D. Arcila, R. A. Pyron, J. C. Tyler, G. Ortí, and R. Betancur-r, An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae), Molecular Phylogenetics and Evolution, vol.82, pp.131-145, 2015.

D. Bapst, A. Wright, N. Matzke, L. , and G. , Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria), Biology Letters, vol.12, issue.7, p.20160237, 2016.

M. J. Benton and P. C. Donoghue, Paleontological evidence to date the tree of life, Molecular Biology and Evolution, vol.24, issue.1, pp.26-53, 2007.

B. Boussau and C. Scornavacca, Reconciling gene trees with species trees, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02535529

L. ;. Bromham, F. Delsuc, and N. Galtier, Substitution rate analysis and molecular evolution, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02536329

S. Claramunt and J. Cracraft, A new time tree reveals Earth history's imprint on the evolution of modern birds, Science Advances, vol.1, issue.11, p.1501005, 2015.

A. A. Davín, E. Tannier, T. A. Williams, B. Boussau, V. Daubin et al., Gene transfers can date the tree of life, Nature Ecology & Evolution, vol.2, issue.5, p.904, 2018.

G. Didier, M. Fau, and M. Laurin, Likelihood of tree topologies with fossils and diversification rate estimation, Systematic Biology, vol.66, issue.6, pp.964-987, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01270368

G. Didier, M. Royer-carenzi, and M. Laurin, The reconstructed evolutionary process with the fossil record, Journal of Theoretical Biology, vol.315, pp.26-37, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01105197

P. C. Donoghue and M. J. Benton, Rocks and clocks: calibrating the tree of life using fossils and molecules, Trends in Ecology & Evolution, vol.22, issue.8, pp.424-431, 2007.

A. Dornburg, J. M. Beaulieu, J. C. Oliver, and T. J. Near, Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation, Systematic Biology, vol.60, issue.4, pp.519-527, 2011.

, REFERENCES 5, vol.1, p.15

M. Dos-reis, Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times, Philosophical Transactions of the Royal Society B, vol.371, 1699.

M. Dos-reis and Z. Yang, The unbearable uncertainty of Bayesian divergence time estimation, Journal of Systematics and Evolution, vol.51, issue.1, pp.30-43, 2013.

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed phylogenetics and dating with confidence, PLoS Biology, vol.4, issue.5, p.88, 2006.

R. Fernández, G. D. Edgecombe, and G. Giribet, Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction, Systematic Biology, vol.65, issue.5, pp.871-889, 2016.

M. Foote, On the probability of ancestors in the fossil record, Paleobiology, vol.22, pp.141-151, 1996.

M. Foote, J. P. Hunter, C. M. Janis, and J. J. Sepkoski, Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals, Science, vol.283, issue.5406, pp.1310-1314, 1999.

M. Foote and J. J. Sepkoski, Absolute measures of the completeness of the fossil record, Nature, vol.398, issue.6726, p.415, 1999.

A. Gavryushkina, T. A. Heath, D. T. Ksepka, T. Stadler, D. Welch et al., Bayesian total-evidence dating reveals the recent crown radiation of penguins, Systematic Biology, vol.66, issue.1, pp.57-73, 2017.

A. Gavryushkina, D. Welch, T. Stadler, and A. J. Drummond, Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration, PLoS Computational Biology, vol.10, issue.12, p.1003919, 2014.

T. Gernhard, The conditioned reconstructed process, Journal of Theoretical Biology, vol.253, pp.769-778, 2008.

G. W. Grimm, P. Kapli, B. Bomfleur, S. Mcloughlin, and S. S. Renner, Using more than the oldest fossils: dating Osmundaceae with three Bayesian clock approaches, Systematic Biology, vol.64, issue.3, pp.396-405, 2014.

S. Guindon, Accounting for calibration uncertainty: Bayesian molecular dating as a "doubly intractable" problem, Systematic Biology, vol.67, issue.4, pp.651-661, 2018.
URL : https://hal.archives-ouvertes.fr/lirmm-01800299

T. A. Heath, Understanding the importance of taxonomic sampling for large-scale phylogenetic analyses by simulating evolutionary processes under complex models, 2008.

T. A. Heath, A hierarchical Bayesian model for calibrating estimates of species divergence times, Systematic Biology, vol.61, issue.5, pp.793-809, 2012.

T. A. Heath, J. P. Huelsenbeck, and T. Stadler, The fossilized birth-death process for coherent calibration of divergence-time estimates, Proceedings of the National Academy of Sciences, vol.111, issue.29, pp.2957-2966, 2014.

