M. Long, E. Betrán, K. Thornton, and W. Wang, The origin of new genes: glimpses from the young and old, Nature Reviews Genetics, vol.4, issue.11, pp.865-875, 2003.
DOI : 10.1038/nrg1204

M. Lynch, The Origins of Genome Architecture (Sinauer Associates, 2007.

R. Rogers and D. Hartl, Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster, Molecular Biology and Evolution, vol.29, issue.2, 2011.
DOI : 10.1093/molbev/msr184

A. Marques, I. Dupanloup, N. Vinckenbosch, A. Reymond, and H. Kaessmann, Emergence of Young Human Genes after a Burst of Retroposition in Primates, PLoS Biology, vol.22, issue.11, p.357, 2005.
DOI : 10.1371/journal.pbio.0030357.st001

R. Singh and R. Kulathinal, Male sex drive and the masculinization of the genome, BioEssays, vol.100, issue.5, pp.518-525, 2005.
DOI : 10.1002/bies.20212

R. Singh and C. Artieri, Male Sex Drive and the Maintenance of Sex: Evidence from Drosophila, Journal of Heredity, vol.101, issue.Supplement 1, pp.100-106, 2010.
DOI : 10.1093/jhered/esq006

K. Kleene, Sexual selection, genetic conflict, selfish genes, and the atypical patterns of gene expression in spermatogenic cells, Developmental Biology, vol.277, issue.1, pp.16-26, 2005.
DOI : 10.1016/j.ydbio.2004.09.031

E. Betrán, K. Thornton, and M. Long, Retroposed New Genes Out of the X in Drosophila, Genome Research, vol.12, issue.12, pp.1854-1859, 2002.
DOI : 10.1101/gr.6049

S. Dorus, Z. Freeman, E. Parker, B. Heath, and T. Karr, Recent Origins of Sperm Genes in Drosophila, Molecular Biology and Evolution, vol.25, issue.10, pp.2157-2166, 2008.
DOI : 10.1093/molbev/msn162

J. Emerson, H. Kaessmann, E. Betrán, and M. Long, Extensive Gene Traffic on the Mammalian X Chromosome, Science, vol.303, issue.5657, pp.537-540, 2004.
DOI : 10.1126/science.1090042

R. Kalamegham, D. Sturgill, E. Siegfried, and B. Oliver, Drosophila mojoless, a Retroposed GSK-3, Has Functionally Diverged to Acquire an Essential Role in Male Fertility, Molecular Biology and Evolution, vol.24, issue.3, pp.732-742, 2007.
DOI : 10.1093/molbev/msl201

B. Loppin, D. Lepetit, S. Dorus, P. Couble, and T. Karr, Origin and Neofunctionalization of a Drosophila Paternal Effect Gene Essential for Zygote Viability, Current Biology, vol.15, issue.2, pp.87-93, 2005.
DOI : 10.1016/j.cub.2004.12.071
URL : https://hal.archives-ouvertes.fr/hal-00145029

Y. Ding, A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes, PLoS Genetics, vol.463, issue.12, p.1001255, 2010.
DOI : 10.1371/journal.pgen.1001255.s008

T. Heinen, F. Staubach, D. Häming, and D. Tautz, Emergence of a New Gene from an Intergenic Region, Current Biology, vol.19, issue.18, pp.1527-1531, 2009.
DOI : 10.1016/j.cub.2009.07.049

H. Dai, The evolution of courtship behaviors through the origination of a new gene in Drosophila, Proceedings of the National Academy of Sciences, vol.105, issue.21, pp.7478-7483, 2008.
DOI : 10.1073/pnas.0800693105

K. Tamura, S. Subramanian, and S. Kumar, Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks, Molecular Biology and Evolution, vol.21, issue.1, pp.36-44, 2004.
DOI : 10.1093/molbev/msg236

D. Nurminsky, M. Nurminskaya, D. Aguiar, D. Hartl, and D. , Selective sweep of a newly evolved sperm-specific gene in Drosophila, Nature, vol.396, issue.6711, pp.572-575, 1998.
DOI : 10.1038/25126

J. Ranz, A. Ponce, D. Hartl, and D. Nurminsky, Origin and evolution of a new gene expressed in the Drosophila sperm axoneme, Genetica, vol.118, pp.233-244, 2003.
DOI : 10.1007/978-94-010-0229-5_12

R. Ponce and D. Hartl, The evolution of the novel Sdic gene cluster in Drosophila melanogaster, Gene, vol.376, issue.2, pp.174-183, 2006.
DOI : 10.1016/j.gene.2006.02.011

R. Kulathinal, Selective sweep in the evolution of a new sperm-specific gene. Drosophila. Selective Sweep, Nurminsky D, 2004.

