A. Estoup, Is there a genetic paradox of biological invasion?, Annu. Rev. Ecol. Evol. Syst, vol.47, pp.51-72, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01608618

C. E. Lee, Evolutionary genetics of invasive species, Trends Ecol. Evol, vol.17, pp.386-391, 2002.

K. D. Whitney and C. A. Gabler, Rapid evolution in introduced species, 'invasive traits' and recipient communities: challenges for predicting invasive potential, Divers. Distrib, vol.14, pp.569-580, 2008.

D. Charlesworth and J. H. Willis, The genetics of inbreeding depression, Nat. Rev. Genet, vol.10, pp.783-796, 2009.

R. Lanfear, H. Kokko, and A. Eyre-walker, Population size and the rate of evolution, Trends Ecol. Evol, vol.29, pp.33-41, 2014.

S. R. Grossman, Identifying recent adaptations in large-scale genomic data, Cell, vol.152, pp.703-713, 2013.

K. Nam, Evidence that the rate of strong selective sweeps increases with population size in the great apes, Proc. Natl. Acad. Sci, vol.114, pp.1613-1618, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02626809

J. Hermisson and P. S. Pennings, Soft Sweeps: Molecular population genetics of adaptation from standing genetic variation, Genetics, vol.169, pp.2335-2352, 2005.

F. W. Allendorf and L. L. Lundquist, Introduction: population biology, evolution, and control of invasive Species, Conserv. Biol, vol.17, pp.24-30, 2003.

R. B. Corbett-detig, J. Zhou, A. G. Clark, D. L. Hartl, and J. F. Ayroles, Genetic incompatibilities are widespread within species, Nature, vol.504, pp.135-137, 2013.

D. G. Montezano, Host plants of Spodoptera frugiperda (Lepidoptera: Noctuidae) in the Americas, Afr. Entomol, vol.26, pp.286-300, 2018.

J. K. Westbrook, R. N. Nagoshi, R. L. Meagher, S. J. Fleischer, and S. Jairam, Modeling seasonal migration of fall armyworm moths, Int. J. Biometeorol, vol.60, pp.255-267, 2016.

R. Gutiérrez-moreno, Field-Evolved Resistance of the Fall Armyworm (Lepidoptera: Noctuidae) to Synthetic Insecticides in Puerto Rico and Mexico, J. Econ. Entomol, vol.112, pp.792-802, 2019.

D. Mota-sanchez, C. John, and W. , Arthropod Pesticide Resistance Database

N. P. Storer, Discovery and Characterization of Field Resistance to Bt Maize: Spodoptera 18 415 . CC-BY-NC-ND 4.0 International license (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint this version posted, 2020.

, doi: bioRxiv preprint frugiperda (Lepidoptera: Noctuidae) in Puerto Rico, J. Econ. Entomol, vol.103, pp.1031-1038, 2010.

S. R. Jakka, Field-Evolved Mode 1 Resistance of the Fall Armyworm to Transgenic Cry1Fa-Expressing Corn Associated with Reduced Cry1Fa Toxin Binding and Midgut Alkaline Phosphatase Expression, Appl. Environ. Microbiol, vol.82, pp.1023-1034, 2016.

C. Omoto, Field-evolved resistance to Cry1Ab maize by Spodoptera frugiperda in Brazil, Pest Manag. Sci, vol.72, pp.1727-1736, 2016.

D. I. Chandrasena, Characterization of field-evolved resistance to Bacillus thuringiensis-derived Cry1F ?-endotoxin in Spodoptera frugiperda populations from Argentina, Pest Manag. Sci, vol.74, pp.746-754, 2018.

A. N. Sparks, A review of the biology of the fall armyworm, Fla. Entomol, pp.82-87, 1979.

G. Goergen, P. L. Kumar, S. B. Sankung, A. Togola, and M. Tamò, First report of outbreaks of the fall armyworm Spodoptera frugiperda, Lepidoptera, Noctuidae), a new alien invasive pest in west and central Africa, vol.11, p.165632, 2016.

R. Day, Fall Armyworm: impacts and implications for Africa. Outlooks Pest Manag, vol.28, pp.196-201, 2017.

D. P. Pashley, Host-associated genetic differentiation in fall armyworm (Lepidoptera: Noctuidae): a sibling species complex?, Ann. Entomol. Soc. Am, vol.79, pp.898-904, 1986.

