E. Mayr, Animal Species and Evolution, 1963.
DOI : 10.4159/harvard.9780674865327

S. Simpson, G. Sword, and N. Lo, Polyphenism in Insects, Current Biology, vol.21, issue.18, pp.738-787, 2011.
DOI : 10.1016/j.cub.2011.06.006

N. Moran, The Evolutionary Maintenance of Alternative Phenotypes, The American Naturalist, vol.139, issue.5, pp.971-89, 1992.
DOI : 10.1086/285369

J. Brisson, G. Davis, and D. Stern, Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum), Evolution & Development, vol.42, issue.4, pp.338-384, 2007.
DOI : 10.1111/j.1525-142X.2007.00170.x

C. Grozinger, Y. Fan, S. Hoover, and M. Winston, Genome-wide analysis reveals differences in brain gene expression patterns associated with caste and reproductive status in honey bees (Apis mellifera), Molecular Ecology, vol.26, issue.1, pp.4837-4885, 2007.
DOI : 10.1146/annurev.ento.51.110104.151011

S. Ohno, Evolution by gene duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

F. Kondrashov, Gene duplication as a mechanism of genomic adaptation to a changing environment, Proceedings of the Royal Society B: Biological Sciences, vol.184, issue.4, pp.5048-57, 1749.
DOI : 10.1534/genetics.109.111963

D. Boubals, Sur les attaques de Phylloxera des racines dans le monde, Progrès Agricole et Viticole, vol.110, pp.416-437, 1993.

D. Downie, Phylogeography in a galling insect, grape phylloxera, Daktulosphaira vitifoliae (Phylloxeridae) in the fragmented habitat of the Southwest USA, Journal of Biogeography, vol.18, issue.11, pp.1759-68, 2004.
DOI : 10.1046/j.1365-294x.1998.00309.x

J. Planchon, Les vignes américaines : leur culture, leur résistance au phylloxéra et leur avenir en Europe

R. Pouget, Histoire de la lutte contre le phylloxera de la vigne en France (1868?1895), 1990.

C. Campbell, Phylloxera: How Wine was Saved for the World, 2004.

Y. Carton, C. Sorensen, J. Smith, and E. Smith, An exemplary partnership of American entomologist (C. V. Riley) with French entomologists in control of the Grape Phylloxera in France (1868?1895) Annales De La Societe Entomologique De France, pp.103-128, 2007.

D. Benheim, S. Rochfort, E. Robertson, I. Potter, and K. Powell, Grape phylloxera (Daktulosphaira vitifoliae) - a review of??potential detection and alternative management options, Annals of Applied Biology, vol.29, issue.Suppl. 1, pp.91-115, 2012.
DOI : 10.1111/j.1744-7348.2012.00561.x

J. Planchon and J. Lichtenstein, De l'identité spécifique du phylloxera des feuilles et du phylloxera des racines de la vigne. Comptes Rendus de l, Académie des Sciences, vol.71, pp.298-300, 1870.

I. Consortium, Genome Sequence of the Pea Aphid Acyrthosiphon pisum, Plos Biol, vol.8, issue.2, p.1000313, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00459970

G. Davis, Cyclical Parthenogenesis and Viviparity in Aphids as Evolutionary Novelties, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol.69, issue.1700-1701, pp.448-59, 2012.
DOI : 10.1002/jez.b.22441

K. Kingston, K. Powell, and P. Cooper, GRAPE PHYLLOXERA: NEW INVESTIGATIONS INTO THE BIOLOGY OF AN OLD GRAPEVINE PEST, Acta Horticulturae, vol.816, issue.816, pp.63-70, 2009.
DOI : 10.17660/ActaHortic.2009.816.9

F. Finseth and R. Harrison, A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly and Utility for RNA-Seq in a Non-Model Bird, PLoS ONE, vol.13, issue.10
DOI : 10.1371/journal.pone.0108550.s001

