F. Abascal, R. Zardoya, and M. J. Telford, TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations, Nucleic Acids Res, vol.38, pp.7-13, 2010.
DOI : 10.1093/nar/gkq291
URL : https://academic.oup.com/nar/article-pdf/38/suppl_2/W7/16771268/gkq291.pdf

V. Ahola, R. Lehtonen, P. Somervuo, L. Salmela, P. Koskinen et al.,

V. Mäkinen, M. R. Goldsmith, L. Holm, P. Auvinen, M. J. Frilander et al., The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera, Nat. Commun, vol.5, p.4737, 2014.

J. M. Allen, D. I. Huang, Q. C. Cronk, and K. P. Johnson, aTRAM -automated target restricted assembly method: a fast method for assembling loci across divergent taxa from nextgeneration sequencing data, BMC Bioinformatics, vol.16, p.98, 2015.
DOI : 10.1186/s12859-015-0515-2
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0515-2

J. M. Allen, B. Boyd, N. P. Nguyen, P. Vachaspati, T. Warnow et al.,

K. P. Johnson, Phylogenomics from whole genome sequences using aTRAM, Syst. Biol, vol.66, pp.786-798, 2017.

G. Altekar, S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist, Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference, Bioinformatics, vol.20, pp.407-415, 2004.
DOI : 10.1093/bioinformatics/btg427
URL : https://academic.oup.com/bioinformatics/article-pdf/20/3/407/455968/btg427.pdf

S. F. Altschul, J. C. Wootton, E. Zaslavsky, and Y. K. Yu, The construction and use of logodds substitution scores for multiple sequence alignment, PLoS Comput. Biol, vol.6, p.1000852, 2010.

, , 2019.

A. S. , Shotgun DNA sequencing using cloned DNase I-generated fragments, Nucleic Acids Res, vol.9, pp.3015-3027, 1981.

K. Angelis, S. Álvarez-carretero, M. Dos-reis, and Z. Yang, An evaluation of different partitioning strategies for Bayesian estimation of species divergence times, Syst. Biol, vol.67, pp.61-77, 2017.

M. Ballenghien, N. Faivre, and N. Galtier, Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions, BMC Biol, vol.15, p.25, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01815358

A. L. Bazinet, K. T. Mitter, D. R. Davis, E. J. Van-nieukerken, M. P. Cummings et al., Phylotranscriptomics resolves ancient divergences in the Lepidoptera, 2017.

. Entomol, , vol.42, pp.82-93

C. D. Bell, D. E. Soltis, and P. S. Soltis, The age and diversification of the angiosperms rerevisited, Am. J. Bot, vol.97, pp.1296-1303, 2010.

M. R. Berenbaum and P. P. Feeny, Chemical mediation of host-plant specialization: the Papilionid paradigm, Specialization, Speciation, and Radiation: The Evolutionary Biology of Herbivorous Insects, pp.3-19, 2008.

B. B. Blaimer, M. W. Lloyd, W. X. Guillory, and S. G. Brady, Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens, PLoS One, vol.11, p.161531, 2016.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a exible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

M. G. Branstetter, B. N. Danforth, J. P. Pitts, B. C. Faircloth, P. S. Ward et al., Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees, Curr. Biol, vol.27, pp.1019-1025, 2017.

M. G. Branstetter, J. T. Longino, P. S. Ward, and B. C. Faircloth, Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera, 2017.

, Meth. Ecol. Evol, vol.8, pp.768-776

J. W. Breinholt and A. Y. Kawahara, Phylotranscriptomics: saturated third codon positions radically in uence the estimation of trees based on next-gen data, Genome Biol. Evol, vol.5, pp.2082-2092, 2013.

J. W. Breinholt, C. Earl, A. R. Lemmon, E. M. Lemmon, L. Xiao et al., Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics, Syst. Biol, vol.67, pp.78-93, 2018.

J. W. Brown and S. A. Smith, The past sure is tense: on interpreting phylogenetic divergence time estimates, Syst. Biol, vol.67, pp.340-353, 2018.

