P. Nosil, B. J. Crespi, and C. P. Sandoval, Host-plant adaptation drives the parallel evolution of reproductive isolation, Nature, vol.28, issue.6887, pp.440-443, 2002.
DOI : 10.1146/annurev.ecolsys.28.1.437

H. D. Rundle and P. Nosil, Ecological speciation, Ecology Letters, vol.5, issue.3, pp.336-352, 2005.
DOI : 10.1111/j.0014-3820.2000.tb00707.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2004.00715.x/pdf

N. Wahlberg, C. W. Wheat, and C. Pena, Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths), PLoS ONE, vol.59, issue.11, p.80875, 2013.
DOI : 10.1371/journal.pone.0080875.s002

D. P. Pashley and J. A. Martin, Reproductive Incompatibility Between Host Strains of the Fall Armyworm (Lepidoptera: Noctuidae), Annals of the Entomological Society of America, vol.80, issue.6, pp.731-733, 1987.
DOI : 10.1093/aesa/80.6.731

D. P. Pashley, Quantitative genetics, development and physiological adaptation in sympatric host strains of fall armyworm, Evolution, vol.42, pp.93-102, 1988.

F. Whitford, S. S. Quisenberry, T. J. Riley, and J. W. Lee, Oviposition Preference, Mating Compatibility, and Development of Two Fall Armyworm Strains, The Florida Entomologist, vol.71, issue.3, pp.234-243, 1988.
DOI : 10.2307/3495426

G. J. Kergoat, Disentangling dispersal, vicariance and adaptive radiation patterns: A case study using armyworms in the pest genus Spodoptera (Lepidoptera: Noctuidae), Molecular Phylogenetics and Evolution, vol.65, issue.3, pp.855-870, 2012.
DOI : 10.1016/j.ympev.2012.08.006

A. T. Groot, M. Marr, D. G. Heckel, G. Schöfl, ?. Schã et al., The roles and interactions of reproductive isolation mechanisms in fall armyworm (Lepidoptera: Noctuidae) host strains, Ecological Entomology, vol.10, pp.105-118, 2010.
DOI : 10.1111/j.0014-3820.2000.tb00707.x

Y. J. Lu and M. J. Adang, Distinguishing Fall Armyworm (Lepidoptera: Noctuidae) Strains Using a Diagnostic Mitochondrial DNA Marker, The Florida Entomologist, vol.79, issue.1, pp.48-55, 1996.
DOI : 10.2307/3495753
URL : https://doi.org/10.2307/3495753

M. M. Michael and D. P. Prowell, Differences in Amplified Fragment-Length Polymorphisms in Fall Armyworm (Lepidoptera: Noctuidae) Host Strains, pp.175-181, 1999.

H. C. Levy, A. Garcia-maruniak, and J. Maruniak, STRAIN IDENTIFICATION OF SPODOPTERA FRUGIPERDA (LEPIDOPTERA: NOCTUIDAE) INSECTS AND CELL LINE: PCR-RFLP OF CYTOCHROME OXIDASE C SUBUNIT I GENE, Florida Entomologist, vol.85, issue.1, pp.186-190, 2002.
DOI : 10.1653/0015-4040(2002)085[0186:SIOSFL]2.0.CO;2

R. N. Nagoshi, J. S. Armstrong, P. Silvie, and R. L. Meagher, Structure and Distribution of a Strain-Biased Tandem Repeat Element in Fall Armyworm (Lepidoptera: Noctuidae) Populations in Florida, Texas, and Brazil, Annals of the Entomological Society of America, vol.101, issue.6, pp.1112-1120, 2008.
DOI : 10.1603/0013-8746-101.6.1112

R. L. Meagher and M. Gallo-meagher, IDENTIFYING HOST STRAINS OF FALL ARMYWORM (LEPIDOPTERA\ NOCTUIDAE) IN FLORIDA USING MITOCHONDRIAL MARKERS, Florida Entomologist, vol.86, issue.4, pp.450-455, 2003.
DOI : 10.1653/0015-4040(2003)086[0450:IHSOFA]2.0.CO;2

M. C. Arias, Permanent genetic resources added to Molecular Ecology Resources Database 1, Mol Ecol Resour, vol.12, pp.570-572, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00687667

