J. W. Alfaro, L. Cortés-ortiz, D. Fiore, A. Boubli, and J. P. , Special issue: Comparative biogeography of Neotropical primates, Molecular Phylogenetics and Evolution, vol.82, pp.518-529, 2015.
DOI : 10.1016/j.ympev.2014.09.027

A. Antonelli, J. A. Nylander, C. Persson, and I. Sanmartín, Tracing the impact of the Andean uplift on Neotropical plant evolution, Proceedings of the National Academy of Sciences, vol.35, issue.3, pp.9749-9754, 2009.
DOI : 10.1016/j.ympev.2004.12.006

A. Antonelli and I. Sanmartín, Why are there so many plant species in the Neotropics? Taxon, pp.403-414, 2011.

C. D. Bacon, D. Silvestro, C. Jaramillo, B. T. Smith, P. Chakrabarty et al., Biological evidence supports an early and complex emergence of the Isthmus of Panama, Proceedings of the National Academy of Sciences, vol.5, issue.2, pp.6110-6115, 2015.
DOI : 10.1126/science.1116412

C. D. Bacon, D. Silvestro, C. Jaramillo, B. T. Smith, P. Chakrabarty et al., Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases: Fig. 1., Proceedings of the National Academy of Sciences, vol.112, issue.43, pp.5767-5768, 2015.
DOI : 10.1029/2007PA001574

C. Badgley, E. J. Beckman, and C. C. Witt, Tectonics, topography, and mammalian diversity Phylogeny and biogeography of the new world siskins and goldfinches: Rapid diversification in the Central Andes, Ecography Molecular Phylogenetics and Evolution, vol.33, issue.87, pp.220-231, 2010.

P. Blandin and B. Purser, Evolution and diversification of neotropical butterflies: Insights from the biogeography and phylogeny of the genus Morpho Fabricius, 1807 (Nymphalidae: Morphinae), with a review of the geodynamics of South America, Tropical Lepidoptera Research, vol.23, pp.62-85, 2013.

J. I. Bloch, E. D. Woodruff, A. R. Wood, A. F. Rincon, A. R. Harrington et al., First North American fossil monkey and early Miocene tropical biotic interchange, Nature, vol.117, issue.7602, pp.533-243, 2016.
DOI : 10.1029/2011JB008959

A. V. Brower, A. V. Freitas, M. M. Lee, K. L. Silva-brandão, A. Whinnett et al., Phylogenetic relationships among the Ithomiini (Lepidoptera: Nymphalidae) inferred from one mitochondrial and two nuclear gene regions, Systematic Entomology, vol.271, issue.2, pp.288-301, 2006.
DOI : 10.1163/187631296X00205

A. V. Brower, K. R. Willmott, K. L. Silva-brandão, I. J. Garzón-orduña, and A. V. Freitas, Phylogenetic relationships of ithomiine butterflies (Lepidoptera: Nymphalidae: Danainae) as implied by combined morphological and molecular data, Systematics and Biodiversity, vol.111, issue.35, pp.133-147, 2014.
DOI : 10.1603/0013-8746(2007)100[449:AROPAN]2.0.CO;2

R. T. Brumfield and S. V. Edwards, ANTSHRIKES, Evolution, vol.68, issue.111, pp.346-367, 2007.
DOI : 10.1663/0006-8101(2002)068[0004:PEAEIA]2.0.CO;2

J. C. Buckner, J. W. Alfaro, A. B. Rylands, and M. E. Alfaro, Biogeography of the marmosets and tamarins (Callitrichidae), Molecular Phylogenetics and Evolution, vol.82, pp.413-425, 2015.
DOI : 10.1016/j.ympev.2014.04.031

K. L. Casner and T. W. Pyrcz, Patterns and timing of diversification in a tropical montane butterfly genus, Lymanopoda (Nymphalidae, Satyrinae), Ecography, vol.213, issue.2, pp.251-259, 2010.
DOI : 10.1111/j.0014-3820.2006.tb01140.x

