E. Abouheif, M. Favé, A. S. Ibarrarán-viniegra, M. P. Lesoway, A. M. Rafiqi et al., Eco-Evo-Devo: The Time Has Come, Ecological genomics, pp.107-125, 2014.
DOI : 10.1007/978-94-007-7347-9_6

A. Abzhanov, M. Protas, B. R. Grant, P. R. Grant, and C. J. Tabin, Bmp4 and Morphological Variation of Beaks in Darwin's Finches, Science, vol.305, issue.5689, pp.1462-1465, 2004.
DOI : 10.1126/science.1098095

B. Altincicek, J. L. Kovacs, and N. M. Gerardo, Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae, Biology Letters, vol.55, issue.7, pp.253-257, 2012.
DOI : 10.1016/j.jinsphys.2009.04.005

L. Avery and S. Wasserman, Ordering gene function: the interpretation of epistasis in regulatory hierarchies, Trends in Genetics, vol.8, issue.9, pp.312-316, 1992.
DOI : 10.1016/0168-9525(92)90263-4

R. S. Baucom, The remarkable repeated evolution of herbicide resistance, American Journal of Botany, vol.103, issue.2, pp.181-183, 2016.
DOI : 10.3732/ajb.1500510

P. M. Bingham and B. H. Judd, A copy of the copia transposable element is very tightly linked to the wa allele at the white locus of D. melanogaster, Cell, vol.25, issue.3, pp.705-711, 1981.
DOI : 10.1016/0092-8674(81)90177-X

P. M. Bingham, R. Levis, and G. M. Rubin, Cloning of DNA sequences from the white locus of D. melanogaster by a novel and general method, Cell, vol.25, issue.3, pp.693-704, 1981.
DOI : 10.1016/0092-8674(81)90176-8

V. A. Blomen, P. Májek, L. T. Jae, J. W. Bigenzahn, J. Nieuwenhuis et al., Gene essentiality and synthetic lethality in haploid human cells, Science, vol.350, issue.6264, pp.1092-1096, 2015.
DOI : 10.1126/science.aac7557

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau et al., Super-resolution imaging reveals distinct chromatin folding for different epigenetic states, Nature, vol.13, issue.7586, pp.418-422, 2016.
DOI : 10.1038/nature16496

C. Bridges and K. Brehme, The mutants of Drosophila melanogaster. With foreword by TH Morgan, 1944.

I. Brigandt and A. Love, Reductionism in biology The Stanford encyclopedia of philosophy, 2008.

J. D. Cande, V. S. Chopra, and M. Levine, Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum, Development, vol.136, issue.18, pp.3153-3160, 2009.
DOI : 10.1242/dev.038034

S. B. Carroll, Evolution at Two Levels: On Genes and Form, PLoS Biology, vol.21, issue.7, 2005.
DOI : 10.1371/journal.pbio.0030245.g003

E. Cassirer, Substance and function, 1910.

C. Cobbs, J. Heath, J. O. Stireman, and P. Abbot, Carotenoids in unexpected places: Gall midges, lateral gene transfer, and carotenoid biosynthesis in animals, Molecular Phylogenetics and Evolution, vol.68, issue.2, pp.221-228, 2013.
DOI : 10.1016/j.ympev.2013.03.012

H. J. Cordell, Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans, Human Molecular Genetics, vol.11, issue.20, pp.2463-2468, 2002.
DOI : 10.1093/hmg/11.20.2463

C. Darwin, On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, 1859.

C. Darwin, The variation of animals and plants under domestication, 1868.

C. Darwin, Pangenesis, Nature, vol.3, issue.78, pp.502-503, 1871.
DOI : 10.1038/003502a0

P. David and S. Samadi, La the´orie de l'e´volution: Une logique pour la biologie, 2011.

D. Davison, C. H. Chapman, C. Wedeen, and P. M. Bingham, Genetic and physical studies of a portion of the white locus participating in transcriptional regulation and in synapsis-dependent interactions in Drosophila adult tissues, Genetics, issue.3, pp.110-479, 1985.

R. Dawkins, The selfish gene, 1976.

H. De-vries, Intracellular pangenesis. Chicago: The Open Court Publishing Co LeGène: Un concept en e´volution, Deutsch, J, 1889.

