S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

E. Bapteste, Prokaryotic evolution and the tree of life are two different things, Biology Direct, vol.4, issue.1, p.34, 2009.
DOI : 10.1186/1745-6150-4-34

R. Belshaw, Long-term reinfection of the human genome by endogenous retroviruses, Proceedings of the National Academy of Sciences, vol.81, issue.2, pp.4894-4899, 2004.
DOI : 10.1016/S0888-7543(02)00027-7

T. Dagan, Y. Artzy-randrup, and W. Martin, Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution, Proceedings of the National Academy of Sciences, vol.7, issue.7, pp.10039-10044, 2008.
DOI : 10.1186/1471-2105-7-488

T. Dagan and W. Martin, The tree of one percent, Genome Biology, vol.7, issue.10, p.118, 2006.
DOI : 10.1186/gb-2006-7-10-118

T. Dagan and M. W. , Getting a better picture of microbial evolution en route to a network of genomes, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.98, issue.26, pp.2187-2196, 1527.
DOI : 10.1073/pnas.252529799

P. Deschamps, Y. Zivanovic, D. Moreira, F. Rodriguez-valera, and P. Garc, Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota, Genome Biology and Evolution, vol.7, issue.7, pp.1549-1563, 2014.
DOI : 10.1186/1745-6150-7-46

A. Dick, T. Harlow, P. Gogarten, and J. , Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction, Molecular Phylogenetics and Evolution, vol.107, pp.338-344, 2017.
DOI : 10.1016/j.ympev.2016.11.016

W. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2129, 1999.
DOI : 10.1126/science.284.5423.2124

W. Doolittle, Eradicating Typological Thinking in Prokaryotic Systematics and Evolution, Cold Spring Harbor Symposia on Quantitative Biology, vol.74, issue.0, pp.197-204, 2009.
DOI : 10.1101/sqb.2009.74.002

W. Doolittle, The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.51, issue.2, pp.2221-2228, 1527.
DOI : 10.1139/W07-029

W. Doolittle and E. Bapteste, Pattern pluralism and the Tree of Life hypothesis, Proceedings of the National Academy of Sciences, vol.102, issue.40, pp.2043-2049, 2007.
DOI : 10.1073/pnas.0504068102

B. Dridi, M. Fardeau, B. Ollivier, D. Raoult, and M. Drancourt, Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.12, issue.2, pp.1902-1907, 2012.
DOI : 10.1016/j.anaerobe.2006.02.002

D. Hotopp and J. , Horizontal gene transfer between bacteria and animals, Trends in Genetics, vol.27, issue.4, pp.157-163, 2011.
DOI : 10.1016/j.tig.2011.01.005

C. Esser, A Genome Phylogeny for Mitochondria Among ??-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes, Molecular Biology and Evolution, vol.21, issue.9, pp.1643-1660, 2004.
DOI : 10.1093/molbev/msh160

K. Georgiades and D. Raoult, How microbiology helps define the rhizome of life, Frontiers in Cellular and Infection Microbiology, vol.2, p.60, 2012.
DOI : 10.3389/fcimb.2012.00060

J. Gogarten, W. Doolittle, and J. Lawrence, Prokaryotic Evolution in Light of Gene Transfer, Molecular Biology and Evolution, vol.19, issue.12, pp.2226-2238, 2002.
DOI : 10.1186/1471-2164-3-4

J. Gogarten and J. Townsend, Horizontal gene transfer, genome innovation and evolution, Nature Reviews Microbiology, vol.306, issue.9, pp.679-687, 2005.
DOI : 10.1046/j.1365-2958.2003.03778.x

S. Gould, The empire of the apes, Nat Hist, vol.96, p.20, 1987.

E. Koonin, P. Puigb-o, and Y. Wolf, Comparison of Phylogenetic Trees and Search for a Central Trend in the ???Forest of Life???, Journal of Computational Biology, vol.18, issue.7, pp.917-924, 2011.
DOI : 10.1089/cmb.2010.0185

E. Koonin and N. Yutin, The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of Eukaryotes, Cold Spring Harbor Perspectives in Biology, vol.6, issue.4, p.16188, 2014.
DOI : 10.1101/cshperspect.a016188

