D. Irwin, T. Kocher, and A. Wilson, Evolution of the cytochromeb gene of mammals, Journal of Molecular Evolution, vol.26, issue.2, pp.128-144, 1991.
DOI : 10.1007/BF02515385

M. Springer and E. Douzery, Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules, Journal of Molecular Evolution, vol.9, issue.4, pp.357-373, 1996.
DOI : 10.1007/BF02339010

D. Erchia, A. Gissi, C. Pesole, G. Saccone, C. Arnason et al., The guinea-pig is not a rodent, Nature, vol.381, issue.6583, pp.597-600, 1996.
DOI : 10.1038/381597a0

M. Stanhope, J. Czelusniak, J. Si, J. Nickerson, and M. Goodman, A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly, Molecular Phylogenetics and Evolution, vol.1, issue.2, pp.148-160, 1992.
DOI : 10.1016/1055-7903(92)90026-D

C. Porter, M. Goodman, and M. Stanhope, Evidence on Mammalian Phylogeny from Sequences of Exon 28 of the von Willebrand Factor Gene, Molecular Phylogenetics and Evolution, vol.5, issue.1, pp.89-101, 1996.
DOI : 10.1006/mpev.1996.0008

O. Madsen, M. Scally, C. Douady, D. Kao, R. Debry et al., Parallel adaptive radiations in two major clades of placental mammals, Nature, vol.409, issue.6820, pp.610-614, 2001.
DOI : 10.1038/35054544

P. Waddell and S. Shelley, Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, ??-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models, Molecular Phylogenetics and Evolution, vol.28, issue.2, pp.197-224, 2003.
DOI : 10.1016/S1055-7903(03)00115-5

M. Springer, G. Cleven, O. Madsen, W. De-jong, V. Waddell et al., Endemic African mammals shake the phylogenetic tree, Nature, vol.388, issue.6637, pp.61-64, 1997.
DOI : 10.1038/40386

C. Montgelard, E. Douzery, and J. Michaux, Classification and molecular phylogeny In Reproductive biology and phylogeny of Cetacea (whales, dolphins and porpoises), pp.95-125

C. Douady, P. Chatelier, O. Madsen, W. De-jong, F. Catzeflis et al., Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews???, Molecular Phylogenetics and Evolution, vol.25, issue.1, pp.200-209, 2002.
DOI : 10.1016/S1055-7903(02)00232-4

J. Townsend, Profiling Phylogenetic Informativeness, Systematic Biology, vol.56, issue.2, pp.222-231, 2007.
DOI : 10.1080/10635150701311362

URL : http://sysbio.oxfordjournals.org/cgi/content/short/56/2/222

N. Goldman, Phylogenetic information and experimental design in molecular systematics, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1407, pp.1779-1786, 1998.
DOI : 10.1098/rspb.1998.0502

Z. Yang, On the Best Evolutionary Rate for Phylogenetic Analysis, Systematic Biology, vol.47, issue.1, pp.125-133, 1998.
DOI : 10.1080/106351598261067

A. Graybeal, Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates, Systematic Biology, vol.43, issue.2, pp.174-193, 1994.
DOI : 10.1093/sysbio/43.2.174

H. Philippe, U. Sorhannus, A. Baroin, R. Perasso, and F. Gasse, Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record, Journal of Evolutionary Biology, vol.7, issue.2, pp.247-265, 1994.
DOI : 10.1046/j.1420-9101.1994.7020247.x

W. Murphy, E. Eizirik, W. Johnson, Y. Zhang, O. Ryder et al., Molecular phylogenetics and the origins of placental mammals, Nature, vol.409, issue.6820, pp.614-618, 2001.
DOI : 10.1038/35054550

W. Murphy, P. Pevzner, O. Brien, and S. , Mammalian phylogenomics comes of age, Trends in Genetics, vol.20, issue.12, pp.631-639, 2004.
DOI : 10.1016/j.tig.2004.09.005

D. Thomas, K. Rosenbloom, H. Clawson, A. Hinrichs, H. Trumbower et al., The ENCODE Project at UC Santa Cruz, Nucleic Acids Research, vol.35, issue.Database, pp.663-667, 2007.
DOI : 10.1093/nar/gkl1017

M. Remm, C. Storm, and E. Sonnhammer, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, Journal of Molecular Biology, vol.314, issue.5, pp.1041-1052, 2001.
DOI : 10.1006/jmbi.2000.5197

L. Li, C. Stoeckert, and D. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003.
DOI : 10.1101/gr.1224503

F. Chen, A. Mackey, C. Stoeckert, and D. Roos, OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups, Nucleic Acids Research, vol.34, issue.90001, pp.363-368, 2006.
DOI : 10.1093/nar/gkj123

O. Brien, K. Remm, M. Sonnhammer, and E. , Inparanoid: a comprehensive database of eukaryotic orthologs, Nucleic Acids Research, vol.33, issue.Database issue, pp.476-480, 2005.
DOI : 10.1093/nar/gki107

