K. D. Baker, L. M. Shewchuk, T. Kozlova, M. Makishima, A. Hassell et al., The Drosophila Orphan Nuclear Receptor DHR38 Mediates an Atypical Ecdysteroid Signaling Pathway, Cell, vol.113, issue.6, pp.731-742, 2003.
DOI : 10.1016/S0092-8674(03)00420-3

Y. Beck, C. Dauer, and G. Richards, Dynamic localisation of KR-H during an ecdysone response in Drosophila, Gene Expression Patterns, vol.5, issue.3, pp.403-409, 2005.
DOI : 10.1016/j.modgep.2004.09.008

URL : https://hal.archives-ouvertes.fr/hal-00187436

I. M. Billas, L. Moulinier, N. Rochel, and D. Moras, Crystal Structure of the Ligand-binding Domain of the Ultraspiracle Protein USP, the Ortholog of Retinoid X Receptors in Insects, Journal of Biological Chemistry, vol.276, issue.10, pp.7465-7474, 2001.
DOI : 10.1074/jbc.M008926200

F. Bonneton, F. G. Brunet, J. Kathirithamby, and V. Laudet, The rapid divergence of the ecdysone receptor is a synapomorphy for Mecopterida that clarifies the Strepsiptera problem, Insect Molecular Biology, vol.46, issue.3, pp.351-362, 2006.
DOI : 10.1146/annurev.ento.44.1.397

F. Bonneton, D. Zelus, T. Iwema, M. Robinson-rechavi, and V. Laudet, Rapid Divergence of the Ecdysone Receptor in Diptera and Lepidoptera Suggests Coevolution Between ECR and USP-RXR, Molecular Biology and Evolution, vol.20, issue.4, pp.541-553, 2003.
DOI : 10.1093/molbev/msg054

URL : https://hal.archives-ouvertes.fr/ensl-00285059

G. Bucher, L. Farzana, S. J. Brown, and M. Klingler, Anterior localization of maternal mRNAs in a short germ insect lacking bicoid, Evolution and Development, vol.125, issue.2, pp.142-149, 2005.
DOI : 10.1126/science.287.5462.2476

C. Burge and S. Karlin, Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997.
DOI : 10.1006/jmbi.1997.0951

D. Chessel, . Dufour, and . Thioulouse, The ade4 package-I-One-table methods, R News, vol.4, pp.5-10, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427558

G. M. Clayton, S. Y. Peak-chew, R. M. Evans, and J. W. Schwabe, The structure of the ultraspiracle ligand-binding domain reveals a nuclear receptor locked in an inactive conformation, Proc. Natl. Acad. Sci. USA, pp.1549-1554, 2001.
DOI : 10.1073/pnas.98.4.1549

J. Cruz, D. Mane-padros, X. Belles, and D. Martin, Functions of the ecdysone receptor isoform-A in the hemimetabolous insect Blattella germanica revealed by systemic 18, p.8, 2006.

J. Cruz, D. Martin, and X. Belles, Redundant ecdysis regulatory functions of three nuclear receptor HR3 isoforms in the direct-developing insect Blattella germanica, Mechanisms of Development, vol.124, issue.3, 2007.
DOI : 10.1016/j.mod.2006.12.003

H. B. Fraser, A. E. Hirsh, D. P. Wall, and M. B. Eisen, Coevolution of gene expression among interacting proteins, Proceedings of the National Academy of Sciences, vol.101, issue.24, pp.9033-9038, 2004.
DOI : 10.1073/pnas.0402591101

M. Friedrich and D. Tautz, An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera, Molecular Biology and Evolution, vol.14, issue.6, pp.644-653, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025804

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543

URL : https://hal.archives-ouvertes.fr/hal-00435028

R. Garcia-serna, L. Opatowski, and J. Mestres, FCP: functional coverage of the proteome by structures, Bioinformatics, vol.22, issue.14, pp.1792-1793, 2006.
DOI : 10.1093/bioinformatics/btl188

