in Fish, J. Exp. Zool. Part B Mol. Dev. Evol, 2017.

A. Fadeev, Zebrafish Leucocyte tyrosine kinase controls iridophore establishment, proliferation and survival, Pigment Cell Melanoma Res, vol.29, pp.284-296, 2016.

Y. Nagao, Sox5 Functions as a Fate Switch in Medaka Pigment Cell Development, PLoS Genet, vol.10, p.80, 2014.

Y. Nagao, Distinct interactions of Sox5 and Sox10 in fate specification of pigment cells in medaka and zebrafish, PLOS Genet, vol.14, p.1007260, 2018.

C. L. Mcgrath, Differential retention and divergent resolution of duplicate genes following whole-genome duplication, Genome Res, vol.24, pp.1665-1675, 2014.

S. Ohno, Evolution by gene duplication, p.83, 1970.

I. Braasch, Pigmentation pathway evolution after whole-genome duplication in fish, Genome Biol. Evol, vol.1, pp.479-493, 2009.

A. M. Turing, The Chemical Basis of Morphogenesis THE CHEMICAL BASIS OF MORPHOGENESIS, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.237, pp.37-72, 1952.

T. W. Hiscock and S. G. Megason, Mathematically guided approaches to distinguish models of periodic patterning, Development, vol.142, pp.409-419, 2015.

K. J. Painter, Stripe formation in juvenile Pomacanthus explained by a generalized Turing mechanism with chemotaxis, Proc. Natl. Acad. Sci, vol.96, pp.5549-5554, 1999.

M. Yamaguchi, Pattern regulation in the stripe of zebrafish suggests an underlying dynamic and autonomous mechanism, Proc. Natl. Acad. Sci. U. S. A, vol.104, pp.4790-4793, 2007.

S. Sick, WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism, Science, vol.314, pp.1447-1450, 2006.

M. P. Harris, Molecular evidence for an activator-inhibitor mechanism in development of embryonic feather branching, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.11734-11739, 2005.

T. Miura and K. Shiota, Depletion of FGF acts as a lateral inhibitory factor in lung branching morphogenesis in vitro, Mech. Dev, vol.116, pp.29-38, 2002.

I. Salazar-ciudad, Tooth patterning and evolution. , Current Opinion in Genetics and Development, vol.22, pp.585-592, 2012.

A. Abol-munafi, N. Norazmi-lokman, N. Asma, S. Sarmiza, and M. Abduh, , 2011.

, Histological study on the gonad of the protandrous anemonefish Amphiprion ocellaris, J Anim Vet Adv, vol.10, pp.3031-3036

K. Adams, Genomic Clues to the Ancestral Flowering Plant. Science (80-), vol.342, pp.1456-1457, 2013.

S. Ahn and S. D. Tanksley, Comparative linkage maps of the rice and maize genomes, Proc Natl Acad Sci U S A, vol.90, pp.7980-7984, 1993.

S. J. Ainsworth, R. L. Stanley, and D. Evans, Developmental stages of the Japanese quail, J Anat, vol.216, pp.3-15, 2010.

R. Albalat and C. Cañestro, Evolution by gene loss, Nat Rev Genet, vol.17, pp.379-391, 2016.

W. Albertin and P. Marullo, Polyploidy in fungi: evolution after whole-genome duplication, Proc R Soc B Biol Sci, vol.279, pp.2497-2509, 2012.

M. A. Alexandrou, B. A. Swartz, N. J. Matzke, and T. H. Oakley, Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae, 2013.

, Mol Phylogenet Evol, vol.69, pp.514-523

M. E. Alfaro, F. Santini, and C. D. Brock, Do reefs drive diversification in marine teleosts? Evidence from the pufferfish and their allies (Order Tetraodontiformes), Evolution (N Y), vol.61, pp.2104-2126, 2007.

B. M. Allen, The Results of Extirpation of the Anterior Lobe of the Hypophysis and of the Thyroid of Rana Pipiens Larvae, Science (80-), vol.44, p.755, 1916.

G. R. Allen, The Anemonefishes: Their Classification and Biology, 1972.

G. R. Allen, Damselfishes of the world, 1991.

C. J. Allender, O. Seehausen, M. E. Knight, G. F. Turner, and N. Maclean, Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration, Proc Natl Acad Sci, vol.100, pp.14074-14079, 2003.

F. W. Allendorf and R. G. Danzmann, Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout, Genetics, vol.145, p.1083, 1997.

G. R. Almany, M. L. Berumen, S. R. Thorrold, S. Planes, and G. P. Jones, Local Replenishment of Coral Reef Fish Populations in a Marine Reserve, Science (80-), vol.316, pp.742-744, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00170715

G. R. Almany, S. Planes, S. R. Thorrold, M. L. Berumen, M. Bode et al., Larval fish dispersal in a coral-reef seascape, Nat Ecol Evol, vol.1, p.148, 2017.

W. J. Alonso, Evolution of bright colours in animals: worlds of prohibition and oblivion, vol.4, p.115, 1000.

B. Altincicek, J. L. Kovacs, and N. M. Gerardo, Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae, Biol Lett, vol.8, pp.253-257, 2012.

A. L. Ambrosio, J. A. Boyle, A. E. Aradi, K. A. Christian, D. Pietro et al., TPC2 controls pigmentation by regulating melanosome pH and size, Proc Natl Acad Sci, vol.113, pp.5622-5627, 2016.

A. Amores, A. Force, Y. L. Yan, L. Joly, C. Amemiya et al., Zebrafish hox clusters and vertebrate genome evolution, Science, vol.282, pp.1711-1715, 1998.

G. D. Amoutzias, Y. He, J. Gordon, D. Mossialos, S. G. Oliver et al., Posttranslational regulation impacts the fate of duplicated genes, Proc Natl Acad Sci, vol.107, pp.2967-2971, 2010.

. Amundsen, Why are female birds ornamented?, Trends Ecol Evol, vol.15, p.149, 2000.

T. Amundsen and E. Forsgren, Male mate choice selects for female coloration in a fish, Proc Natl Acad Sci, vol.98, pp.13155-13160, 2001.

L. Anavy, M. Levin, S. Khair, N. Nakanishi, S. L. Fernandez-valverde et al., BLIND ordering of large-scale transcriptomic developmental timecourses, Development, vol.141, pp.1161-1166, 2014.

M. Andersson and L. W. Simmons, Sexual selection and mate choice, Trends Ecol Evol, vol.21, pp.296-302, 2006.

S. Aparicio, J. Chapman, E. Stupka, N. Putnam, J. Chia et al., WholeGenome Shotgun Assembly and Analysis of the Genome of Fugu rubripes, Science (80-), vol.297, pp.1301-1310, 2002.

, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Arabidopsis Genome Initiative, vol.408, pp.796-815, 2000.

L. Arnoult, K. Su, D. Manoel, C. Minervino, J. Magrina et al., , 2013.

, Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module, Science (80-), vol.339, pp.1423-1426

M. Arvedlund, T. M. Brolund, and L. E. Nielsen, Morphology and cytology of the olfactory organs in small juvenile Dascyllus aruanus and Amphiprion ocellaris (Pisces: Pomacentridae), J Mar Biol Assoc UK, vol.83, pp.1321-1326, 2003.

M. Arvedlund, I. Bundgaard, and L. E. Nielsen, Host imprinting in anemonefishes (Pisces: Pomacentridae): does it dictate spawning site preferences? Environ Biol fishes, pp.203-213, 2000.

M. Arvedlund, M. Mccormick, and T. Ainsworth, Effects of photoperiod on growth of larvae and juveniles of the anemonefish Amphiprion melanopus, WorldFish Cent, vol.23, pp.18-23, 2000.

M. Arvedlund, M. Mccormick, D. Fautin, and M. Bildsøe, Host recognition and possible imprinting in the anemonefish Amphiprion melanopus (Pisces:Pomacentridae), Mar Ecol Prog Ser, vol.188, pp.207-218, 1999.

J. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin et al., Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol.444, pp.171-178, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00090904

M. A. Avella, I. Olivotto, G. Gioacchini, F. Maradonna, and O. Carnevali, The role of fatty acids enrichments in the larviculture of false percula clownfish Amphiprion ocellaris, Aquaculture, vol.273, pp.87-95, 2007.

M. A. Avella, I. Olivotto, S. Silvi, A. R. Place, and O. Carnevali, Effect of dietary probiotics on clownfish: a molecular approach to define how lactic acid bacteria modulate development in a marine fish, Am J Physiol Integr Comp Physiol, vol.298, pp.359-371, 2010.

H. Badouin, J. Gouzy, C. J. Grassa, F. Murat, S. E. Staton et al., The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution, Nature, vol.546, pp.148-152, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01603287

J. T. Bagnara, Developmental Aspects of Vertebrate Chromatophores, Am Zool, vol.23, pp.465-478, 1983.

J. T. Bagnara, P. J. Fernandez, and R. Fujii, On the blue coloration of vertebrates, Pigment Cell Res, vol.20, pp.14-26, 2007.

J. T. Bagnara and E. M. Hadley, Chromatophores and Color Change. The Comparative Physiology of Animal Pigmentation, 1973.

J. T. Bagnara and J. Matsumoto, Comparative Anatomy and Physiology of Pigment Cells in Nonmammalian Tissues, The Pigmentary System, pp.11-59, 2006.

J. T. Bagnara, J. D. Taylor, and M. E. Hadley, The dermal chromatophore unit, J Cell Biol, vol.38, pp.67-79, 1968.

C. C. Baldwin, The phylogenetic significance of colour patterns in marine teleost larvae, Zool J Linn Soc, vol.168, pp.496-563, 2013.

R. J. Balment, W. Lu, E. Weybourne, and J. M. Warne, Arginine vasotocin a key hormone in fish physiology and behaviour: A review with insights from mammalian models, Gen Comp Endocrinol, vol.147, pp.9-16, 2006.

E. Ban, A. Kasai, M. Sato, A. Yokozeki, O. Hisatomi et al., The signaling pathway in photoresponses that may be mediated by visual pigments in erythrophores of Nile tilapia, Pigment Cell Res, vol.18, pp.360-369, 2005.

Z. Bar-joseph, A. Gitter, and I. Simon, Studying and modelling dynamic biological processes using time-series gene expression data, Nat Rev Genet, vol.13, pp.552-564, 2012.

M. Baron and I. Yanai, It's about time: studying gene regulatory programs across serial organs, Genome Biol, vol.18, p.30, 2017.

A. S. Barreira, M. G. Lagorio, D. A. Lijtmaer, S. C. Lougheed, and P. L. Tubaro, Fluorescent and ultraviolet sexual dichromatism in the blue-winged parrotlet (A Kitchener, J Zool, vol.288, pp.135-142, 2012.

G. S. Barsh, What Controls Variation in Human Skin Color?, PLoS Biol, vol.1, p.27, 2003.

H. B. Bates, Contributions to an insect fauna of the Amazon valley (Lepidoptera: Heliconidae), Trans Linn Soc London, vol.23, pp.495-556, 1862.

W. Bateson, Mendel's principles of heredity, 1902.

A. Baumel, M. L. Ainouche, and J. E. Levasseur, Molecular investigations in populations of Spartina anglica C.E. Hubbard (Poaceae) invading coastal Brittany (France), Mol Ecol, vol.10, pp.1689-1701, 2001.

C. W. Beck, , 1997.

R. Beldade, S. J. Holbrook, R. J. Schmitt, S. Planes, D. Malone et al., , 2012.

, Larger female fish contribute disproportionately more to self-replenishment

, Proc R Soc B Biol Sci, vol.279, pp.2116-2121

D. R. Bellwood, What are reef fishes? -Comment on the report by D. R. Robertson: Do coral-reef fish faunas have a distinctive taxonomic structure?, Coral Reefs, vol.17, pp.187-189, 1998.

D. R. Bellwood, T. P. Hughes, S. R. Connolly, and J. Tanner, Environmental and geometric constraints on Indo-Pacific coral reef biodiversity, Ecol Lett, vol.8, p.643, 2005.

D. R. Bellwood, T. P. Hughes, C. Folke, and M. Nyström, Confronting the coral reef crisis, Nature, vol.429, pp.827-860, 2004.

Y. Benjamini and T. P. Speed, Summarizing and correcting the GC content bias in high-throughput sequencing, Nucleic Acids Res, vol.40, pp.72-72, 2012.

D. C. Bennett and M. L. Lamoreux, The Color Loci of Mice -A Genetic Century, Pigment Cell Res, vol.16, pp.333-344, 2003.

J. L. Bergé-lefranc, G. Cartouzou, Y. Malthiéry, F. Perrin, B. Jarry et al., , 1981.

M. F. Berger, J. Z. Levin, K. Vijayendran, A. Sivachenko, X. Adiconis et al.,

, Integrative analysis of the melanoma transcriptome, Genome Res, vol.20, pp.413-427

G. Bernardi, Monophyletic origin of brood care in damselfishes, Mol Phylogenet Evol, vol.59, pp.245-248, 2011.

G. Bernardi, N. L. Crane, G. C. Longo, and A. L. Quiros, The ecology of Altrichthys azurelineatus and A. curatus, two damselfishes that lack a pelagic larval phase, Environ Biol Fishes, vol.100, pp.111-120, 2017.

C. Berthelot, F. Brunet, D. Chalopin, A. Juanchich, M. Bernard et al., , 2014.

M. Besson, P. Salis, V. Laudet, and D. Lecchini, Complete and rapid reversal of the body color pattern in juveniles of the convict surgeonfish Acanthurus triostegus at Moorea Island (French Polynesia), Coral Reefs, vol.37, pp.31-35, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01628304

. Betancur-r-r, E. O. Wiley, G. Arratia, A. Acero, N. Bailly et al., , 2017.

, Phylogenetic classification of bony fishes, BMC Evol Biol, vol.17, p.162

P. Béziers, A. Ducrest, C. Simon, and A. Roulin, Circulating testosterone and feather-gene expression of receptors and metabolic enzymes in relation to melanin-based colouration in the barn owl, Gen Comp Endocrinol, vol.250, pp.36-45, 2017.

A. Bianco and B. Kim, Deiodinases: implications of the local control of thyroid hormone action, J Clin Invest, vol.116, pp.2571-2579, 2006.

J. A. Birchler, N. C. Riddle, D. L. Auger, and R. A. Veitia, Dosage balance in gene regulation: biological implications, Trends Genet, vol.21, pp.219-226, 2005.

J. Blaxter, Pattern and Variety in Development, The Physiology of Developing Fish, pp.1-58, 1988.

J. A. Bolker, Model systems in developmental biology, BioEssays, vol.17, p.451, 1995.

J. Bolker, Model organisms: There's more to life than rats and flies, Nature, vol.491, pp.31-33, 2012.

G. C. Boorse and R. J. Denver, Expression and hypophysiotropic actions of corticotropin-releasing factor in Xenopus laevis, Gen Comp Endocrinol, vol.137, p.272, 2004.

J. A. Botía, J. Vandrovcova, P. Forabosco, S. Guelfi, D. Sa et al., An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks, BMC Syst Biol, vol.11, p.47, 2017.

L. Boto, Horizontal gene transfer in the acquisition of novel traits by metazoans, Proc R Soc B Biol Sci, vol.281, 2014.

C. Bower, D. Turner, and R. Biever, A standardized method of propagating the marine fish parasite, Amyloodinium ocellatum, J Parasitol, vol.73, pp.85-88, 1887.

I. Braasch, F. Brunet, J. Volff, and M. Schartl, Pigmentation pathway evolution after whole-genome duplication in fish, Genome Biol Evol, vol.1, pp.479-493, 2009.

I. Braasch, A. R. Gehrke, J. J. Smith, K. Kawasaki, T. Manousaki et al., The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons, Nat Genet, vol.48, pp.427-437, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01595410

I. Braasch, S. M. Peterson, T. Desvignes, B. M. Mccluskey, P. Batzel et al., A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo, J Exp Zool Part B Mol Dev Evol, vol.324, pp.316-341, 2015.

I. Braasch and J. H. Postlethwait, The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genome, Proc Natl Acad Sci, vol.108, pp.47-48, 2011.

I. Braasch, M. Schartl, and J. Volff, Evolution of pigment synthesis pathways by gene and genome duplication in fish, BMC Evol Biol, vol.7, p.74, 2007.

I. Braasch, J. N. Volff, and M. Schartl, The evolution of teleost pigmentation and the fish-specific genome duplication, J Fish Biol, vol.73, pp.1891-1918, 2008.

D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field et al., Evolution of flower color pattern through selection on regulatory small RNAs, Science (80-), vol.358, pp.925-928, 2017.

N. L. Bray, H. Pimentel, P. Melsted, and L. Pachter, Near-optimal probabilistic RNA-seq quantification, Nat Biotechnol, vol.34, pp.525-527, 2016.

M. Brenner and V. J. Hearing, The Protective Role of Melanin Against UV Damage in Human Skin ?, Photochem Photobiol, vol.84, pp.539-549, 2008.

