E. Zuckerkandl and . Pauling, Molecular Disease, Evolution, and Genic Heterogeneity, 1962.

M. Dos-reis, Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny, Proc. Biol. Sci, vol.279, pp.3491-3500, 2012.

M. A. O'leary, The placental mammal ancestor and the post-K-Pg radiation of placentals, Science, vol.339, pp.662-667, 2013.

P. C. Donoghue and M. J. Benton, Rocks and clocks: calibrating the Tree of Life using fossils and molecules, Trends Ecol. Evol, vol.22, pp.424-431, 2007.

Z. Yang and P. C. Donoghue, Dating species divergences using rocks and clocks, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.371, p.20150126, 2016.

A. H. Knoll, The Fossil Record of Microbial Life, Fundamentals of Geobiology, pp.297-314, 2012.

A. H. Knoll, Paleobiological perspectives on early eukaryotic evolution, Cold Spring Harb. Perspect. Biol, vol.6, 2014.

W. F. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, pp.2124-2128, 1999.

S. S. Abby, E. Tannier, M. Gouy, and V. Daubin, Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences, vol.109, pp.4962-4967, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00752055

G. J. Szöll?si, B. Boussau, S. S. Abby, E. Tannier, and V. Daubin, Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, PNAS, vol.109, pp.17513-17518, 2012.

T. A. Williams, Integrative modelling of gene and genome evolution roots the archaeal tree of life, 2017.

J. Huang and J. P. Gogarten, Ancient gene transfer as a tool in phylogenetic reconstruction, Methods Mol. Biol, vol.532, pp.127-139, 2009.

J. Huang, Y. Xu, and J. P. Gogarten, The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic, Mol. Biol. Evol, vol.22, pp.2142-2146, 2005.

J. M. Wolfe and G. P. Fournier, Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution, 2017.

W. P. Maddison, Gene Trees in Species Trees. Syst. Biol, vol.46, p.523, 1997.

G. J. Szöll?si and V. Daubin, Modeling Gene Family Evolution and Reconciling Phylogenetic Discord, Methods in Molecular Biology, vol.29, p.51, 2012.

J. Sjöstrand, A Bayesian method for analyzing lateral gene transfer, Syst. Biol, vol.63, pp.409-420, 2014.

G. J. Szöll?si, E. Tannier, V. Daubin, and B. Boussau, The Inference of Gene Trees with Species Trees, Syst. Biol, vol.64, issue.1, pp.42-62, 2015.

V. Daubin and G. J. Szöll?si, Horizontal Gene Transfer and the History of Life, Cold Spring Harb. Perspect. Biol, vol.8, p.18036, 2016.

J. P. Gogarten, R. D. Murphey, and L. Olendzenski, Horizontal gene transfer: pitfalls and promises, Biol. Bull, vol.196, pp.361-363, 1999.

G. J. Szöll?si, B. Boussau, S. S. Abby, E. Tannier, and V. Daubin, Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, PNAS, vol.109, pp.17513-17518, 2012.

G. J. Szöll?si, E. Tannier, N. Lartillot, and V. Daubin, Lateral Gene Transfer from the Dead. Syst. Biol, vol.62, pp.386-397, 2013.

A. Dufresne, L. Garczarek, and F. Partensky, Accelerated evolution associated with genome reduction in a free-living prokaryote, Genome Biol, 2005.

M. J. Benton and P. C. Donoghue, Paleontological evidence to date the tree of life, Mol. Biol. Evol, vol.24, pp.26-53, 2007.

M. Dos-reis, P. C. Donoghue, and Z. Yang, Bayesian molecular clock dating of species divergences in the genomics era, Nat. Rev. Genet, vol.17, pp.71-80, 2016.

C. Chauve, MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01532738

G. J. Szöll?si, A. A. Davín, E. Tannier, V. Daubin, and B. Boussau, Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.370, p.20140335, 2015.

T. A. Williams, Integrative modelling of gene and genome evolution roots the archaeal tree of life, 2017.

L. G. Nagy, Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts, Nat. Commun, vol.5, p.4471, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01268896

G. J. Szöll?si, W. Rosikiewicz, B. Boussau, E. Tannier, and V. Daubin, Efficient exploration of the space of reconciled gene trees, Syst. Biol, vol.62, pp.901-912, 2013.

J. Felsenstein, Phylogenies and the Comparative Method, Am. Nat, vol.125, pp.1-15, 1985.

N. Lartillot and H. Philippe, A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process, Mol. Biol. Evol, vol.21, pp.1095-1109, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00108585

N. Lartillot, T. Lepage, and S. Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, pp.2286-2288, 2009.

T. Lepage, D. Bryant, H. Philippe, and N. Lartillot, A General Comparison of Relaxed Molecular Clock Models, Mol. Biol. Evol, vol.24, pp.2669-2680, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00193697

C. Chauve, MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01532738

A. Tomitani, A. H. Knoll, C. M. Cavanaugh, and T. Ohno, The evolutionary diversification of cyanobacteria: Molecular-phylogenetic and paleontological perspectives, Proceedings of the National Academy of Sciences, vol.103, pp.5442-5447, 2006.

C. E. Blank and P. Sánchez-baracaldo, Timing of morphological and ecological innovations in the cyanobacteria â a key to understanding the rise in atmospheric oxygen, Geobiology, vol.8, pp.1-23, 2010.

P. M. Shih, J. Hemp, L. M. Ward, N. J. Matzke, and W. W. Fischer, Crown group Oxyphotobacteria postdate the rise of oxygen, Geobiology, vol.15, pp.19-29, 2017.

Y. Ueno, K. Yamada, N. Yoshida, S. Maruyama, and Y. Isozaki, Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era, Nature, vol.440, pp.516-519, 2006.

J. W. Spatafora, A phylum-level phylogenetic classification of zygomycete fungi based on genomescale data, Mycologia, vol.108, pp.1028-1046, 2016.

L. Eme, S. C. Sharpe, M. W. Brown, and A. J. Roger, On the age of eukaryotes: evaluating evidence from fossils and molecular clocks, Cold Spring Harb. Perspect. Biol, vol.6, 2014.

N. Wybouw, A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning, Elife, vol.3, p.2365, 2014.

M. Groussin, Unraveling the processes shaping mammalian gut microbiomes over evolutionary time, Nat. Commun, vol.8, p.14319, 2017.

A. H. Knoll, K. D. Bergmann, and J. V. Strauss, Life: the first two billion years, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.371, p.20150493, 2016.

J. M. Wolfe and G. P. Fournier, Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution, p.129494, 2017.

R. M. Soo, J. Hemp, D. H. Parks, W. W. Fischer, and P. Hugenholtz, On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria, Science, vol.355, pp.1436-1440, 2017.

G. J. Szöll?si, E. Tannier, V. Daubin, and B. Boussau, The inference of gene trees with species trees, Syst. Biol, vol.64, pp.42-62, 2015.