L. Koski and G. Golding, The Closest BLAST Hit Is Often Not the Nearest Neighbor, Journal of Molecular Evolution, vol.51, issue.6, pp.540-542, 2001.
DOI : 10.1006/mpev.1999.0675

M. Krzywinski, Circos: An information aesthetic for comparative genomics, Genome Research, vol.19, issue.9, pp.1639-1645, 2009.
DOI : 10.1101/gr.092759.109

J. Lake, C. Herbold, M. Rivera, J. Servin, and R. Skophammer, Rooting the Tree of Life Using Nonubiquitous Genes, Molecular Biology and Evolution, vol.227, issue.1, pp.130-136, 2007.
DOI : 10.1007/s00709-005-0135-1

J. Lake, R. Skophammer, C. Herbold, and J. Servin, Genome beginnings: rooting the tree of life, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.227, issue.1, pp.2177-2185, 1527.
DOI : 10.1007/s00709-005-0135-1

V. Merhej, C. Notredame, M. Royer-carenzi, P. Pontarotti, and D. Raoult, The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences, Molecular Biology and Evolution, vol.51, issue.2, pp.3213-3223, 2011.
DOI : 10.1186/gb-2007-8-8-r156

URL : https://hal.archives-ouvertes.fr/hal-01105200

S. Nelson-sathi, Origins of major archaeal clades correspond to gene acquisitions from bacteria, Nature, vol.21, issue.7532, pp.77-80, 2015.
DOI : 10.1093/bioinformatics/bti191

N. Pace, Time for a change, Nature, vol.441, issue.7091, p.289, 2006.
DOI : 10.1038/441289a

D. Raoult, The post-Darwinist rhizome of life, The Lancet, vol.375, issue.9709, pp.104-105
DOI : 10.1016/S0140-6736(09)61958-9

D. Raoult, Dé passer Darwin

D. Raoult, Of ignorance and blindness, 2013.

D. Raoult and E. Koonin, Microbial genomics challenge Darwin, Front Cell Infect Microbiol, vol.2, p.127, 2012.

M. Rivera and J. Lake, The ring of life provides evidence for a genome fusion origin of eukaryotes, Nature, vol.87, issue.7005, pp.152-155, 2004.
DOI : 10.1073/pnas.87.12.4576

A. Rokas, B. Williams, N. King, and S. Carroll, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, vol.14, issue.6960, pp.798-804, 2003.
DOI : 10.1093/bioinformatics/14.9.817

A. Spang, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, vol.26, issue.7551, pp.173-179, 2015.
DOI : 10.1093/bioinformatics/btq413

J. Viezens and M. Arvand, Simultaneous presence of two different copies of the 16S rRNA gene in Bartonella henselae, Microbiology, vol.179, issue.10, pp.2881-2886, 2008.
DOI : 10.1016/S0891-5520(05)70414-1

C. Woese and G. Fox, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proceedings of the National Academy of Sciences, vol.20, issue.3, pp.5088-5090, 1977.
DOI : 10.1525/ctx.2006.5.3.41

C. Woese, Bacterial evolution, Microbiol Rev, vol.51, issue.2, pp.221-271, 1987.

C. Woese, O. Kandler, and M. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya., Proceedings of the National Academy of Sciences, vol.87, issue.12, pp.4576-4579, 1990.
DOI : 10.1073/pnas.87.12.4576

Y. Wolf, I. Rogozin, N. Grishin, and E. Koonin, Genome trees and the tree of life, Trends in Genetics, vol.18, issue.9, pp.472-479, 2002.
DOI : 10.1016/S0168-9525(02)02744-0

N. Yutin, K. Makarova, S. Mekhedov, Y. Wolf, and E. Koonin, The Deep Archaeal Roots of Eukaryotes, Molecular Biology and Evolution, vol.51, issue.4, pp.1619-1630, 2008.
DOI : 10.1080/10635150290102339

O. Zhaxybayeva and J. Gogarten, Cladogenesis, coalescence and the evolution of the three domains of life, Trends in Genetics, vol.20, issue.4, pp.182-187, 2004.
DOI : 10.1016/j.tig.2004.02.004