P. K. Kakumani, P. Malhotra, S. K. Mukherjee, and R. K. Bhatnagar, A draft genome assembly of the army worm, Spodoptera frugiperda, Genomics, vol.104, issue.2, pp.134-143005, 2014.
DOI : 10.1016/j.ygeno.2014.06.005

J. L. Vaughn, R. H. Goodwin, G. J. Tompkins, and P. Mccawley, The establishment of two cell lines from the insectspodoptera frugiperda (lepidoptera; noctuidae), In Vitro, vol.25, issue.4, pp.213-217, 1977.
DOI : 10.1016/B978-0-12-429740-1.50037-0

E. D-'alençon, Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements, Proceedings of the National Academy of Sciences, vol.107, issue.17, pp.7680-76850910413107, 2010.
DOI : 10.1101/gr.086009.108

M. Osanai-futahashi, Y. Suetsugu, K. Mita, and H. Fujiwara, Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori, Insect Biochemistry and Molecular Biology, vol.38, issue.12, pp.1046-1057, 2008.
DOI : 10.1016/j.ibmb.2008.05.012

J. C. Simon, Genomics of adaptation to host-plants in herbivorous insects, Briefings in Functional Genomics, vol.14, issue.6, p.15, 2015.
DOI : 10.1093/bfgp/elv015
URL : https://hal.archives-ouvertes.fr/hal-01132673

A. Sanchez-gracia, F. G. Vieira, and J. Rozas, Molecular evolution of the major chemosensory gene families in insects, Heredity, vol.17, issue.3, pp.208-21655, 2009.
DOI : 10.1111/j.1432-1033.1995.tb20864.x

K. Isono and H. Morita, Molecular and cellular designs of insect taste receptor system, Frontiers in Cellular Neuroscience, vol.4, issue.20, p.20, 2010.
DOI : 10.3389/fncel.2010.00020

B. Van-schooten, C. D. Jiggins, A. D. Briscoe, and R. Papa, Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies, BMC Genomics, vol.200, issue.4, pp.10-1186, 2016.
DOI : 10.1371/journal.pgen.1000796

M. Giraudo, ): responses to plant allelochemicals and pesticides, Insect Molecular Biology, vol.66, issue.Suppl. 2, p.12140, 2014.
DOI : 10.1002/ps.1832

Y. H. Wang, Changes in the activity and the expression of detoxification enzymes in silkworms (Bombyx mori) after phoxim feeding, Pesticide Biochemistry and Physiology, vol.105, issue.1, pp.13-17, 2013.
DOI : 10.1016/j.pestbp.2012.11.001

X. Y. Tao, X. Y. Xue, Y. P. Huang, X. Y. Chen, and Y. B. Mao, Gossypol-enhanced P450 gene pool contributes to cotton bollworm tolerance to a pyrethroid insecticide, Molecular Ecology, vol.66, issue.17, pp.4371-4385, 2012.
DOI : 10.1002/ps.1832

M. G. Teese, Gene identification and proteomic analysis of the esterases of the cotton bollworm, Helicoverpa armigera, Insect Biochemistry and Molecular Biology, vol.40, issue.1, pp.1-16002, 2010.
DOI : 10.1016/j.ibmb.2009.12.002

K. W. Bock, Vertebrate UDP-glucuronosyltransferases: functional and evolutionary aspects, Biochemical Pharmacology, vol.66, issue.5, pp.691-69600296, 2003.
DOI : 10.1016/S0006-2952(03)00296-X

A. Srinivasan, A. P. Giri, and V. S. Gupta, Structural and functional diversities in Lepidopteran serine proteases Cellular &amp, Molecular Biology Letters, vol.11, pp.132-15410, 2006.
DOI : 10.2478/s11658-006-0012-8
URL : http://www.degruyter.com/downloadpdf/j/cmble.2006.11.issue-1/s11658-006-0012-8/s11658-006-0012-8.xml

X. Cao, Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta, Insect Biochemistry and Molecular Biology, vol.62, pp.51-63006, 2015.
DOI : 10.1016/j.ibmb.2014.10.006

C. L. Chai, A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori, Insect Biochemistry and Molecular Biology, vol.38, issue.12, pp.1111-1120, 2008.
DOI : 10.1016/j.ibmb.2008.06.008

K. H. Veenstra, D. P. Pashley, and J. A. Ottea, Host-Plant Adaptation in Fall Armyworm Host Strains: Comparison of Food Consumption, Utilization, and Detoxication Enzyme Activities, Annals of the Entomological Society of America, vol.88, issue.1, pp.80-91, 1995.
DOI : 10.1093/aesa/88.1.80

J. J. Adamczyk, J. W. Holloway, B. R. Leonard, and J. B. Graves, Susceptibility of fall armyworm collected from different plant hosts to selected insecticides and transgenic Bt cotton, JOURNAL OF COTTON SCIENCE, vol.1, pp.21-28, 1997.