F. Chen, A. Mackey, J. Vermunt, and D. Roos, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, PLoS ONE, vol.17, issue.4, p.383, 2007.
DOI : 10.1371/journal.pone.0000383.s008

T. Hubbard, B. Aken, K. Beal, B. Ballester, M. Caccamo et al., Ensembl 2007, Nucleic Acids Research, vol.35, issue.Database, pp.610-617, 2007.
DOI : 10.1093/nar/gkl996

URL : http://doi.org/10.1093/nar/gkl996

F. Wu, L. Mueller, D. Crouzillat, V. Petiard, and S. Tanksley, Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade, Genetics, vol.174, issue.3, pp.1407-1420, 2006.
DOI : 10.1534/genetics.106.062455

C. Li, G. Orti, G. Zhang, and G. Lu, A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study, BMC Evolutionary Biology, vol.7, issue.1, p.44, 2007.
DOI : 10.1186/1471-2148-7-44

F. Delsuc, H. Brinkmann, and P. H. , Phylogenomics and the reconstruction of the tree of life, Nature Reviews Genetics, vol.3, issue.5, pp.361-375, 2005.
DOI : 10.1038/nrg1603

URL : https://hal.archives-ouvertes.fr/halsde-00193293

T. Collins, O. Fedrigo, and G. Naylor, Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics, Systematic Biology, vol.54, pp.493-500, 2005.

M. Phillips and D. Penny, The root of the mammalian tree inferred from whole mitochondrial genomes, Molecular Phylogenetics and Evolution, vol.28, issue.2, pp.171-185, 2003.
DOI : 10.1016/S1055-7903(03)00057-5

Z. Yang, N. Goldman, and A. Friday, Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation, Mol Biol Evol, vol.11, pp.316-324, 1994.

V. Curwen, E. Eyras, T. Andrews, L. Clarke, E. Mongin et al., The Ensembl Automatic Gene Annotation System, Genome Research, vol.14, issue.5
DOI : 10.1101/gr.1858004

O. Bininda-emonds, transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences, BMC Bioinformatics, vol.6, issue.1, p.156, 2005.
DOI : 10.1186/1471-2105-6-156

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.

D. Swofford and . Paup-*, Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4.0b10, 2002.

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

D. Posada and K. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

H. Akaike, A new look at the statistical model identification, IEEE Trans Autom Contr, vol.1974, pp.19716-723

Z. Yang, Estimating the pattern of nucleotide substitution, Journal of Molecular Evolution, vol.39, issue.1, pp.105-111, 1994.
DOI : 10.1007/BF00178256

Z. Yang, Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution, pp.367-372, 1996.

A. Criscuolo, V. Berry, E. Douzery, and O. Gascuel, SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics, Systematic Biology, vol.55, issue.5, pp.740-755, 2006.
DOI : 10.1080/10635150600969872

URL : https://hal.archives-ouvertes.fr/lirmm-00136655

R. Adkins, E. Gelke, D. Rowe, and R. Honeycutt, Molecular Phylogeny and Divergence Time Estimates for Major Rodent Groups: Evidence from Multiple Genes, Molecular Biology and Evolution, vol.18, issue.5, pp.777-791, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003860

F. Delsuc, M. Scally, O. Madsen, M. Stanhope, W. De-jong et al., Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting, Molecular Biology and Evolution, vol.19, issue.10, pp.1656-1671, 2002.
DOI : 10.1093/oxfordjournals.molbev.a003989

URL : https://hal.archives-ouvertes.fr/halsde-00192981

M. Scally, O. Madsen, C. Douady, W. De-jong, M. Stanhope et al., Molecular evidence for the major clades of placental mammals, J Mammal Evol, pp.239-277, 2001.

W. Murphy, T. Pringle, T. Crider, M. Springer, and W. Miller, Using genomic data to unravel the root of the placental mammal phylogeny, Genome Research, vol.17, issue.4, pp.413-421, 2007.
DOI : 10.1101/gr.5918807

D. Huchon, P. Chevret, U. Jordan, C. Kilpatrick, V. Ranwez et al., Multiple molecular evidences for a living mammalian fossil, Proceedings of the National Academy of Sciences, vol.104, issue.18, pp.7495-7499, 2007.
DOI : 10.1073/pnas.0701289104

URL : https://hal.archives-ouvertes.fr/halsde-00453695

D. Huchon, O. Madsen, M. Sibbald, K. Ament, M. Stanhope et al., Rodent Phylogeny and a Timescale for the Evolution of Glires: Evidence from an Extensive Taxon Sampling Using Three Nuclear Genes, Molecular Biology and Evolution, vol.19, issue.7, pp.1053-1065, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004164

W. Murphy, E. Eizirik, O. Brien, S. Madsen, O. Scally et al., Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics, Science, vol.294, issue.5550, pp.2348-2351, 2001.
DOI : 10.1126/science.1067179

