E. Baack, K. Whitney, and L. Rieseberg, Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species, New Phytologist, vol.75, issue.2, pp.623-630, 2005.
DOI : 10.1111/j.1469-8137.2005.01433.x

B. Carvalho, A. Koerich, L. Clark, and A. , Origin and evolution of the Drosophila Y chromosome, Current Opinion in Genetics & Development, vol.12, issue.6, pp.270-277, 2009.
DOI : 10.1016/S0959-437X(02)00356-8

G. Bosco, P. Campbell, J. Leiva-neto, and T. Markow, Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species, Genetics, vol.177, issue.3, pp.1277-1290, 2007.
DOI : 10.1534/genetics.107.075069

M. Boulesteix, M. Weiss, and C. Bié-mont, Differences in Genome Size Between Closely Related Species: The Drosophila melanogaster Species Subgroup, Molecular Biology and Evolution, vol.23, issue.1, pp.162-167, 2006.
DOI : 10.1093/molbev/msj012

URL : https://hal.archives-ouvertes.fr/hal-00294844

J. Camillo, Reassessment of the genome size in Elaeis guineensis and Elaeis oleifera, and its interspecific hybrid, Genomics Insights, vol.7, pp.13-22, 2014.

E. Carnelossi, Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids, Genome Biology and Evolution, vol.6, issue.7, pp.1806-1817, 2014.
DOI : 10.1093/gbe/evu141

URL : https://hal.archives-ouvertes.fr/hal-01079996

A. Dion-cô-té, S. Renaut, E. Normandeau, and L. Bernatchez, RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species, Molecular Biology and Evolution, vol.31, issue.5, pp.1188-1199, 2014.
DOI : 10.1093/molbev/msu069

L. Ellis, Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity, PLoS Genetics, vol.20, issue.7, p.1004522, 2014.
DOI : 10.1371/journal.pgen.1004522.s017

M. Evgen-'ev, G. Yenikolopov, N. Peunova, and Y. Ilyin, Transposition of mobile genetic elements in interspecific hybrids of Drosophila, Chromosoma, vol.76, issue.3, pp.375-386, 1982.
DOI : 10.1007/BF00330360

A. Fontdevila, Hybrid genome evolution by transposition, Cytogenetic and Genome Research, vol.110, issue.1-4, pp.49-55, 2005.
DOI : 10.1159/000084937

A. Fontdevila, Drosophila koepferae: a New Member of the Drosophila serido (Diptera: Drosophilidae) Superspecies Taxon, Annals of the Entomological Society of America, vol.81, issue.3, pp.380-385, 1988.
DOI : 10.1093/aesa/81.3.380

G. Guerreiro and M. , What makes transposable elements move in the Drosophila genome?, Heredity, vol.31, issue.5, pp.461-468, 2012.
DOI : 10.1134/S1022795406060056

G. Guerreiro and M. , Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae, Molecular Genetics and Genomics, vol.7, issue.4, pp.1471-1483, 2015.
DOI : 10.1007/s00438-015-1012-z

A. Girard and G. Hannon, Conserved themes in small-RNA-mediated transposon control, Trends in Cell Biology, vol.18, issue.3, pp.136-148, 2008.
DOI : 10.1016/j.tcb.2008.01.004

T. Gregory, Genome Size Evolution in Animals, pp.3-87
DOI : 10.1016/B978-012301463-4/50003-6

T. Gregory, The C-value Enigma in Plants and Animals: A Review of Parallels and an Appeal for Partnership, Annals of Botany, vol.95, issue.1, pp.133-146, 2005.
DOI : 10.1093/aob/mci009

T. Gregory and J. Johnston, Genome size diversity in the family Drosophilidae, Heredity, vol.19, issue.3, pp.228-238, 2008.
DOI : 10.1007/BF00056783

Y. Guillé-n, Genomics of Ecological Adaptation in Cactophilic Drosophila, Genome Biology and Evolution, vol.7, issue.1, pp.349-366, 2015.
DOI : 10.1093/gbe/evu291

T. Kawakami, P. Dhakal, A. Katterhenry, C. Heatherington, and M. Ungerer, Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons, Genome Biology and Evolution, vol.3, issue.0, pp.156-167, 2011.
DOI : 10.1093/gbe/evr005

E. Kelleher, N. Edelman, and D. Barbash, Drosophila Interspecific Hybrids Phenocopy piRNA-Pathway Mutants, PLoS Biology, vol.18, issue.11, p.1001428, 2012.
DOI : 10.1371/journal.pbio.1001428.s022

M. Kidwell, Transposable elements and the evolution of genome size in eukaryotes, Genetica, vol.115, issue.1, pp.49-63, 2002.
DOI : 10.1023/A:1016072014259

K. Kraaijeveld, Genome Size and Species Diversification, Evolutionary Biology, vol.3, issue.4, pp.227-233, 2010.
DOI : 10.1007/s11692-010-9093-4

M. Labrador, M. Farré, F. Utzet, and A. Fontdevila, Interspecific hybridization increases transposition rates of Osvaldo, Molecular Biology and Evolution, vol.16, issue.7, pp.931-937, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026182

B. Liu and J. Wendel, Retrotransposon activation followed by rapid repression in introgressed rice plants, Genome, vol.43, issue.5, pp.874-880, 2000.
DOI : 10.1139/g00-058

V. Mahelka, J. Suda, V. Jarolímová, P. Trá-vnicek, and F. Krahulec, Genome size discriminates between closely related taxaElytrigia repens andE. intermedia (Poaceae: Triticeae) and their hybrid, Folia Geobotanica, vol.39, issue.4, pp.367-384, 2005.
DOI : 10.1007/BF02804286