S. Capella-gutiérrez, J. M. Silla-martínez, and T. Gabaldón, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

F. M. Carpenter, Treatise on invertebrate paleontology, 1992.

M. S. Caterino, R. D. Reed, M. M. Kuo, and F. A. Sperling, A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae), Syst. Biol, vol.50, pp.106-127, 2001.

J. M. Carter, S. C. Baker, R. Pink, D. R. Carter, A. Collins et al., Unscrambling butterfly oogenesis, BMC Genom, vol.14, p.283, 2013.

N. Chazot, N. Wahlberg, A. V. Freitas, C. Mitter, C. C. Labandeira et al., Priors and posteriors in Bayesian timing of divergence analyses: The age of butterflies revisited, Syst. Biol, 2019.

, , 2019.

Q. Cong, J. Shen, D. Borek, R. K. Robbins, Z. Otwinowski et al., Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence, Sci. Rep, vol.6, p.24863, 2016.

Q. Cong, J. Shen, W. Li, D. Borek, Z. Otwinowski et al., The first complete genomes of metalmarks and the classification of butterfly families, Genomics, vol.109, pp.485-493

J. W. Davey, M. Chouteau, S. L. Barker, L. Maroja, S. W. Baxter et al., Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution, Genes Genomes Genet, vol.6, pp.695-708, 2016.

D. Franco, A. Poujol, R. Baurain, D. Philippe, and H. , Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences, 2019.

, BMC Evol. Biol, vol.19, p.21

M. Dos-reis, J. Inoue, M. Hasegawa, R. J. Asher, P. C. Donoghue et al., Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny, Proc. R. Soc. B, vol.279, pp.3491-3500, 2012.

M. Dos-reis, Y. Thawornwattana, K. Angelis, M. J. Telford, P. C. Donoghue et al., Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales, Curr. Biol, vol.25, pp.2939-2950, 2015.

M. Dos-reis, P. C. Donoghue, and Z. Yang, Bayesian molecular clock dating of species divergences in the genomics era, Nat. Rev. Genet, vol.17, pp.71-80, 2016.

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed phylogenetics and dating with confidence, PLoS Biol, vol.4, p.88, 2006.

J. R. Dupuis and F. A. Sperling, Repeated reticulate evolution in North American Papilio machaon group swallowtail butterflies, PLoS One, vol.10, p.141882, 2015.

, , 2019.

J. R. Dupuis and F. A. Sperling, Hybrid dynamics in a species group of swallowtail butterflies, J. Evol. Biol, vol.29, pp.1932-1951, 2016.

C. J. Durden and H. Rose, Butterflies from the middle Eocene: the earliest occurrence of fossil Papilionidae, Prarce-Sellards Ser. Tax. Mem. Mus, vol.29, pp.1-25, 1978.

P. R. Ehrlich and P. H. Raven, Butterflies and plants: a study in coevolution, Evolution, vol.18, pp.586-608, 1964.

D. M. Emms and S. Kelly, OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol, vol.16, p.157, 2015.

M. Espeland, J. P. Hall, P. J. Devries, D. C. Lees, M. Cornwall et al., , 2015.

, Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea), Mol. Phylogenet. Evol, vol.93, pp.296-306

M. Espeland, J. Breinholt, K. R. Willmott, A. D. Warren, R. Vila et al., A comprehensive and dated phylogenomic analysis of butterflies, Curr. Biol, vol.28, pp.770-778, 2018.

B. C. Faircloth, J. E. Mccormack, N. G. Crawford, M. G. Harvey, R. T. Brumfield et al., Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales, Syst. Biol, vol.61, pp.717-726, 2012.

B. C. Faircloth, M. G. Branstetter, N. D. White, and S. G. Brady, Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera, Mol. Ecol. Res, vol.15, pp.489-501, 2015.

B. C. Faircloth, Identifying conserved genomic elements and designing universal bait sets to enrich them, Meth. Ecol. Evol, vol.8, pp.1103-1112, 2017.

E. B. Ford, Studies on the chemistry of pigments in the Lepidoptera, with reference to their bearing on systematics. 4. The classification of the Papilionidae, Trans. R. Entomol. Soc. L, vol.94, pp.201-223, 1944.