D. P. Pashley and J. A. Martin, Reproductive incompatibility between host strains of the fall armyworm (Lepidoptera: Noctuidae), Ann. Entomol. Soc. Am, vol.80, pp.731-733, 1987.

P. Dumas, Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?, Genetica, vol.143, pp.305-316, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01208780

L. Zhang, High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China, bioRxiv, vol.813154, 2019.

R. N. Nagoshi, Comparative molecular analyses of invasive fall armyworm in Togo reveal strong similarities to populations from the eastern United States and the Greater Antilles, PLoS ONE, vol.12, 2017.

R. N. Nagoshi, G. Goergen, H. D. Plessis, . Van-den, J. Berg et al., Genetic comparisons of fall armyworm populations from 11 countries spanning sub-Saharan Africa provide insights into strain composition and migratory behaviors, Sci. Rep, vol.9, p.8311, 2019.

, International license (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint this version posted, 2020.

,

W. T. Tay, Whole genome sequencing of global Spodoptera frugiperda populations: evidence for complex, multiple introductions across the Old World, 2020.

E. Lieberman-aiden, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, pp.289-293, 2009.

F. A. Simão, 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, pp.3210-3212, 2015.

K. Nam, Adaptation by copy number variation increases insecticide resistance in fall armyworms, bioRxiv, vol.812958, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02945633

K. Nam, Divergent selection causes whole genome differentiation without physical linkage among the targets in Spodoptera frugiperda (Noctuidae), bioRxiv, vol.452870, 2018.

H. Liu, Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China. bioRxiv 671560, 2019.

A. Mckenna, The Genome Analysis Toolkit: A MapReduce framework for analyzing nextgeneration DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

Y. Lu and M. J. Adang, Distinguishing fall armyworm (Lepidoptera: Noctuidae) strains using a diagnostic mitochondrial DNA marker, Fla. Entomol, vol.79, pp.48-55, 1996.

D. H. Alexander, J. Novembre, and K. Lange, Fast model-based estimation of ancestry in unrelated individuals, Genome Res, vol.19, pp.1655-1664, 2009.

R. N. Nagoshi, Analysis of strain distribution, migratory potential, and invasion history of fall armyworm populations in northern Sub-Saharan Africa, Sci. Rep, vol.8, p.3710, 2018.

A. J. Mongue, M. V. Tsai, M. L. Wayne, and J. C. De-roode, Inbreeding depression in monarch butterflies, J. Insect Conserv, vol.20, pp.477-483, 2016.

M. Degiorgio, K. E. Lohmueller, and R. Nielsen, A model-based approach for identifying signatures of ancient balancing selection in genetic data, PLoS Genet, vol.10, p.1004561, 2014.

C. J. Anderson, Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa. Proc. Natl. Acad. Sci, vol.115, pp.5034-5039, 2018.

P. Pavlidis, D. ?ivkovi?, A. Stamatakis, and N. Alachiotis, SweeD: likelihood-based detection of selective sweeps in thousands of genomes, Mol. Biol. Evol, vol.30, pp.2224-2234, 2013.

, International license (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint this version posted, 2020.

,

B. Charlesworth, M. T. Morgan, and D. Charlesworth, The effect of deleterious mutations on neutral molecular variation, Genetics, vol.134, pp.1289-1303, 1993.

A. M. Mcdonnell and C. H. Dang, Basic review of the cytochrome P450 system, J. Adv. Pract. Oncol, vol.4, pp.263-268, 2013.

M. Giraudo, Cytochrome P450s from the fall armyworm (Spodoptera frugiperda): responses to plant allelochemicals and pesticides, Insect Mol. Biol, vol.24, pp.115-128, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02631337

F. Cui, Carboxylesterase-mediated insecticide resistance: Quantitative increase induces broader metabolic resistance than qualitative change. Pestic, Biochem. Physiol, vol.121, pp.88-96, 2015.

M. G. Tapadia and S. C. Lakhotia, Expression of mdr49 and mdr65 multidrug resistance genes in larval tissues of Drosophila melanogaster under normal and stress conditions, Cell Stress Chaperones, vol.10, pp.7-11, 2005.