S. Castroviejo-fisher, J. M. Guayasamin, A. Gonzalez-voyer, and C. Vilà, Neotropical diversification seen through glassfrogs, Journal of Biogeography, vol.101, issue.1, pp.66-80, 2014.
DOI : 10.1038/hdy.2008.30
URL : http://onlinelibrary.wiley.com/doi/10.1111/jbi.12208/pdf

J. A. Chaves, J. T. Weir, and T. B. Smith, Diversification in Adelomyia hummingbirds follows Andean uplift, Molecular Ecology, vol.56, issue.21, pp.4564-4576, 2011.
DOI : 10.1016/j.ympev.2010.04.011

N. Chazot, K. R. Willmott, F. L. Condamine, D. L. De-silva, A. V. Freitas et al., Into the Andes: multiple independent colonizations drive montane diversity in the Neotropical clearwing butterflies Godyridina, Molecular Ecology, vol.22, issue.22, pp.5765-5784, 2016.
DOI : 10.1111/j.1096-0031.2006.00108.x

N. Chazot, K. R. Willmott, P. G. Santacruz-endara, A. Toporov, R. I. Hill et al., Mutualistic Mimicry and Filtering by Altitude Shape the Structure of Andean Butterfly Communities, The American Naturalist, vol.183, issue.1, pp.26-39, 2014.
DOI : 10.1086/674100

A. G. Coates, J. B. Jackson, L. S. Collins, T. M. Cronin, H. J. Dowsett et al., Closure of the Isthmus of Panama: The near-shore marine record of Costa Rica and western Panama, Geological Society of America Bulletin, vol.104, issue.7, pp.814-8280016, 1992.
DOI : 10.1130/0016-7606(1992)104<0814:COTIOP>2.3.CO;2

A. G. Coates and R. F. Stallard, How old is the Isthmus of Panama?, Bulletin of Marine Science, vol.89, issue.4, pp.801-814, 2013.
DOI : 10.5343/bms.2012.1076

F. L. Condamine, K. L. Silva-brandão, G. J. Kergoat, and F. A. Sperling, Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia, BMC Evolutionary Biology, vol.12, issue.1, 2012.
DOI : 10.1093/sysbio/syq032

S. M. Dantas, J. D. Weckstein, J. M. Bates, N. K. Krabbe, C. D. Cadena et al., Molecular systematics of the new world screech-owls ( Megascops : Aves, Strigidae): biogeographic and taxonomic implications, Molecular Phylogenetics and Evolution, vol.94, pp.626-634, 2016.
DOI : 10.1016/j.ympev.2015.09.025

D. L. De-silva, J. J. Day, M. Elias, K. Willmott, A. Whinnett et al., Molecular phylogenetics of the neotropical butterfly subtribe Oleriina (Nymphalidae: Danainae: Ithomiini), Molecular Phylogenetics and Evolution, vol.55, issue.3, pp.1032-1041, 2010.
DOI : 10.1016/j.ympev.2010.01.010

D. L. De-silva, M. Elias, K. Willmott, J. Mallet, and J. J. Day, Diversification of clearwing butterflies with the rise of the Andes, Journal of Biogeography, vol.26, issue.1, pp.44-58, 2016.
DOI : 10.1046/j.1365-3113.2001.00157.x

D. L. De-silva, L. L. Mota, N. Chazot, R. Mallarino, K. L. Silva-brandao et al., North Andean origin and diversification of the largest ithomiine butterfly genus Bayesian phylogenetics with BEAUti and the BEAST 1.7, Scientific Reports Molecular Biology and Evolution, vol.7, issue.29, pp.1969-1973, 2012.

P. R. Ehrlich and P. H. Raven, BUTTERFLIES AND PLANTS: A STUDY IN COEVOLUTION, Evolution, vol.13, issue.4, pp.586-608, 1964.
DOI : 10.1146/annurev.en.05.010160.001205

M. Elias, M. Joron, K. Willmott, K. L. Silva-brandão, V. Kaiser et al., Out of the Andes: patterns of diversification in clearwing butterflies, Molecular Ecology, vol.19, issue.8, pp.1716-1729, 2009.
DOI : 10.1111/j.0014-3820.2006.tb01161.x

L. A. Evenstar, F. M. Stuart, A. J. Hartley, and B. Tattitch, He in alluvial boulders from the Pacific Planation Surface, Geophysical Research Letters, vol.345, issue.1-4, pp.8448-8455, 2015.
DOI : 10.1016/S0040-1951(01)00212-8