G. Cannarozzi, A. Schneider, and G. Gonnet, A Phylogenomic Study of Human, Dog, and Mouse, PLoS Computational Biology, vol.16, issue.1, p.2, 2007.
DOI : 1367-4803(2000)016[0619:UTSPAF]2.0.CO;2

A. Hughes and R. Friedman, The effect of branch lengths on phylogeny: An empirical study using highly conserved orthologs from mammalian genomes, Molecular Phylogenetics and Evolution, vol.45, issue.1, pp.81-88, 2007.
DOI : 10.1016/j.ympev.2007.04.022

G. Huttley, M. Wakefield, and S. Easteal, Rates of Genome Evolution and Branching Order from Whole Genome Analysis, Molecular Biology and Evolution, vol.24, issue.8, pp.1722-1730, 2007.
DOI : 10.1093/molbev/msm094

H. Amrine-madsen, K. Koepfli, R. Wayne, and M. Springer, A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships, Molecular Phylogenetics and Evolution, vol.28, issue.2, pp.225-240, 2003.
DOI : 10.1016/S1055-7903(03)00118-0

S. Nikolaev, J. Montoya-burgos, E. Margulies, J. Rougemont, and B. Nyffeler, Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data, PLoS Genetics, vol.5, issue.1, p.2, 2007.
DOI : 10.1371/journal.pgen.0030002.st002

A. Reyes, C. Gissi, F. Catzeflis, E. Nevo, G. Pesole et al., Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods, Molecular Biology and Evolution, vol.21, issue.2, pp.397-403, 2004.
DOI : 10.1093/molbev/msh033

URL : http://mbe.oxfordjournals.org/cgi/content/short/21/2/397

C. Poux, T. Van-rheede, O. Madsen, and W. De-jong, Sequence Gaps Join Mice and Men: Phylogenetic Evidence from Deletions in Two Proteins, Molecular Biology and Evolution, vol.19, issue.11, pp.2035-2037, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004028

J. Kriegs, G. Churakov, M. Kiefmann, U. Jordan, J. Brosius et al., Retroposed Elements as Archives for the Evolutionary History of Placental Mammals, PLoS Biology, vol.15, issue.4, p.91, 2006.
DOI : 10.1371/journal.pbio.0040091.st002

H. Philippe, N. Lartillot, and H. Brinkmann, Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia, Molecular Biology and Evolution, vol.22, issue.5, pp.1246-1253, 2005.
DOI : 10.1093/molbev/msi111

URL : https://hal.archives-ouvertes.fr/lirmm-00105354

J. Felsenstein, Cases in which Parsimony or Compatibility Methods Will be Positively Misleading, Systematic Zoology, vol.27, issue.4, pp.401-410, 1978.
DOI : 10.2307/2412923

H. Philippe and E. Douzery, The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships, Journal of Mammalian Evolution, vol.42, issue.2, pp.133-152, 1994.
DOI : 10.1007/BF01464365

E. Douzery and D. Huchon, Rabbits, if anything, are likely Glires, Molecular Phylogenetics and Evolution, vol.33, issue.3, pp.922-935, 2004.
DOI : 10.1016/j.ympev.2004.07.014

J. Sullivan and D. Swofford, Are Guinea pigs Rodents ? The importance of adequate models in molecular phylogenetics, Journal of Mammalian Evolution, vol.4, issue.2, pp.77-86, 1997.
DOI : 10.1023/A:1027314112438

G. Lunter, Dog as an Outgroup to Human and Mouse, PLoS Computational Biology, vol.14, issue.4, p.74, 2007.
DOI : 1088-9051(2004)014[0708:AMGSWT]2.0.CO;2

M. Mckenna, Toward a phylogenetic classification of the Mammalia In Phylogeny of the primates Edited by: Luckett WP, Szalay FS, pp.21-46

P. Waddell, Y. Cao, J. Hauf, and M. Hasegawa, Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant, Systematic Biology, vol.48, issue.1, pp.31-53, 1999.

B. Hallstrom, M. Kullberg, M. Nilsson, and A. Janke, Phylogenomic Data Analyses Provide Evidence that Xenarthra and Afrotheria Are Sister Groups, Molecular Biology and Evolution, vol.24, issue.9, pp.2059-2068, 2007.
DOI : 10.1093/molbev/msm136

D. Wildman, M. Uddin, J. Opazo, G. Liu, V. Lefort et al., Genomics, biogeography, and the diversification of placental mammals, Proceedings of the National Academy of Sciences, vol.104, issue.36, pp.14395-14400, 2007.
DOI : 10.1073/pnas.0704342104

URL : https://hal.archives-ouvertes.fr/lirmm-00193171

H. Nishihara, N. Okada, and M. Hasegawa, Rooting the eutherian tree: the power and pitfalls of phylogenomics, Genome Biology, vol.8, issue.9, p.199, 2007.
DOI : 10.1186/gb-2007-8-9-r199