L. J. Bright, J. Gout, and M. Lynch, Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in Paramecium species (PJ Brennwald, Mol Biol Cell, vol.28, pp.1101-1110, 2017.

T. M. Brolund, L. E. Nielsen, and M. Arvedlund, Do juvenile Amphiprion ocellaris (Pisces: Pomacentridae) recognize conspecifics by chemical or visual cues?, J Mar Biol Assoc UK, vol.83, p.0025315403008385, 2003.

R. M. Brooker and D. L. Dixson, Assessing the role of olfactory cues in the early life history of coral reef fish: current methods and future directions, Chemical Signals in Vertebrates, pp.229-244, 2016.

D. D. Brown, The role of thyroid hormone in zebrafish and axolotl development, Proc Natl Acad Sci U S A, vol.94, pp.13011-13017, 1997.

D. D. Brown and L. Cai, Amphibian metamorphosis, Dev Biol, vol.306, pp.20-33, 2007.

R. Brumbaugh, Protecting Million Dollar Reefs is Key to Sustaining Global Tourism, 2017.

F. G. Brunet, R. Crollius, H. Paris, M. Aury, J. Gibert et al., , 2006.

, Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes, Mol Biol Evol, vol.23, pp.1808-1816

F. G. Brunet, J. Volff, and M. Schartl, Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates, Genome Biol Evol, vol.8, pp.1600-1613, 2016.

R. Burgus, T. F. Dunn, D. Desiderio, and R. Guillemin, Molecular structure of the hypothalamic hypophysiotropic TRF factor of ovine origin: mass spectrometry demonstration of the PCA-His-Pro-NH2 sequence, C R Acad Sci Hebd Seances Acad Sci D, vol.269, pp.1870-1873, 1969.

P. Buston, Size and growth modification in clownfish, Nature, vol.424, pp.145-146, 2003.

P. M. Buston and M. B. García, An extraordinary life span estimate for the clown anemonefish Amphiprion percula, J Fish Biol, vol.70, pp.1710-1719, 2007.

L. Cai and D. D. Brown, Expression of type II iodothyronine deiodinase marks the time that a tissue responds to thyroid hormone-induced metamorphosis in Xenopus laevis, Dev Biol, vol.266, pp.87-95, 2004.

L. Cal, M. Megías, -. Cerdá, I. Braasch, and J. Rotllant, BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish, J Exp Zool Part B Mol Dev Evol, 2017.

M. A. Campinho, M. Galay-burgos, G. E. Sweeney, and D. M. Power, Coordination of deiodinase and thyroid hormone receptor expression during the larval to juvenile transition in sea bream (Sparus aurata, Linnaeus), Gen Comp Endocrinol, vol.165, pp.181-194, 2010.

Z. Cao, Y. Yu, Y. Wu, P. Hao, Z. Di et al., , 2013.

T. Caro, The Adaptive Significance of Coloration in Mammals, Bioscience, vol.55, pp.125-136, 2005.

T. Caro, Wallace on Coloration: Contemporary Perspective and Unresolved Insights, Trends Ecol Evol, vol.32, pp.23-30, 2017.

D. Casane and S. Rétaux, Evolutionary Genetics of the Cavefish Astyanax mexicanus, pp.117-159, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01366160

L. Casas, F. Saborido-rey, T. Ryu, C. Michell, T. Ravasi et al., Sex Change in Clownfish: Molecular Insights from, Transcriptome Analysis. Sci Rep, vol.6, p.35461, 2016.

L. Casas, P. Saenz-agudelo, and X. Irigoien, High-Throughput Sequencing and Linkage Mapping of a Clownfish Genome Provide Insights on the Distribution of Molecular Players Involved in Sex Change, Sci Rep, vol.8, p.4073, 2018.

R. M. Ceinos, R. Guillot, R. N. Kelsh, J. M. Cerdá-reverter, and J. Rotllant, Pigment patterns in adult fish result from superimposition of two largely independent pigmentation mechanisms, Pigment Cell Melanoma Res, vol.28, pp.196-209, 2015.

D. Chalopin and J. Volff, , 2017.

S. Chamala, A. S. Chanderbali, J. P. Der, T. Lan, B. Walts et al., , 2013.

, Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella, Science (80-), vol.342, pp.1516-1517

B. A. Chapman, J. E. Bowers, F. A. Feltus, and A. H. Paterson, Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication, Proc Natl Acad Sci, vol.103, pp.2730-2735, 2006.

N. Chaudhari and W. Hahn, Genetic expression in the developing brain, Science (80-), vol.220, pp.924-928, 1983.

Z. J. Chen, Molecular mechanisms of polyploidy and hybrid vigor, Trends Plant Sci, vol.15, pp.57-71, 2010.

T. Chen and C. Hsieh, Fighting Nemo: Effect of 17?-ethinylestradiol (EE2) on aggressive behavior and social hierarchy of the false clown anemonefish Amphiprion ocellaris, Mar Pollut Bull, vol.124, pp.760-766, 2017.

S. Chen, R. M. Robertson, and C. W. Hawryshyn, Possible Involvement of Cone Opsins in Distinct Photoresponses of Intrinsically Photosensitive Dermal Chromatophores in Tilapia Oreochromis niloticus, PLoS One, vol.8, p.70342, 2013.

S. Chen, X. C. Troje, N. F. Robertson, R. M. Hawryshyn, and C. W. , Functional characterisation of the chromatically antagonistic photosensitive mechanism of erythrophores in the tilapia Oreochromis niloticus, J Exp Biol, vol.218, pp.748-756, 2015.

K. L. Cheney, C. Newport, E. C. Mcclure, and N. J. Marshall, Colour vision and response bias in a coral reef fish, J Exp Biol, vol.216, pp.2967-2973, 2013.

J. L. Cherry, Expression Level, Evolutionary Rate, and the Cost of Expression, Genome Biol Evol, vol.2, pp.757-769, 2010.

J. H. Choat and D. R. Bellwood, Reef Fishes: Their History and Evolution, The Ecology of Fishes on Coral Reefs, pp.39-66, 1991.

J. T. Clarke, G. T. Lloyd, and M. Friedman, Little evidence for enhanced phenotypic evolution in early teleosts relative to their living fossil sister group, Proc Natl Acad Sci, vol.113, pp.11531-11536, 2016.

S. Clement, J. Lichtenbert, and C. Kohler, Stripping clowns: induced meristic changes in common clownfish (Amphiprion ocellaris), 2001.

J. Clobert, M. Baguette, T. G. Benton, and J. M. Bullock, Dispersal ecology and evolution, 2012.

N. Cloonan, A. Forrest, G. Kolle, B. Gardiner, G. J. Faulkner et al.,

, Nat Methods, vol.5, pp.613-619

T. Clutton-brock, We do not need a Sexual Selection 2.0-nor a theory of Genial Selection, Anim Behav, vol.79, pp.7-10, 2010.

C. Cobbs, J. Heath, J. O. Stireman, and P. Abbot, Carotenoids in unexpected places: Gall midges, lateral gene transfer, and carotenoid biosynthesis in animals, Mol Phylogenet Evol, vol.68, pp.221-228, 2013.

, Emerging Model Organisms: A Laboratory Manual, 2010.

O. Colleye, B. Frederich, P. Vandewalle, M. Casadevall, and E. Parmentier, , 2009.

, Agonistic sounds in the skunk clownfish Amphiprion akallopisos : size-related variation in acoustic features, J Fish Biol, vol.75, pp.908-916

O. Colleye, E. Iwata, and E. Parmentier, Clownfishes, Biology of Damselfishes, pp.246-266, 2016.
URL : https://hal.archives-ouvertes.fr/hal-00722771

O. Colleye and E. Parmentier, Overview on the Diversity of Sounds Produced by Clownfishes (Pomacentridae): Importance of Acoustic Signals in Their Peculiar Way of Life (SCF Neuhauss, PLoS One, vol.7, p.49179, 2012.

O. Colleye, P. Vandewalle, D. Lanterbecq, D. Lecchini, and E. Parmentier, Interspecific variation of calls in clownfishes: degree of similarity in closely related species, BMC Evol Biol, vol.11, p.365, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00722771

G. C. Conant, J. A. Birchler, and J. C. Pires, Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time, Curr Opin Plant Biol, vol.19, pp.91-98, 2014.

G. C. Conant and K. H. Wolfe, Turning a hobby into a job: How duplicated genes find new functions, Nat Rev Genet, vol.9, pp.938-950, 2008.

A. Conesa, P. Madrigal, S. Tarazona, D. Gomez-cabrero, A. Cervera et al., A survey of best practices for RNA-seq data analysis, Genome Biol, vol.17, p.13, 2016.

W. J. Cooper and M. W. Westneat, Form and function of damselfish skulls: rapid and repeated evolution into a limited number of trophic niches, BMC Evol Biol, vol.9, p.24, 2009.

F. Cortesi, W. E. Feeney, M. Ferrari, P. A. Waldie, G. Phillips et al., Phenotypic Plasticity Confers Multiple Fitness Benefits to a Mimic, Curr Biol, vol.25, pp.949-954, 2015.

F. Cortesi, Z. Musilová, S. M. Stieb, N. S. Hart, U. E. Siebeck et al., From crypsis to mimicry: changes in colour and the configuration of the visual system during ontogenetic habitat transitions in a coral reef fish, J Exp Biol, vol.219, pp.2545-2558, 2016.

R. Costanza, R. De-groot, P. Sutton, S. Van-der-ploeg, S. J. Anderson et al., Changes in the global value of ecosystem services, Glob Environ Chang, vol.26, pp.152-158, 2014.

H. Cott, Adaptive Coloration in Animals, 1940.

R. K. Cowen, C. B. Paris, and A. Srinivasan, Scaling of Connectivity in Marine Populations, Science (80-), vol.311, pp.522-527, 2005.

R. K. Cowen and S. Sponaugle, Larval Dispersal and Marine Population Connectivity, Annu Rev Mar Sci, vol.1, pp.443-66, 2009.

P. F. Cowman and D. R. Bellwood, Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots, J Evol Biol, vol.24, pp.2543-2562, 2011.

N. G. Crawford, D. E. Kelly, M. Hansen, M. H. Beltrame, S. Fan et al., Loci associated with skin pigmentation identified in African populations, Science, vol.80, p.8433, 2017.

K. Curran, J. A. Lister, G. R. Kunkel, A. Prendergast, D. M. Parichy et al., Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest, Dev Biol, vol.344, pp.107-118, 2010.

I. C. Cuthill, W. L. Allen, K. Arbuckle, B. Caspers, G. Chaplin et al., The biology of color, Science, p.221, 2017.

I. C. Cuthill, M. Stevens, J. Sheppard, T. Maddocks, C. A. Párraga et al., Disruptive coloration and background pattern matching, Nature, vol.434, pp.72-74, 2005.

L. D&apos;alba, L. Kieffer, and M. D. Shawkey, Relative contributions of pigments and biophotonic nanostructures to natural color production: a case study in budgerigar (Melopsittacus undulatus) feathers, J Exp Biol, vol.215, pp.1272-1277, 2012.

S. D&apos;mello, G. Finlay, B. Baguley, and M. Askarian-amiri, Signaling Pathways in Melanogenesis, Int J Mol Sci, vol.17, p.1144, 2016.

C. Darwin, The Variation of Animals and Plants Under Domestication, 1868.

C. Darwin, The Descent of Man, and Selection in Relation to Sex, 1871.

L. David, S. Blum, M. Feldman, U. Lavi, and J. Hillel, Recent Duplication of the Common Carp (Cyprinus carpio L.) Genome as Revealed by Analyses of Microsatellite Loci, Mol Biol Evol, vol.20, pp.1425-1434, 2003.

J. Davis and D. Petrov, Do disparate mechanisms of duplication add similar genes to the genome?, Trends Genet, vol.21, pp.548-551, 2005.

G. De&apos;ath, K. E. Fabricius, H. Sweatman, and M. Puotinen, The 27-year decline of coral cover on the Great Barrier Reef and its causes, Proc Natl Acad Sci, vol.109, pp.17995-17999, 2012.

R. Deangelis, J. Gogola, L. Dodd, and J. S. Rhodes, Opposite effects of nonapeptide antagonists on paternal behavior in the teleost fish Amphiprion ocellaris, Horm Behav, vol.90, pp.113-119, 2017.

R. S. Deangelis and J. S. Rhodes, Sex Differences in Steroid Hormones and Parental Effort across the Breeding Cycle in Amphiprion ocellaris, Copeia, vol.104, pp.586-593, 2016.

P. Dehal and J. L. Boore, Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate (P Holland, PLoS Biol, vol.3, p.314, 2005.

B. Demeneix, Cocktail toxique -Comment les perturbateurs endocriniens empoisonnent notre cerveau, 2017.

S. Dennenmoser, F. J. Sedlazeck, E. Iwaszkiewicz, X. Li, J. Altmüller et al., Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin, Mol Ecol, vol.26, pp.4712-4724, 2017.

R. J. Denver, Several hypothalamic peptides stimulate in vitro thyrotropin secretion by pituitaries of anuran amphibians, Gen Comp Endocrinol, vol.72, p.383, 1988.

N. Dhayanithi, T. Kumar, and K. Kathiresan, Effect of neem extract against the bacteria isolated from marine fish, J Env Biol, vol.31, pp.409-412, 2010.

D. Dickson, Gene estimate rises as US and UK discuss freedom of access, Nature, vol.401, pp.311-311, 1999.

I. Djurdjevi?, M. E. Kreft, S. Bajec, and S. , Comparison of pigment cell ultrastructure and organisation in the dermis of marble trout and brown trout, and first description of erythrophore ultrastructure in salmonids, J Anat, vol.227, pp.583-595, 2015.

S. Dodsworth, M. W. Chase, and A. R. Leitch, Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?, Bot J Linn Soc, vol.180, pp.1-5, 2016.

P. J. Doherty, Variable replenishment and the dynamics of reef fish populations, Coral Reef Fishes: Dynamics and Diversity in a Complex Ecosystem, pp.327-355, 2002.

E. T. Domyan and M. D. Shapiro, Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation, Dev Biol, vol.427, pp.241-250, 2017.

P. Donoghue and M. Purnell, Genome duplication, extinction and vertebrate evolution, Trends Ecol Evol, vol.20, pp.312-319, 2005.

C. M. Dooley, A. Mongera, B. Walderich, and C. Nusslein-volhard, On the embryonic origin of adult melanophores: the role of ErbB and Kit signalling in establishing melanophore stem cells in zebrafish, Development, vol.140, pp.1003-1013, 2013.

N. M. Le-douarin and E. Dupin, Multipotentiality of the neural crest, Curr Opin Genet Dev, vol.13, pp.529-536, 2003.

J. A. Doudna and E. Charpentier, The new frontier of genome engineering with CRISPR-Cas9, Science (80-), vol.346, pp.1258096-1258096, 2014.

G. M. Douglas, G. Gos, K. A. Steige, A. Salcedo, K. Holm et al., , 2015.

, Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris, Proc Natl Acad Sci, vol.112, pp.2806-2811

A. N. Dreiss, R. Séchaud, P. Béziers, N. Villain, M. Genoud et al., , 2016.

, Social huddling and physiological thermoregulation are related to melanism in the nocturnal barn owl, Oecologia, vol.180, pp.371-381

D. Duboule, Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony, Dev, pp.135-177, 1994.

A. Ducrest, L. Keller, and A. Roulin, Pleiotropy in the melanocortin system, coloration and behavioural syndromes, Trends Ecol Evol, vol.23, pp.502-510, 2008.

B. Dujon, The yeast genome project: what did we learn, Trends Genet, vol.12, pp.263-270, 1996.

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.430, pp.35-44, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00104411

J. K. Elliott, S. C. Lougheed, B. Bateman, L. K. Mcphee, and P. T. Boag, Molecular phylogenetic evidence for the evolution of specialization in anemonefishes, Proc R Soc B Biol Sci, vol.266, pp.677-685, 1999.

S. B. Emerson, T. A. Cooper, and J. R. Ehleringer, Convergence in Reflectance Spectra Among Treefrogs, Funct Ecol, vol.4, p.47, 1990.

P. Ensminger, Life Under the Sun, 2001.

D. S. Eom, E. J. Bain, L. B. Patterson, M. E. Grout, and D. M. Parichy, Long-distance communication by specialized cellular projections during pigment pattern development and evolution, 2015.

D. S. Eom and D. M. Parichy, A macrophage relay for long-distance signaling during postembryonic tissue remodeling, Science (80-), vol.355, pp.1317-1320, 2017.

R. M. Evans and D. J. Mangelsdorf, Nuclear Receptors, RXR, and the Big Bang, Cell, vol.157, pp.255-266, 2014.

B. D. Eyre, T. Cyronak, P. Drupp, D. Carlo, E. H. Sachs et al., Coral reefs will transition to net dissolving before end of century, Science, vol.80, pp.908-911, 2018.

R. I. Eytan, B. R. Evans, A. Dornburg, A. R. Lemmon, E. M. Lemmon et al., Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment, BMC Evol Biol, vol.15, p.113, 2015.