D. W. Farris, C. Jaramillo, G. Bayona, S. A. Restrepo-moreno, C. Montes et al., Fracturing of the Panamanian Isthmus during initial collision with South America, Geology, vol.39, issue.11, pp.1007-1010, 2011.
DOI : 10.1130/G32237.1

R. G. Fitzjohn, : comparative phylogenetic analyses of diversification in R, Methods in Ecology and Evolution, vol.279, issue.6, pp.1084-1092, 2012.
DOI : 10.1098/rspb.2011.1045

A. Fouquet, C. C. Santana, F. B. Haddad, N. Pech, and R. M. Trefaut, (Anura, Leptodactylidae), Journal of Biogeography, vol.41, issue.248, pp.855-870, 2014.
DOI : 10.1126/science.1059412
URL : https://hal.archives-ouvertes.fr/hal-01032133

I. J. Garzón-orduña, K. L. Silva-brandão, K. R. Willmott, A. V. Freitas, and . Brower, Incompatible Ages for Clearwing Butterflies Based on Alternative Secondary Calibrations, Systematic Biology, vol.2013, issue.5, pp.752-767, 2015.
DOI : 10.1098/rsbl.2004.0184

T. J. Givnish, M. H. Barfuss, B. Van-ee, R. Riina, K. Schulte et al., Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae, Molecular Phylogenetics and Evolution, vol.71, pp.55-78, 2014.
DOI : 10.1016/j.ympev.2013.10.010
URL : https://repository.si.edu/bitstream/handle/10088/21985/stri_Brom-Giv-2014.pdf

E. E. Goldberg and B. Igic, TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION, Evolution, vol.19, issue.12, pp.3701-3709, 2012.
DOI : 10.1093/oxfordjournals.molbev.a004139
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01730.x/pdf

J. P. Hall, Montane speciation patterns in Ithomiola butterflies (Lepidoptera: Riodinidae): are they consistently moving up in the world?, Proceedings of the Royal Society B: Biological Sciences, vol.26, issue.1386, pp.2457-24663254, 2005.
DOI : 10.1046/j.1365-3113.2001.00157.x

C. Hoorn, F. Wesselingh, H. Ter-steege, M. Bermudez, A. Mora et al., Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity, Science, vol.27, issue.7176, pp.927-931, 2010.
DOI : 10.1111/j.0906-7590.2004.03732.x
URL : http://www.zora.uzh.ch/id/eprint/42535/10/Figure2.pdf

C. E. Hughes, R. T. Pennington, and A. Antonelli, Neotropical Plant Evolution: Assembling the Big Picture, Botanical Journal of the Linnean Society, vol.19, issue.1, pp.1-18, 2013.
DOI : 10.1016/j.tree.2004.09.011
URL : https://academic.oup.com/botlinnean/article-pdf/171/1/1/14086864/boj12006.pdf

C. Hughes and R. Eastwood, Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes, Proceedings of the National Academy of Sciences, vol.17, issue.8, pp.10334-10339, 2006.
DOI : 10.1093/bioinformatics/17.8.754

C. R. Hutter, J. M. Guayasamin, and J. J. Wiens, Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns, Ecology Letters, vol.14, issue.9, pp.1135-1144, 2013.
DOI : 10.1111/j.1461-0248.2011.01625.x

N. Janz, S. Nylin, and N. Wahlberg, Diversity begets diversity: Host expansions and the diversification of plant-feeding insects, BMC Evolutionary Biology, vol.6, issue.4, pp.1471-2148, 2006.

L. P. Lagomarsino, F. L. Condamine, A. Antonelli, A. Mulch, and C. C. Davis, The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae), New Phytologist, vol.451, issue.372, pp.1430-1442, 2016.
DOI : 10.1038/nature06588

G. Lamas, Ithomiinae in Atlas of Neotropical Lepidoptera. Checklist: Part 4A. Hesperioidea -Papilionoidea. (Association for Tropical Lepidoptera, 2004.