I. Ezkurdia, D. Juan, J. M. Rodriguez, A. Frankish, M. Diekhans et al., Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes, Human Molecular Genetics, vol.23, issue.22, pp.5866-5878, 2014.
DOI : 10.1093/hmg/ddu309

D. S. Falconer and T. F. Mackay, Introduction to quantitative genetics, 1996.

R. Falk, The gene in search of an identity, Human Genetics, vol.171, issue.3, pp.195-204, 1984.
DOI : 10.1007/BF00418388

R. Falk, What is a gene????Revisited, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, vol.41, issue.4, pp.396-406, 2010.
DOI : 10.1016/j.shpsc.2010.10.014

S. H. Fuss, M. Omura, and P. Mombaerts, Local and cis Effects of the H Element on Expression of Odorant Receptor Genes in Mouse, Cell, vol.130, issue.2, pp.373-384, 2007.
DOI : 10.1016/j.cell.2007.06.023

W. J. Gehring, R. Klemenz, U. Weber, and U. Kloter, Functional analysis of the white gene of Drosophila by P-factor-mediated transformation, The EMBO Journal, vol.3, pp.2077-2085, 1984.

W. J. Gehring and R. Paro, Isolation of a hybrid plasmid with homologous sequences to a transposing element of drosophila melanogaster, Cell, vol.19, issue.4, pp.897-904, 1980.
DOI : 10.1016/0092-8674(80)90081-1

M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du et al., What is a gene, post-ENCODE? History and updated definition, Genome Research, vol.17, issue.6, pp.669-681, 2007.
DOI : 10.1101/gr.6339607

S. F. Gilbert, Genes classical and genes developmental: The different uses of genes in evolutionary syntheses The concept of The Concept of Gene ARTICLE IN PRESS the gene in development and evolution, pp.178-192, 2000.

S. F. Gilbert and D. Epel, Ecological Developmental Biology, 2009.
DOI : 10.1186/s12915-014-0097-x

M. M. Green, Putative non-reciprocal crossing over in Drosophila melanogaster, Zeitschrift f???r Vererbungslehre, vol.33, issue.3, pp.375-384, 1959.
DOI : 10.1007/BF00888812

M. M. Green, The " genesis of the white-eyed mutant " in Drosophila melanogaster: A reappraisal, Genetics, pp.142-329, 1996.

P. Griffiths and K. Stotz, Genetics and philosophy: An introduction, 2013.
DOI : 10.1017/CBO9780511744082

T. Hazelrigg, R. Levis, and G. M. Rubin, Transformation of white locus DNA in Drosophila: Dosage compensation, zeste interaction, and position effects, Cell, vol.36, issue.2, pp.469-481, 1984.
DOI : 10.1016/0092-8674(84)90240-X

P. W. Hedrick, Genetics of populations, 2011.

C. G. Hempel and P. Oppenheim, Studies in the Logic of Explanation, Philosophy of Science, vol.15, issue.2, pp.135-175, 1948.
DOI : 10.1086/286983

J. Hou, A. Friedrich, J. Gounot, and J. Schacherer, Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast, Nature Communications, vol.4, p.7214, 2015.
DOI : 10.1186/2047-217X-1-18

D. Houle, Numbering the hairs on our heads: The shared challenge and promise of phenomics, Proceedings of the National Academy of Sciences, vol.107, issue.suppl_1, pp.1793-1799, 2010.
DOI : 10.1073/pnas.0906195106

D. L. Hull, THE EFFECT OF ESSENTIALISM ON TAXONOMY???TWO THOUSAND YEARS OF STASIS (I), The British Journal for the Philosophy of Science, vol.XV, issue.60, 1965.
DOI : 10.1093/bjps/XV.60.314

T. R. Hurd, F. Liang, and R. Lehmann, Curly encodes dual oxidase, which acts with heme peroxidase Curly Su to shape the adult Drosophila wing, PLoS Genetics, vol.11, 2015.

F. Imsland, C. Feng, H. Boije, B. Bed-'hom, V. Fillon et al., The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility, PLoS Genetics, vol.59, issue.6, 2012.
DOI : 10.1371/journal.pgen.1002775.s014

URL : https://hal.archives-ouvertes.fr/hal-01019806

W. Johannsen, The Genotype Conception of Heredity, The American Naturalist, vol.45, issue.531, pp.129-159, 1911.
DOI : 10.1086/279202

E. F. Keller, The century of the gene, 2009.

E. F. Keller, The mirage of a space between nature and nurture, 2010.
DOI : 10.1215/9780822392811

R. Levis, T. Hazelrigg, and G. M. Rubin, Separable cis-acting control elements for expression of the white gene of Drosophila, The EMBO Journal, vol.4, pp.3489-3499, 1985.

