C. Biémont, WORLDWIDE DISTRIBUTION OF TRANSPOSABLE ELEMENT COPY NUMBER IN NATURAL POPULATIONS OF DROSOPHILA SIMULANS, Evolution, vol.59, issue.1, pp.159-167, 2003.
DOI : 10.1007/s004380050910

H. Cerutti and J. A. Casas-mollano, On the origin and functions of RNA-mediated silencing: from protists to man, Current Genetics, vol.299, issue.2, pp.81-99, 2006.
DOI : 10.1007/s00294-006-0078-x

S. Chambeyron, piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline, Proceedings of the National Academy of Sciences of the United States of America, pp.14964-14969, 2008.
DOI : 10.1073/pnas.0508192102

URL : https://hal.archives-ouvertes.fr/hal-00331712

H. A. Cook, The Drosophila SDE3 Homolog armitage Is Required for oskar mRNA Silencing and Embryonic Axis Specification, Cell, vol.116, issue.6, pp.817-829, 2004.
DOI : 10.1016/S0092-8674(04)00250-8

D. N. Cox, A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal, Genes & Development, vol.12, issue.23, pp.3715-3727, 1998.
DOI : 10.1101/gad.12.23.3715

R. D. Dowell, Genotype to Phenotype: A Complex Problem, Science, vol.327, issue.5964, pp.328-469, 2010.
DOI : 10.1126/science.1180823

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269

A. González-reyes, H. Elliott, and D. St-johnston, Oocyte determination and the origin of polarity in Drosophila: the role of the spindle genes, Development, issue.24, pp.124-4927, 1997.

S. Henikoff and J. G. Henikoff, Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences of the United States of America, pp.10915-10919, 1992.
DOI : 10.1073/pnas.89.22.10915

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/pdf

A. I. Kalmykova, M. S. Klenov, and V. A. Gvozdev, Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline, Nucleic Acids Research, vol.33, issue.6, pp.2052-2059, 2005.
DOI : 10.1093/nar/gki323

E. S. Kelleher and D. A. Barbash, Analysis of piRNA-Mediated Silencing of Active TEs in Drosophila melanogaster Suggests Limits on the Evolution of Host Genome Defense, Molecular Biology and Evolution, vol.30, issue.8, pp.1816-1829, 2013.
DOI : 10.1093/molbev/mst081

J. S. Khurana, Adaptation to P Element Transposon Invasion in Drosophila melanogaster, Cell, vol.147, issue.7, pp.1551-1563, 2011.
DOI : 10.1016/j.cell.2011.11.042

URL : http://doi.org/10.1016/j.cell.2011.11.042

C. Klattenhoff and W. Theurkauf, Biogenesis and germline functions of piRNAs, Development, vol.135, issue.1, pp.3-9, 2008.
DOI : 10.1242/dev.006486

URL : http://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=2251&context=oapubs

B. Kolaczkowski, D. N. Hupalo, and A. D. Kern, Recurrent Adaptation in RNA Interference Genes Across the Drosophila Phylogeny, Molecular Biology and Evolution, vol.28, issue.2, pp.1033-1042, 2011.
DOI : 10.1093/molbev/msq284

D. Lachaise, Historical Biogeography of the Drosophila melanogaster Species Subgroup, pp.159-225, 1988.
DOI : 10.1007/978-1-4613-0931-4_4

M. K. Lawniczak, Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans, Genome Biology, vol.9, issue.8, p.125, 2008.
DOI : 10.1186/gb-2008-9-8-r125

B. Lemos, Evolution of Proteins and Gene Expression Levels are Coupled in Drosophila and are Independently Associated with mRNA Abundance, Protein Length, and Number of Protein-Protein Interactions, Molecular Biology and Evolution, vol.22, issue.5, pp.1345-1354, 2005.
DOI : 10.1093/molbev/msi122

C. Li, Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies, Cell, vol.137, issue.3, pp.509-521, 2009.
DOI : 10.1016/j.cell.2009.04.027

J. Lu and A. G. Clark, Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila, Genome Research, vol.20, issue.2, pp.212-227, 2010.
DOI : 10.1101/gr.095406.109

C. D. Malone and G. J. Hannon, Small RNAs as Guardians of the Genome, Cell, vol.136, issue.4, pp.656-668, 2009.
DOI : 10.1016/j.cell.2009.01.045

G. Meister, Argonaute proteins: functional insights and emerging roles, Nature Reviews Genetics, vol.136, issue.7, pp.447-459, 2013.
DOI : 10.1038/nrg3462

S. V. Nuzhdin, Common Pattern of Evolution of Gene Expression Level and Protein Sequence in Drosophila, Molecular Biology and Evolution, vol.21, issue.7, pp.1308-1317, 2004.
DOI : 10.1093/molbev/msh128

D. J. Obbard and J. J. Welch, Quantifying Adaptive Evolution in the Drosophila Immune System, PLoS Genetics, vol.355, issue.10, p.1000698, 2009.
DOI : 10.1371/journal.pgen.1000698.s030

D. J. Obbard and K. H. Gordon, The evolution of RNAi as a defence against viruses and transposable elements, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.20, issue.23, pp.36499-115, 1513.
DOI : 10.1101/gad.1495506

D. Olivieri, An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila, The EMBO Journal, vol.1, issue.19, pp.3301-3317, 2010.
DOI : 10.1002/gene.20070

A. Pane, K. Wehr, and T. Schüpbach, zucchini and squash Encode Two Putative Nucleases Required for rasiRNA Production in the Drosophila Germline, Developmental Cell, vol.12, issue.6, pp.851-862, 2007.
DOI : 10.1016/j.devcel.2007.03.022

A. Pélisson, A Novel Repeat-Associated Small Interfering RNA-Mediated Silencing Pathway Downregulates Complementary Sense gypsy Transcripts in Somatic Cells of the Drosophila Ovary, Journal of Virology, vol.81, issue.4, pp.1951-1960, 2007.
DOI : 10.1128/JVI.01980-06

K. Saito and M. C. Siomi, Small RNA-Mediated Quiescence of Transposable Elements in Animals, Developmental Cell, vol.19, issue.5, pp.687-697, 2010.
DOI : 10.1016/j.devcel.2010.10.011

T. Schüpbach and E. Wieschaus, Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology, Genetics, vol.129, issue.4, pp.1119-1136, 1991.

K. Senti and J. Brennecke, The piRNA pathway: a fly's perspective on the guardian of the genome, Trends in Genetics, vol.26, issue.12, pp.499-509, 2010.
DOI : 10.1016/j.tig.2010.08.007

M. C. Siomi, PIWI-interacting small RNAs: the vanguard of genome defence, Nature Reviews Molecular Cell Biology, vol.103, issue.4, pp.246-258, 2011.
DOI : 10.1038/nrm3089

L. Thomas and A. , Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state, Genes & Development, vol.27, issue.4, pp.390-399, 2013.
DOI : 10.1101/gad.209841.112

V. V. Vagin, A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline, Science, vol.313, issue.5785, pp.313320-324, 2006.
DOI : 10.1126/science.1129333

V. V. Vagin, The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster, RNA biology, vol.1, issue.1, pp.54-58, 2004.

C. Vieira, Wake up of transposable elements following Drosophila simulans worldwide colonization, Molecular Biology and Evolution, vol.16, issue.9, pp.1251-1255, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026215

URL : https://hal.archives-ouvertes.fr/hal-00428465