R. Lanfear, B. Calcott, S. Y. Ho, and S. H. Guindon, PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses The great American schism: Divergence of marine organisms after the rise of the Central American Isthmus, Molecular Biology and Evolution Annual Review of Ecology, Evolution, and Systematics, vol.29, issue.39, pp.1695-1701, 2008.

D. S. Lewis, F. A. Sperling, S. Nakahara, A. M. Cotton, A. Y. Kawahara et al., swallowtails, Cladistics, vol.53, issue.3, pp.291-314, 2015.
DOI : 10.1080/10635150490423403

W. P. Maddison and R. G. Fitzjohn, The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters, Systematic Biology, vol.417, issue.1, pp.127-136, 2015.
DOI : 10.1038/nature750

S. Madriñán, A. J. Cortés, and J. E. Richardson, P??ramo is the world's fastest evolving and coolest biodiversity hotspot, Frontiers in Genetics, vol.4, pp.1-7, 2013.
DOI : 10.3389/fgene.2013.00192

S. Magallón, S. Gómez-acevedo, L. I. Sánchez-reyes, and T. Hernández-hernández, A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity, New Phytologist, vol.195, issue.2, pp.437-453, 2015.
DOI : 10.1111/j.1469-8137.2012.04212.x

R. Mallarino, E. Bermingham, K. R. Willmott, A. Whinnett, and C. D. Jiggins, Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes, Molecular Phylogenetics and Evolution, vol.34, issue.3, pp.625-644, 2005.
DOI : 10.1016/j.ympev.2004.10.021

P. F. Matos-maraví, C. Peña, K. R. Willmott, A. V. Freitas, and N. Wahlberg, Systematics and evolutionary history of butterflies in the ???Taygetis clade??? (Nymphalidae: Satyrinae: Euptychiina): Towards a better understanding of Neotropical biogeography, Molecular Phylogenetics and Evolution, vol.66, issue.1, pp.54-68, 2013.
DOI : 10.1016/j.ympev.2012.09.005

N. J. Matzke, Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades, Systematic Biology, vol.62, issue.6, pp.951-970, 2014.
DOI : 10.1017/CBO9780511735882.010

J. A. Mcguire, C. C. Witt, D. L. Altshuler, and J. Remsen, Phylogenetic Systematics and Biogeography of Hummingbirds: Bayesian and Maximum Likelihood Analyses of Partitioned Data and Selection of an Appropriate Partitioning Strategy, Systematic Biology, vol.95, issue.5, pp.837-856, 2007.
DOI : 10.1080/10635150500234625

J. A. Mcguire, C. C. Witt, J. Remsen, A. Corl, D. L. Rabosky et al., Molecular Phylogenetics and the Diversification of Hummingbirds, Current Biology, vol.24, issue.8, pp.910-916, 2014.
DOI : 10.1016/j.cub.2014.03.016

R. Menéndez, A. González-megías, Y. Collingham, R. Fox, D. B. Roy et al., DIRECT AND INDIRECT EFFECTS OF CLIMATE AND HABITAT FACTORS ON BUTTERFLY DIVERSITY, Ecology, vol.88, issue.3, pp.605-61106, 2007.
DOI : 10.2307/3544109

B. Q. Minh, M. A. Nguyen, and A. Haeseler, Ultrafast Approximation for Phylogenetic Bootstrap, Molecular Biology and Evolution, vol.14, issue.7, 2013.
DOI : 10.1093/oxfordjournals.molbev.a025811
URL : https://academic.oup.com/mbe/article-pdf/30/5/1188/6388241/mst024.pdf

C. Montes, A. Cardona, C. Jaramillo, A. Pardo, J. C. Silva et al., Middle Miocene closure of the Central American Seaway, Science, vol.296, issue.1, pp.226-229, 2015.
DOI : 10.1144/SP296.2

C. Montes, A. Cardona, R. Mcfadden, S. E. Morón, C. A. Silva et al., Evidence for middle Eocene and younger land emergence in central Panama: Implications for Isthmus closure, Geological Society of America Bulletin, vol.124, issue.5-6, pp.780-799, 2012.
DOI : 10.1130/B30528.1