C. S. Foster, H. Sauquet, M. Van-der-merwe, H. Mcpherson, M. Rossetto et al., Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale, Syst. Biol, vol.66, pp.338-351, 2017.

A. P. Fuentes-pardo and D. E. Ruzzante, Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations, 2017.

. Ecol, , vol.26, pp.5369-5406

R. C. Gardner, A. J. Howarth, P. Hahn, M. Brown-luedi, R. J. Shepherd et al., The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing, Nucleic Acids Res, vol.9, pp.2871-2888, 1981.

N. L. Garrison, J. Rodriguez, I. Agnarsson, J. A. Coddington, C. E. Griswold et al., Spider phylogenomics: untangling the Spider Tree of Life, vol.4, p.1719, 2016.

T. Gernhard, The conditioned reconstructed process, J. Theoret. Biol, vol.253, pp.769-778, 2008.

J. P. Gillung, S. L. Winterton, K. M. Bayless, Z. Khouri, M. L. Borowiec et al., Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids, Mol. Phylogenet. Evol, vol.128, pp.233-245, 2018.

S. Gnerre, I. Maccallum, D. Przybylski, F. J. Ribeiro, J. N. Burton et al., , 2019.

R. Nicol, A. Gnirke, C. Nusbaum, E. S. Lander, and D. B. Jaffe, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proc. Natl Acad. Sci. USA, vol.108, pp.1513-1518, 2011.

L. Guéguen, S. Gaillard, B. Boussau, M. Gouy, M. Groussin et al.,

L. Dachary, N. Galtier, K. Belkir, and J. Y. Dutheil, Bio++: efficient extensible libraries and tools for computational molecular evolution, Mol. Biol. Evol, vol.30, pp.1745-1750, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01209906

K. Guschanski, J. Krause, S. Sawyer, L. M. Valente, S. Bailey et al., Nextgeneration museomics disentangles one of the largest primate radiations, Syst. Biol, vol.62, pp.539-554, 2013.

D. L. Hancock, Classification of the Papilionidae (Lepidoptera): a phylogenetic approach, Smithersia, vol.2, pp.1-48, 1983.

K. M. Harkins, R. S. Schwartz, R. A. Cartwright, and A. C. Stone, Phylogenomic reconstruction supports supercontinent origins for Leishmania, Infect. Genet. Evol, vol.38, pp.101-109, 2016.

M. Heikkilä, L. Kaila, M. Mutanen, C. Peña, and N. Wahlberg, Cretaceous origin and repeated tertiary diversification of the redefined butterflies, Proc. R. Soc. B, vol.279, pp.1093-1099, 2012.

D. T. Hoang, O. Chernomor, A. Von-haeseler, B. Q. Minh, and L. S. Vinh, UFBoot2: improving the ultrafast bootstrap approximation, Mol. Biol. Evol, vol.35, pp.518-522, 2018.

G. M. Hughes and E. C. Teeling, AGILE: an assembled genome mining pipeline, Bioinformatics, vol.35, pp.1252-1254, 2018.

, , 2019.

S. Igarashi, The classification of the Papilionidae mainly based on the morphology of their immature stages, Trans. Lepido. Soc. Japan, vol.34, pp.41-96, 1984.

E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde et al.,

S. Subramanian, T. Gabaldón, S. Capella-gutiérrez, J. Huerta-cepas, B. Rekepalli et al.,

D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro et al.,

L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando et al.,

W. Johnson, K. P. Koepfli, S. O'brien, D. Haussler, O. A. Ryder et al., Whole-genome analyses resolve early branches in the tree of life of modern birds, vol.346, pp.1320-1331, 2014.

O. Jeffroy, H. Brinkmann, F. Delsuc, and H. Philippe, Phylogenomics: the beginning of incongruence?, Trends Genet, vol.22, pp.225-231, 2006.
URL : https://hal.archives-ouvertes.fr/halsde-00315496

W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers, The global diversity of birds in space and time, Nature, vol.491, pp.444-448, 2012.

, , 2019.

F. Jia, N. Lo, and S. Y. Ho, The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and timescales, PLoS One, vol.9, p.95722, 2014.

R. De-jong, Are there butterflies with Gondwanan ancestry in the Australian region?, Invert. Syst, vol.17, pp.143-156, 2003.