J. Debenedictis and J. Granett, Variability of Responses of Grape Phylloxera (Homoptera: Phylloxeridae) to Bioassays That Discriminate Between California Biotypes, Journal of Economic Entomology, vol.85, issue.4, pp.1527-1561, 1992.
DOI : 10.1093/jee/85.4.1527

M. Grabherr, B. Haas, M. Yassour, J. Levin, D. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-130, 2011.
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002

S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman et al., Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

F. Simão, R. Waterhouse, P. Ioannidis, E. Kriventseva, and E. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, issue.19
DOI : 10.1093/bioinformatics/btv351

L. Li, C. Stoeckert, and D. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-89, 2003.
DOI : 10.1101/gr.1224503

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-354
DOI : 10.1093/bioinformatics/btp352

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

C. Notredame, D. Higgins, J. Heringa, and . T-coffee, T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-222, 2000.
DOI : 10.1006/jmbi.2000.4042

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-52, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2734, 2013.
DOI : 10.1093/molbev/mst197

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010.
DOI : 10.1186/gb-2010-11-10-r106

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J Roy Statist Soc Ser B (Methodological), vol.57, pp.289-300, 1995.

S. Purandare, R. Bickel, J. Jaquiery, C. Rispe, and J. Brisson, Accelerated Evolution of Morph-Biased Genes in Pea Aphids, Molecular Biology and Evolution, vol.31, issue.8, pp.2073-83, 2014.
DOI : 10.1093/molbev/msu149
URL : https://hal.archives-ouvertes.fr/hal-01178949

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-561, 1997.
DOI : 10.1093/bioinformatics/13.5.555

T. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-791, 2011.
DOI : 10.1016/0005-2795(75)90109-9

J. Jaquiery, C. Rispe, R. D. Legeai, F. , L. Trionnaire et al., Masculinization of the X Chromosome in the Pea Aphid, PLoS Genetics, vol.15, issue.8, p.1003690, 2013.
DOI : 10.1371/journal.pgen.1003690.s006
URL : https://hal.archives-ouvertes.fr/hal-00916967

S. Chen, P. Yang, F. Jiang, Y. Wei, Z. Ma et al., De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits, PLoS ONE, vol.17, issue.Suppl 1, p.15633, 2010.
DOI : 10.1371/journal.pone.0015633.s030

N. Gerardo, B. Altincicek, C. Anselme, H. Atamian, S. Barribeau et al., Immunity and other defenses in pea aphids, Acyrthosiphon pisum, Genome Biology, vol.11, issue.2, p.21, 2010.
DOI : 10.1186/gb-2010-11-2-r21
URL : https://hal.archives-ouvertes.fr/hal-00459961

H. Moghadam, P. Harrison, G. Zachar, T. Szekely, and J. Mank, The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome, Molecular Ecology Resources, vol.12, issue.4, pp.696-705, 2013.
DOI : 10.1111/1755-0998.12096

C. Rispe, M. Kutsukake, V. Doublet, S. Hudaverdian, F. Legeai et al., Large Gene Family Expansion and Variable Selective Pressures for Cathepsin B in Aphids, Molecular Biology and Evolution, vol.25, issue.1, pp.5-17, 2008.
DOI : 10.1093/molbev/msm222
URL : https://hal.archives-ouvertes.fr/inria-00180087

J. Colbourne, M. Pfrender, D. Gilbert, W. Thomas, A. Tucker et al., The Ecoresponsive Genome of Daphnia pulex, Science, vol.331, issue.6017, pp.555-61, 2011.
DOI : 10.1126/science.1197761

B. Johnson and N. Tsutsui, Taxonomically restricted genes are associated with the evolution of sociality in the honey bee, BMC Genomics, vol.27, issue.11, p.164, 2011.
DOI : 10.1007/978-3-662-10306-7

F. Meng, I. Braasch, J. Phillips, X. Lin, T. Titus et al., Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish, Molecular Biology and Evolution, vol.30, issue.7, pp.1527-1570, 2013.
DOI : 10.1093/molbev/mst079