S. B. Hedges and S. Kumar, Precision of molecular time estimates, Trends in Genetics, vol.20, issue.5, pp.242-247, 2004.

J. Heled and A. J. Drummond, Calibrated tree priors for relaxed phylogenetics and divergence time estimation, Systematic Biology, vol.61, issue.1, pp.138-149, 2012.

J. P. Herrera and L. M. Dávalos, Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree, Systematic Biology, vol.65, issue.5, pp.772-791, 2016.

S. Y. Ho, Calibrating molecular estimates of substitution rates and divergence times in birds, Journal of Avian Biology, vol.38, issue.4, pp.409-414, 2007.

S. Y. Ho and M. J. Phillips, Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times, Systematic Biology, vol.58, pp.367-380, 2009.

S. Höhna, T. A. Heath, B. Boussau, M. J. Landis, F. Ronquist et al., Probabilistic graphical model representation in phylogenetics, Systematic Biology, vol.63, issue.5, pp.753-771, 2014.

S. Höhna, T. Stadler, F. Ronquist, and T. Britton, Inferring speciation and extinction rates under different sampling schemes, Molecular Biology and Evolution, vol.28, issue.9, pp.2577-2589, 2011.

J. Inoue, P. C. Donoghue, Y. , and Z. , The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times, Systematic Biology, vol.59, issue.1, pp.74-89, 2009.

E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde et al., Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, vol.346, issue.6215, pp.1320-1331, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02046801

D. G. Kendall, On the generalized "birth-and-death" process, The Annals of Mathematical Statistics, vol.19, issue.1, pp.1-15, 1948.

A. M. Kozlov and A. Stamatakis, Using raxml-ng in practice, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02535311

M. J. Landis, Biogeographic dating of speciation times using paleogeographically informed processes, Systematic Biology, vol.66, issue.2, pp.128-144, 2017.

N. Lartillot, Should we condition on non-extinction?, Blog: The Bayesian Kitchen, 2014.

N. ;. Lartillot, F. Delsuc, and N. Galtier, The bayesian approach to molecular phylogeny, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02535330

N. ;. Lartillot, F. Delsuc, and N. Galtier, Phylobayes: Bayesian phylogenetics using site-heterogeneous models, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02535342

A. Luo, D. A. Duchêne, C. Zhang, C. Zhu, and S. Y. Ho, A simulationbased evaluation of tip-dating under the fossilized birth-death process, Systematic Biology, vol.69, issue.2, pp.325-344, 2020.

C. R. Marshall, A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points, The American Naturalist, vol.171, issue.6, pp.726-742, 2008.

J. Müller and R. R. Reisz, Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates, BioEssays, vol.27, issue.10, pp.1069-1075, 2005.

S. Nee, R. M. May, and P. H. Harvey, The reconstructed evolutionary process, Philosophical Transactions of the Royal Society B, vol.344, pp.305-311, 1994.

L. Orlando, A. Ginolhac, G. Zhang, D. Froese, A. Albrechtsen et al., Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse, Nature, vol.499, issue.7456, p.74, 2013.

J. F. Parham, P. C. Donoghue, C. J. Bell, T. D. Calway, J. J. Head et al., Best practices for justifying fossil calibrations, Systematic Biology, vol.61, issue.2, pp.346-359, 2012.

, REFERENCES 5, vol.1, p.17

T. Pupko and I. Mayrose, A gentle introduction to probabilistic evolutionary models, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02535102

R. A. Pyron, Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia, Systematic Biology, vol.60, pp.466-481, 2011.

R. A. Pyron, Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians), Systematic Biology, vol.66, issue.1, pp.38-56, 2016.

B. Rannala, Conceptual issues in Bayesian divergence time estimation, Philosophical Transactions of the Royal Society B, vol.371, 1699.

D. M. Raup, Taxonomic diversity during the Phanerozoic, Science, vol.177, issue.4054, pp.1065-1071, 1972.

D. M. Raup, Species diversity in the Phanerozoic: an interpretation, Paleobiology, vol.2, issue.4, pp.289-297, 1976.

R. R. Reisz and J. Müller, Molecular timescales and the fossil record: a paleontological perspective, Trends in Genetics, vol.20, issue.5, pp.237-241, 2004.

F. Ronquist, S. Klopfstein, L. Vilhelmsen, S. Schulmeister, D. L. Murray et al., A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera, Systematic Biology, issue.6, pp.973-999, 2012.