D. Nurminsky, D. Aguiar, C. Bustamante, and D. Hartl, Chromosomal Effects of Rapid Gene Evolution in Drosophila melanogaster, Science, vol.291, issue.5501, pp.128-130, 2001.
DOI : 10.1126/science.291.5501.128

B. Charlesworth and D. Charlesworth, How was the Sdic gene fixed?, Nature, vol.400, issue.6744, pp.519-520, 1999.
DOI : 10.1038/22922

K. Golic and M. Golic, Engineering the Drosophila genome: Chromosome rearrangements by design, Genetics, vol.144, pp.1693-1711, 1996.

A. Parks, Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome, Nature Genetics, vol.36, issue.3, pp.288-292, 2004.
DOI : 10.1038/ng1312

B. Graveley, The developmental transcriptome of Drosophila melanogaster, Nature, vol.31, issue.7339, pp.473-479, 2010.
DOI : 10.1038/nature09715

D. Lindsley and G. Zimm, The Genome f Drosophila Melanogaster (Academic, p.1133, 1992.

K. Boylan and T. Hays, The gene for the intermediate chain subunit of cytoplasmic dynein is essential in Drosophila, Genetics, vol.162, pp.1211-1220, 2002.

S. Tweedie, FlyBase: enhancing Drosophila Gene Ontology annotations, Nucleic Acids Research, vol.37, issue.Database, pp.555-559, 2009.
DOI : 10.1093/nar/gkn788

T. Markow, Evolution of Drosophila mating systems, Evolutionary Biology Hecht MK, vol.29, pp.73-106, 1996.

C. Ting, Gene duplication and speciation in Drosophila: Evidence from the Odysseus locus, Proceedings of the National Academy of Sciences, vol.101, issue.33, pp.12232-12235, 2004.
DOI : 10.1073/pnas.0401975101

R. Milkmann and R. Zeitler, Concurrent multiple paternity in natural and laboratory populations of Drosophila melanogaster, Genetics, vol.78, pp.1191-1193, 1974.

G. Parker, SPERM COMPETITION AND ITS EVOLUTIONARY CONSEQUENCES IN THE INSECTS, Biological Reviews, vol.52, issue.4, pp.525-567, 1970.
DOI : 10.1007/BF00304158

R. Griffiths, S. Mckechnie, and J. Mckenzie, Multiple mating and sperm displacement in natural populations of Drosophila melanogaster, Theor Appl Genet, vol.62, pp.89-96, 1982.

M. Gromko, K. Sheehan, and R. Richmond, Random Mating in Two Species of Drosophila, The American Naturalist, vol.115, issue.4, pp.467-479, 1980.
DOI : 10.1086/283574

G. Lefevre, J. Jonsson, and U. , Sperm transfer, storage, displacement, and utilization in Drosophila melanogaster, Genetics, vol.47, pp.1719-1736, 1962.

A. Civetta, Direct visualization of sperm competition and sperm storage in Drosophila, Current Biology, vol.9, issue.15, pp.841-844, 1999.
DOI : 10.1016/S0960-9822(99)80370-4

M. Manier, Resolving Mechanisms of Competitive Fertilization Success in Drosophila melanogaster, Science, vol.328, issue.5976, pp.354-357, 2010.
DOI : 10.1126/science.1187096

A. Clark, M. Aguadé, T. Prout, L. Harshman, and C. Langley, Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster, Genetics, vol.139, pp.189-201, 1995.