R. Feyereisen, Evolution of insect P450, Biochemical Society Transactions, vol.34, issue.6, pp.1252-1255, 2006.
DOI : 10.1042/BST0341252
URL : http://www.biochemsoctrans.org/content/ppbiost/34/6/1252.full.pdf

L. Yu, Characterization and expression of the cytochrome P450 gene family in diamondback moth, Plutella xylostella (L.). Sci Rep 5, pp.10-1038, 2015.

R. N. Nagoshi, R. L. Meagher, and M. Hay-roe, Inferring the annual migration patterns of fall armyworm (Lepidoptera: Noctuidae) in the United States from mitochondrial haplotypes, Ecology and Evolution, vol.328, issue.7, pp.1458-146710, 2012.
DOI : 10.1098/rstb.1990.0132

M. G. Pogue, World revision of the genus Spodoptera Guenée (Lepidoptera: Noctuidae) Memoirs of the, pp.1-202, 2002.

A. D. Briscoe, Female Behaviour Drives Expression and Evolution of Gustatory Receptors in Butterflies, PLoS Genetics, vol.103, issue.2, 2013.
DOI : 10.1371/journal.pgen.1003620.s016
URL : https://hal.archives-ouvertes.fr/hal-01190382

K. W. Wanner and H. M. Robertson, is characterized by a large expansion of a single lineage of putative bitter receptors, Insect Molecular Biology, vol.9, issue.6, pp.621-629, 2008.
DOI : 10.1093/ae/51.3.166

W. Xu, A. Papanicolaou, H. J. Zhang, and A. Anderson, Expansion of a bitter taste receptor family in a polyphagous insect herbivore, Sci Rep, vol.6, pp.10-1038, 2016.

O. Imura, A Comparative Study of the Feeding Habits of Tribolium freemani HINTON and Tribolium castaneum(HERBST)(Coleoptera:Tenebrionidae), Applied Entomology and Zoology, vol.26, issue.2, pp.173-182, 1991.
DOI : 10.1303/aez.26.173

S. Richards, The genome of the model beetle and pest Tribolium castaneum, Nature, vol.107, issue.7190, pp.949-955, 2008.
DOI : 10.1128/MCB.8.1.114

S. Gnerre, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proceedings of the National Academy of Sciences, vol.462, issue.7269, pp.1513-151810, 2011.
DOI : 10.1038/462021a
URL : http://www.pnas.org/content/108/4/1513.full.pdf

R. Kajitani, Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads, Genome Research, vol.24, issue.8, p.113, 2014.
DOI : 10.1101/gr.170720.113
URL : http://genome.cshlp.org/content/24/8/1384.full.pdf

A. Bankevich, SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-4770021, 2012.
DOI : 10.1089/cmb.2012.0021
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf

K. L. Howe, T. Chothia, and R. Durbin, GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming, Genome Research, vol.12, issue.9, pp.1418-1427, 2002.
DOI : 10.1101/gr.149502

I. Korf, Gene finding in novel genomes, BMC Bioinformatics, vol.5, issue.59, 2004.

M. S. Campbell, C. Holt, B. Moore, and M. Yandell, Genome Annotation and Curation Using MAKER and MAKER-P, Curr Protoc Bioinformatics, vol.151, issue.11, pp.11-0411, 2014.
DOI : 10.1104/pp.109.140632
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/pdf

E. Lee, Web Apollo: a web-based genomic annotation editing platform, Genome Biology, vol.14, issue.8, pp.10-1186, 2013.
DOI : 10.1093/bioinformatics/btp120
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2013-14-8-r93?site=genomebiology.biomedcentral.com

F. A. Simao, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, issue.19, pp.3210-321210, 2015.
DOI : 10.1093/bioinformatics/btv351

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.25, issue.3, 2011.
DOI : 10.1371/journal.pone.0016526.s021
URL : https://hal.archives-ouvertes.fr/hal-00956366