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

D. Henley and K. Korach, Endocrine-Disrupting Chemicals Use Distinct Mechanisms of Action to Modulate Endocrine System Function, Endocrinology, vol.147, issue.6, pp.25-32, 2006.
DOI : 10.1210/en.2005-1117

V. Henrich, The ecdysteroid receptor, pp.243-285, 2005.

M. Hirai, T. Shinoda, M. Kamimura, S. Tomita, and T. Shiotsuki, Bombyx mori orphan receptor, BmHR78: cDNA cloning, testis abundant expression and putative dimerization partner for Bombyx ultraspiracle, Molecular and Cellular Endocrinology, vol.189, issue.1-2, pp.201-211, 2002.
DOI : 10.1016/S0303-7207(01)00604-9

K. Hiruma and L. M. Riddiford, Differential control of MHR3 promoter activity by isoforms of the ecdysone receptor and inhibitory effects of E75A and MHR3, Developmental Biology, vol.272, issue.2, pp.510-521, 2004.
DOI : 10.1016/j.ydbio.2004.04.028

P. Jolicoeur and J. E. Mosimann, Size and shape variation in the painted turtle. A principal component analysis, Growth, vol.24, pp.339-354, 1960.

D. T. Jones, W. R. Taylor, and J. M. Thornton, The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, issue.3, pp.275-282, 1992.
DOI : 10.1093/bioinformatics/8.3.275

K. King-jones, J. P. Charles, G. Lam, and C. S. , The Ecdysone-Induced DHR4 Orphan Nuclear Receptor Coordinates Growth and Maturation in Drosophila, Cell, vol.121, issue.5, pp.773-784, 2005.
DOI : 10.1016/j.cell.2005.03.030

URL : https://hal.archives-ouvertes.fr/hal-00451232

K. King-jones and C. S. , Nuclear receptors ??? a perspective from Drosophila, Nature Reviews Genetics, vol.125, issue.4, pp.311-323, 2005.
DOI : 10.1016/j.ydbio.2004.01.009

N. P. Kristensen, Phylogeny of Insect Orders, Annual Review of Entomology, vol.26, issue.1, pp.135-157, 1981.
DOI : 10.1146/annurev.en.26.010181.001031

N. P. Kristensen, Phylogeny of endopterygote insects, the most successful lineage of living organisms, Eur. J. Entomol, vol.96, pp.237-253, 1999.

R. Lafont, C. Dauphin-villemant, J. T. Warren, and H. Rees, Ecdysteroid chemistry and biochemistry. Pp. 125-195 in, Comprehensive Molecular Insect Science, 2005.
DOI : 10.1016/b978-0-12-384749-2.10004-4

V. Laudet and F. Bonneton, Evolution of Nuclear Hormone Receptors in Insects, Comprehensive Molecular Insect Science, pp.287-318, 2005.
DOI : 10.1016/B0-44-451924-6/00038-7

V. Laudet and H. Gronemeyer, The Nuclear Receptor FactsBook, p.8, 2002.

O. Lichtarge, H. Yao, D. M. Kristensen, S. Madabushi, and I. Mihalek, Accurate and scalable identification of functional sites by evolutionary tracing, Journal of Structural and Functional Genomics, vol.4, issue.2/3, pp.159-166, 2003.
DOI : 10.1023/A:1026115125950

K. Lunde, J. L. Trimble, A. Guichard, K. A. Guss, U. Nauber et al., Activation of the knirps locus links patterning to morphogenesis of the second wing vein in Drosophila, Development, vol.130, issue.2, pp.235-248, 2003.
DOI : 10.1242/dev.00207

D. Martin, O. Maestro, J. Cruz, D. Mane-padros, and X. Belles, RNAi studies reveal a conserved role for RXR in molting in the cockroach Blattella germanica, Journal of Insect Physiology, vol.52, issue.4, pp.410-416, 2006.
DOI : 10.1016/j.jinsphys.2005.12.002

K. Miura, J. Zhu, N. T. Dittmer, L. Chen, and A. S. , A COUP-TF/Svp homolog is highly expressed during vitellogenesis in the mosquito Aedes aegypti, Journal of Molecular Endocrinology, vol.29, issue.2, pp.223-238, 2002.
DOI : 10.1677/jme.0.0290223

C. Pal, B. Papp, and M. J. Lercher, An integrated view of protein evolution, Nature Reviews Genetics, vol.272, issue.5, pp.337-348, 2006.
DOI : 10.1038/nrg1838

. Krause, Dynamic regulation of Drosophila nuclear receptor activity in vivo, Development, vol.133, pp.3549-3562, 2006.