R. De-jong, Estimating time and space in the evolution of the Lepidoptera, Tijdschrift voor Entomologie, vol.150, pp.319-346, 2007.

R. De-jong, Reconstructing a 55-million-year-old butterfly (Lepidoptera: Hesperiidae), 2016.

, European J. Entomol, vol.113, pp.423-428

R. De-jong, Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea), Zootaxa, vol.4270, pp.1-63, 2017.

R. Kajitani, K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura et al., Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads, Genome Res, vol.24, pp.1384-1395, 2014.

S. Kalyaanamoorthy, B. Q. Minh, T. K. Wong, A. Von-haeseler, and L. S. Jermiin, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Meth, vol.14, pp.587-589, 2017.

A. Y. Kawahara, Phylogeny of snout butter ies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from morphology of extant, fossil, and recently extinct taxa, Cladistics, vol.25, pp.263-278, 2009.

A. Y. Kawahara and J. W. Breinholt, Phylogenomics provides strong evidence for relationships of butterflies and moths, Proc. R. Soc. B, vol.281, p.20140970, 2014.
DOI : 10.1098/rspb.2014.0970
URL : http://rspb.royalsocietypublishing.org/content/281/1788/20140970.full.pdf

K. Kunte, The diversity and evolution of Batesian mimicry in Papilio swallowtails butterflies, Evolution, vol.63, pp.2707-2716, 2009.

, , 2019.

K. Kunte, W. Zhang, A. Tenger-trolander, D. H. Palmer, A. Martin et al., Doublesex is a mimicry supergene, Nature, vol.507, pp.229-232, 2014.
DOI : 10.1038/nature13112

N. Lartillot and H. Philippe, A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process, Mol. Biol. Evol, vol.21, pp.1095-1109, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00108585

N. Lartillot, T. Lepage, and S. Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, pp.2286-2288, 2009.
DOI : 10.1093/bioinformatics/btp368
URL : https://academic.oup.com/bioinformatics/article-pdf/25/17/2286/16888307/btp368.pdf

N. Lartillot, N. Rodrigue, D. Stubbs, and J. Richer, PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment, Syst. Biol, vol.62, pp.611-615, 2013.

S. Laurin-lemay, H. Brinkmann, and H. Philippe, Origin of land plants revisited in the light of sequence contamination and missing data, Curr. Biol, vol.22, pp.593-594, 2012.

S. Q. Le and O. Gascuel, An improved general amino acid replacement matrix, Mol. Biol. Evol, vol.25, pp.1307-1320, 2008.
DOI : 10.1093/molbev/msn067
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

S. Q. Le, O. Gascuel, and N. Lartillot, Empirical profile mixture models for phylogenetic reconstruction, Bioinformatics, vol.24, pp.2317-2323, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324090

S. Q. Le, C. C. Dang, and O. Gascuel, Modeling protein evolution with several amino acid replacement matrices depending on site rates, Mol. Biol. Evol, vol.29, pp.2921-2936, 2012.
DOI : 10.1093/molbev/mss112
URL : https://hal.archives-ouvertes.fr/lirmm-00715443

E. M. Lemmon and A. R. Lemmon, High-throughput genomic data in systematics and phylogenetics, Annu. Rev. Ecol. Evol. Syst, vol.44, pp.99-121, 2013.
DOI : 10.1146/annurev-ecolsys-110512-135822

A. R. Lemmon, S. A. Emme, and E. M. Lemmon, Anchored hybrid enrichment for massively high-throughput phylogenomics, Syst. Biol, vol.61, pp.727-744, 2012.

X. Li, D. Fan, W. Zhang, G. Liu, L. Zhang et al., Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies, Nat. Commun, vol.6, p.8212, 2015.
DOI : 10.1038/ncomms9212
URL : https://www.nature.com/articles/ncomms9212.pdf

, , 2019.