D. Fautin and G. R. Allen, Field Guide to Anemone Fishes and Their Host Sea Anemones, 1992.

D. Fautin and G. R. Allen, Anemone fishes and their host sea anemones, 1997.

J. Feitosa, A. M. Concentino, S. F. Teixeira, and B. P. Ferreira, Food resource use by two territorial damselfish (Pomacentridae: Stegastes) on South-Western Atlantic algal-dominated reefs, J Sea Res, vol.70, pp.42-49, 2012.

S. Ferraresso, A. Bonaldo, L. Parma, S. Cinotti, P. Massi et al., Exploring the larval transcriptome of the common sole (Solea solea L.), BMC Genomics, vol.14, p.315, 2013.

S. D. Ferris and G. S. Whitt, Duplicate gene expression in diploid and tetraploid loaches (Cypriniformes, Cobitidae), Biochem Genet, vol.15, pp.1097-112, 1977.

R. Fisher, The Genetical Theory of Natural Selection, 1958.

R. Fisher, Swimming speeds of larval coral reef fishes: Impacts on selfrecruitment and dispersal, Mar Ecol Prog Ser, vol.285, pp.223-232, 2005.

R. Fisher, D. Bellwood, and S. Job, Development of swimming abilities in reef fish larvae, Mar Ecol Prog Ser, vol.202, pp.163-173, 2000.

R. Fisher, J. M. Leis, D. L. Clark, and S. K. Wilson, Critical swimming speeds of latestage coral reef fish larvae: variation within species, among species and between locations, Mar Biol, vol.147, pp.1201-1212, 2005.

D. A. Fitzpatrick, Horizontal gene transfer in fungi, FEMS Microbiol Lett, vol.329, pp.1-8, 2012.

V. C. Fleisch, H. B. Schonthaler, J. Von-lintig, and S. Neuhauss, Subfunctionalization of a Retinoid-Binding Protein Provides Evidence for Two Parallel Visual Cycles in the Cone-Dominant Zebrafish Retina, J Neurosci, vol.28, pp.8208-8216, 2008.

J. Flot, B. Hespeels, X. Li, B. Noel, I. Arkhipova et al., , 2013.

, Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga, Nature, vol.500, pp.453-457

A. Force, M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al., , 1999.

, Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, pp.1531-1576

R. H. Fraser and D. J. Currie, The Species Richness-Energy Hypothesis in a System Where Historical Factors Are Thought to Prevail: Coral Reefs, Am Nat, vol.148, pp.138-159, 1996.

B. Frédérich, G. Fabri, G. Lepoint, P. Vandewalle, and E. Parmentier, Trophic niches of thirteen damselfishes (Pomacentridae) at the Grand Récif of Toliara, Madagascar. Ichthyol Res, vol.56, pp.10-17, 2009.

B. Frédérich and E. Parmentier, Biology of Damselfishes, 2016.

B. Frédérich, L. Sorenson, F. Santini, G. J. Slater, and M. E. Alfaro, Iterative Ecological Radiation and Convergence during the Evolutionary History of Damselfishes (Pomacentridae), Am Nat, vol.181, pp.94-113, 2013.

M. Freeling and B. C. Thomas, Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity, Genome Res, vol.16, pp.805-814, 2006.

H. W. Fricke, Individual partner recognition in fish: Field studies onAmphiprion bicinctus, Naturwissenschaften, vol.60, pp.204-204, 1973.

H. W. Fricke, Mating System, Resource Defence and Sex Change in the Anemonefish Amphiprion akallopisos, Z Tierpsychol, vol.50, pp.313-326, 1979.

H. W. Fricke and S. Fricke, Monogamy and sex change by aggressive dominance in coral reef fish, Nature, vol.266, pp.830-832, 1977.

H. Fricke and S. Holzberg, Social units and hermaphroditism in a pomacentrid fish, Naturwissenschaften, vol.61, pp.367-368, 1974.

R. Friedman and A. L. Hughes, The Temporal Distribution of Gene Duplication Events in a Set of Highly Conserved Human Gene Families, Mol Biol Evol, vol.20, pp.154-161, 2003.

C. Frith, Charles Darwin's Life With Birds: His Complete Ornithology, 2016.

R. Froese and D. Pauly, , 2018.

I. Fuentes, S. Stegemann, H. Golczyk, D. Karcher, and R. Bock, Horizontal genome transfer as an asexual path to the formation of new species, Nature, vol.511, pp.232-235, 2014.

R. Fujii, Cytophysiology of Fish Chromatophores, International Review of Cytology, pp.191-255, 1993.

T. Fukuzawa, Unusual leucophore-like cells specifically appear in the lineage of melanophores in the periodic albino mutant of Xenopus laevis, Pigment Cell Res, vol.17, pp.252-261, 2004.

T. Fukuzawa, Unusual development of light-reflecting pigment cells in intact and regenerating tail in the periodic albino mutant of Xenopus laevis, Cell Tissue Res, vol.342, pp.53-66, 2010.

J. Fumey, H. Hinaux, C. Noirot, C. Thermes, S. Rétaux et al., Evidence for late Pleistocene origin of Astyanax mexicanus cavefish, BMC Evol Biol, vol.18, p.43, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01828523

J. D. Furlow and E. S. Neff, A developmental switch induced by thyroid hormone: Xenopus laevis metamorphosis, Trends Endocrinol Metab, vol.17, pp.40-47, 2006.

G. Gachelin, De l'animal expérimental au modèle en recherche biomédicale, Rev Philos France Let, vol.133, p.319, 2008.

M. H. Gallardo, J. W. Bickham, R. L. Honeycutt, R. A. Ojeda, and N. Köhler, Discovery of tetraploidy in a mammal, Nature, vol.401, pp.341-341, 1999.

I. Galván and F. Solano, Bird Integumentary Melanins: Biosynthesis, Forms, Function and Evolution, Int J Mol Sci, vol.17, p.520, 2016.

M. Garber, M. G. Grabherr, M. Guttman, and C. Trapnell, Computational methods for transcriptome annotation and quantification using RNA-seq, Nat Methods, vol.8, pp.469-477, 2011.

. Gardner-t-a, I. M. Côté, A. Grant, and A. R. Watkinson, Long-term regionwide declines in Caribbean corals, Science, vol.301, pp.958-960, 2003.

B. S. Gaut and J. F. Doebley, DNA sequence evidence for the segmental allotetraploid origin of maize, Proc Natl Acad Sci U S A, vol.94, pp.6809-6823, 1997.

E. N. Geissler, M. A. Ryan, and D. E. Housman, The dominant-white spotting (W) locus of the mouse encodes the c-kit proto-oncogene, Cell, vol.55, pp.185-192, 1988.

A. Genin, G. Yahel, M. Reidenbach, S. Monismith, and J. Koseff, Intense Benthic Grazing on Phytoplankton in Coral Reefs Revealed Using the Control Volume Approach, Oceanography, vol.15, pp.90-96, 2002.

G. Gerlach, J. Atema, M. J. Kingsford, K. P. Black, and V. Miller-sims, Smelling home can prevent dispersal of reef fish larvae, Proc Natl Acad Sci, vol.104, pp.858-863, 2007.

R. S. Ginger, S. E. Askew, R. M. Ogborne, S. Wilson, D. Ferdinando et al., SLC24A5 Encodes a trans -Golgi Network Protein with Potassiumdependent Sodium-Calcium Exchange Activity That Regulates Human Epidermal Melanogenesis, J Biol Chem, vol.283, pp.5486-5495, 2008.

S. Glasauer and S. Neuhauss, Whole-genome duplication in teleost fishes and its evolutionary consequences, Mol Genet Genomics, vol.289, pp.1045-1060, 2014.

M. Goda, Rapid integumental color changes due to novel iridophores in the chameleon sand tilefish Hoplolatilus chlupatyi, Pigment Cell Melanoma Res, vol.30, pp.368-371, 2017.

M. Goda and R. Fujii, Blue Chromatophores in Two Species of Callionymid Fish, Zoolog Sci, vol.12, pp.811-813, 1995.

M. Goda, Y. Fujiyoshi, M. Sugimoto, and R. Fujii, Novel Dichromatic Chromatophores in the Integument of the Mandarin Fish Synchiropus splendidus, Biol Bull, vol.224, pp.14-17, 2013.

M. Goda, M. Ohata, H. Ikoma, Y. Fujiyoshi, M. Sugimoto et al., Integumental reddish-violet coloration owing to novel dichromatic chromatophores in the teleost fish, Pseudochromis diadema. Pigment Cell Melanoma Res, vol.24, pp.614-617, 2011.

J. Godin and H. E. Mcdonough, Predator preference for brightly colored males in the guppy: a viability cost for a sexually selected trait, Behav Ecol, vol.14, pp.194-200, 2003.

A. Goffeau, B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon et al., Life with 6000 Genes, Science (80-), vol.274, pp.546-567, 1996.

N. Gompel, B. Prud&apos;homme, P. J. Wittkopp, V. A. Kassner, and S. B. Carroll, Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila, Nature, vol.433, pp.481-487, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00310898

R. Gopurappilly, S. Ogawa, and I. S. Parhar, Functional Significance of GnRH and Kisspeptin, and Their Cognate Receptors in Teleost Reproduction, Front Endocrinol, p.4, 2013.

J. Gout, D. Kahn, and L. Duret, The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00539474

, PLoS Genet, vol.6, p.1000944

J. Gout and M. Lynch, Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization, Mol Biol Evol, vol.32, pp.2141-2148, 2015.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., , 2011.

, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat Biotechnol, vol.29, pp.644-652

E. O. Gracheva, N. T. Ingolia, Y. M. Kelly, J. F. Cordero-morales, G. Hollopeter et al., Molecular basis of infrared detection by snakes, Nature, vol.464, pp.1006-1011, 2010.

L. A. Graham, J. Li, W. S. Davidson, and P. L. Davies, Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes, BMC Evol Biol, vol.12, p.190, 2012.

L. A. Graham, S. C. Lougheed, K. V. Ewart, and P. L. Davies, Lateral Transfer of a Lectin-Like Antifreeze Protein Gene in Fishes (M Isalan, PLoS One, vol.3, p.2616, 2008.

S. A. Green and M. E. Bronner, Gene duplications and the early evolution of neural crest development, Semin Cell Dev Biol, vol.24, pp.95-100, 2013.

A. L. Green, A. P. Maypa, G. R. Almany, K. L. Rhodes, R. Weeks et al., Larval dispersal and movement patterns of coral reef fishes, and implications for marine reserve network design, Biol Rev, vol.90, pp.1215-1247, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01334353

S. A. Green, M. Simoes-costa, and M. E. Bronner, Evolution of vertebrates as viewed from the crest, Nature, vol.520, pp.474-482, 2015.

B. De-groef, S. Van-der-geyten, V. M. Darras, and E. R. Kühn, Role of corticotropinreleasing hormone as a thyrotropin-releasing factor in non-mammalian vertebrates, Gen Comp Endocrinol, vol.146, pp.62-68, 2006.

D. J. Grunwald and J. S. Eisen, Headwaters of the zebrafish -emergence of a new model vertebrate, Nat Rev Genet, vol.3, pp.717-724, 2002.

L. Gu, C. Zhang, and C. Xia, Revelation of the Genetic Basis for Convergent Innovative Anal Fin Pigmentation Patterns in Cichlid Fishes, 2017.

J. F. Gudernatsch, Feeding Experiments on tadpoles, Arch für Entwicklungsmechanik der Org, vol.35, pp.457-483, 1912.

R. Guillot, R. M. Ceinos, C. R. Rotllant, J. Cerdá-reverter, and J. M. , Transient Ectopic Overexpression of Agouti-Signalling Protein 1 (Asip1) Induces Pigment Anomalies in Flatfish, PLoS One, vol.7, p.48526, 2012.

R. Guillot, B. Muriach, A. Rocha, J. Rotllant, R. N. Kelsh et al., , 2016.

, Thyroid Hormones Regulate Zebrafish Melanogenesis in a Gender-Specific Manner (Z Yin, PLoS One, vol.11, p.166152

B. Guo, Complex Genes Are Preferentially Retained After Whole-Genome Duplication in Teleost Fish, J Mol Evol, vol.84, pp.253-258, 2017.

P. Haffter, J. Odenthal, M. C. Mullins, S. Lin, M. J. Farrell et al., Mutations affecting pigmentation and shape of the adult zebrafish, Dev Genes Evol, vol.206, pp.260-276, 1996.

M. W. Hahn, Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates, J Hered, vol.100, pp.605-617, 2009.

L. Hakes, J. W. Pinney, S. C. Lovell, S. G. Oliver, and D. L. Robertson, All duplicates are not equal: the difference between small-scale and genome duplication, 2007.

, Genome Biol, vol.8, p.209

B. K. Hall, The neural crest as a fourth germ layer and vertebrates as quadroblastic not triploblastic, Evol Dev, vol.2, pp.3-5, 2000.

H. Hamada, M. Watanabe, H. E. Lau, T. Nishida, T. Hasegawa et al., Involvement of Delta/Notch signaling in zebrafish adult pigment stripe patterning, Development, vol.141, pp.318-324, 2014.

V. Hamburger and H. L. Hamilton, A series of normal stages in the development of the chick embryo, Dev Dyn, vol.195, pp.231-272, 1951.

W. J. Hamilton and R. M. Peterman, Countershading in the colourful reef fish Chaetodon lunula: Concealment, communication or both?, Anim Behav, vol.19, p.357, 1971.

M. Harada, T. Yoshinaga, D. Ojima, and M. Iwata, cDNA cloning and expression analysis of thyroid hormone receptor in the coho salmon Oncorhynchus kisutch during smoltification, Gen Comp Endocrinol, vol.155, pp.658-667, 2008.

M. L. Harmelin-vivien, Energetics and Fish Diversity on Coral Reefs, Coral Reef Fishes, pp.265-274, 2002.

T. Hashimshony, M. Feder, M. Levin, B. K. Hall, and I. Yanai, Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer, Nature, vol.519, pp.219-222, 2015.

M. Havelka, D. Bytyutskyy, R. Symonová, P. Ráb, and M. Flaj?hans, , 2016.

S. B. Heard and D. L. Hauser, Key evolutionary innovations and their ecological mechanisms, Hist Biol, vol.10, pp.151-173, 1995.

X. He and J. Zhang, Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution, Genetics, vol.169, pp.1157-1164, 2005.

M. J. Hegarty and S. J. Hiscock, Genomic Clues to the Evolutionary Success of Polyploid Plants, Curr Biol, vol.18, pp.435-444, 2008.

R. A. Heimeier, B. Das, D. R. Buchholz, M. Fiorentino, and Y. Shi, , 2010.

, Genome Biol, vol.11, p.55

R. Herranz, O. J. Larkin, R. J. Hill, I. Lopez-vidriero, J. J. Van-loon et al., , 2013.

R. S. Hetem, B. A. De-witt, L. G. Fick, A. Fuller, G. Kerley et al., Body temperature, thermoregulatory behaviour and pelt characteristics of three colour morphs of springbok (Antidorcas marsupialis), Comp Biochem Physiol Part A Mol Integr Physiol, vol.152, pp.379-388, 2009.

C. W. Higdon, R. D. Mitra, and S. L. Johnson, Gene Expression Analysis of Zebrafish Melanocytes, Iridophores, and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin (YF Leung, PLoS One, vol.8, p.67801, 2013.

C. Higuera, K. J. Gardiner, and K. J. Cios, Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome (Y Herault, PLoS One, vol.10, p.129126, 2015.

G. Hill, Female choice for ornamental coloration, Coloration: Function and evolution2, pp.137-200, 2006.

G. Hill and K. Mcgraw, Bird Coloration: Mechanisms and measurements, 2006.

Y. Hinits, V. C. Williams, D. Sweetman, T. M. Donn, T. P. Ma et al., , 2011.

, Defective cranial skeletal development, larval lethality and haploinsufficiency in Myod mutant zebrafish, Dev Biol, vol.358, pp.102-112

C. T. Hittinger and S. B. Carroll, Gene duplication and the adaptive evolution of a classic genetic switch, Nature, vol.449, pp.677-681, 2007.

A. Ho, S. K. Shea, and H. F. Pomeroy, Dietary esterified astaxanthin effects on color, carotenoid concentrations, and compositions of clown anemonefish, Amphiprion ocellaris, skin, Aquac Int, vol.21, pp.361-374, 2013.

O. Hoegh-guldberg, P. J. Mumby, A. Hooten, R. S. Steneck, P. Greenfield et al., Coral reefs under rapid climate change and ocean acidification, Science (80-), vol.318, pp.1737-1742, 2007.

M. Van-hoek and P. Hogeweg, Metabolic Adaptation after Whole Genome Duplication, Mol Biol Evol, vol.26, pp.2441-2453, 2009.

H. E. Hoekstra, Genetics, development and evolution of adaptive pigmentation in vertebrates, Heredity (Edinb), vol.97, pp.222-234, 2006.

