C. Darwin, On the Origins of Species by Means of Natural Selection
DOI : 10.5962/bhl.title.24329

T. Flatt, M. P. Tu, and M. Tatar, Hormonal pleiotropy and the juvenile hormone regulation ofDrosophila development and life history, BioEssays, vol.131, issue.10, pp.999-1010, 2005.
DOI : 10.1002/bies.20290

R. Altig, R. W. Mcdiarmid, and . Tadpoles, The Biology of Anuran Larvae, pp.24-51, 1999.

R. Altig, M. R. Whiles, and C. L. Taylor, What do tadpoles really eat? Assessing the trophic status of an understudied and imperiled group of consumers in freshwater habitats, Freshwater Biology, vol.26, issue.2, pp.386-395, 2007.
DOI : 10.2307/1443378

G. S. Pryor, Tadpole nutritional ecology and digestive physiology: Implications for captive rearing of larval anurans, Zoo Biology, vol.4, issue.6, pp.502-507, 2014.
DOI : 10.1002/zoo.21152

K. Roelants, A. Haas, and F. Bossuyt, Anuran radiations and the evolution of tadpole morphospace, Proc. Natl Acad. Sci. USA, pp.8731-8736, 2011.
DOI : 10.1371/journal.pbio.0040088

A. Haas, Phylogeny of frogs as inferred from primarily larval characters, Cladistics, vol.19, pp.23-89, 2003.
DOI : 10.1016/s0748-3007(03)00006-9

R. Altig and G. Johnston, Guilds of Anuran Larvae: Relationships among Developmental Modes, Morphologies, and Habitats, Herpetological Monographs, vol.3, pp.81-109, 1989.
DOI : 10.2307/1466987

D. S. Moen, H. Morlon, and J. J. Wiens, Testing Convergence Versus History: Convergence Dominates Phenotypic Evolution for over 150 Million Years in Frogs, Systematic Biology, vol.65, issue.1, pp.146-160, 2016.
DOI : 10.1093/sysbio/syv073

D. S. Falconer, Introduction to Quantitative Genetics, 1989.

N. Shubin, C. Tabin, and S. Carroll, Fossils, genes and the evolution of animal limbs, Nature, vol.388, issue.6643, pp.639-648, 1997.
DOI : 10.1038/41710

D. L. Berry, C. S. Rose, B. F. Remo, and D. D. Brown, The Expression Pattern of Thyroid Hormone Response Genes in Remodeling Tadpole Tissues Defines Distinct Growth and Resorption Gene Expression Programs, Developmental Biology, vol.203, issue.1, pp.24-35, 1998.
DOI : 10.1006/dbio.1998.8975

F. Bossuyt and M. C. Milinkovitch, Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits, Proc. Natl Acad. Sci. USA 97, pp.6585-6590, 2000.
DOI : 10.2307/2408678

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18667/pdf

R. G. Perl, DNA barcoding Madagascar???s amphibian fauna, Amphibia-Reptilia, vol.35, issue.2, pp.197-206, 2014.
DOI : 10.1163/15685381-00002942

K. C. Wollenberg, D. R. Vieites, F. Glaw, and M. Vences, Speciation in little: the role of range and body size in the diversification of Malagasy mantellid frogs, BMC Evolutionary Biology, vol.11, issue.1, p.217, 2011.
DOI : 10.1111/j.1558-5646.2008.00538.x

F. Glaw and M. Vences, A Field Guide to the Amphibians and Reptiles of Madagascar, 2007.

R. M. Blommers-schlösser, Biosystematics of the Malagasy frogs. I. Mantellinae (Ranidae), Beaufortia, vol.29, pp.1-77, 1979.

R. M. Blommers-schlösser, Biosystematics of the Malagasy frogs. II. The genus Boophis (Rhacophoridae), Bijdr. Dierkd, vol.49, pp.261-312, 1979.