S. Palli, R. Hormann, U. Schlattner, and M. Lezzi, Ecdysteroid Receptors and their Applications in Agriculture and Medicine, Vitam Horm, vol.73, pp.59-100, 2005.
DOI : 10.1016/S0083-6729(05)73003-X

URL : https://hal.archives-ouvertes.fr/inserm-00390881

F. Pazos, M. Helmer-citterich, G. Ausiello, and A. Valencia, Correlated mutations contain information about protein-protein interaction, Journal of Molecular Biology, vol.271, issue.4, pp.511-523, 1997.
DOI : 10.1006/jmbi.1997.1198

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.360.2386

F. Pecasse, Y. Beck, C. Ruiz, and G. Richards, Kruppel-homolog, a stage-specific 18, p.8, 2000.

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2006.

M. Rothe, M. Pehl, H. Taubert, and H. Jackle, Loss of gene function through rapid mitotic cycles in the Drosophila embryo, Nature, vol.359, issue.6391, pp.156-159, 1992.
DOI : 10.1038/359156a0

D. Ruau, J. Duarte, T. Ourjdal, G. Perriere, V. Laudet et al., Update of NUREBASE: nuclear hormone receptor functional genomics, Nucleic Acids Research, vol.32, issue.90001, pp.165-167, 2004.
DOI : 10.1093/nar/gkh062

URL : https://hal.archives-ouvertes.fr/hal-00427648

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987.

J. Savard, D. Tautz, and M. J. Lercher, Genome-wide acceleration of protein evolution in flies (Diptera), BMC Evolutionary Biology, vol.6, issue.1, p.7, 2006.
DOI : 10.1186/1471-2148-6-7

J. Savard, D. Tautz, S. Richards, G. M. Weinstock, R. A. Gibbs et al., Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects, Genome Research, vol.16, issue.11, pp.1334-1338, 2006.
DOI : 10.1101/gr.5204306

R. Schroder, C. Eckert, C. Wolff, and D. Tautz, Conserved and divergent aspects of terminal patterning in the beetle Tribolium castaneum, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.6591-6596, 2000.
DOI : 10.1073/pnas.100005497

M. Stanke, A. Tzvetkova, and B. Morgenstern, AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome, 2006.

R. Wilson, R. H. Durbin, and . Waterston, The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics, PLoS Biol, vol.1, p.45, 2003.

L. Swevers, K. Ito, and K. Iatrou, The BmE75 Nuclear Receptors Function as Dominant Repressors of the Nuclear Receptor BmHR3A, Journal of Biological Chemistry, vol.277, issue.44, pp.41637-41644, 2002.
DOI : 10.1074/jbc.M203581200

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

C. S. Thummel, Molecular Mechanisms of Developmental Timing in C. elegans and Drosophila, Developmental Cell, vol.1, issue.4, pp.453-465, 2001.
DOI : 10.1016/S1534-5807(01)00060-0

R. A. Velarde, G. E. Robinson, and S. E. Fahrbach, Nuclear receptors of the honey bee: annotation and expression in the adult brain, Insect Molecular Biology, vol.15, issue.5, pp.583-595, 2006.
DOI : 10.1038/366476a0

K. P. White, P. Hurban, T. Watanabe, and D. S. Hogness, Coordination of Drosophila Metamorphosis by Two Ecdysone-Induced Nuclear Receptors, Science, vol.276, issue.5309, pp.114-117, 1997.
DOI : 10.1126/science.276.5309.114