E. B. Lewis, The Pseudoallelism of White and Apricot in Drosophila Melanogaster, Proceedings of the National Academy of Sciences, vol.38, issue.11, pp.953-961, 1952.
DOI : 10.1073/pnas.38.11.953

E. B. Lewis, An unstable gene in Drosophila melanogaster, Genetics, pp.41-651, 1956.

E. B. Lewis, Remembering Sturtevant, Genetics, pp.141-1227, 1995.

R. C. Lewontin, The Units of Selection, Annual Review of Ecology and Systematics, vol.1, issue.1, pp.1-18, 1970.
DOI : 10.1146/annurev.es.01.110170.000245

R. C. Lewontin, The triple helix: Gene, organism, and environment, 2001.

M. Lynch and B. Walsh, Genetics and analysis of quantitative traits, 1998.

M. E. Mackendrick and G. Pontecorvo, Crossing-over between alleles at thew locus inDrosophila melanogaster, Experientia, vol.3, issue.10, pp.390-391, 1952.
DOI : 10.1007/BF02176203

A. Martin and V. Orgogozo, THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION, Evolution, vol.109, pp.1235-1250, 2013.
DOI : 10.1111/evo.12081

E. Mayr, Evolution and the diversity of life, 1975.

A. Mcgregor, V. Orgogozo, I. Delon, J. Zanet, D. Srinivasan et al., Morphological evolution through multiple cis-regulatory mutations at a single gene, Nature, vol.87, issue.7153, pp.587-590, 2007.
DOI : 10.1038/nature05988

URL : https://hal.archives-ouvertes.fr/hal-00169725

G. Mendel, Versuche u ¨ber Pflanzenhybriden, Verhandlungen Naturforschenden Vereines Brunn, vol.4, pp.3-47, 1866.

N. A. Moran and T. Jarvik, Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids, Science, vol.328, issue.5978, pp.624-627, 2010.
DOI : 10.1126/science.1187113

M. Morange, Une histoire de la biologie, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01373891

T. Morgan, SEX LIMITED INHERITANCE IN DROSOPHILA, Science, vol.32, issue.812, pp.120-122, 1910.
DOI : 10.1126/science.32.812.120

L. Moss, $59.95. xvi + 384 p; ill.; index. ISBN: 0???521???77187???0. 2000., The Quarterly Review of Biology, vol.78, issue.1, pp.57-67, 2003.
DOI : 10.1086/367581

O. 'hare, K. Levis, R. Rubin, and G. M. , Transcription of the white locus in Drosophila melanogaster, Proceedings of the National Academy of Sciences of the United States of America, issue.22, pp.80-6917, 1983.

O. 'hare, K. Murphy, C. Levis, R. Rubin, and G. M. , DNA sequence of the white locus of Drosophila melanogaster, Journal of Molecular Biology, vol.180, issue.3, pp.437-455, 1984.
DOI : 10.1016/0022-2836(84)90021-4

R. Olby, Mendel No Mendelian?, History of Science, vol.17, issue.1, pp.53-72, 1979.
DOI : 10.1177/007327537901700103

K. M. Olsen and J. F. Wendel, A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes, Annual Review of Plant Biology, vol.64, issue.1, pp.47-70, 2013.
DOI : 10.1146/annurev-arplant-050312-120048

V. Orgogozo, K. W. Broman, and D. L. Stern, High-Resolution Quantitative Trait Locus Mapping Reveals Sign Epistasis Controlling Ovariole Number Between Two Drosophila Species, Genetics, vol.173, issue.1, pp.197-205, 2006.
DOI : 10.1534/genetics.105.054098

V. Orgogozo, B. Morizot, and A. Martin, The differential view of genotype? phenotype relationships, Frontiers in Genetics, vol.6, issue.179, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01354348

S. Oyama, The ontogeny of information: Developmental systems and evolution, 2000.
DOI : 10.1215/9780822380665

A. B. Paaby and M. V. Rockman, The many faces of pleiotropy, Trends in Genetics, vol.29, issue.2, pp.66-73, 2013.
DOI : 10.1016/j.tig.2012.10.010

H. Pearson, Genetics: What is a gene? Nature, pp.398-401, 2006.

C. Pei, H. Wang, J. Zhang, Y. Wang, D. M. Francis et al., Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3, Theoretical and Applied Genetics, vol.41, issue.5, pp.533-542, 2012.
DOI : 10.1007/s00122-011-1726-1

R. J. Petit and L. Excoffier, Gene flow and species delimitation, Trends in Ecology & Evolution, vol.24, issue.7, pp.386-393, 2009.
DOI : 10.1016/j.tree.2009.02.011

P. C. Phillips, Epistasis ??? the essential role of gene interactions in the structure and evolution of genetic systems, Nature Reviews Genetics, vol.1, issue.11, pp.855-867, 2008.
DOI : 10.1038/nrg2452

V. Pirrotta and C. Br?-ockl, Transcription of the Drosophila white locus and some of its mutants, The EMBO Journal, vol.3, issue.3, p.563, 1984.

V. Pirrotta, H. Steller, and M. P. Bozzetti, Multiple upstream regulatory elements control the expression of the Drosophila white gene, The EMBO Journal, vol.4, pp.3501-3508, 1985.