R. Altig and R. W. Mcdiarmid, Descriptions and biological notes on three unusual mantellid tadpoles (Amphibia: Anura: Mantellidae) from southeastern Madagascar, Proceedings of the Biological Society of Washington, vol.119, issue.3, pp.418-425, 2006.
DOI : 10.2988/0006-324X(2006)119[418:DABNOT]2.0.CO;2

S. Grosjean, R. D. Randrianiaina, A. Strau, and M. Vences, Sand-eating tadpoles in Madagascar: morphology and ecology of the unique larvae of the treefrog Boophis picturatus, Salamandra, vol.47, pp.63-76, 2011.

S. Grosjean, Morphological and ecological uniformity in the funnel-mouthed tadpoles of Malagasy litter frogs, subgenus Chonomantis, Zoological Journal of the Linnean Society, vol.162, issue.1, pp.149-183, 2011.
DOI : 10.1111/j.1096-3642.2010.00667.x

A. Strau, R. D. Randrianiaina, M. Vences, and J. Glos, Species distribution and assembly patterns of frog larvae in rainforest streams of Madagascar, Hydrobiologia, vol.23, issue.1, pp.27-43, 2013.
DOI : 10.1007/s10750-012-1301-z

A. Strau, Opposing patterns of seasonal change in functional and phylogenetic diversity of tadpole assemblages, PLoS ONE, vol.11, p.151744, 2016.

D. P. Scantlebury, Diversification rates have declined in the Malagasy herpetofauna, Proceedings of the Royal Society B: Biological Sciences, vol.173, issue.5, p.20131109, 2013.
DOI : 10.1086/597378

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730589

T. Hansen, STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION, Evolution, vol.41, issue.no. 53, pp.1341-1351, 1997.
DOI : 10.2307/3544261

T. Ingram and D. L. Mahler, SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion, Methods in Ecology and Evolution, vol.6, issue.5, pp.416-425, 2013.
DOI : 10.1111/2041-210X.12034

R. D. Martin, Review Lecture: Adaptive Radiation and Behaviour of the Malagasy Lemurs, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.264, issue.862, pp.295-352, 1972.
DOI : 10.1098/rstb.1972.0013

H. Wirta, L. Orsini, and I. Hanski, An old adaptive radiation of forest dung beetles in Madagascar, Molecular Phylogenetics and Evolution, vol.47, issue.3, pp.1076-1089, 2008.
DOI : 10.1016/j.ympev.2008.03.010

L. Christidis, S. M. Goodman, K. Naughton, and B. Appleton, Insights into the Evolution of a Cryptic Radiation of Bats: Dispersal and Ecological Radiation of Malagasy Miniopterus (Chiroptera: Miniopteridae), PLoS ONE, vol.12, issue.4, p.92440, 2014.
DOI : 10.1371/journal.pone.0092440.s002

A. Soulebeau, The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept, Organisms Diversity & Evolution, vol.23, issue.8, pp.747-761, 2015.
DOI : 10.1007/s13127-015-0220-z

K. A. Jønsson, Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas, Proc. Natl Acad. Sci. USA, pp.6620-6625, 2012.
DOI : 10.1093/bioinformatics/bti175

S. Reddy, A. Driskell, D. L. Rabosky, S. J. Hackett, and T. S. Schulenberg, Diversification and the adaptive radiation of the vangas of Madagascar, Proceedings of the Royal Society B: Biological Sciences, vol.31, issue.12, pp.2062-2071, 2012.
DOI : 10.1002/bies.200900102

W. Moore and J. A. Robertson, Explosive Adaptive Radiation and Extreme Phenotypic Diversity within Ant-Nest Beetles, Current Biology, vol.24, issue.20, pp.2435-2439, 2014.
DOI : 10.1016/j.cub.2014.09.022

C. Poux, O. Madsen, J. Glos, W. W. De-jong, and M. Vences, Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses, BMC Evolutionary Biology, vol.8, issue.1, p.102, 2008.
DOI : 10.1186/1471-2148-8-102

L. P. Warren and J. Kutzbach, Sensitivity of the Indian monsoon to forcing parameters and implications for its evolution, Nature, vol.360, pp.647-652, 1992.