J. Good, C. Ross, and T. Markow, Multiple paternity in wild-caught Drosophila mojavensis, Molecular Ecology, vol.17, issue.8, pp.2253-2260, 2006.
DOI : 10.1111/j.1365-294X.2006.02847.x

B. Jones and A. Clark, Bayesian sperm competition estimates, Genetics, vol.163, pp.1193-1199, 2003.

T. Karasov, P. Messer, and D. Petrov, Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites, PLoS Genetics, vol.30, issue.6, p.1000924, 2010.
DOI : 10.1371/journal.pgen.1000924.s006

A. Ghosh-roy, B. Desai, and K. Ray, Dynein Light Chain 1 Regulates Dynamin-mediated F-Actin Assembly during Sperm Individualization in Drosophila, Molecular Biology of the Cell, vol.16, issue.7, pp.3107-3116, 2005.
DOI : 10.1091/mbc.E05-02-0103

P. Pevzner, H. Tang, and G. Tesler, De Novo Repeat Classification and Fragment Assembly, Genome Research, vol.14, issue.9, pp.1786-1796, 2004.
DOI : 10.1101/gr.2395204

M. Adams, The Genome Sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-2195, 2000.
DOI : 10.1126/science.287.5461.2185

S. Celniker, Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence, Genome Biol, vol.314, issue.12, pp.79-80, 2002.

A. Carvalho, B. Lazzaro, and A. Clark, Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides, Proceedings of the National Academy of Sciences, vol.97, issue.24, pp.13239-13244, 2000.
DOI : 10.1073/pnas.230438397

L. Greenspan and A. Clark, Associations between variation in X chromosome male reproductive genes and sperm competitive ability in Drosophila melanogaster, Int J Evol Biol, p.214280, 2011.

W. Swanson, A. Clark, H. Waldrip-dail, M. Wolfner, and C. Aquadro, Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila, Proceedings of the National Academy of Sciences, vol.98, issue.13, pp.7375-7379, 2001.
DOI : 10.1073/pnas.131568198

J. Mueller, Cross-Species Comparison of Drosophila Male Accessory Gland Protein Genes, Genetics, vol.171, issue.1, pp.131-143, 2005.
DOI : 10.1534/genetics.105.043844

M. Ashburner, Drosophila: A Laboratory Manual, 1989.

E. Boorman and G. Parker, Sperm (ejaculate) competition in Drosophila melanogaster, and the reproductive value of females to males in relation to female age and mating status, Ecological Entomology, vol.8, issue.3, pp.145-155, 1976.
DOI : 10.1007/BF00304158

M. Gromko, D. Gilbert, and R. Richmond, Sperm transfer and use in the multiple mating system of Drosophila. Sperm Competition and the Evolution of Animal Mating Systems, Smith RL, pp.372-427, 1984.

S. Shapiro and M. Wilk, An analysis of variance test for normality (complete samples), Biometrika, vol.52, issue.3-4, pp.591-611, 1965.
DOI : 10.1093/biomet/52.3-4.591

R. Sokal and F. Rohlf, Biometry: The Principles and Practice of, Statistics in Biological Research, 1994.

S. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

R. Durbin, S. Eddy, S. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, p.pp, 1998.
DOI : 10.1017/CBO9780511790492

K. Katoh and H. Toh, Recent developments in the MAFFT multiple sequence alignment program, Briefings in Bioinformatics, vol.9, issue.4, pp.286-298, 2008.
DOI : 10.1093/bib/bbn013

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-595, 2010.
DOI : 10.1093/bioinformatics/btp698

A. Vilella, A. Blanco-garcia, S. Hutter, and J. Rozas, VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data, Bioinformatics, vol.21, issue.11, pp.2791-2793, 2005.
DOI : 10.1093/bioinformatics/bti403

S. Pimpinelli and D. P. , Cytogenetic analysis of segregation distortion in Drosophila melanogaster: The cytological organization of the Responder (Rsp) locus, Genetics, vol.121, pp.765-772, 1989.

M. Accardo and D. P. , Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (BACs) to Mitotic Heterochromatin of Drosophila, Methods Mol Biol, vol.659, pp.389-400, 2010.
DOI : 10.1007/978-1-60761-789-1_30