P. Hof-ae-van&apos;t,-campagne, D. J. Rigden, C. J. Yung, J. Lingley, and M. A. Quail, The industrial melanism mutation in British peppered moths is a transposable element, Nature, vol.534, pp.102-105, 2016.

E. A. Hoffman, F. W. Schueler, A. G. Jones, and M. S. Blouin, An analysis of selection on a colour polymorphism in the northern leopard frog, Mol Ecol, vol.15, pp.2627-2641, 2006.

G. Holzer, Origine de la signalisation thyroïdienne chez les métazoaires et implication dans leur métamorphose, 2015.

G. Holzer, M. Besson, A. Lambert, L. François, P. Barth et al., Fish larval recruitment to reefs is a thyroid hormone-mediated metamorphosis sensitive to the pesticide chlorpyrifos, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01633712

G. Holzer and V. Laudet, Thyroid Hormones: A Triple-Edged Sword for Life History Transitions, Curr Biol, vol.25, pp.344-347, 2015.

N. Hopwood, A history of normal plates, tables and stages in vertebrate embryology, Int J Dev Biol, vol.51, pp.1-26, 2007.

K. Howe, M. D. Clark, C. F. Torroja, J. Torrance, C. Berthelot et al., The zebrafish reference genome sequence and its relationship to the human genome, Nature, vol.496, pp.498-503, 2013.

H. Huang, L. Cai, B. F. Remo, and D. D. Brown, Timing of metamorphosis and the onset of the negative feedback loop between the thyroid gland and the pituitary is controlled by type II iodothyronine deiodinase in Xenopus laevis, Proc Natl Acad Sci, vol.98, pp.7348-7353, 2001.

R. Huang, F. Hippauf, D. Rohrbeck, M. Haustein, K. Wenke et al., Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates, Proc Natl Acad Sci, vol.109, pp.2966-2971, 2012.

J. K. Hubbard, J. Uy, M. E. Hauber, H. E. Hoekstra, and R. J. Safran, Vertebrate pigmentation: from underlying genes to adaptive function, Trends Genet, vol.26, pp.231-239, 2010.

A. L. Hughes, The Evolution of Functionally Novel Proteins after Gene Duplication, Proc R Soc B Biol Sci, vol.256, pp.119-124, 1994.

T. P. Hughes, A. H. Baird, D. R. Bellwood, M. Card, S. R. Connolly et al., Climate change, human impacts, and the resilience of coral reefs, Science, vol.301, pp.929-962, 2003.

T. P. Hughes, J. Kerry, M. Álvarez-noriega, J. Álvarez-romero, A. K. Baird et al., Global warming and recurrent mass bleaching of corals, Nature, vol.543, pp.373-386, 2017.

I. A. Hurley, R. L. Mueller, K. A. Dunn, E. J. Schmidt, M. Friedman et al., , 2007.

, A new time-scale for ray-finned fish evolution, Proc R Soc B Biol Sci, vol.274, p.489

P. G. Hysi, A. M. Valdes, F. Liu, N. A. Furlotte, D. M. Evans et al., , 2018.

J. Ihmels, S. Bergmann, M. Gerami-nejad, I. Yanai, M. Mcclellan et al., Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage, Science (80-), vol.309, pp.938-940, 2005.

H. Innan and F. Kondrashov, The evolution of gene duplications: classifying and distinguishing between models, Nat Rev Genet, vol.11, pp.97-108, 2010.

J. Inoue, Y. Sato, R. Sinclair, K. Tsukamoto, and M. Nishida, Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling, Proc Natl Acad Sci, vol.112, pp.14918-14923, 2015.

U. Irion, A. P. Singh, and C. Nüsslein-volhard, The Developmental Genetics of Vertebrate Color Pattern Formation, Wassarman PM, pp.141-169, 2016.

J. Irisson and D. Lecchini, In situ observation of settlement behaviour in larvae of coral reef fishes at night, J Fish Biol, vol.72, pp.2707-2713, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00293976

S. Ito, A Chemist's View of Melanogenesis, Pigment Cell Res, vol.16, pp.230-236, 2003.

E. Iwata, K. Mikami, J. Manbo, K. Moriya-ito, and H. Sasaki, Social Interaction Influences Blood Cortisol Values and Brain Aromatase Genes in the Protandrous False Clown Anemonefish, Amphiprion ocellaris, Zoolog Sci, vol.29, pp.849-855, 2012.

E. Iwata, Y. Nagai, M. Hyoudou, and H. Sasaki, Social Environment and Sex Differentiation in the False Clown Anemonefish, Amphiprion ocellaris, Zoolog Sci, vol.25, pp.123-128, 2008.

E. Iwata, Y. Nagai, and H. Sasaki, Social rank modulates brain arginine vasotocin immunoreactivity in false clown anemonefish, 2010.

, Fish Physiol Biochem, vol.36, pp.337-345

I. J. Jackson, A cDNA encoding tyrosinase-related protein maps to the brown locus in mouse, Proc Natl Acad Sci U S A, vol.85, pp.4392-4398, 1988.

G. A. Jackson and R. R. Strathmann, Larval Mortality from Offshore Mixing as a Link between Precompetent and Competent Periods of Development, Am Nat, vol.118, pp.16-26, 1981.

F. Jacob, Evolution and tinkering, Science (80-), vol.196, pp.1161-1166, 1977.

H. Jacob, S. Pouil, D. Lecchini, F. Oberhänsli, P. Swarzenski et al., , 2017.

, Trophic transfer of essential elements in the clownfish Amphiprion ocellaris in the context of ocean acidification, PLoS One, vol.12, p.174344

A. Jacquier, The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs, Nat Rev Genet, vol.10, pp.833-844, 2009.

O. Jaillon, J. Aury, F. Brunet, J. Petit, N. Stange-thomann et al.,

, Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol.431, pp.946-957

P. Janvier, Comparative Anatomy: All Vertebrates Do Have Vertebrae, Curr Biol, vol.21, pp.661-663, 2011.

Y. Jiang, S. Zhang, J. Xu, J. Feng, S. Mahboob et al., , 2014.

, Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp (AT Slominski, PLoS One, vol.9, p.108200

Y. Jiao, N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr et al., Ancestral polyploidy in seed plants and angiosperms, Nature, vol.473, p.97, 2011.

S. Johnsen, The Optics of Life A Biologist's Guide to Light in Nature, 2012.

S. Joly, P. B. Heenan, and P. J. Lockhart, A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand, Mol Phylogenet Evol, vol.51, pp.365-372, 2009.

G. P. Jones, M. I. Mccormick, M. Srinivasan, and J. Eagle, Coral decline threatens fish biodiversity in marine reserves, Proc Natl Acad Sci, vol.101, pp.8251-8254, 2004.

G. P. Jones, S. Planes, and S. R. Thorrold, Coral Reef Fish Larvae Settle Close to Home, Curr Biol, vol.15, pp.1314-1318, 2005.

J. Marshall and N. , Communication and camouflage with the same 'bright' colours in reef fishes, Philos Trans R Soc B Biol Sci, vol.355, pp.1243-1248, 2000.

H. Kaessmann, Origins, evolution, and phenotypic impact of new genes, 2010.

, Genome Res, vol.20, pp.1313-1326

H. Kaessmann, N. Vinckenbosch, and M. Long, RNA-based gene duplication: mechanistic and evolutionary insights, Nat Rev Genet, vol.10, pp.19-31, 2009.

A. T. Kalinka, K. M. Varga, D. T. Gerrard, S. Preibisch, D. L. Corcoran et al., Gene expression divergence recapitulates the developmental hourglass model, Nature, vol.468, pp.811-814, 2010.

Y. Kawakami, J. Nozaki, M. Seoka, H. Kumai, and H. Ohta, Characterization of thyroid hormones and thyroid hormone receptors during the early development of Pacific bluefin tuna (Thunnus orientalis), Gen Comp Endocrinol, vol.155, pp.597-606, 2008.

R. N. Kelsh, Genetics and Evolution of Pigment Patterns in Fish, Pigment Cell Res, vol.17, pp.326-336, 2004.

R. N. Kelsh, M. L. Harris, S. Colanesi, and C. A. Erickson, Stripes and belly-spots-A review of pigment cell morphogenesis in vertebrates, Semin Cell Dev Biol, vol.20, pp.90-104, 2009.

N. J. Kenny, K. W. Chan, W. Nong, Z. Qu, I. Maeso et al., Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs, Heredity (Edinb), vol.116, pp.190-199, 2016.

W. Kiessling, C. Simpson, and M. Foote, Reefs as Cradles of Evolution and Sources of Biodiversity in the Phanerozoic, Science (80-), vol.327, pp.196-198, 2010.

C. B. Kimmel, Genetics and early development of zebrafish, Trends Genet, vol.5, pp.283-288, 1989.

T. Kimura, Y. Nagao, H. Hashimoto, Y. Yamamoto-shiraishi, S. Yamamoto et al., Leucophores are similar to xanthophores in their specification and differentiation processes in medaka, Proc Natl Acad Sci, vol.111, pp.7343-7348, 2014.

M. Kirkpatrick, Sexual selection and the evolution of female choice, Evolution (N Y), vol.36, pp.1-12, 1982.

J. Kitano, S. C. Lema, J. A. Luckenbach, S. Mori, Y. Kawagishi et al., Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation, Curr Biol, vol.20, pp.2124-2130, 2010.

L. Kleppe, R. B. Edvardsen, T. Furmanek, G. L. Taranger, and A. Wargelius, Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in atlantic cod, Mol Reprod Dev, vol.81, pp.619-635, 2014.

A. K. Knecht and M. Bronner-fraser, Induction of the neural crest: a multigene process, Nat Rev Genet, vol.3, pp.453-461, 2002.

D. G. Knowles and A. Mclysaght, Recent de novo origin of human proteincoding genes, Genome Res, vol.19, pp.1752-1759, 2009.

H. R. Kobel, D. Pasquier, and L. , Genetics of polyploid Xenopus, Trends Genet, vol.2, pp.310-315, 1986.

T. D. Kocher, Adaptive evolution and explosive speciation: the cichlid fish model, Nat Rev Genet, vol.5, pp.288-298, 2004.

A. Kodric-brown, Dietary carotenoids and male mating success in the guppy: an environmental component to female choice, Behav Ecol Sociobiol, vol.25, pp.393-401, 1989.

A. Kodric-brown, Sexual Dichromatism and Temporary Color Changes in the Reproduction of Fishes, Am Zool, vol.38, pp.70-81, 1998.

N. Kollias, The spectroscopy of human melanin pigmentation, Melanin: Its Role in Human Photoprotection, pp.31-38, 1994.

S. Kondo and R. Asai, A reaction-diffusion wave on the skin of the marine angelfish Pomacanthus, Nature, vol.376, pp.765-768, 1995.

S. Kondo and T. Miura, Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation, Science (80-), vol.329, pp.1616-1620, 2010.

T. B. Kornberg, Macrophages Help Cells Connect to Pattern Zebrafish Stripes, Dev Cell, vol.40, pp.520-521, 2017.

V. A. Kottler, A. Fadeev, D. Weigel, and C. Dreyer, Pigment Pattern Formation in the Guppy, Poecilia reticulata, Involves the Kita and Csf1ra Receptor Tyrosine Kinases, Genetics, vol.194, pp.631-646, 2013.

V. A. Kottler, A. Künstner, and M. Schartl, Pheomelanin in fish?, Pigment Cell Melanoma Res, vol.28, pp.355-356, 2015.

T. Kuriyama, K. Miyaji, M. Sugimoto, and M. Hasegawa, Ultrastructure of the Dermal Chromatophores in a Lizard (Scincidae: Plestiodon latiscutatus) with Conspicuous Body and Tail Coloration, Zoolog Sci, vol.23, pp.793-799, 2006.

L. De and M. Brooke, Ecological factors influencing the occurrence of 'flash marks' in wading birds, Funct Ecol, vol.12, pp.339-346, 1998.

R. L. Lamason, M. Mohideen, J. R. Mest, A. C. Wong, H. L. Norton et al.,

, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans, Science, vol.310, pp.1782-1788

E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

D. Larhammar and C. Risinger, Molecular Genetic Aspects of Tetraploidy in the Common Carp Cyprinus carpio, Mol Phylogenet Evol, vol.3, pp.59-68, 1994.

V. Laudet, The Origins and Evolution of Vertebrate Metamorphosis, Curr Biol, vol.21, pp.726-737, 2011.

S. Laurent, N. Salamin, and M. Robinson-rechavi, No evidence for the radiation time lag model after whole genome duplications in Teleostei (A von Haeseler, Ed.). PLoS One, vol.12, p.176384, 2017.

E. Leclercq, J. F. Taylor, and H. Migaud, Morphological skin colour changes in teleosts, Fish Fish, vol.11, pp.159-193, 2009.

A. P. Lee, S. Y. Kerk, Y. Y. Tan, S. Brenner, and B. Venkatesh, Ancient Vertebrate Conserved Noncoding Elements Have Been Evolving Rapidly in Teleost Fishes, 2011.

, Mol Biol Evol, vol.28, pp.1205-1215

J. M. Leis and M. I. Mccormick, The Biology, Behavior, and Ecology of the Pelagic Larval Stage of Coral Reef Fishes, Coral Reef Fishes, pp.171-199, 2002.

J. M. Leis, U. Siebeck, and D. L. Dixson, How Nemo Finds Home: The Neuroecology of Dispersal and of Population Connectivity in Larvae of Marine Fishes, Integr Comp Biol, vol.51, pp.826-843, 2011.

I. J. Leitch and A. R. Leitch, , 2013.

, Genome Size Diversity and Evolution in Land Plants, Plant Genome Diversity, vol.2, pp.307-322

S. Leonelli and R. A. Ankeny, What makes a model organism, Endeavour, vol.37, pp.209-212, 2013.

M. Levin, L. Anavy, A. G. Cole, E. Winter, N. Mostov et al., The middevelopmental transition and the evolution of animal body plans, Nature, vol.531, pp.637-641, 2016.

M. Levin, T. Hashimshony, F. Wagner, and I. Yanai, Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo, Dev Cell, vol.22, p.1101, 2012.

Z. Li, A. E. Baniaga, E. B. Sessa, M. Scascitelli, S. W. Graham et al., , 2015.

, Early genome duplications in conifers and other seed plants, Sci Adv, vol.1, pp.1501084-1501084

J. Li, G. Hou, X. Kong, C. Li, J. Zeng et al., The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, Cyprinus carpio). Sci Rep, vol.5, p.8199, 2015.

P. Li, L. Ponnala, N. Gandotra, L. Wang, Y. Si et al., The developmental dynamics of the maize leaf transcriptome, Nat Genet, vol.42, p.1060, 2010.

Z. Li, G. P. Tiley, S. R. Galuska, C. R. Reardon, T. I. Kidder et al., , 2018.

, Multiple large-scale gene and genome duplications during the evolution of hexapods, Proc Natl Acad Sci, 201710791.

S. Lien, L. Gidskehaug, T. Moen, B. J. Hayes, P. R. Berg et al., A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns, BMC Genomics, vol.12, p.615, 2011.

S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent et al., The Atlantic salmon genome provides insights into rediploidization, Nature, vol.533, pp.200-205, 2016.

E. Lieske and R. Myers, Coral Reef Fishes -Caribbean, Indian Ocean and Pacific Ocean, 2002.

H. J. Liew, M. Ambak, A. Abol-munafi, and T. Chuah, Embryonic development of clownfish Amphiprion ocellaris under laboratory condition, J Sustain Sci Manag, vol.1, pp.64-73, 2006.

S. J. Lin, J. Foley, T. X. Jiang, C. Y. Yeh, P. Wu et al., Topology of Feather Melanocyte Progenitor Niche Allows Complex Pigment Patterns to Emerge, Science (80-), vol.340, pp.1442-1445, 2013.

J. A. Lister, J. Close, and D. W. Raible, Duplicate mitf Genes in Zebrafish: Complementary Expression and Conservation of Melanogenic Potential, Dev Biol, vol.237, pp.333-344, 2001.

G. Litsios, A. Kostikova, and N. Salamin, Host specialist clownfishes are environmental niche generalists, Proc R Soc B Biol Sci, vol.281, pp.20133220-20133220, 2014.

G. Litsios, P. Pearman, D. Lanterbecq, N. Tolou, and N. Salamin, The radiation of the clownfishes has two geographical replicates, J Biogeogr, vol.41, pp.2140-2149, 2014.

G. Litsios and N. Salamin, Hybridisation and diversification in the adaptive radiation of clownfishes, BMC Evol Biol, vol.14, p.245, 2014.

G. Litsios, C. A. Sims, R. O. Wüest, P. B. Pearman, N. E. Zimmermann et al., , 2012.

, Mutualism with sea anemones triggered the adaptive radiation of clownfishes, BMC Evol Biol, vol.12, p.212

J. Lokki and A. Saura, Polyploidy in insect evolution, Basic Life Sci, vol.13, pp.277-312, 1979.

R. J. Lopes, J. D. Johnson, M. B. Toomey, M. S. Ferreira, P. M. Araujo et al., Genetic Basis for Red Coloration in Birds, Curr Biol, vol.26, pp.1427-1434, 2016.