F. Ronquist, N. Lartillot, and M. J. Phillips, Closing the gap between rocks and clocks using total-evidence dating, Philosophical Transactions of the Royal Society B, vol.371, p.20150136, 1699.
URL : https://hal.archives-ouvertes.fr/hal-02049882

M. Sakamoto, C. Venditti, and M. J. Benton, Residual diversity estimates' do not correct for sampling bias in palaeodiversity data, Methods in Ecology and Evolution, vol.8, issue.4, pp.453-459, 2017.

B. Saladin, A. B. Leslie, R. O. Wüest, G. Litsios, E. Conti et al., Fossils matter: improved estimates of divergence times in Pinus reveal older diversification, BMC Evolutionary Biology, vol.17, issue.1, p.95, 2017.

K. L. Sanders and M. S. Lee, Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds, Biology Letters, vol.3, issue.3, pp.275-279, 2007.

J. J. Schenk, Consequences of secondary calibrations on divergence time estimates, PLoS One, vol.11, issue.1, p.148228, 2016.

A. Schuster, S. Vargas, I. S. Knapp, S. A. Pomponi, R. J. Toonen et al., Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model, BMC Evolutionary Biology, vol.18, issue.1, p.114, 2018.

J. J. Sepkoski, R. K. Bambach, D. M. Raup, and J. W. Valentine, Phanerozoic marine diversity and the fossil record, Nature, vol.293, issue.5832, p.435, 1981.

G. J. Slater, P. Cui, A. M. Forasiepi, D. Lenz, K. Tsangaras et al., Evolutionary relationships among extinct and extant sloths: the evidence of mitogenomes and retroviruses, Genome Biology and Evolution, vol.8, issue.3, pp.607-621, 2016.

G. J. Slater, J. A. Goldbogen, and N. D. Pyenson, Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics, Royal Society B: Biological Sciences, vol.284, p.20170546, 1855.

A. B. Smith and A. J. Mcgowan, The shape of the Phanerozoic marine palaeodiversity curve: how much can be predicted from the sedimentary rock record of Western Europe?, Palaeontology, vol.50, issue.4, pp.765-774, 2007.

T. Stadler, On incomplete sampling under birth-death models and connections to the sampling-based coalescent, Journal of Theoretical Biology, vol.261, issue.1, pp.58-66, 2009.

T. Stadler, Sampling-through-time in birth-death trees, Journal of Theoretical Biology, vol.267, issue.3, pp.396-404, 2010.

T. Stadler, A. Gavryushkina, R. C. Warnock, A. J. Drummond, and T. A. Heath, The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes, Journal of Theoretical Biology, vol.447, pp.41-55, 2018.

D. Strauss and P. M. Sadler, Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges, Mathematical Geology, vol.21, issue.4, pp.411-427, 1989.

S. Tavaré, C. R. Marshall, O. Will, C. Soligo, and R. D. Martin, Using the fossil record to estimate the age of the last common ancestor of extant primates, Nature, vol.416, issue.6882, p.726, 2002.

E. A. Thompson, Human Evolutionary Trees, 1975.

N. S. Upham, J. A. Esselstyn, J. , and W. , Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation, PLoS Biology, vol.17, issue.12, p.3000494, 2019.

I. M. Vea and D. A. Grimaldi, Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts, Scientific Reports, vol.6, p.23487, 2016.

R. C. Warnock, Z. Yang, and P. C. Donoghue, Exploring uncertainty in the calibration of the molecular clock, Biology Letters, vol.8, issue.1, pp.156-159, 2012.

R. D. Wilkinson, M. E. Steiper, C. Soligo, R. D. Martin, Z. Yang et al., Dating primate divergences through an integrated analysis of palaeontological and molecular data, Systematic Biology, vol.60, pp.16-31, 2011.

D. F. Wright, S. Zamora, and I. A. Rahman, Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata), Journal of Paleontology, vol.91, issue.4, pp.799-814, 2017.

Z. Yang and B. Rannala, Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds, Molecular Biology and Evolution, vol.23, issue.1, pp.212-226, 2005.

Z. Yang and A. D. Yoder, Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species, Systematic Biology, vol.52, issue.5, pp.705-716, 2003.

G. U. Yule, A mathematical theory of evolution, based on the conclusions of Dr, J. C. Wills, F. R. S. Philosophical Transactions of the Royal Society of London, vol.213, pp.21-87, 1924.

C. Zhang, T. Stadler, S. Klopfstein, T. A. Heath, and F. Ronquist, Total-evidence dating under the fossilized birth-death process, Systematic Biology, vol.65, issue.2, pp.228-249, 2016.

A. Zhukova, O. Gascuel, S. Duchêne, D. L. Ayres, P. Lemey et al., Efficiently analysing large viral data sets in computational phylogenomics, Phylogenetics in the Genomic Era, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02536435