S. Fischer, Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups, Curr Protoc Bioinformatics Chapter, vol.13, pp.12-23, 2011.
DOI : 10.1101/gr.1224503
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196566/pdf

G. Ostlund, InParanoid 7: new algorithms and tools for eukaryotic orthology analysis, Nucleic Acids Research, vol.38, issue.Database, pp.196-203, 2010.
DOI : 10.1093/nar/gkp931
URL : https://academic.oup.com/nar/article-pdf/38/suppl_1/D196/16772408/gkp931.pdf

A. Loytynoja and N. Goldman, Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis, Science, vol.319, issue.5862, pp.1632-163510, 2008.
DOI : 10.1126/science.1151532

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088
URL : https://academic.oup.com/mbe/article-pdf/24/8/1586/3853532/msm088.pdf

W. J. Kent, R. Baertsch, A. Hinrichs, W. Miller, and D. Haussler, Evolution' s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes, 2003.

C. Lemaitre, E. Tannier, C. Gautier, and M. F. Sagot, Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol.9, issue.1, p.286, 2008.
DOI : 10.1186/1471-2105-9-286
URL : https://hal.archives-ouvertes.fr/inria-00278553

D. Plotree and D. Plotgram, PHYLIP-phylogeny inference package cladistics, pp.5163-166, 1989.

P. Danecek, The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2158, 2011.
DOI : 10.1093/bioinformatics/btr330
URL : https://academic.oup.com/bioinformatics/article-pdf/27/15/2156/1125001/btr330.pdf

L. J. Revell, phytools: an R package for phylogenetic comparative biology (and other things), Methods in Ecology and Evolution, vol.62, issue.2, pp.217-223, 2012.
DOI : 10.1111/j.1558-5646.2008.00519.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00169.x/pdf

M. R. Kanost, Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta, Insect Biochemistry and Molecular Biology, vol.76, pp.118-147005, 2016.
DOI : 10.1016/j.ibmb.2016.07.005

T. H. Consortium, Butterfly genome reveals promiscuous exchange of mimicry adaptations among species, Nature, vol.487, pp.94-9810, 2012.

S. Zhan, C. Merlin, J. L. Boore, and S. M. Reppert, The Monarch Butterfly Genome Yields Insights into Long-Distance Migration, Cell, vol.147, issue.5, pp.1171-1185, 2011.
DOI : 10.1016/j.cell.2011.09.052
URL : https://doi.org/10.1016/j.cell.2011.09.052

R. G. Vogt, E. Grosse-wilde, and J. J. Zhou, The Lepidoptera Odorant Binding Protein gene family: Gene gain and loss within the GOBP/PBP complex of moths and butterflies, Insect Biochemistry and Molecular Biology, vol.62, pp.142-153, 2015.
DOI : 10.1016/j.ibmb.2015.03.003

V. Croset, Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction, PLoS Genetics, vol.21, issue.8, 2010.
DOI : 10.1371/journal.pgen.1001064.s008

R. Chauhan, R. Jones, P. Wilkinson, Y. Pauchet, and R. H. Ffrench-constant, genome as candidates for cyanogenesis, Insect Molecular Biology, vol.17, issue.5, pp.532-54010, 2013.
DOI : 10.1093/bioinformatics/17.9.847

T. Tsubota and T. Shiotsuki, Genomic and phylogenetic analysis of insect carboxyl/cholinesterase genes, Journal of Pesticide Science, vol.35, issue.3, pp.310-314, 2010.
DOI : 10.1584/jpestics.R10-04
URL : https://www.jstage.jst.go.jp/article/jpestics/35/3/35_R10-04/_pdf

R. V. Rane, Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Current Opinion in, Insect Science, vol.13, pp.70-76, 2016.

S. J. Ahn, H. Vogel, and D. G. Heckel, Comparative analysis of the UDP-glycosyltransferase multigene family in insects, Insect Biochemistry and Molecular Biology, vol.42, issue.2, pp.133-147, 2012.
DOI : 10.1016/j.ibmb.2011.11.006

P. Zhao, Genome-wide identification and expression analysis of serine proteases and homologs in the silkworm Bombyx mori, BMC Genomics, vol.11, issue.1, pp.10-1186, 2010.
DOI : 10.1186/1471-2164-11-405

A. Genoscope, I. , U. G. , J. O. , F. C. et al., Starting material preparation Annotation summary writing Orthology and genes under selection Evolution of host-plant range, Author Contributions Projects design, writing and supervision