H. Morlon, T. L. Parsons, and J. B. Plotkin, Reconciling molecular phylogenies with the fossil record, Proceedings of the National Academy of Sciences of the United States of America, pp.16327-16332, 2011.
DOI : 10.1093/oxfordjournals.molbev.a003974
URL : http://www.pnas.org/content/108/39/16327.full.pdf

J. J. Morrone, <strong>Biogeographical regionalisation of the Neotropical region</strong>, Zootaxa, vol.3782, issue.1, pp.1-110, 2014.
DOI : 10.11646/zootaxa.3782.1.1

S. P. Mullen, W. K. Savage, N. Wahlberg, and K. R. Willmott, Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies, Proceedings of the Royal Society B: Biological Sciences, vol.63, issue.5, pp.1777-1785, 2011.
DOI : 10.1111/j.1558-5646.2009.00610.x
URL : http://rspb.royalsocietypublishing.org/content/royprsb/278/1713/1777.full.pdf

N. Myers, R. G. Mittermeier, C. G. Mittermeier, G. A. Da-fonseca, and J. Kent, Biodiversity hotspots for conservation priorities, Nature, vol.401, issue.6772, pp.853-858, 2000.
DOI : 10.1038/32761

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, Molecular Biology and Evolution, vol.51, issue.1, pp.268-274, 2015.
DOI : 10.1007/s002390010105
URL : https://academic.oup.com/mbe/article-pdf/32/1/268/13171186/msu300.pdf

A. Parada, G. D-'elía, and R. E. Palma, The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents, BMC Evolutionary Biology, vol.12, issue.3, 2015.
DOI : 10.1038/nature13687

D. L. Rabosky, D. L. Rabosky, E. E. Goldberg, O. M. Warsi, and L. M. Dávalos, Extinction rates should not be estimated from molecular phylogenies Model inadequacy and mistaken inferences of trait-dependent speciation Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity, Systematic Biology Systematic Biology, vol.6, issue.65, pp.1816-1824, 2010.

R. E. Sedano and K. J. Burns, Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini), Journal of Biogeography, vol.48, issue.2, pp.325-343, 2010.
DOI : 10.1093/oxfordjournals.molbev.a003974

G. L. Stebbins, Flowering plants: Evolution above the species level (p. 399), 1974.
DOI : 10.4159/harvard.9780674864856

P. R. Stephens and J. J. Wiens, Explaining species richness from continents to communities: The time-for-speciation effect in emydid turtles, The American Naturalist, vol.161, pp.112-128, 2003.

J. Trifinopoulos, L. T. Nguyen, A. Von-haeseler, and B. Q. Minh, W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis, Nucleic Acids Research, vol.44, issue.W1, 2016.
DOI : 10.1098/rspb.2001.1862

N. Wahlberg, J. Leneveu, U. Kodandaramaiah, C. Peña, S. Nylin et al., Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary, Proceedings of the Royal Society B: Biological Sciences, vol.313, issue.5790, pp.4295-43021303, 2009.
DOI : 10.1126/science.1129569
URL : http://rspb.royalsocietypublishing.org/content/royprsb/276/1677/4295.full.pdf

N. Wahlberg and C. Wheat, Genomic Outposts Serve the Phylogenomic Pioneers: Designing Novel Nuclear Markers for Genomic DNA Extractions of Lepidoptera, Systematic Biology, vol.33, issue.2, pp.231-242, 2008.
DOI : 10.1111/j.1365-3113.2007.00410.x

J. T. Weir, DIVERGENT TIMING AND PATTERNS OF SPECIES ACCUMULATION IN LOWLAND AND HIGHLAND NEOTROPICAL BIRDS, Evolution, vol.213, issue.4, pp.842-855, 2006.
DOI : 10.1098/rstb.2003.1392

F. P. Wesselingh and J. Salo, A Miocene perspective on the evolution of the Amazonian biota, Scripta Geologica, vol.133, pp.439-458, 2006.

K. R. Willmott and A. V. Freitas, Higher-level phylogeny of the Ithomiinae (Lepidoptera: Nymphalidae): classification, patterns of larval hostplant colonization and diversification, Cladistics, vol.14, issue.35, pp.297-368, 2006.
DOI : 10.1098/rspb.2005.3247