G. Li, B. W. Davis, E. Eizirik, and W. J. Murphy, Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae), 2016.

, Genome Res, vol.26, pp.1-11

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short, vol.1, p.18, 2012.
DOI : 10.1186/2047-217x-1-18
URL : https://academic.oup.com/gigascience/article-pdf/1/1/2047-217X-1-18/25510880/13742_2012_article_18.pdf

S. Magallón, S. Gómez-acevedo, and L. L. Sánchez-reyes, Hernández-Hernández T. 2015. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity, New Phytol, vol.207, pp.437-453

J. E. Mccormack, S. M. Hird, A. J. Zellmer, B. C. Carstens, and R. T. Brumfield, Applications of next-generation sequencing to phylogeography and phylogenetics, Mol. Phylogenet. Evol, vol.66, pp.526-538, 2013.

M. L. Metzker, Sequencing technologies-the next generation, Nat. Rev. Genet, vol.11, pp.31-46, 2010.

F. Michel, C. Rebourg, E. Cosson, and H. Descimon, Molecular phylogeny of Parnassiinae butterflies (Lepidoptera: Papilionidae) based on the sequences of four mitochondrial DNA segments, Ann. Soc. Entomol. Fr, vol.44, pp.1-36, 2008.

J. S. Miller, Phylogenetic studies in the Papilioninae (Lepidoptera: Papilionidae), Bull. Am. Mus. Nat. Hist, vol.186, pp.365-512, 1987.

B. Q. Minh, M. Hahn, and R. Lanfear, New methods to calculate concordance factors for phylogenomic datasets. bioRxiv, p.487801, 2018.

B. Q. Minh, M. A. Nguyen, and A. Von-haeseler, Ultrafast approximation for phylogenetic bootstrap, Mol. Biol. Evol, vol.30, pp.1188-1195, 2013.

S. Mirarab, R. Reaz, M. S. Bayzid, T. Zimmermann, M. S. Swenson et al., ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, vol.30, pp.541-548, 2014.

B. Misof, S. Liu, K. Meusemann, R. S. Peters, A. Donath et al.,

T. R. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui et al.,

L. Podsiadlowski, H. Pohl, B. M. Von-reumont, K. Schütte, K. Sekiya et al.,

J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou et al.,

J. Wang, J. Wang, K. M. Kjer, and X. Zhou, Phylogenomics resolves the timing and pattern of insect evolution, Science, vol.346, pp.763-767, 2014.

K. Mita, M. Kasahara, S. Sasaki, Y. Nagayasu, T. Yamada et al.,

S. Morishita and T. Sasaki, The genome sequence of silkworm, Bombyx mori, DNA Res, vol.11, pp.27-35, 2004.

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Methods, vol.5, pp.621-628, 2008.

, , 2019.

E. Munroe, The classification of the Papilionidae (Lepidoptera), Canad. Entomologist: Suppl, vol.17, pp.1-51, 1961.

M. Mutanen, N. Wahlberg, and L. Kaila, Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies, Proc. R. Soc. B, vol.277, pp.2839-2848, 2010.

A. R. Nabhan and I. N. Sarkar, The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy, Brief. Bioinfo, vol.13, pp.122-134, 2012.

V. Nazari, E. V. Zakharov, and F. A. Sperling, Phylogeny, historical biogeography, and taxonomic ranking of Parnassiinae (Lepidoptera: Papilionidae) based on morphology and seven genes, Mol. Phylogenet. Evol, vol.42, pp.131-156, 2007.

L. T. Nguyen, H. A. Schmidt, A. Von-haeseler, and B. Q. Minh, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol, vol.32, pp.268-274, 2015.

E. J. Van-nieukerken, L. Kaila, and I. J. Kitching, Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness, Z.Q. Zhang). Zootaxa, vol.3148, pp.212-221, 2011.

H. Nishikawa, T. Iijima, R. Kajitani, J. Yamaguchi, T. Ando et al.,

H. Hori, T. Itoh, and H. Fujiwara, A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly, Nature Genet, vol.47, pp.405-409, 2015.

R. W. Nowell, B. Elsworth, V. Oostra, B. J. Zwaan, C. W. Wheat et al., A high-coverage draft genome of the mycalesine butterfly, Bicyclus anynana. GigaScience, vol.6, pp.1-7, 2017.

, , 2019.