S. S. Lopes, X. Yang, J. Müller, T. J. Carney, A. R. Mcadow et al., , 2008.

, Leukocyte Tyrosine Kinase Functions in Pigment Cell Development (G Barsh, PLoS Genet, vol.4, p.1000026

M. Lorgen, E. Casadei, E. Król, A. Douglas, M. J. Birnie et al., Functional Divergence of Type 2 Deiodinase Paralogs in the Atlantic Salmon, Curr Biol, vol.25, pp.936-941, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01194956

T. Lorin, F. G. Brunet, V. Laudet, and J. Volff, Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates. G3 Genes|Genomes|Genetics: g3, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806995

G. S. Losey, T. W. Cronin, T. H. Goldsmith, D. Hyde, N. J. Marshall et al., The UV visual world of fishes: a review, J Fish Biol, vol.54, pp.921-943, 1999.

G. S. Losey, W. N. Mcfarland, E. R. Loew, J. P. Zamzow, P. A. Nelson et al., , 2003.

, Visual Biology of Hawaiian Coral Reef Fishes. I. Ocular Transmission and Visual Pigments (WL Montgomery, Copeia, pp.433-454, 2003.

J. B. Losos, Convergence, adaptation and constraint, Evolution (N Y), vol.65, pp.1827-1840, 2011.

R. Lumb, S. Buckberry, G. Secker, D. Lawrence, and Q. Schwarz, Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels, BMC Dev Biol, vol.17, p.5, 2017.

E. Lunghi, A. Monti, A. Binda, I. Piazzi, M. Salvadori et al., Cases of albinism and leucism in amphibians in Italy: new reports, Nat Hist Sci, vol.4, p.73, 2017.

M. Lynch and J. S. Conery, The evolutionary fate and consequences of duplicate genes, Science, vol.290, pp.1151-1156, 2000.

M. Lynch and A. G. Force, The Origin of Interspecific Genomic Incompatibility via Gene Duplication, Am Nat, vol.156, pp.590-605, 2000.

R. Macarthur and R. Levins, Competition, habitat selection and character displacement in a patchy environment, Proc Natl Acad Sci U S A, vol.6, pp.1207-1210, 1964.

I. C. Macaulay, V. Svensson, C. Labalette, L. Ferreira, F. Hamey et al., , 2016.

, Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells, Cell Rep, vol.14, pp.966-977

I. Machuca, G. Esslemont, L. Fairclough, and J. R. Tata, Analysis of structure and expression of the Xenopus thyroid hormone receptor-beta gene to explain its autoinduction, Mol Endocrinol, vol.9, pp.96-107, 1995.

D. J. Macqueen and I. A. Johnston, A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification, Proc R Soc B Biol Sci, vol.281, pp.20132881-20132881, 2014.

H. Madduppa, J. Timm, and M. Kochzius, Reduced genetic diversity in clown anemonefish (Amphiprion ocellaris) in exploited reefs of the Spermonde Archipelago, 2018.

C. Madeira, D. Madeira, M. S. Diniz, H. N. Cabral, and C. Vinagre, Comparing biomarker responses during thermal acclimation: A lethal vs non-lethal approach in a tropical reef clownfish, Comp Biochem Physiol Part A Mol Integr Physiol, vol.204, pp.104-112, 2017.

F. Maderspacher, Colour Patterns: Channelling Turing, Curr Biol, vol.22, pp.266-268, 2012.

S. Maere, D. Bodt, S. Raes, J. Casneuf, T. Van-montagu et al., , 2005.

, Modeling gene and genome duplications in eukaryotes, Proc Natl Acad Sci, vol.102, pp.5454-5459

P. Mahalwar, B. Walderich, A. P. Singh, and C. Nusslein-volhard, Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish, Science, vol.80, pp.1362-1364, 2014.

P. K. Maini, R. E. Baker, and C. Chuong, Developmental Biology: The Turing Model Comes of Molecular Age, Science (80-), vol.314, pp.1397-1398, 2006.

T. Makino, K. Hokamp, and A. Mclysaght, The complex relationship of gene duplication and essentiality, Trends Genet, vol.25, pp.152-155, 2009.

T. Makino and A. Mclysaght, Ohnologs in the human genome are dosage balanced and frequently associated with disease, Proc Natl Acad Sci, vol.107, p.9270, 2010.

T. Makino, A. Mclysaght, and M. Kawata, , 2013.

R. Mallarino, C. Henegar, M. Mirasierra, M. Manceau, C. Schradin et al.,

, Developmental mechanisms of stripe patterns in rodents, Nature, vol.539, pp.518-523

R. Mallarino, T. A. Linden, C. R. Linnen, and H. E. Hoekstra, The role of isoforms in the evolution of cryptic coloration in Peromyscus mice, Mol Ecol, vol.26, pp.245-258, 2017.

M. Manceau, V. S. Domingues, C. R. Linnen, E. B. Rosenblum, and H. E. Hoekstra, , 2010.

, Convergence in pigmentation at multiple levels: mutations, genes and function, Philos Trans R Soc B Biol Sci, vol.365, pp.2439-2450

M. Manceau, V. S. Domingues, R. Mallarino, and H. E. Hoekstra, The Developmental Role of Agouti in Color Pattern Evolution, Science (80-), vol.331, pp.1062-1065, 2011.

D. Marais, D. L. Rausher, and M. D. , Escape from adaptive conflict after duplication in an anthocyanin pathway gene, Nature, vol.454, pp.762-765, 2008.

S. Marburger, M. A. Alexandrou, J. B. Taggart, S. Creer, G. Carvalho et al.,

, Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes, Proc R Soc B Biol Sci, vol.285, 20172732.

M. Marcet-houben and T. Gabaldón, Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage, PLOS Biol, vol.13, p.1002220, 2015.

A. Marcionetti, V. Rossier, J. Bertrand, G. Litsios, and N. Salamin, First draft genome of an iconic clownfish species ( Amphiprion frenatus ), Mol Ecol Resour, 2018.

J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad, RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays, Genome Res, vol.18, pp.1509-1517, 2008.

R. N. Mariscal, The symbiosis between tropical sea anemones and fishes: a review, The Galápagos: Proceedings of the Symposia of the Galápagos International Scientific Project, p.318, 1966.

V. Del-marmol and F. Beermann, Tyrosinase and related proteins in mammalian pigmentation, FEBS Lett, vol.381, pp.165-168, 1996.

N. J. Marshall, The Visual Ecology of Reef Fish Colours, Animal Signals: Signalling and Signal Design in Animal Communication, p.83, 2000.

N. J. Marshall, K. Jennings, W. N. Mcfarland, E. R. Loew, and G. S. Losey, Visual Biology of Hawaiian Coral Reef Fishes. II. Colors of Hawaiian Coral Reef Fish (WL Montgomery, Copeia, pp.455-466, 2003.

A. Martin and V. Courtier-orgogozo, Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes, Diversity and Evolution of Butterfly Wing Patterns, pp.59-87, 2017.

A. Martin and V. Orgogozo, The loci of repeated evolution: A catalog of genetic hotspots of phenotypic variation, Evolution (N Y), vol.67, pp.1235-1250, 2013.

J. P. Masly, C. D. Jones, M. Noor, J. Locke, and H. A. Orr, Gene Transposition as a Cause of Hybrid Sterility in Drosophila, Science (80-), vol.313, pp.1448-1450, 2006.

S. Mathavan, S. Lee, A. Mak, L. D. Miller, K. Murthy et al., Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays, PLoS Genet, vol.1, p.29, 2005.

L. M. Mäthger, M. F. Land, U. E. Siebeck, and N. J. Marshall, Rapid colour changes in multilayer reflecting stripes in the paradise whiptail, Pentapodus paradiseus, J Exp Biol, vol.206, pp.3607-3620, 2003.

D. Mazurais, M. Darias, J. L. Zambonino-infante, and C. L. Cahu, Transcriptomics for understanding marine fish larval development 1 This review is part of a virtual symposium on current topics in aquaculture of marine fish and shellfish, Can J Zool, vol.89, pp.599-611, 2011.

B. Mcclintock, The origin and behavior of mutable loci in maize, Proc Natl Acad Sci, vol.36, pp.344-355, 1950.

M. Mccormick, Delayed metamorphosis of a tropical reef fish (Acanthurus triostegus):a field experiment, Mar Ecol Prog Ser, vol.176, pp.25-38, 1999.

M. I. Mccormick, L. J. Makey, and V. Dufour, Comparative study of metamorphosis in tropical reef fishes, Mar Biol, vol.141, pp.841-853, 2002.

M. I. Mccormick, L. Makey, and V. Dufour, Comparative study of metamorphosis in tropical reef fishes, Mar Biol, vol.141, pp.841-853, 2002.

C. L. Mcgrath, J. Gout, T. G. Doak, A. Yanagi, and M. Lynch, Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence, Genetics, vol.197, pp.1417-1428, 2014.

C. L. Mcgrath, J. Gout, P. Johri, T. G. Doak, and M. Lynch, Differential retention and divergent resolution of duplicate genes following whole-genome duplication, Genome Res, vol.24, pp.1665-1675, 2014.

K. J. Mcgraw, Mechanics of Uncommon colors: Pterins, Porphyrins and Psittacofulvins, Coloration: Function and evolution, pp.354-398, 2006.

K. J. Mcgraw and M. C. Nogare, Carotenoid pigments and the selectivity of psittacofulvin-based coloration systems in parrots, Comp Biochem Physiol -B Biochem Mol Biol, vol.138, pp.229-233, 2004.

K. J. Mcgraw, M. B. Toomey, P. M. Nolan, N. I. Morehouse, M. Massaro et al., A description of unique fluorescent yellow pigments in penguin feathers, Pigment Cell Res, vol.20, pp.301-304, 2007.

A. Mclysaght, K. Hokamp, and K. H. Wolfe, Extensive genomic duplication during early chordate evolution, Nat Genet, vol.31, pp.200-204, 2002.

S. K. Mcmenamin and D. M. Parichy, Metamorphosis in Teleosts, Curr Top Dev Biol, vol.103, pp.127-165, 2013.

S. K. Mcmenamin, E. J. Bain, A. E. Mccann, L. B. Patterson, D. S. Eom et al., Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish, Science (80-), vol.345, issue.602, pp.1358-1361, 2014.

M. G. Meadows, N. Anthes, S. Dangelmayer, M. A. Alwany, T. Gerlach et al., Red fluorescence increases with depth in reef fishes, supporting a visual function, not UV protection, Proc R Soc B Biol Sci, vol.281, pp.20141211-20141211, 2014.

D. Mebs, Chemical biology of the mutualistic relationships of sea anemones with fish and crustaceans, Toxicon, vol.54, pp.1071-1074, 2009.

T. K. Mehta, V. Ravi, S. Yamasaki, A. P. Lee, M. M. Lian et al., Evidence for at least six Hox clusters in the Japanese lamprey, 2013.

, Proc Natl Acad Sci, vol.110, pp.16044-16049

H. Meinhardt and A. Gierer, Pattern formation by local self-activation and lateral inhibition, BioEssays, vol.22, pp.753-760, 2000.

E. M. Mellgren and S. L. Johnson, The evolution of morphological complexity in zebrafish stripes, Trends Genet, vol.18, pp.128-162, 2002.

D. G. Menter, M. Obika, T. T. Tchen, and J. D. Taylor, Leucophores and iridophores ofFundulus heteroclitus: Biophysical and ultrastructural properties, J Morphol, vol.160, pp.103-119, 1979.

A. Meyer and Y. Van-de-peer, From 2R to 3R: evidence for a fish-specific genome duplication (FSGD), BioEssays, vol.27, pp.937-945, 2005.

A. Meyer and M. Schartl, Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions, Curr Opin Cell Biol, vol.11, pp.699-704, 1999.

N. K. Michiels, N. Anthes, N. S. Hart, J. Herler, A. J. Meixner et al.,

, Red fluorescence in reef fish: A novel signalling mechanism?, BMC Ecol, vol.8, p.16

E. L. Milam, Looking for a Few Good Males, 2010.

E. L. Milam, R. L. Millstein, A. Potochnik, and J. E. Roughgarden, Sex and sensibility: The role of social selection, Metascience, vol.20, pp.253-277, 2011.

T. A. Militz and S. Foale, The 'Nemo Effect': Perception and reality of Finding Nemo 's impact on marine aquarium fisheries, Fish Fish, vol.18, pp.596-606, 2017.

L. S. Mills, E. V. Bragina, A. V. Kumar, M. Zimova, D. Lafferty et al.,

M. G. Mills and L. B. Patterson, Not just black and white: Pigment pattern development and evolution in vertebrates, Semin Cell Dev Biol, vol.20, pp.72-81, 2009.

J. S. Mitchell, Mobility of Stichodactyla Gigantea Sea Anemones and Implications for Resident False Clown Anemonefish, Amphiprion Ocellaris, Environ Biol Fishes, vol.66, pp.85-90, 2003.

J. Mitchell, Queue selection and switching by false clown anemonefish, Amphiprion ocellaris, Anim Behav, vol.69, pp.643-652, 2005.

K. Miyagawa-kohshima, H. Miyahara, S. Uchida, S. Odoriba, D. Okabe et al., Embryonic learning of chemical cues via the parents' host in anemonefish (Amphiprion ocellaris), J Exp Mar Bio Ecol, vol.457, pp.160-172, 2014.

F. F. Moberg and C. Folke, Ecological goods and services of coral reef ecosystems, Ecol Econ, vol.29, pp.215-233, 1999.

N. A. Moran and T. Jarvik, Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids, Science (80-), vol.328, pp.624-627, 2010.

T. H. Morgan, Sex limited inheritance in Drosophila, Science, vol.32, issue.80, p.120, 1910.

T. H. Morgan, Notes on two different crosses between races of pigeons, Biol Bull, vol.21, pp.215-221, 1911.

R. L. Morrison, M. S. Rand, . Frost-mason, and . Sk, Cellular Basis of Color Differences in Three Morphs of the Lizard Sceloporus undulatus erythrocheilus, Copeia, p.397, 1995.

R. L. Morrison, W. C. Sherbrooke, . Frost-mason, and . Sk, Temperature-Sensitive, Physiologically Active Iridophores in the Lizard Urosaurus ornatus: An Ultrastructural Analysis of Color Change, Copeia, p.804, 1996.

R. L. Mort, I. J. Jackson, and E. E. Patton, The melanocyte lineage in development and disease, Development, vol.142, pp.620-632, 2015.

A. Mortazavi, E. M. Schwarz, B. Williams, L. Schaeffer, I. Antoshechkin et al., Scaffolding a Caenorhabditis nematode genome with RNA-seq, 2010.

, Genome Res, vol.20, pp.1740-1747

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat Methods, vol.5, pp.621-628, 2008.

K. G. Mountjoy, L. S. Robbins, M. T. Mortrud, and R. D. Cone, The cloning of a family of genes that encode the melanocortin receptors, Science, vol.257, pp.1248-51, 1992.

J. Moyer and A. Nakazano, Protandrous hermaphroditism in six species of the anemonefish genus Amphiprion in Japan, Japanese J Ichthyol, vol.25, pp.101-106, 1978.

F. Müller, Ituna and Thyridia: a remarkable case of mimicry in butterflies, 1879.

, Trans Entomol Soc London, pp.20-29

P. J. Mumby, The impact of exploiting grazers (Scaridae) on the dynamics of Caribbean coral reefs, Ecol Appl, vol.16, pp.747-69, 2006.

N. I. Mundy, J. Stapley, C. Bennison, R. Tucker, H. Twyman et al., , 2016.

, Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster, Curr Biol, vol.26, pp.1435-1440

M. M. Muñoz, N. G. Crawford, T. J. Mcgreevy, N. J. Messana, R. D. Tarvin et al.,

, Divergence in coloration and ecological speciation in the Anolis marmoratus species complex, Mol Ecol, vol.22, pp.2668-2682

J. L. Munro, V. C. Gaut, R. Thompson, and P. H. Reeson, The spawning seasons of Caribbean reef fishes, J Fish Biol, vol.5, pp.69-84, 1973.

M. Murata, K. Miyagawa-kohshima, K. Nakanishi, and Y. Naya, Characterization of Compounds That Induce Symbiosis Between Sea Anemone and Anemone Fish, Science (80-), vol.234, pp.585-587, 1986.

A. A. Myrberg and L. A. Fuiman, The Sensory World of Coral Reef Fishes, Coral Reef Fishes, pp.123-148, 2002.

N. J. Nadeau, C. Pardo-diaz, A. Whibley, M. A. Supple, S. V. Saenko et al., The gene cortex controls mimicry and crypsis in butterflies and moths, Nature, vol.534, pp.106-110, 2016.

