Raup, D. M. Biological extinction in Earth history. Science 231, 1528–1533 (1986).
Benton, M. J. The Red Queen and the Court Jester: species diversity and the role of biotic and abiotic factors through time. Science 323, 728–732 (2009).
Harmon, L. J. & Harrison, S. Species diversity is dynamic and unbounded at local and continental scales. Am. Nat. 185, 584–593 (2015).
Rabosky, D. L. & Hurlbert, A. H. Species richness at continental scales is dominated by ecological limits. Am. Nat. 185, 572–583 (2015).
Gavrilets, S. & Losos, J. B. Adaptive radiation: contrasting theory with data. Science 323, 732–737 (2009).
Gould, S. J., Gilinsky, N. L. & German, R. Z. Asymmetry of lineages and the direction of evolutionary time. Science 236, 1437–1441 (1987).
Žliobaitė, I., Fortelius, M. & Stenseth, N. C. Reconciling taxon senescence with the Red Queen’s hypothesis. Nature 552, 92–95 (2017).
Morlon, H., Parsons, T. L. & Plotkin, J. B. Reconciling molecular phylogenies with the fossil record. Proc. Natl Acad. Sci. USA 108, 16327–16332 (2011).
Quental, T. B. & Marshall, C. R. How the Red Queen drives terrestrial mammals to extinction. Science 341, 290–292 (2013).
Alfaro, M. E. et al. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl Acad. Sci. USA 106, 13410–13414 (2009).
Stadler, T. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl Acad. Sci. USA 108, 6187–6192 (2011).
Etienne, R. S. & Haegeman, B. A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence. Am. Nat. 180, E75–E89 (2012).
Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9, e89543 (2014).
Heath, T. A., Huelsenbeck, J. P. & Stadler, T. The fossilized birth–death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957–E2966 (2014).
Gavryushkina, A. et al. Bayesian total-evidence dating reveals the recent crown radiation of penguins. Syst. Biol. 66, 57–73 (2017).
Quintero, I., Lartillot, N. & Morlon, H. Imbalanced speciation pulses sustain the radiation of mammals. Science 384, 1007–1012 (2024).
Hauffe, T., Cantalapiedra, J. L. & Silvestro, D. Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks. Sci. Adv. 10, eadl2643 (2024).
Burin, G., Alencar, L. R., Chang, J., Alfaro, M. E. & Quental, T. B. How well can we estimate diversity dynamics for clades in diversity decline? Syst. Biol. 68, 47–62 (2019).
Silvestro, D., Warnock, R. C., Gavryushkina, A. & Stadler, T. Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nat. Commun. 9, 5237 (2018).
Warnock, R. C., Heath, T. A. & Stadler, T. Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates. Paleobiology 46, 137–157 (2020).
Billaud, O., Moen, D., Parsons, T. L. & Morlon, H. Estimating diversity through time using molecular phylogenies: old and species-poor frog families are the remnants of a diverse past. Syst. Biol. 69, 363–383 (2020).
Rabosky, D. L. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 12, 735–743 (2009).
Sepkoski, J. J. Ten years in the library: new data confirm paleontological patterns. Paleobiology 19, 43–51 (1993).
Alroy, J. Dynamics of origination and extinction in the marine fossil record. Proc. Natl Acad. Sci. USA 105, 11536–11542 (2008).
Foote, M. Symmetric waxing and waning of marine invertebrate genera. Paleobiology 33, 517–529 (2007).
Morlon, H., Potts, M. D. & Plotkin, J. B. Inferring the dynamics of diversification: a coalescent approach. PLoS Biol. 8, e1000493 (2010).
Hohmann, N. & Jarochowska, E. Enforced symmetry: the necessity of symmetric waxing and waning. PeerJ 7, e8011 (2019).
Nee, S. Birth–death models in macroevolution. Annu. Rev. Ecol. Evol. Syst. 37, 1–17 (2006).
Simpson, G. G.Tempo and Mode in Evolution (Columbia Univ. Press, 1953).
Schluter, D.The Ecology of Adaptive Radiations (Oxford Univ. Press, 2000).
Calderón del Cid, C. et al. The clade replacement theory: a framework to study age-dependent extinction. J. Evol. Biol. 37, 290–301 (2024).
Hughes, M., Gerber, S. & Wills, M. A. Clades reach highest morphological disparity early in their evolution. Proc. Natl Acad. Sci. USA 110, 13875–13879 (2013).
Raup, D. M. & Sepkoski, J. J. Mass extinctions in the marine fossil record. Science 215, 1501–1503 (1982).
Bambach, R. K., Knoll, A. H. & Wang, S. C. Origination, extinction, and mass depletions of marine diversity. Paleobiology 30, 522–542 (2004).
Stadler, T. Sampling-through-time in birth–death trees. J. Theor. Biol. 267, 396–404 (2010).
Truman, K., Vaughan, T. G., Gavryushkin, A. & Gavryushkina, A. S. The fossilised birth–death model is identifiable. Syst. Biol. 74, 112–123 (2025).
Jablonski, D. Heritability at the species level: analysis of geographic ranges of cretaceous mollusks. Science 238, 360–363 (1987).
Tanner, M. A. & Wong, W. H. The calculation of posterior distributions by data augmentation. J. Am. Stat. Assoc. 82, 528–540 (1987).
Höhna, S. et al. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst. Biol. 65, 726–736 (2016).