T. H. Oakley, J. M. Wolfe, A. R. Lindgren, and A. K. Zaharoff, Phylotranscriptomics to bring the understudied into the fold: Monophyletic Ostracoda, fossil placement and Pancrustacean phylogeny, Mol. Biol. Evol, vol.30, pp.215-233, 2012.

M. J. Parsons, Gondwanan evolution of the troidine swallowtails (Lepidoptera: Papilionidae): cladistic reappraisals using mainly immature stage characters, with focus on the birdwings Ornithoptera Boisduval, Bull. Kitakyushu Mus. Nat. Hist, vol.15, pp.43-118, 1996.

P. De-la, M. Celorio-mancera, C. W. Wheat, H. Vogel, L. Söderlind et al., Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq, Mol. Ecol, vol.22, pp.4884-4895, 2013.

H. Philippe, D. M. Vienne, V. Ranwez, B. Roure, D. Baurain et al., Pitfalls in supermatrix phylogenomics, European J. Taxon, vol.283, pp.1-25, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606389

C. Pouchon, A. Fernández, J. M. Nassar, F. Boyer, S. Aubert et al., Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the tropical Andes, Syst. Biol, vol.67, pp.1041-1060, 2018.

R. O. Prum, J. S. Berv, A. Dornburg, D. J. Field, J. P. Townsend et al., A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing, Nature, vol.526, pp.569-573, 2015.

J. L. Rainford, M. Hofreiter, D. B. Nicholson, and P. J. Mayhew, Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects, PLoS One, vol.9, p.109085, 2014.

V. Ranwez, A. Criscuolo, and E. J. Douzery, SuperTriplets: a triplet-based supertree approach to phylogenomics, Bioinformatics, vol.26, pp.115-123, 2010.

H. Rebel, Fossile Lepidopteren aus der Miocänformation von Gabbro, Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften. Mathematisch-Naturwissenschaftliche Classe, vol.107, pp.731-745, 1898.

, , 2019.

J. C. Regier, A. Zwick, M. P. Cummings, A. Y. Kawahara, S. Cho et al., Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study, BMC Evol. Biol, vol.9, p.280, 2009.

S. Roch and M. Steel, Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent, Theoret. Pop. Biol, vol.100, pp.56-62, 2015.

B. Roure, D. Baurain, and H. Philippe, Impact of missing data on phylogenies inferred from empirical phylogenomic data sets, Mol. Biol. Evol, vol.30, pp.197-214, 2013.

R. K. Sahoo, A. D. Warren, S. C. Collins, and U. Kodandaramaiah, Hostplant change and paleoclimatic events explain diversification shifts in skipper butterflies (Family: Hesperiidae), BMC Evol. Biol, vol.17, p.174, 2017.

R. S. Schwartz, K. M. Harkins, A. C. Stone, and R. A. Cartwright, A composite genome approach to identify phylogenetically informative data from next-generation sequencing, BMC Bioinformatics, vol.16, p.193, 2015.

J. M. Scriber, Y. Tsubaki, and R. C. Lederhouse, Swallowtail butterflies: their ecology and evolutionary biology, 1995.

S. H. Scudder, 1875. Fossil butterflies. Mem. Am. Assoc. Advanc. Sci, vol.1, pp.1-99

P. Simion, K. Belkhir, C. François, J. Veyssier, J. C. Rink et al., A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data, BMC Biol, vol.16, p.28, 2018.
DOI : 10.1186/s12915-018-0486-7
URL : https://bmcbiol.biomedcentral.com/track/pdf/10.1186/s12915-018-0486-7

T. J. Simonsen, E. V. Zakharov, M. Djernaes, A. M. Cotton, R. I. Vane-wright et al., Phylogenetics and divergence times of Papilioninae (Lepidoptera) with special reference to the enigmatic genera Teinopalpus and Meandrusa, Cladistics, vol.27, pp.113-137, 2011.

, , 2019.

M. E. Smith, B. Singer, and A. Carroll, 40 Ar/ 39 Ar geochronology of the Eocene Green River Formation, Wyoming. Geol. Soc. Am. Bull, vol.115, pp.549-565, 2003.

S. A. Smith, J. W. Brown, and J. F. Walker, So many genes, so little time: A practical approach to divergence-time estimation in the genomic era, PLoS One, vol.13, p.197433, 2018.