Y. Nagao, T. Suzuki, A. Shimizu, T. Kimura, R. Seki et al., Sox5 Functions as a Fate Switch in Medaka Pigment Cell Development, PLoS Genet, vol.10, 2014.

Y. Nagao, H. Takada, M. Miyadai, T. Adachi, R. Seki et al., Distinct interactions of Sox5 and Sox10 in fate specification of pigment cells in medaka and zebrafish, PLoS Genet, vol.14, p.1007260, 2018.

A. Nakamasu, G. Takahashi, A. Kanbe, and S. Kondo, Interactions between zebrafish pigment cells responsible for the generation of Turing patterns, Proc Natl Acad Sci, vol.106, pp.8429-8434, 2009.

K. Nakashima, L. Yamada, Y. Satou, J. Azuma, and N. Satoh, The evolutionary origin of animal cellulose synthase, Dev Genes Evol, vol.214, pp.81-88, 2004.

Y. Nakatani, H. Takeda, Y. Kohara, and S. Morishita, Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates, pp.307-322, 2011.

M. Naville, D. Chalopin, and J. Volff, Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths (H Escriva, vol.9, p.114382, 2014.

M. Naville and J. Volff, Endogenous Retroviruses in Fish Genomes: From Relics of Past Infections to Evolutionary Innovations?, 2016.

T. J. Near, A. Dornburg, R. I. Eytan, B. P. Keck, W. L. Smith et al., , 2013.

, Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes, Proc Natl Acad Sci, vol.110, pp.12738-12743

T. J. Near, R. I. Eytan, A. Dornburg, K. L. Kuhn, J. A. Moore et al., Resolution of ray-finned fish phylogeny and timing of diversification, Proc Natl Acad Sci, vol.109, pp.13698-13703, 2012.

A. P. Negri, S. Uthicke, F. Mueller, and J. , Chemical Pollution on Coral Reefs: Exposure and Ecological Effects, Impacts of Toxic Chemicals (Open Access), pp.187-211, 2011.

J. S. Nelson, T. C. Grande, and M. Wilson, Fishes of the World, 5th edn, 2016.

R. Neme, C. Amador, B. Yildirim, E. Mcconnell, and D. Tautz, Random sequences are an abundant source of bioactive RNAs or peptides, Nat Ecol Evol, vol.1, p.127, 2017.

H. Nilsson-sköld, S. Aspengren, and M. Wallin, Rapid color change in fish and amphibians -function, regulation, and emerging applications, Pigment Cell Melanoma Res, vol.26, pp.29-38, 2013.

M. Nishioka and H. Ueda, Electron-microscopic observation on the dermal chromatophores of normal frogs and three kinds of color variants in Rhacophorus schlegelii, Sci Rep Lab Amphib Biol, vol.7, pp.123-155, 1985.

D. Niu, F. Wang, S. Xie, F. Sun, Z. Wang et al., Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta, Mar Biotechnol, vol.18, pp.168-175, 2016.

C. S. Norman, L. O&apos;gorman, J. Gibson, R. J. Pengelly, D. Baralle et al., Identification of a functionally significant tri-allelic genotype in the Tyrosinase gene (TYR) causing hypomorphic oculocutaneous albinism (OCA1B), 2017.

, Sci Rep, vol.7, p.4415

C. W. Nossa, P. Havlak, J. Yue, J. Lv, K. Y. Vincent et al., Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication, Gigascience, vol.3, p.9, 2014.

V. L. Nunes, A. Miraldo, M. A. Beaumont, R. K. Butlin, and O. S. Paulo, Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida, J Evol Biol, vol.24, pp.2289-2298, 2011.

E. Oancea, J. Vriens, S. Brauchi, J. Jun, I. Splawski et al., , p.1, 2009.

, Forms Ion Channels Associated with Melanin Content in Melanocytes. Sci Signal, vol.2, pp.21-21

J. Odenthal, K. Rossnagel, P. Haffter, R. N. Kelsh, E. Vogelsang et al., Mutations affecting xanthophore pigmentation in the zebrafish, Danio rerio, Development, vol.123, pp.391-399, 1996.

J. M. Odiorne, The Occurrence of Guanophores in Fundulus, Proc Natl Acad Sci U S A, vol.19, pp.750-754, 1933.

J. C. Ogden and T. P. Quinn, Migration in coral reef fishes: ecological significance and orientation mechanisms, Mechanisms of migration in fishes, p.293, 1984.

S. Ohno, Evolution by gene duplication, 1970.

S. Ohno, J. Muramoto, L. Christian, and N. B. Atkin, , 1967.

L. W. Oliphant, Pteridines and purines as major pigments of the avian iris, Pigment cell Res, vol.1, pp.129-160, 1987.

L. W. Oliphant and J. Hudon, Pteridines as reflecting pigments and components of reflecting organelles in vertebrates, Pigment cell Res, vol.6, pp.205-213, 1993.

S. G. Oliver, Q. Van-der-aart, M. L. Agostoni-carbone, M. Aigle, L. Alberghina et al., The complete DNA sequence of yeast chromosome III, Nature, vol.357, pp.38-46, 1992.

K. R. Oliver, J. A. Mccomb, and W. K. Greene, Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity, Genome Biol Evol, vol.5, p.1886, 2013.

I. Olivotto, D. Stefano, M. Rosetti, S. Cossignani, L. Pugnaloni et al., Live prey enrichment, with particular emphasis on HUFAs, as limiting factor in false percula clownfish (Amphiprion ocellaris, Pomacentridae) larval development and metamorphosis: Molecular and biochemical implications, 2011.

, Comp Biochem Physiol Part A Mol Integr Physiol, vol.159, pp.207-218

J. Ollerton, D. Mccollin, D. G. Fautin, and G. R. Allen, Finding NEMO: nestedness engendered by mutualistic organization in anemonefish and their hosts, Proc R Soc B Biol Sci, vol.274, pp.591-598, 2007.

M. Olsson, D. Stuart-fox, and C. Ballen, Genetics and evolution of colour patterns in reptiles, Semin Cell Dev Biol, vol.24, pp.529-541, 2013.

H. A. Orr, Why Polyploidy is Rarer in Animals Than in Plants' Revisited, Am Nat, vol.136, pp.759-770, 1990.

T. C. Osborn, C. Pires, J. Birchler, J. A. Auger, D. L. et al.,

S. P. Otto and J. Whitton, Polyploid Incidence and Evolution, Annu Rev Genet, vol.34, pp.401-437, 2000.

J. Ou, H. Deng, S. Zheng, L. Huang, Q. Feng et al., , 2014.

K. J. Painter, P. K. Maini, and H. G. Othmer, Stripe formation in juvenile Pomacanthus explained by a generalized turing mechanism with chemotaxis, Proc Natl Acad Sci U S A, vol.96, pp.5549-5554, 1999.

N. Panchy, M. D. Lehti-shiu, and S. Shiu, Evolution of gene duplication in plants, Plant Physiol, p.523, 2016.

J. M. Pandolfi, S. R. Connolly, D. J. Marshall, and A. L. Cohen, Projecting Coral Reef Futures Under Global Warming and Ocean Acidification, Science (80-), vol.333, p.418, 2011.

S. Pantalacci, L. Guéguen, C. Petit, A. Lambert, R. Peterkovà et al., , 2017.

S. Pantalacci and M. Sémon, Transcriptomics of developing embryos and organs: A raising tool for evo-devo, J Exp Zool Part B Mol Dev Evol, vol.324, p.363, 2015.

D. Papatsenko, M. Levine, and Y. Goltsev, Clusters of Temporal Discordances Reveal Distinct Embryonic Patterning Mechanisms in Drosophila and Anopheles, vol.9, p.1000584, 2011.

B. Papp, C. Pál, and L. D. Hurst, Dosage sensitivity and the evolution of gene families in yeast, Nature, vol.424, pp.194-197, 2003.

D. M. Parichy, Evolution of danio pigment pattern development, Heredity (Edinb), vol.97, pp.200-210, 2006.

D. M. Parichy, Homology and the evolution of novelty duringDanio adult pigment pattern development, J Exp Zool Part B Mol Dev Evol, vol.308, pp.578-590, 2007.

D. M. Parichy, M. R. Elizondo, M. G. Mills, T. N. Gordon, and R. E. Engeszer, Normal table of postembryonic zebrafish development: Staging by externally visible anatomy of the living fish, Dev Dyn, vol.238, pp.2975-3015, 2009.

D. M. Parichy, D. G. Ransom, B. Paw, L. I. Zon, and S. L. Johnson, An orthologue of the kit-related gene fms is required for development of neural crest-derived xanthophores and a subpopulation of adult melanocytes in the zebrafish, Danio rerio, Development, vol.127, pp.3031-3075, 2000.

D. M. Parichy and J. M. Turner, Zebrafish puma mutant decouples pigment pattern and somatic metamorphosis, Dev Biol, vol.256, pp.242-257, 2003.

E. Parmentier, O. Colleye, and D. Mann, Hearing ability in three clownfish species, J Exp Biol, vol.212, pp.2023-2026, 2009.

E. Parmentier, L. Kéver, M. Casadevall, and D. Lecchini, Diversity and complexity in the acoustic behaviour of Dacyllus flavicaudus, 2010.

, Mar Biol, vol.157, pp.2317-2327

J. Pasquier, I. Braasch, P. Batzel, C. Cabau, J. Montfort et al., Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome, J Exp Zool Part B Mol Dev Evol, vol.328, pp.709-721, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01788671

M. J. Pebusque, F. Coulier, D. Birnbaum, and P. Pontarotti, Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution, Mol Biol Evol, vol.15, pp.1145-1159, 1998.

Y. Van-de-peer, S. Maere, and A. Meyer, The evolutionary significance of ancient genome duplications, Nat Rev Genet, vol.10, pp.725-732, 2009.

I. Pelletier, L. Bally-cuif, and I. Ziegler, Cloning and developmental expression of zebrafish GTP cyclohydrolase I, Mech Dev, vol.109, pp.99-103, 2001.

G. A. Petsko, What's in a name?, Genome Biol, vol.3, 2002.

G. Phillips, M. J. How, J. E. Lange, N. J. Marshall, and K. L. Cheney, Disruptive colouration in reef fish: does matching the background reduce predation risk?, J Exp Biol, vol.220, pp.1962-1974, 2017.

R. Piault, J. Gasparini, P. Bize, S. Jenni-eiermann, and A. Roulin, PheomelaninBased Coloration and the Ability to Cope with Variation in Food Supply and Parasitism, Am Nat, vol.174, pp.548-556, 2009.

M. De-pinna, Teleostean Monophyly, Interrelationships of Fishes, pp.147-162, 1996.

N. Pirarat, W. Pratakpiriya, K. Jongnimitpaiboon, K. Sajjawiriyakul, C. Rodkhum et al., Lymphocystis disease in cultured false clown anemonefish (Amphiprion ocellaris), Aquaculture, vol.315, pp.414-416, 2011.

S. Planes, G. P. Jones, and S. R. Thorrold, Larval dispersal connects fish populations in a network of marine protected areas, Proc Natl Acad Sci, vol.106, pp.5693-5697, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00431334

J. H. Postlethwait, Y. Yan, M. A. Gates, S. Horne, A. Amores et al., , 1998.

, Vertebrate genome evolution and the zebrafish gene map, Nat Genet, vol.18, pp.345-349

E. Poulton, The Colours of Animals: Their Meaning and Use, Especially Considered in the Case of Insects, p.1890, 1890.

R. A. Powell, Evolution of Black-Tipped Tails in Weasels: Predator Confusion, Am Nat, vol.119, pp.126-131, 1982.

D. Power, L. Llewellyn, F. M. Nowell, M. Björnsson, B. T. Einarsdottir et al., Thyroid hormones in growth and development of fish, Comp Biochem Physiol Part C Toxicol Pharmacol, vol.130, pp.447-459, 2001.

T. Pradeu, L. Laplane, K. Prévot, T. Hoquet, V. Reynaud et al., , 2016.

, Wassarman PM (ed) Essays on Developmental Biology, pp.171-183

S. A. Price, T. Claverie, T. J. Near, and P. C. Wainwright, Phylogenetic insights into the history and diversification of fishes on reefs, Coral Reefs, vol.34, pp.997-1009, 2015.

S. A. Price, R. Holzman, T. J. Near, and P. C. Wainwright, Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes, Ecol Lett, vol.14, pp.462-469, 2011.

M. E. Protas, C. Hersey, D. Kochanek, Y. Zhou, H. Wilkens et al., , 2006.

, Nat Genet, vol.38, pp.107-111

R. O. Prum, Aesthetic evolution by mate choice: Darwin's really dangerous idea, Philos Trans R Soc B Biol Sci, vol.367, pp.2253-2265, 2012.

R. O. Prum, R. H. Torres, S. Williamson, and J. Dyck, Coherent light scattering by blue feather barbs, Nature, vol.396, pp.28-29, 1998.

R. O. Prum, R. Torres, S. Williamson, and J. Dyck, Two-dimensional Fourier analysis of the spongy medullary keratin of structurally coloured feather barbs, Proc R Soc B Biol Sci, vol.266, pp.13-22, 1999.

N. H. Putnam, T. Butts, D. Ferrier, R. F. Furlong, U. Hellsten et al.,

, The amphioxus genome and the evolution of the chordate karyotype, Nature, vol.453, pp.1064-1071

J. Randall, A Review of Mimicry in Marine Fishes, Zool Stud, vol.44, pp.299-328, 2005.

J. Randall and D. G. Fautin, Fishes other than anemonefishes that associate with sea anemones, Coral Reefs, vol.21, pp.188-190, 2002.

V. Ravi and B. Venkatesh, The Divergent Genomes of Teleosts, Annu Rev Anim Biosci, vol.6, pp.47-68, 2018.

R. D. Reed, R. Papa, A. Martin, H. M. Hines, B. A. Counterman et al.,

, optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry, Science (80-), vol.333, pp.1137-1141

J. C. Regier, J. W. Shultz, A. Zwick, A. Hussey, B. Ball et al., , 2010.

, Arthropod relationships revealed by phylogenomic analysis of nuclear proteincoding sequences, Nature, vol.463, pp.1079-1083

R. A. Relyea, Getting out alive: how predators affect the decision to metamorphose, Oecologia, vol.152, pp.389-400, 2007.

W. J. Richards and K. C. Lindeman, Recruitment dynamics of reef fishes: planktonic processes, settlement and demersal ecologies, and fishery analysis, Bull Mar Sci, vol.41, pp.392-410, 1987.

D. R. Riley, K. B. Sieber, K. M. Robinson, J. R. White, A. Ganesan et al., Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples, PLoS Comput Biol, vol.9, p.1003107, 2013.

D. R. Robertson, Do coral-reef fish faunas have a distinctive taxonomic structure?, Coral Reefs, vol.17, pp.179-186, 1998.

F. M. Robertson, M. K. Gundappa, F. Grammes, T. R. Hvidsten, A. K. Redmond et al., Lineage-specific rediploidization is a mechanism to explain timelags between genome duplication and evolutionary diversification, Genome Biol, vol.18, p.111, 2017.

M. Robinson-rechavi, O. Marchand, H. Escriva, P. Bardet, D. Zelus et al., Euteleost Fish Genomes are Characterized by Expansion of Gene Families, Genome Res, vol.11, pp.781-788, 2001.

S. T. Rohrlich and K. R. Porter, Fine structural observations relating to the production of color by the iridophores of a lizard, Anolis carolinensis, J Cell Biol, vol.53, pp.38-52, 1972.

S. Rohwer, Passerine Subadult Plumages and the Deceptive Acquisition of Resources: Test of a Critical Assumption, Condor, vol.80, p.173, 1978.

E. B. Rosenblum, H. Rompler, T. Schoneberg, and H. E. Hoekstra, Molecular and functional basis of phenotypic convergence in white lizards at White Sands, Proc Natl Acad Sci, vol.107, pp.2113-2117, 2010.

A. Roulin, Covariation between eumelanic pigmentation and body mass only under specific conditions, Naturwissenschaften, vol.96, pp.375-382, 2009.

A. Roulin, Condition-dependence, pleiotropy and the handicap principle of sexual selection in melanin-based colouration, Biol Rev, vol.91, pp.328-348, 2015.

A. Roulin and A. Ducrest, Genetics of colouration in birds, Semin Cell Dev Biol, vol.24, pp.594-608, 2013.

K. Rousseau and S. Dufour, Introduction to Fish First and Secondary Metamorphoses, Metamorphosis in Fish, 2012.

J. Roux, M. Rosikiewicz, and M. Robinson-rechavi, What to compare and how: Comparative transcriptomics for Evo-Devo, J Exp Zool Part B Mol Dev Evol, vol.324, pp.372-382, 2015.

L. Rowen, G. Mahairas, and L. Hood, Sequencing the human genome, Science (80-), vol.278, pp.605-612, 1997.

H. M. Rowland, The history, theory and evidence for a cryptic function of countershading, pp.53-72, 2011.

H. M. Rowland, J. Mappes, G. D. Ruxton, and M. P. Speed, Mimicry between unequally defended prey can be parasitic: evidence for quasi-Batesian mimicry, 2010.