H. Mann and D. Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, The Annals of Mathematical Statistics, vol.18, issue.1, pp.50-60, 1947.
DOI : 10.1214/aoms/1177730491

I. Marin, A. Ruiz, C. Pla, and A. Fontdevila, Reproductive Relationships among Ten Species of the Drosophila repleta Group from South America and the West Indies, Evolution, vol.47, issue.5, pp.1616-1624, 1993.
DOI : 10.2307/2410173

C. Metcalfe, Genomic Instability Within Centromeres of Interspecific Marsupial Hybrids, Genetics, vol.177, issue.4, pp.2507-2517, 2007.
DOI : 10.1534/genetics.107.082313

P. Michalak, Epigenetic, transposon and small RNA determinants of hybrid dysfunctions, Heredity, vol.11, issue.1, pp.45-50, 2009.
DOI : 10.1002/1521-1878(200010)22:10<938::AID-BIES9>3.0.CO;2-9

T. Morá-n and F. A. , Genome-Wide Dissection of Hybrid Sterility in Drosophila Confirms a Polygenic Threshold Architecture, Journal of Heredity, vol.105, issue.3, pp.381-396
DOI : 10.1093/jhered/esu003

A. Nagao, T. Mituyama, H. Huang, D. Chen, and M. Siomi, Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis, RNA, vol.16, issue.12, pp.2503-2515, 2010.
DOI : 10.1261/rna.2270710

C. Nardon, M. Weiss, C. Vieira, and C. Bié-mont, Variation of the genome size estimate with environmental conditions in Drosophila melanogaster, Cytometry A, vol.55, pp.43-49, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00427444

O. Neill, R. , O. Neill, M. , M. Graves et al., Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid, Nature, vol.393, issue.6680, pp.68-73, 1998.
DOI : 10.1038/29985

D. Petrov and D. Hartl, High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups, Molecular Biology and Evolution, vol.15, issue.3, pp.293-302, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025926

R. Rebollo, B. Horard, B. Hubert, and C. Vieira, Jumping genes and epigenetics: Towards new species, Gene, vol.454, issue.1-2, pp.1-7, 2010.
DOI : 10.1016/j.gene.2010.01.003

URL : https://hal.archives-ouvertes.fr/hal-00850384

S. Renaut, H. Rowe, M. Ungerer, and L. Rieseberg, Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.16, issue.13, p.20130345, 2014.
DOI : 10.1016/j.cub.2006.05.045

V. Romero-soriano, G. Guerreiro, and M. , Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids, PLOS ONE, vol.47, issue.1, 2016.
DOI : 10.1371/journal.pone.0147903.s010

P. Sanmiguel, Nested Retrotransposons in the Intergenic Regions of the Maize Genome, Science, vol.274, issue.5288, pp.765-768, 1996.
DOI : 10.1126/science.274.5288.765

N. Senerchia, C. Parisod, and C. Parisod, Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation, Proceedings of the Royal Society B: Biological Sciences, vol.45, issue.42, p.20142874, 2015.
DOI : 10.1073/pnas.0907003106

K. Senti, D. Jurczak, R. Sachidanandam, and J. Brennecke, piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire, Genes & Development, vol.29, issue.16, pp.1747-1762, 2015.
DOI : 10.1101/gad.267252.115

M. Siomi, T. Miyoshi, and H. Siomi, piRNA-mediated silencing in Drosophila germlines, Seminars in Cell & Developmental Biology, vol.21, issue.7, pp.754-759, 2010.
DOI : 10.1016/j.semcdb.2010.01.011

M. Ungerer, S. Strakosh, and Y. Zhen, Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation, Current Biology, vol.16, issue.20, pp.872-873, 2006.
DOI : 10.1016/j.cub.2006.09.020

V. Peralta and D. , Estudio de la inestabilidad genó mica inducida por transposició n en los híbridos interespecíficos de Drosophila buzzatii y Drosophila koepferae, 2012.

D. Vela, A. Fontdevila, C. Vieira, G. Guerreiro, and M. , A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids, PLoS ONE, vol.91, issue.2, p.88992, 2014.
DOI : 10.1371/journal.pone.0088992.s005

URL : https://hal.archives-ouvertes.fr/hal-01092626

D. Vela, G. Guerreiro, M. Fontdevila, and A. , Adaptation of the AFLP technique as a new tool to detect genetic instability and transposition in interspecific hybrids, Biotechniques, vol.50, pp.247-250, 2011.

C. Vieira, C. Nardon, C. Arpin, D. Lepetit, and C. Bié-mont, Evolution of Genome Size in Drosophila. Is the Invader's Genome Being Invaded by Transposable Elements?, Molecular Biology and Evolution, vol.19, issue.7, pp.1154-1161, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004173

URL : https://hal.archives-ouvertes.fr/hal-00427308

M. Wasserman, Cytological studies of the repleta group of the genus Drosophila. V. The mulleri subgroup, pp.85-118, 1962.

F. Wilcoxon, Individual Comparisons of Grouped Data by Ranking Methods, Journal of Economic Entomology, vol.39, issue.2, pp.80-83, 1945.
DOI : 10.1093/jee/39.2.269

X. Zhou, Genome size of the diploid hybrid species Hippophae goniocarpa and its parental species, H. rhamnoides ssp. sinensis and H. neurocarpa ssp. neurocarpa (Elaeagnaceae) Acta Biol Cracoviensia Ser Bot, pp.12-16, 2010.