H. Lin, Characterization and expression profiling of serine protease inhibitors in the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae), BMC Genomics, vol.18, p.162, 2017.

A. De-fouchier, Functional evolution of Lepidoptera olfactory receptors revealed by deorphanization of a moth repertoire, Nat. Commun, vol.8, p.15709, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01938636

G. Goergen, P. L. Kumar, S. B. Sankung, A. Togola, and M. Tamò, First report of outbreaks of the Fall Armyworm Spodoptera frugiperda, Lepidoptera, Noctuidae), a new alien invasive pest in West and Central Africa, vol.11, p.165632, 2016.

O. Tataroglu and P. Emery, The molecular ticks of the Drosophila circadian clock, Curr. Opin. Insect Sci, vol.7, pp.51-57, 2015.

S. Haenniger, Sexual communication of Spodoptera frugiperda from West Africa: Adaptation of an invasive species and implications for pest management, Sci. Rep, vol.10, p.2892, 2020.

S. D. Cinel and S. J. Taylor, Prolonged bat call exposure induces a broad transcriptional response in the male fall armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) brain, Front. Behav. Neurosci, vol.13, 2019.

K. M. Herkt, G. Barnikel, A. K. Skidmore, and J. Fahr, A high-resolution model of bat diversity and endemism for continental Africa, Ecol. Model, vol.320, pp.9-28, 2016.

E. Lombaert, Bridgehead effect in the worldwide invasion of the biocontrol Harlequin ladybird, PLoS ONE, vol.5, p.9743, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02664647

C. Bertelsmeier and L. Keller, CC-BY-NC-ND 4.0 International license (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint this version posted, vol.21, 2020.

, Trends Ecol. Evol, vol.33, pp.527-534, 2018.

A. Rortais, A new enemy of honeybees in Europe: the Asian Hornet, Vespa velutina, 2010.

A. Gouin, Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges, Sci. Rep, vol.7, p.11816, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01633879

M. Hunt, REAPR: a universal tool for genome assembly evaluation, Genome Biol, vol.14, p.47, 2013.

J. Ghurye, Integrating Hi-C links with assembly graphs for chromosome-scale assembly, PLOS Comput.Biol, vol.15, p.1007273, 2019.

O. Dudchenko, De novo assembly of the Aedes aegypti genome using Hi-C yields chromosomelength scaffolds, Science, vol.356, pp.92-95, 2017.

R. Luo, Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.4, p.30, 2015.

G. Xu, LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly, GigaScience, vol.8, 2018.

T. D. Otto, G. P. Dillon, W. S. Degrave, and M. Berriman, RATT: Rapid Annotation Transfer Tool, Nucleic Acids Res, vol.39, p.57, 2011.

. Sharanabasappa, Lepidoptera: Noctuidae), an alien invasive pest on maize in India, Pest Manag. Hortic. Ecosyst, vol.24, pp.23-29, 2018.

M. Schubert, S. Lindgreen, and L. Orlando, AdapterRemoval v2: rapid adapter trimming, identification, and read merging, BMC Res. Notes, vol.9, p.88, 2016.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012.

X. Wang, CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations, GigaScience, vol.6, 2017.

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

G. Meng, Y. Li, C. Yang, and S. Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Res, vol.47, pp.63-63, 2019.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

, International license (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint this version posted, 2020.

,

S. Guindon, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL) v4: recent updates and new developments, Nucleic Acids Res, vol.47, pp.256-259, 2019.

V. Lefort, R. Desper, and O. Gascuel, FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program, Mol. Biol. Evol, vol.32, pp.2798-2800, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01283927

D. Plotree and D. Plotgram, PHYLIP-phylogeny inference package (version 3.2), cladistics, vol.5, pp.163-166, 1989.

M. E. Rentería, A. Cortes, and S. E. Medland, Using PLINK for genome-wide association studies (GWAS) and data analysis. in Genome-Wide Association Studies and Genomic Prediction, pp.193-213, 2013.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, vol.38, pp.1358-1370, 1984.

P. Danecek, The variant call format and VCFtools, Bioinformatics, vol.27, pp.2156-2158, 2011.

C. Zhang, S. Dong, J. Xu, W. He, and T. Yang, PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files, Bioinformatics, vol.35, pp.1786-1788, 2019.