, Ecol Lett, vol.13, pp.1494-1502

M. A. Rudnicki, T. Braun, S. Hinuma, and R. Jaenisch, Inactivation of MyoD in mice leads to up-regulation of the myogenic HLH gene Myf-5 and results in apparently normal muscle development, Cell, vol.71, pp.383-390, 1992.

L. M. Sachs, P. L. Jones, E. Havis, N. Rouse, B. A. Demeneix et al., Nuclear receptor corepressor recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development, Mol Cell Biol, vol.22, pp.8527-8565, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00106244

S. Saenko, J. Teyssier, D. Van-der-marel, and M. C. Milinkovitch, Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards, BMC Biol, vol.11, p.105, 2013.

R. Safi, S. Bertrand, O. Marchand, M. Duffraisse, A. De-luze et al., The Axolotl ( Ambystoma mexicanum ), a Neotenic Amphibian, Expresses Functional Thyroid Hormone Receptors, Endocrinology, vol.145, pp.760-772, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00106231

J. Salse, Ancestors of modern plant crops, Curr Opin Plant Biol, vol.30, pp.134-142, 2016.

B. Salvat, Coral reefs -a challenging ecosystem for human societies, Glob Environ Chang, vol.2, pp.12-18, 1992.

L. M. San-jose and A. Roulin, Genomics of coloration in natural animal populations, Philos Trans R Soc B Biol Sci, vol.372, 2017.

F. Sanger, S. Nicklen, and A. R. Coulson, DNA sequencing with chain-terminating inhibitors, Proc Natl Acad Sci U S A, vol.74, pp.5463-5470, 1977.

S. E. Santana, J. Lynch-alfaro, and M. E. Alfaro, Adaptive evolution of facial colour patterns in Neotropical primates, Proc R Soc B Biol Sci, vol.279, pp.2204-2211, 2012.

F. Santini, L. J. Harmon, G. Carnevale, and M. E. Alfaro, Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes, BMC Evol Biol, vol.9, p.194, 2009.

E. Santos, I. Braasch, N. Boileau, B. S. Meyer, A. Bo et al., The evolution of cichlid fish egg-spots is linked with a cis-regulatory change, Nat Commun, 2014.

D. R. Scannell, A. C. Frank, G. C. Conant, K. P. Byrne, M. Woolfit et al., Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication, Proc Natl Acad Sci, vol.104, pp.8397-8402, 2007.

A. Schally, T. W. Redding, C. Y. Bowers, and J. F. Barrett, Isolation and properties of porcine thyrotropin-releasing hormone, J Biol Chem, vol.244, pp.4077-88, 1969.

M. Schartl, L. Larue, M. Goda, M. W. Bosenberg, H. Hashimoto et al., What is a vertebrate pigment cell?, Pigment Cell Melanoma Res, vol.29, pp.8-14, 2016.

H. B. Schioth, A. Vastermark, and R. D. Cone, Reply to Braasch and Postlethwait: Evolutionary origin of the teleost A2 agouti genes (agouti signaling protein 2 and agouti-related protein 2) remains unclear, Proc Natl Acad Sci, vol.108, pp.49-50, 2011.

D. Schluter, The ecology of adaptive radiation, 2000.

T. W. Schoener, Resource Partitioning in Ecological Communities, Science (80-), vol.185, pp.27-39, 1974.

M. Schranz, S. Mohammadin, and P. P. Edger, Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model, Curr Opin Plant Biol, vol.15, pp.147-153, 2012.

A. M. Schreiber, L. Cai, and D. D. Brown, Remodeling of the intestine during metamorphosis of Xenopus laevis, Proc Natl Acad Sci, vol.102, pp.3720-3725, 2005.

A. M. Schreiber and J. L. Specker, Metamorphosis in the summer flounder (Paralichthys dentatus): stage-specific developmental response to altered thyroid status, Gen Comp Endocrinol, vol.111, pp.156-66, 1998.

C. Schunter, M. J. Welch, G. E. Nilsson, J. L. Rummer, P. L. Munday et al., An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish, Nat Ecol Evol, vol.2, pp.334-342, 2018.

E. E. Schwager, P. P. Sharma, T. Clarke, D. J. Leite, T. Wierschin et al.,

J. Schwartz, Sonic Hedgehog' sounded funny, at first, 2006.

A. Scott and D. L. Dixson, Reef fishes can recognize bleached habitat during settlement: sea anemone bleaching alters anemonefish host selection, Proc R Soc B Biol Sci, vol.283, 2016.

A. Scott and B. Francisco, Observations on the feeding behaviour of resident anemonefish during host sea anemone spawning, Coral Reefs, vol.25, pp.451-451, 2006.

O. Seehausen, Y. Terai, I. S. Magalhaes, K. L. Carleton, H. Mrosso et al.,

, Speciation through sensory drive in cichlid fish, Nature, vol.455, pp.620-626

M. Semon and K. H. Wolfe, Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis, Proc Natl Acad Sci, vol.105, p.8333, 2008.

J. Senar, Color displays as intrasexual signals of aggression and dominance, Coloration: Function and evolution, pp.87-136, 2006.

M. R. Seringhaus, P. D. Cayting, and M. B. Gerstein, Uncovering trends in gene naming, Genome Biol, vol.9, p.401, 2008.

A. M. Session, Y. Uno, T. Kwon, J. A. Chapman, A. Toyoda et al., , 2016.

, Genome evolution in the allotetraploid frog Xenopus laevis, Nature, vol.538, p.336

G. Shamim, S. K. Ranjan, D. M. Pandey, and R. Ramani, Biochemistry and biosynthesis of insect pigments, Eur J Entomol, vol.111, pp.149-164, 2014.

P. P. Sharma, C. M. Baker, J. G. Cosgrove, J. E. Johnson, J. T. Oberski et al.,

, A revised dated phylogeny of scorpions: Phylogenomic support for ancient divergence of the temperate Gondwanan family Bothriuridae, Mol Phylogenet Evol, vol.122, pp.37-45

G. Sharon, D. Benharroch, L. Kachko, N. Reis-hevlin, and D. Zilberg, , 2015.

, Amphiprion ocellaris Cuvier, produced in indoor aquaculture, Liposarcoma in clownfish, vol.38, pp.575-580

M. D. Shawkey and G. E. Hill, Carotenoids need structural colours to shine, Biol Lett, vol.1, pp.121-124, 2005.

J. Shendure, The beginning of the end for microarrays?, Nat Methods, vol.5, pp.585-587, 2008.

J. Shendure, R. D. Mitra, C. Varma, and G. M. Church, Advanced sequencing technologies: methods and goals, Nat Rev Genet, vol.5, pp.335-344, 2004.

S. Shibahara, Y. Tomita, T. Sakakura, C. Nager, B. Chaudhuri et al., , 1986.

, Cloning and expression of cDNA encoding mouse tyrosinase, Nucleic Acids Res, vol.14, pp.2413-2440

S. Sick, S. Reinker, J. Timmer, and T. Schlake, WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism, Science (80-), vol.314, pp.1447-1450, 2006.

U. E. Siebeck, Communication in the Ultraviolet: Unravelling the Secret Language of Fish, Biocommunication of Animals, pp.299-320, 2014.

U. E. Siebeck, A. N. Parker, D. Sprenger, L. M. Mäthger, and G. Wallis, A Species of Reef Fish that Uses Ultraviolet Patterns for Covert Face Recognition, Curr Biol, vol.20, pp.407-410, 2010.

M. Simoes-costa and M. E. Bronner, Establishing neural crest identity: a gene regulatory recipe, Development, vol.142, pp.242-257, 2015.

M. Simons, A. A. Cohen, and S. Verhulst, What Does Carotenoid-Dependent Coloration Tell? Plasma Carotenoid Level Signals Immunocompetence and Oxidative Stress State in Birds-A Meta-Analysis (JJ Bolhuis, PLoS One, vol.7, p.43088, 2012.

M. Simons and S. Verhulst, Zebra finch females prefer males with redder bills independent of song rate-a meta-analysis, Behav Ecol, vol.22, pp.755-762, 2011.

S. D. Simpson, Homeward Sound. Science (80-), vol.308, pp.221-221, 2005.

S. D. Simpson, M. G. Meekan, N. J. Larsen, R. D. Mccauley, and A. Jeffs, Behavioral plasticity in larval reef fish: orientation is influenced by recent acoustic experiences, Behav Ecol, vol.21, pp.1098-1105, 2010.

A. P. Singh, A. Dinwiddie, P. Mahalwar, U. Schach, C. Linker et al., , 2016.

, Pigment Cell Progenitors in Zebrafish Remain Multipotent through Metamorphosis, Dev Cell, vol.38, pp.316-330

A. P. Singh and C. Nüsslein-volhard, Zebrafish Stripes as a Model for Vertebrate Colour Pattern Formation, Curr Biol, vol.25, pp.81-92, 2015.

A. P. Singh, U. Schach, and C. Nüsslein-volhard, Proliferation, dispersal and patterned aggregation of iridophores in the skin prefigure striped colouration of zebrafish, Nat Cell Biol, vol.16, pp.604-611, 2014.

J. Siroki, J. Hodurkova, I. Negrutiu, and B. Vyskot, Functional and Structural Chromosome Analyses in Autotetraploid Silene latifolia, Ann Bot, vol.84, pp.633-638, 1999.

J. Skelhorn, H. M. Rowland, M. P. Speed, and G. D. Ruxton, Masquerade: Camouflage Without Crypsis, Science (80-), vol.327, pp.51-51, 2010.

L. Skrabanek and K. H. Wolfe, Eukaryote genome duplication -where's the evidence?, Curr Opin Genet Dev, vol.8, pp.694-700, 1998.

A. Slominski, D. J. Tobin, S. Shibahara, and J. Wortsman, Melanin Pigmentation in Mammalian Skin and Its Hormonal Regulation, Physiol Rev, vol.84, pp.1155-1228, 2004.

M. M. Smith, Molecular evolution of the Saccharomyces cerevisiae histone gene loci, J Mol Evol, vol.24, pp.252-261, 1987.

J. J. Smith, F. Antonacci, E. E. Eichler, and C. T. Amemiya, Programmed loss of millions of base pairs from a vertebrate genome, Proc Natl Acad Sci, vol.106, pp.11212-11217, 2009.

J. J. Smith and M. C. Keinath, The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications, Genome Res, vol.25, pp.1081-1090, 2015.

J. J. Smith, S. Kuraku, C. Holt, T. Sauka-spengler, N. Jiang et al., , 2013.

, Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution, Nat Genet, vol.45, pp.415-421

J. J. Smith, N. Timoshevskaya, C. Ye, C. Holt, M. C. Keinath et al., The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution, Nat Genet, vol.50, pp.270-277, 2018.

D. E. Soltis, V. A. Albert, J. Leebens-mack, C. D. Bell, A. H. Paterson et al., Polyploidy and angiosperm diversification, Am J Bot, vol.96, pp.336-348, 2009.

P. S. Soltis, D. B. Marchant, Y. Van-de-peer, and D. E. Soltis, Polyploidy and genome evolution in plants, Curr Opin Genet Dev, vol.35, pp.119-125, 2015.

P. Songwut, D. Sataporn, and T. Opas, A simple method for cell culture of 'Nemo' ocellaris clownfish (Amphiprion ocellaris, Cuvier 1830), Cell Biol Int Rep, vol.21, pp.39-45, 2014.

T. M. Sonneborn, The Paramecium aurelia Complex of Fourteen Sibling Species, Trans Am Microsc Soc, vol.94, p.155, 1975.

S. M. Soucy, J. Huang, and J. P. Gogarten, Horizontal gene transfer: building the web of life, Nat Rev Genet, vol.16, pp.472-482, 2015.

F. De-souza, V. F. Bumaschny, M. J. Low, and M. Rubinstein, Subfunctionalization of Expression and Peptide Domains Following the Ancient Duplication of the Proopiomelanocortin Gene in Teleost Fishes, Mol Biol Evol, vol.22, pp.2417-2427, 2005.

M. Spalding, E. Green, and C. Ravilious, World Atlas of Coral Reefs, 2007.

M. D. Spalding and A. M. Grenfell, New estimates of global and regional coral reef areas, Coral Reefs, vol.16, pp.225-230, 1997.

M. P. Speed, Warning signals, receiver psychology and predator memory, Anim Behav, vol.60, pp.269-278, 2000.

J. Spring, Vertebrate evolution by interspecific hybridisation--are we polyploid?, FEBS Lett, vol.400, pp.2-8, 1997.

E. Stanganello, A. Hagemann, B. Mattes, C. Sinner, D. Meyen et al., Filopodia-based Wnt transport during vertebrate tissue patterning, Nat Commun, vol.6, p.5846, 2015.

D. G. Stavenga, H. L. Leertouwer, N. J. Marshall, and D. Osorio, Dramatic colour changes in a bird of paradise caused by uniquely structured breast feather barbules, Proc R Soc B Biol Sci, vol.278, pp.2098-2104, 2011.

C. C. Steiner, H. Rompler, L. M. Boettger, T. Schoneberg, and H. E. Hoekstra, The Genetic Basis of Phenotypic Convergence in Beach Mice: Similar Pigment Patterns but Different Genes, Mol Biol Evol, vol.26, pp.35-45, 2008.

C. C. Steiner, J. N. Weber, and H. E. Hoekstra, Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes, PLoS Biol, vol.5, p.219, 2007.

D. L. Stern and V. Orgogozo, Is Genetic Evolution Predictable? Science (80-), vol.323, pp.746-751, 2009.

M. Stevens and S. Merilaita, Animal camouflage: current issues and new perspectives, Philos Trans R Soc B Biol Sci, vol.364, pp.423-427, 2009.

S. M. Stieb, F. Cortesi, L. Sueess, K. L. Carleton, W. Salzburger et al., , 2017.

, Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes, Mol Ecol, vol.26, pp.1323-1342

I. Stobutzki and D. Bellwood, Sustained swimming abilities of the late pelagic stages of coral reef fishes, Mar Ecol Prog Ser, vol.149, pp.35-41, 1997.

J. T. Streelman, M. Alfaro, M. W. Westneat, D. R. Bellwood, and S. A. Karl, Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity, Evolution, vol.56, pp.961-71, 2002.

G. Streisinger, C. Walker, N. Dower, D. Knauber, and F. Singer, Production of clones of homozygous diploid zebra fish (Brachydanio rerio), Nature, vol.291, p.293, 1981.

R. A. Sturm, R. D. Teasdale, and N. F. Box, Human pigmentation genes: identification, structure and consequences of polymorphic variation, Gene, vol.277, pp.49-62, 2001.

P. Sulem, D. F. Gudbjartsson, S. N. Stacey, A. Helgason, T. Rafnar et al., Two newly identified genetic determinants of pigmentation in Europeans, Nat Genet, vol.40, pp.835-837, 2008.

M. Svartman, G. Stone, and R. Stanyon, Molecular cytogenetics discards polyploidy in mammals, Genomics, vol.85, pp.425-430, 2005.

J. T. Szczebak, R. P. Henry, F. A. Al-horani, and C. Ne, Anemonefish oxygenate their anemone hosts at night, J Exp Biol, vol.216, pp.970-976, 2013.

P. Tamayo, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan et al., Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation, Proc Natl Acad Sci U S A, vol.96, pp.2907-2919, 1999.

M. H. Tan, K. F. Au, A. L. Yablonovitch, A. E. Wills, J. Chuang et al., RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development, Genome Res, vol.23, pp.201-216, 2013.

M. H. Tan, C. M. Austin, M. P. Hammer, Y. P. Lee, L. J. Croft et al., Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly, 2018.

Y. Tanaka, Social selection and the evolution of animal signals, Evolution (N Y), vol.50, pp.512-523, 1996.

M. Taniguchi, K. Miura, H. Iwao, and S. Yamanaka, Quantitative Assessment of DNA Microarrays-Comparison with Northern Blot Analyses, Genomics, vol.71, p.34, 2001.

D. C. Tank, J. M. Eastman, M. W. Pennell, P. S. Soltis, D. E. Soltis et al., Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications, New Phytol, vol.207, pp.454-467, 2015.

A. K. Tarafder, G. Bolasco, M. S. Correia, F. Pereira, L. Iannone et al.,

, Rab11b Mediates Melanin Transfer between Donor Melanocytes and Acceptor Keratinocytes via Coupled Exo/Endocytosis, J Invest Dermatol, vol.134, pp.1056-1066

M. Tassabehji, V. E. Newton, and A. P. Read, Waardenburg syndrome type 2 caused by mutations in the human microphthalmia (MITF) gene, Nat Genet, vol.8, pp.251-255, 1994.

J. R. Tata, Getting hooked on thyroid hormone action: A semiautobiographical account, J Biosci, vol.33, pp.653-667, 2008.

J. S. Taylor and J. Raes, Duplication and Divergence: The Evolution of New Genes and Old Ideas, Annu Rev Genet, vol.38, pp.615-643, 2004.