J. Sohn, C. C. Labandeira, D. Davis, and C. Mitter, An annotated catalog of fossil and subfossil Lepidoptera (Insecta: Holometabola) of the world, Zootaxa, vol.3286, pp.1-132, 2012.

A. Srivastava, H. Sarkar, N. Gupta, and R. Patro, RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes, Bioinformatics, vol.32, pp.192-200, 2016.
DOI : 10.1093/bioinformatics/btw277
URL : https://academic.oup.com/bioinformatics/article-pdf/32/12/i192/17130476/btw277.pdf

R. Staden, A strategy of DNA sequencing employing computer programs, Nucleic Acids Res, vol.6, pp.2601-2610, 1979.
DOI : 10.1093/nar/6.7.2601
URL : http://europepmc.org/articles/pmc327874?pdf=render

A. Suh, The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves, Zool. Scripta, vol.45, pp.50-62, 2016.

V. Talla, A. Suh, F. Kalsoom, V. Dinc?, R. Vila et al., Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies, Genome Biol. Evol, vol.9, pp.2491-2505, 2017.

K. J. Tong, S. Duchêne, S. Y. Ho, and N. Lo, Comment on "Phylogenomics resolves the timing and pattern of insect evolution, Science, vol.349, p.487, 2015.

H. A. Tyler, K. S. Brown, and K. Wilson, Swallowtail butterflies of the Americas: a study in biological dynamics, ecological diversity, biosystematics and conservation, 1994.

N. Wahlberg, J. Leneveu, U. Kodandaramaiah, C. Peña, S. Nylin et al., , 2009.

, Cretaceous/Tertiary boundary, Proc. R. Soc. B, vol.276, pp.4295-4302

, , 2019.

N. Wahlberg, C. W. Wheat, and C. Peña, Timing and patterns in the taxonomic diversification of Lepidoptera (butterflies and moths), PLoS One, vol.8, p.80875, 2013.

A. R. Wallace, On the phenomena of variation and geographical distribution as illustrated by the Papilionidae of the Malayan region, Trans. Linn. Soc. London, vol.25, pp.1-71, 1865.

H. C. Wang, B. Q. Minh, E. Susko, and A. J. Roger, Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation, 2018.
DOI : 10.1093/sysbio/syx068

, Syst. Biol, vol.67, pp.216-235

T. Warnow, Computational phylogenetics: An introduction to designing methods for phylogeny estimation, 2017.

A. D. Warren, J. R. Ogawa, and A. V. Brower, Revised classification of the family Hesperiidae (Lepidoptera: Hesperioidea) based on combined molecular and morphological data, Syst. Entomol, vol.34, pp.467-523, 2009.

T. Yagi, G. Sasaki, and H. Takebe, Phylogeny of Japanese papilionid butterflies inferred from nucleotide sequences of the mitochondrial ND5 gene, J. Mol. Evol, vol.48, pp.42-48, 1999.

Z. Yang, Among-site rate variation and its impact on phylogenetic analyses, Trends Ecol. Evol, vol.11, pp.367-372, 1996.

Z. Yang and B. Rannala, Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds, Mol. Biol. Evol, vol.23, pp.212-226, 2006.

E. V. Zakharov, M. S. Caterino, and F. A. Sperling, Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae), Syst. Biol, vol.53, pp.193-215, 2004.

S. Zhan, C. Merlin, J. L. Boore, and S. M. Reppert, The monarch butterfly genome yields insights into long-distance migration, Cell, vol.147, pp.1171-1185, 2011.

C. Zhang, M. Rabiee, E. Sayyari, and S. Mirarab, ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees, BMC Bioinfo, vol.19, p.153, 2018.

F. Zhang, Y. Ding, C. Zhu, X. Zhou, M. C. Orr et al., Phylogenomics from low-coverage whole-genome sequencing, Meth. Ecol. Evol, vol.10, pp.507-517, 2019.

A. V. Zimin, G. Marçais, D. Puiu, M. Roberts, S. L. Salzberg et al., The MaSuRCA genome assembler, Bioinformatics, vol.29, pp.2669-2677, 2013.

, , 2019.