C. Rispe, F. Legeai, J. Gauthier, and D. Tagu, Strong Heterogeneity in Nucleotidic Composition and Codon Bias in the Pea Aphid (Acyrthosiphon pisum) Shown by EST-Based Coding Genome Reconstruction, Journal of Molecular Evolution, vol.87, issue.4, pp.413-437, 2007.
DOI : 10.1007/s00239-007-9023-y
URL : https://hal.archives-ouvertes.fr/inria-00180094

P. Buchner, Endosymbiosis of Animals with Plant Microorganisms, 1965.

H. Schanderl, G. Lauff, and H. Becker, Studien über die Myzetom und Darmsymbionten der Aphiden, Zeitschrift für Naturforschg, vol.4, pp.50-58, 1949.

H. Breider, Beiträge zur morphologie der reblaus Dactylosphaera vitifoliae Shim, J Applied Entomology, vol.33, pp.517-560, 1952.

P. Maillet, Biologie du Phylloxera de la Vigne, Annales des Sciences Naturelles Zoologie, vol.11, pp.358-73, 1957.

S. Vorwerk, D. Martinez-torres, and A. Forneck, Pantoea agglomerans-associated bacteria in grape phylloxera (Daktulosphaira vitifoliae, Fitch) Agricultural Forest Entomology, pp.57-64, 2007.

R. Medina, P. Nachappa, and C. Tamborindeguy, Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory, Journal of Evolutionary Biology, vol.13, issue.4, pp.761-71, 2011.
DOI : 10.1111/j.1420-9101.2010.02215.x

G. Martins, B. Lauga, C. Miot-sertier, A. Mercier, A. Lonvaud et al., Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations, PLoS ONE, vol.153, issue.8, p.73013, 2013.
DOI : 10.1371/journal.pone.0073013.t003

A. Campisano, L. Ometto, S. Compant, M. Pancher, L. Antonielli et al., Interkingdom Transfer of the Acne-Causing Agent, Propionibacterium acnes, from Human to Grapevine, Molecular Biology and Evolution, vol.31, issue.5, pp.1059-65, 2014.
DOI : 10.1093/molbev/msu075

B. Grassi, A. Foa, R. Grandori, B. Bonfigli, and M. Topi, Contributo alla conoscenza delle Fillosserine ed in particolare delle Fillossera della vite. Italy: Publícati Ministero d'Agricoltura, Industria e Commercio, 1912.

J. Hoffmann, F. Kafatos, C. Janeway, and R. Ezekowitz, Phylogenetic Perspectives in Innate Immunity, Science, vol.284, issue.5418, pp.1313-1321, 1999.
DOI : 10.1126/science.284.5418.1313

M. Lynch and J. Conery, The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, pp.1151-1156, 2000.
DOI : 10.1126/science.290.5494.1151

L. Duret and D. Mouchiroud, Determinants of Substitution Rates in Mammalian Genes: Expression Pattern Affects Selection Intensity but Not Mutation Rate, Molecular Biology and Evolution, vol.17, issue.1, pp.68-74, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026239
URL : https://hal.archives-ouvertes.fr/hal-00427068

H. Ellegren and J. Parsch, The evolution of sex-biased genes and sex-biased gene expression, Nature Reviews Genetics, vol.416, issue.9, pp.689-98, 2007.
DOI : 10.1038/nrg2167

M. Pointer, P. Harrison, A. Wright, and J. Mank, Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism, PLoS Genetics, vol.102, issue.8, p.1003697, 2013.
DOI : 10.1371/journal.pgen.1003697.s011

E. Snell-rood, A. Cash, M. Han, T. Kijimoto, J. Andrews et al., DEVELOPMENTAL DECOUPLING OF ALTERNATIVE PHENOTYPES: INSIGHTS FROM THE TRANSCRIPTOMES OF HORN-POLYPHENIC BEETLES, Evolution, vol.21, issue.1, pp.231-276, 2011.
DOI : 10.1111/j.1558-5646.2010.01106.x

J. Van-dyken and M. Wade, The Genetic Signature of Conditional Expression, Genetics, vol.184, issue.2, pp.557-70, 2010.
DOI : 10.1534/genetics.109.110163