P. Portin, Historical Development of the Concept of the Gene, The Journal of Medicine and Philosophy, vol.27, issue.3, pp.257-286, 2002.
DOI : 10.1076/jmep.27.3.257.2980

T. Pradeu, Toolbox murders: putting genes in their epigenetic and ecological contexts, Biology & Philosophy, vol.5, issue.3, pp.125-142, 2015.
DOI : 10.1007/s10539-014-9471-x

J. R. Raab, S. Resnick, and T. Magnuson, Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes, PLOS Genetics, vol.473, issue.7345, 2015.
DOI : 10.1371/journal.pgen.1005748.s024

W. C. Salmon, Causality without Counterfactuals, Philosophy of Science, vol.61, issue.2, pp.297-312, 1994.
DOI : 10.1086/289801

W. C. Salmon, Causality and Explanation: A Reply to Two Critiques, Philosophy of Science, vol.64, issue.3, pp.461-477, 1997.
DOI : 10.1086/392561

L. L. Sandell and V. A. Zakian, Loss of a yeast telomere: Arrest, recovery, and chromosome loss, Cell, vol.75, issue.4, pp.729-739, 1993.
DOI : 10.1016/0092-8674(93)90493-A

S. Sarkar, Genetics and reductionism, 1998.
DOI : 10.1017/CBO9781139173216

K. Sathasivan, G. W. Haughn, and N. Murai, Molecular Basis of Imidazolinone Herbicide Resistance in Arabidopsis thaliana var Columbia, PLANT PHYSIOLOGY, vol.97, issue.3, pp.1044-1050, 1991.
DOI : 10.1104/pp.97.3.1044

M. Schumer, R. Cui, G. G. Rosenthal, and P. Andolfatto, Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities, PLOS Genetics, vol.60, issue.3, p.1005041, 2015.
DOI : 10.1371/journal.pgen.1005041.s033

E. Sober, Evolution, Population Thinking, and Essentialism, Philosophy of Science, vol.47, issue.3, pp.350-383, 1980.
DOI : 10.1086/288942

F. Spencer and P. Hieter, Centromere DNA mutations induce a mitotic delay in Saccharomyces cerevisiae., Proceedings of the National Academy of Sciences of the United States of America, pp.8908-8912, 1992.
DOI : 10.1073/pnas.89.19.8908

K. Sterelny and P. Kitcher, The Return of the Gene, The Journal of Philosophy, vol.85, issue.7, pp.339-361, 1988.
DOI : 10.2307/2026953

D. L. Stern, PERSPECTIVE: EVOLUTIONARY DEVELOPMENTAL BIOLOGY AND THE PROBLEM OF VARIATION, Evolution, vol.124, issue.4, pp.1079-1091, 2000.
DOI : 10.1126/science.279.5358.1896

D. L. Stern, Evolution, development, and the predictable genome, 2010.

D. Stern and V. Orgogozo, THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?, Evolution, vol.30, issue.256, pp.2155-2177, 2008.
DOI : 10.1111/j.1558-5646.2008.00450.x

J. P. Stoye and M. W. Yap, Chance favors a prepared genome, Proceedings of the National Academy of Sciences, vol.105, issue.9, pp.3177-3178, 2008.
DOI : 10.1073/pnas.0800667105

M. Tassabehji, Williams-Beuren syndrome: a challenge for genotype-phenotype correlations, Human Molecular Genetics, vol.12, issue.suppl 2, pp.229-237, 2003.
DOI : 10.1093/hmg/ddg299

D. Versluis, M. M. D-'andrea, J. R. Garcia, M. M. Leimena, F. Hugenholtz et al., Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions, Scientific Reports, vol.157, issue.1, p.11981, 2015.
DOI : 10.1038/srep11981

N. Wade, Gene sweepstakes ends, but winner may well be wrong, New York Times www.nytimes.com, issue.06, 2003.

L. Ward, The genetics of curly wing in Drosophila. Another case of balanced lethal factors, Genetics, vol.8, p.276, 1923.

C. K. Waters, Causes That Make a Difference, Journal of Philosophy, vol.104, issue.11, pp.551-579, 2007.
DOI : 10.5840/jphil2007104111

M. Weber, Philosophy of experimental biology, 2005.
DOI : 10.1017/CBO9780511498596

J. Weischenfeldt, O. Symmons, F. Spitz, and J. O. Korbel, Phenotypic impact of genomic structural variation: insights from and for human disease, Nature Reviews Genetics, vol.410, issue.2, pp.125-138, 2013.
DOI : 10.1038/nrg3373

J. Woodward, Making things happen: A theory of causal explanation, 2005.
DOI : 10.1093/0195155270.001.0001

Z. Zachar and P. M. Bingham, Regulation of white locus expression: The structure of mutant alleles at the white locus of Drosophila melanogaster, Cell, vol.30, issue.2, pp.529-541, 1982.
DOI : 10.1016/0092-8674(82)90250-1