Maliet, O. & Morlon, H. Fast and accurate estimation of species-specific diversification rates using data augmentation. Syst. Biol. 71, 353–366 (2022).
Holland, S. M. The non-uniformity of fossil preservation. Phil. Trans. R. Soc. B 371, 20150130 (2016).
Pett, W. & Heath, T. A. in Phylogenetics in the Genomic Era (eds Scornavacca, C. et al.) 5.1:1–5.1:18 (2020); https://hal.science/hal-02536361
Andréoletti, J. et al. The occurrence birth–death process for combined-evidence analysis in macroevolution and epidemiology. Syst. Biol. 71, 1440–1452 (2022).
Cooper, R. B., Flannery-Sutherland, J. T. & Silvestro, D. DeepDive: estimating global biodiversity patterns through time using deep learning. Nat. Commun. 15, 4199 (2024).
Foote, M. Diversity-dependent diversification in the history of marine animals. Am. Nat. 201, 680–693 (2023).
Barnes, B. D., Sclafani, J. A. & Zaffos, A. Dead clades walking are a pervasive macroevolutionary pattern. Proc. Natl Acad. Sci. USA 118, e2019208118 (2021).
Gould, S. J., Raup, D. M., Sepkoski, J. J., Schopf, T. J. & Simberloff, D. S. The shape of evolution: a comparison of real and random clades. Paleobiology 3, 23–40 (1977).
Maliet, O., Hartig, F. & Morlon, H. A model with many small shifts for estimating species-specific diversification rates. Nat. Ecol. Evol. 3, 1086–1092 (2019).
Van Valen, L. The Red Queen. Am. Nat. 111, 809–810 (1977).
Eldredge, N. & Gould, S. J. in Models in Paleobiology (ed. Schopf, T. J. M.) 82–115 (Freeman, Cooper & Co., 1972).
Hunt, G. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proc. Natl Acad. Sci. USA 104, 18404–18408 (2007).
Sanisidro, O., Mihlbachler, M. C. & Cantalapiedra, J. L. A macroevolutionary pathway to megaherbivory. Science 380, 616–618 (2023).
Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973).
Spiridonov, A. & Lovejoy, S. Life rather than climate influences diversity at scales greater than 40 million years. Nature 607, 307–312 (2022).
Pearson, P. N. Investigating age dependency of species extinction rates using dynamic survivorship analysis. Hist. Biol. 10, 119–136 (1995).
Nietzsche, F. Thus Spoke Zarathustra: A Book for All and None (Random House, 1995).
Fischhoff, B. Hindsight is not equal to foresight: the effect of outcome knowledge on judgment under uncertainty. J. Exp. Psychol. 1, 288–299 (1975).
Kidwell, S. M. & Holland, S. M. The quality of the fossil record: implications for evolutionary analyses. Annu. Rev. Ecol. Syst. 33, 561–588 (2002).
Silvestro, D., Salamin, N. & Schnitzler, J. PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods Ecol. Evol. 5, 1126–1131 (2014).
Maddison, W. P., Midford, P. E. & Otto, S. P. Estimating a binary character’s effect on speciation and extinction. Syst. Biol. 56, 701–710 (2007).
Mitchell, J. S., Etienne, R. S. & Rabosky, D. L. Inferring diversification rate variation from phylogenies with fossils. Syst. Biol. 68, 1–18 (2019).
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–1092 (1953).
Hastings, W. K. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97–109 (1970).
Bezanson, J., Edelman, A., Karpinski, S. & Shah, V. B. Julia: a fresh approach to numerical computing. SIAM Rev. 59, 65–98 (2017).
Huelsenbeck, J. P., Rannala, B. & Masly, J. P. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288, 2349–2350 (2000).
Stadler, T., Gavryushkina, A., Warnock, R. C. M., Drummond, A. J. & Heath, T. A. The fossilized birth–death model for the analysis of stratigraphic range data under different speciation modes. J. Theor. Biol. 447, 41–55 (2018).
Stolz, U., Gavryushkina, A., Vaughan, T. G., Stadler, T. & Allen, B. J. Enhancing evolutionary timelines: the impact of stratigraphic range information on phylogenetic inference. Preprint at bioRxiv https://doi.org/10.1101/2025.04.17.649084 (2025).
Varela, S., González Hernández, J. & Fabris Sgarbi, L. paleobioDB: download and process data from the paleobiology database. R package v.0.7.0. CRAN https://CRAN.R-project.org/package=paleobioDB (2020).
Zaffos, A. A. velociraptr: Fossil Analysis. R package v.1.1.0. CRAN https://CRAN.R-project.org/package=velociraptr (2019).
R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2023).
Quintero, I., Landis, M. J., Jetz, W. & Morlon, H. The build-up of the present-day tropical diversity of tetrapods. Proc. Natl Acad. Sci. USA 120, e2220672120 (2023).
Stan Reference Manual: Version 2.36.0 (Stan Development Team, 2024).
Gabry, J., Češnovar, R., Johnson, A. & Bronder, S. CmdStanR: R interface to ’CmdStan’. R package v.0.9.0. Stan https://mc-stan.org/cmdstanr/ (2025).
Rabosky, D. L. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu. Rev. Ecol. Evol. Syst. 44, 481–502 (2013).
Etienne, R. S. et al. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. B 279, 1300–1309 (2012).
Quintero, I. Supplementary dataset for “The rise, decline and fall of clades”. Zenodo https://doi.org/10.5281/zenodo.15535408 (2025).
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