S. A. Teichmann and M. M. Babu, Gene regulatory network growth by duplication, Nat Genet, vol.36, pp.492-496, 2004.

J. Teyssier, S. V. Saenko, D. Van-der-marel, and M. C. Milinkovitch, Photonic crystals cause active colour change in chameleons, Nat Commun, vol.6, p.6368, 2015.

D. B. Thomas, C. M. Mcgoverin, K. J. Mcgraw, H. F. James, and O. Madden, , 2013.

, Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins, J R Soc Interface, vol.10, pp.20121065-20121065

D. B. Thomas, K. J. Mcgraw, M. W. Butler, M. T. Carrano, O. Madden et al., Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds, Proc R Soc B Biol Sci, vol.281, pp.20140806-20140806, 2014.

D. A. Thompson, S. Roy, M. Chan, M. P. Styczynsky, J. Pfiffner et al., Evolutionary principles of modular gene regulation in yeasts, 2013.

A. Thompson, D. Vo, C. Comfort, and H. H. Zakon, Expression Evolution Facilitated the Convergent Neofunctionalization of a Sodium Channel Gene, Mol Biol Evol, vol.31, pp.1941-1955, 2014.

G. H. Thorgaard, G. S. Bailey, D. Williams, D. R. Buhler, S. L. Kaattari et al., Status and opportunities for genomics research with rainbow trout, 2002.

, Comp Biochem Physiol B Biochem Mol Biol, vol.133, pp.609-655

K. Thorisson, Is metamorphosis a critical interval in the early life of marine fishes?, Environ Biol Fishes, vol.40, pp.23-36, 1994.

R. E. Thresher, Reproduction in reef fishes, 1984.

R. E. Thresher, P. L. Colin, and L. J. Bell, Planktonic Duration, Distribution and Population Structure of Western and Central Pacific Damselfishes (Pomacentridae), Copeia, p.420, 1989.

E. A. Tibbetts and J. Dale, A socially enforced signal of quality in a paper wasp, Nature, vol.432, pp.218-222, 2004.

J. Tinbergen, B. D. Wilts, and D. G. Stavenga, Spectral tuning of Amazon parrot feather coloration by psittacofulvin pigments and spongy structures, J Exp Biol, vol.216, pp.4358-4364, 2013.

D. Tisch and M. Schmoll, Light regulation of metabolic pathways in fungi, Appl Microbiol Biotechnol, vol.85, pp.1259-1277, 2010.

M. B. Toomey, R. J. Lopes, P. M. Araújo, J. D. Johnson, M. A. Gazda et al., , 2017.

, High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds, Proc Natl Acad Sci, vol.114, pp.5219-5224

G. M. Toral, J. Figuerola, and J. J. Negro, Multiple ways to become red: Pigment identification in red feathers using spectrometry, Comp Biochem Physiol Part B Biochem Mol Biol, vol.150, pp.147-152, 2008.

V. A. Trifonov, S. S. Romanenko, V. R. Beklemisheva, L. S. Biltueva, A. I. Makunin et al., Evolutionary plasticity of acipenseriform genomes, Chromosoma, vol.125, pp.661-668, 2016.

A. M. Turing, The Chemical Basis of Morphogenesis, Philos Trans R Soc B Biol Sci, vol.237, pp.37-72, 1952.

T. Uyeno and G. R. Smith, Tetraploid origin of the karyotype of catostomid fishes, Science, vol.175, pp.644-650, 1972.

K. Vanneste, S. Maere, and Y. Van-de-peer, Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution, Philos Trans R Soc B Biol Sci, vol.369, 2014.

Å. Västermark, A. Krishnan, M. E. Houle, R. Fredriksson, J. M. Cerdá-reverter et al., Identification of Distant Agouti-Like Sequences and Re-Evaluation of the Evolutionary History of the Agouti-Related Peptide (AgRP) (V Laudet, 2012.

, PLoS One, vol.7, p.40982

B. Venkatesh, A. P. Lee, V. Ravi, A. K. Maurya, M. M. Lian et al., Elephant shark genome provides unique insights into gnathostome evolution, Nature, vol.505, pp.174-179, 2014.

J. C. Venter, M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural et al., The Sequence of the Human Genome, Science (80-), vol.291, pp.1304-1351, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00465088

B. C. Victor, Delayed Metamorphosis with Reduced Larval Growth in a Coral Reef Fish (Thalassoma bifasciatum), Can J Fish Aquat Sci, vol.43, pp.1208-1213, 1986.

N. Vinckenbosch, I. Dupanloup, and H. Kaessmann, Evolutionary fate of retroposed gene copies in the human genome, Proc Natl Acad Sci, vol.103, p.3220, 2006.

J. L. Vitt and P. J. Calwell, Herpetology, Fourth Edition: An Introductory Biology of Amphibians and Reptiles, 2013.

E. Voldoire, F. Brunet, M. Naville, J. Volff, and D. Galiana, Expansion by whole genome duplication and evolution of the sox gene family in teleost fish (H Vaudry, PLoS One, vol.12, p.180936, 2017.

J. Volff, Genome evolution and biodiversity in teleost fish, Heredity (Edinb), vol.94, pp.280-294, 2005.

K. Voordeckers, K. Pougach, and K. J. Verstrepen, How do regulatory networks evolve and expand throughout evolution?, Curr Opin Biotechnol, vol.34, pp.180-188, 2015.

B. S. Vorbach, J. C. Wolf, and R. P. Yanong, Odontomas in two long-finned ocellaris clownfish ( Amphiprion ocellaris ), J Vet Diagnostic Investig, vol.30, pp.136-139, 2018.

D. Vries, G. J. Panzica, and G. C. , Sexual differentiation of central vasopressin and vasotocin systems in vertebrates: Different mechanisms, similar endpoints, Neuroscience, vol.138, pp.947-955, 2006.

C. E. Wagner, L. J. Harmon, and O. Seehausen, Ecological opportunity and sexual selection together predict adaptive radiation, Nature, vol.487, pp.366-369, 2012.

G. P. Wagner, M. Pavlicev, and J. M. Cheverud, The road to modularity, Nat Rev Genet, vol.8, pp.921-931, 2007.

J. T. Wagner, P. P. Singh, A. L. Romney, C. L. Riggs, P. Minx et al., The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development, BMC Genomics, vol.19, p.155, 2018.

P. C. Wainwright and D. R. Bellwood, Ecomorphology of Feeding in Coral Reef Fishes, Coral Reef Fishes, pp.33-55, 2002.

Y. Wakamatsu, S. Pristyazhnyuk, M. Kinoshita, M. Tanaka, and K. Ozato, The see-through medaka: A fish model that is transparent throughout life, Proc Natl Acad Sci, vol.98, pp.10046-10050, 2001.

B. Walderich, A. P. Singh, P. Mahalwar, and C. Nüsslein-volhard, Homotypic cell competition regulates proliferation and tiling of zebrafish pigment cells during colour pattern formation, Nat Commun, vol.7, p.11462, 2016.

A. R. Wallace, The colours of animals and plants, Am Nat, vol.11, pp.713-728, 1877.

A. R. Wallace, Natural selection and tropical nature, Smith CH (ed) Science for All, 1879.

C. N. Walpita, A. D. Crawford, E. Janssens, S. Van-der-geyten, and V. M. Darras, , 2009.

, Iodothyronine Deiodinase Is Essential for Thyroid Hormone-Dependent Embryonic Development and Pigmentation in Zebrafish, Endocrinology, vol.150, pp.530-539

Z. Wang, M. Gerstein, and M. Snyder, RNA-Seq: a revolutionary tool for transcriptomics, Nat Rev Genet, vol.10, pp.57-63, 2009.

J. Wang, J. Li, X. Zhang, and X. Sun, Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio), BMC Genomics, vol.13, p.96, 2012.

Y. Wang, Y. Lu, Y. Zhang, Z. Ning, Y. Li et al., The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation, Nat Genet, vol.47, pp.625-631, 2015.

X. Wang, H. Wang, J. Wang, R. Sun, J. Wu et al., The genome of the mesopolyploid crop species Brassica rapa, Nat Genet, vol.43, pp.1035-1039, 2011.

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, Natural history and evolutionary principles of gene duplication in fungi, Nature, vol.449, pp.54-61, 2007.

I. A. Warren, M. Naville, D. Chalopin, P. Levin, C. S. Berger et al., Evolutionary impact of transposable elements on genomic diversity and lineagespecific innovation in vertebrates, Chromosom Res, vol.23, pp.505-531, 2015.

B. R. Wasik, S. F. Liew, D. A. Lilien, A. J. Dinwiddie, H. Noh et al., Artificial selection for structural color on butterfly wings and comparison with natural evolution, Proc Natl Acad Sci, vol.111, pp.12109-12114, 2014.

M. Watanabe, M. Iwashita, M. Ishii, Y. Kurachi, A. Kawakami et al., , 2006.

, gene. EMBO Rep, vol.7, pp.893-897

M. Watanabe and S. Kondo, Changing clothes easily: connexin41.8 regulates skin pattern variation, Pigment Cell Melanoma Res, vol.25, pp.326-330, 2012.

M. Watanabe and S. Kondo, Is pigment patterning in fish skin determined by the Turing mechanism?, Trends Genet, vol.31, pp.88-96, 2015.

K. Watanabe, Y. Washio, Y. Fujinami, M. Aritaki, S. Uji et al., Adult-type pigment cells, which color the ocular sides of flounders at metamorphosis, localize as precursor cells at the proximal parts of the dorsal and anal fins in early larvae, Dev Growth Differ, vol.50, pp.731-741, 2008.

A. C. Watson, L. A. Siemann, and R. T. Hanlon, Dynamic camouflage by Nassau groupers Epinephelus striatus on a Caribbean coral reef, J Fish Biol, vol.85, pp.1634-1649, 2014.

G. M. Wellington and B. C. Victor, Planktonic larval duration of one hundred species of Pacific and Atlantic damselfishes (Pomacentridae), Mar Biol, vol.101, pp.557-567, 1989.

T. Werner, S. Koshikawa, T. M. Williams, and S. B. Carroll, Generation of a novel wing colour pattern by the Wingless morphogen, Nature, vol.464, pp.1143-1148, 2010.

B. Wertheim, L. W. Beukeboom, and L. Van-de-zande, Polyploidy in Animals: Effects of Gene Expression on Sex Determination, Evolution and Ecology, Cytogenet Genome Res, vol.140, pp.256-269, 2013.

M. West-eberhard, Developmental Plasticity and Evolution, 2003.

H. M. Wilbur and J. P. Collins, Ecological Aspects of Amphibian Metamorphosis: Nonnormal distributions of competitive ability reflect selection for facultative metamorphosis, Science (80-), vol.182, pp.1305-1314, 1973.

R. M. Williams, R. J. Winkfein, R. S. Ginger, M. R. Green, P. P. Schnetkamp et al., A functional approach to understanding the role of NCKX5 in Xenopus pigmentation (EM Verheyen, PLoS One, vol.12, p.180465, 2017.

J. B. Wolf, I. Brodie, . Ed, and A. J. Moore, Interacting Phenotypes and the Evolutionary Process. II. Selection Resulting from Social Interactions, Am Nat, vol.153, pp.254-266, 1999.

W. Horrell, E. M. Boulanger, M. C. , D. Orazio, and J. A. , Melanocortin 1 Receptor: Structure, Function, and Regulation, 2016.

K. H. Wolfe, Yesterday's polyploids and the mystery of diploidization, Nat Rev Genet, vol.2, pp.333-341, 2001.

K. H. Wolfe, Origin of the Yeast Whole-Genome Duplication, PLOS Biol, vol.13, p.1002221, 2015.

K. H. Wolfe and D. C. Shields, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, vol.387, pp.708-713, 1997.

G. M. Wright and K. M. Mcburney, Changes in the ventral dermis and development of iridophores in the anadromous sea lamprey, Petromyzon marinus, during metamorphosis: an ultrastructural study, Histol Histopathol, vol.7, pp.237-50, 1992.

X. Wu and X. Qi, Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication, BMC Evol Biol, vol.10, p.145, 2010.

M. F. Wucherer and N. K. Michiels, A Fluorescent Chromatophore Changes the Level of Fluorescence in a Reef Fish, PLoS One, vol.7, p.37913, 2012.

M. F. Wucherer and N. K. Michiels, Regulation of red fluorescent light emission in a cryptic marine fish, Front Zool, vol.11, p.1, 2014.

P. Xu, X. Zhang, X. Wang, J. Li, G. Liu et al., Genome sequence and genetic diversity of the common carp, Cyprinus carpio, Nat Genet, vol.46, pp.1212-1219, 2014.

P. Xu, X. Zhang, X. Wang, J. Li, G. Liu et al., Genome sequence and genetic diversity of the common carp, Cyprinus carpio, Nat Genet, vol.46, pp.1212-1219, 2014.

Y. Sadovy-de-mitcheson and P. L. Colin, Reef Fish Spawning Aggregations: Biology, Research and Management, Reef Fish Spawning Aggregations: Biology, Research and Management, vol.565, pp.405-565, 2012.

C. Yaeger, A. M. Ros, V. Cross, R. S. Deangelis, D. J. Stobaugh et al., Blockade of arginine vasotocin signaling reduces aggressive behavior and c-Fos expression in the preoptic area and periventricular nucleus of the posterior tuberculum in male Amphiprion ocellaris, Neuroscience, vol.267, pp.205-218, 2014.

Y. Yamagata, E. Yamamoto, K. Aya, K. T. Win, K. Doi et al., , 2010.

, Mitochondrial gene in the nuclear genome induces reproductive barrier in rice, Proc Natl Acad Sci, vol.107, pp.1494-1499

K. Yamano and S. Miwa, Differential gene expression of thyroid hormone receptor alpha and beta in fish development, Gen Comp Endocrinol, vol.109, pp.75-85, 1998.

I. Yanai, L. Peshkin, P. Jorgensen, and M. W. Kirschner, Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility, Dev Cell, vol.20, pp.483-496, 2011.

H. Yang, Y. Zhou, J. Gu, S. Xie, Y. Xu et al., Deep mRNA Sequencing Analysis to Capture the Transcriptome Landscape of Zebrafish Embryos and Larvae, PLoS One, vol.8, p.64058, 2013.

Y. Yaoita, Y. Shi, and D. Brown, Xenopus laevis alpha and beta thyroid hormone receptors, Proc Natl Acad Sci, vol.87, p.8684, 1990.

I. Yasir and J. G. Qin, Embryology and early ontogeny of an anemonefish Amphiprion ocellaris, J Mar Biol Assoc UK, vol.87, p.1025, 2007.

I. Yasir and J. G. Qin, Effect of Light Intensity on Color Performance of False Clownfish, Amphiprion ocellaris Cuvier, J World Aquac Soc, vol.40, pp.337-350, 2009.

I. Yasir and J. G. Qin, Impact of Background on Color Performance of False Clownfish, Amphiprion ocellaris, Cuvier. J World Aquac Soc, vol.40, pp.724-734, 2009.

I. Yasir and J. G. Qin, Effect of dietary carotenoids on skin color and pigments of false clownfish, Amphiprion ocellaris, Cuvier. J World Aquac Soc, vol.41, pp.308-318, 2010.

M. Yúfera, S. Halm, S. Beltran, B. Fusté, J. V. Planas et al., , 2012.

, Transcriptomic Characterization of the Larval Stage in Gilthead Seabream (Sparus aurata) by 454 Pyrosequencing, Mar Biotechnol, vol.14, pp.423-435

A. Zahavi, Mate selection-a selection for a handicap, J Theor Biol, vol.53, p.205, 1975.

A. Zahavi, The cost of honesty, 1977.

, J Theor Biol, vol.67, pp.603-608

F. Zapata, F. E. Goetz, S. A. Smith, M. Howison, S. Siebert et al., , 2015.

, Phylogenomic Analyses Support Traditional Relationships within Cnidaria (RE Steele, PLoS One, vol.10, p.139068

O. Zarnescu, Ultrastructure of the skin melanophores and iridophores in paddlefish, Polyodon spathula, Micron, vol.38, pp.81-84, 2007.

B. Zhang and S. Horvath, A general framework for weighted gene coexpression network analysis, Stat Appl Genet Mol Biol, vol.4, p.17, 2005.

Y. Zhang, J. Liu, W. Fu, W. Xu, H. Zhang et al., Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.), BMC Genet, vol.18, p.95, 2017.

H. Zhang, N. Okamoto, and Y. Ikeda, Two c-myc genes from a tetraploid fish, the common carp (Cyprinus carpio), Gene, vol.153, pp.231-236, 1995.

H. Zhang, V. Ravi, B. Tay, S. Tohari, N. E. Pillai et al., Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters, Proc Natl Acad Sci, vol.114, pp.9146-9151, 2017.

X. Zhou, L. Ren, Q. Meng, Y. Li, Y. Yu et al., The next-generation sequencing technology and application, Protein Cell, vol.1, pp.520-536, 2010.