K. E. Samonds, Imperfect Isolation: Factors and Filters Shaping Madagascar???s Extant Vertebrate Fauna, PLoS ONE, vol.89, issue.4, p.62086, 2013.
DOI : 10.1371/journal.pone.0062086.s001

URL : http://doi.org/10.1371/journal.pone.0062086

J. Gardner, The fossil record of tadpoles. Fossil Imprint, pp.17-44, 2016.

J. B. Karpinka, Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes, Nucleic Acids Research, vol.43, issue.D1, pp.756-763, 2015.
DOI : 10.1093/nar/gku956

URL : http://doi.org/10.1093/nar/gku956

J. Reimand, M. Kull, H. Peterson, J. Hansen, and J. Vilo, g:Profiler???a web-based toolset for functional profiling of gene lists from large-scale experiments, Nucleic Acids Research, vol.35, issue.suppl_2, pp.193-200, 2007.
DOI : 10.1093/nar/gkm226

J. Reimand, T. Arak, and J. Vilo, g:Profiler--a web server for functional interpretation of gene lists (2011 update), Nucleic Acids Research, vol.39, issue.suppl, pp.307-315, 2011.
DOI : 10.1093/nar/gkr378

P. Flicek, Ensembl 2011, Nucleic Acids Research, vol.39, issue.Database, pp.800-806, 2011.
DOI : 10.1093/nar/gkq1064

URL : http://doi.org/10.1093/nar/gkq1064

L. Pachter, Models for transcript quantification from RNA-Seq, p.3889, 2011.

M. Ashburner, Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1038/75556

M. Kanehisa, Y. Sato, M. Kawashima, M. Furumichi, and M. Tanabe, KEGG as a reference resource for gene and protein annotation, Nucleic Acids Research, vol.44, issue.D1, pp.457-462, 2015.
DOI : 10.1093/nar/gkv1070

URL : http://doi.org/10.1093/nar/gkv1070

A. Conesa, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, issue.18, pp.3674-3676, 2005.
DOI : 10.1093/bioinformatics/bti610

B. J. Haas, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, vol.500, issue.8, pp.1494-1512, 2013.
DOI : 10.1038/ng.2295

S. Hunter, InterPro: the integrative protein signature database, Nucleic Acids Research, vol.37, issue.Database, pp.211-215, 2009.
DOI : 10.1093/nar/gkn785

URL : https://hal.archives-ouvertes.fr/hal-00428250

R. C. Gentleman, Bioconductor: open software development for computational biology and bioinformatics, Genome Biol, vol.5, p.1, 2004.

S. Tarazona, Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package, Nucleic Acids Research, vol.43, p.140, 2015.
DOI : 10.1093/nar/gkv711

D. Szklarczyk, STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Research, vol.43, issue.D1, pp.447-452, 2015.
DOI : 10.1093/nar/gku1003

D. L. Swofford and . Paup-*, Phylogenetic Analysis Using Parsimony (*and Other Methods), 2002.

D. Schluter, The Ecology of Adaptive Radiation, 2000.

H. Morlon, M. D. Potts, and J. B. Plotkin, Inferring the Dynamics of Diversification: A Coalescent Approach, PLoS Biology, vol.55, issue.9, p.1000493, 2010.
DOI : 10.1371/journal.pbio.1000493.s001

H. Morlon, RPANDA: Phylogenetic ANalyses of DiversificAtion. R package version 1.0, 2014.

R. Development, C. Team, and R. , A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2011.

J. M. Eastman, M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon, A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES, Evolution, vol.51, issue.5, pp.3578-3589, 2011.
DOI : 10.1111/j.1558-5646.2011.01401.x

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

L. Harmon, J. Weir, C. Brock, R. Glor, and W. Challenger, GEIGER: investigating evolutionary radiations, Bioinformatics, vol.24, issue.1, pp.129-131, 2008.
DOI : 10.1093/bioinformatics/btm538

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.7580

L. Harmon, J. Schulte, A. Larson, and J. Losos, Tempo and Mode of Evolutionary Radiation in Iguanian Lizards, Science, vol.301, issue.5635, pp.961-964, 2003.
DOI : 10.1126/science.1084786

M. Pagel, A. Meade, and D. Barker, Bayesian Estimation of Ancestral Character States on Phylogenies, Systematic Biology, vol.53, issue.5, pp.673-684, 2004.
DOI : 10.1080/10635150490522232