Allan, R. P. Climate Change 2021: The Physical Science Basis: Working Group I Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (WMO, IPCC Secretariat, 2021).
Burke, K. D. et al. Pliocene and Eocene provide best analogs for near-future climates. Proc. Natl Acad. Sci. USA 115, 13288–13293 (2018).
Ceballos, G. et al. Accelerated modern human-induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015).
Freeman, B. G., Lee-Yaw, J. A., Sunday, J. M. & Hargreaves, A. L. Expanding, shifting and shrinking: the impact of global warming on species’ elevational distributions. Glob. Ecol. Biogeogr. 27, 1268–1276 (2018).
Harper, G. A. & Bunbury, N. Invasive rats on tropical islands: their population biology and impacts on native species. Glob. Ecol. Conserv. 3, 607–627 (2015).
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).
Strotz, L. C. et al. Getting somewhere with the Red Queen: chasing a biologically modern definition of the hypothesis. Biol. Lett. 14, 20170734 (2018).
Condamine, F. L., Romieu, J. & Guinot, G. Climate cooling and clade competition likely drove the decline of lamniform sharks. Proc. Natl Acad. Sci. USA 116, 20584–20590 (2019).
Ezard, T. H. G., Aze, T., Pearson, P. N. & Purvis, A. Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science 332, 349–351 (2011).
Nesbitt, S. J. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Thesis, Columbia Univ. (2009).
Grigg, G. Biology and Evolution of Crocodylians (Csiro, 2015).
Baillie, J., Hilton-Taylor, C., Stuart, S. N. & IUCN Species Survival Commission. 2004 IUCN Red List of Threatened Species: A Global Species Assessment (IUCN, 2004).
Somaweera, R., Brien, M. L., Platt, S. G., Manolis, C. & Webber, B. L. Direct and indirect interactions with vegetation shape crocodylian ecology at multiple scales. Freshw. Biol. 64, 257–268 (2018).
Stubbs, T. L. et al. Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation. Proc. Biol. Sci. 288, 20210069 (2021).
Mannion, P. D. et al. Climate constrains the evolutionary history and biodiversity of crocodylians. Nat. Commun. 6, 8438 (2015).
Jouve, S. & Jalil, N.-E. Paleocene resurrection of a crocodylomorph taxon: biotic crises, climatic and sea level fluctuations. Gondwana Res. 85, 1–18 (2020).
Mannion, P. D., Chiarenza, A. A., Godoy, P. L. & Cheah, Y. N. Spatiotemporal sampling patterns in the 230 million year fossil record of terrestrial crocodylomorphs and their impact on diversity. Palaeontology 62, 615–637 (2019).
Leardi, J. M., Yáñez, I. & Pol, D. South American crocodylomorphs (Archosauria; Crocodylomorpha): a review of the early fossil record in the continent and its relevance on understanding the origins of the clade. J. South Am. Earth Sci. 104, 102780 (2020).
Foth, C., Sookias, R. B. & Ezcurra, M. D. Rapid initial morphospace expansion and delayed morphological disparity peak in the first 100 million years of the archosauromorph evolutionary radiation. Front. Earth Sci. Chin. 9, 723973 (2021).
Buffetaut, E. Radiation evolutive, paleoecologie et biogeographie des crocodiliens mesosuchiens. Mem. S. Geo. F. 60, 88 (1981).
Ezcurra, M. D. & Butler, R. J. The rise of the ruling reptiles and ecosystem recovery from the Permo-Triassic mass extinction. Proc. Biol. Sci. 285, 20180361 (2018).
Godoy, P. L., Benson, R. B. J., Bronzati, M. & Butler, R. J. The multi-peak adaptive landscape of crocodylomorph body size evolution. BMC Evol. Biol. 19, 167 (2019).
Melstrom, K. M. & Irmis, R. B. Repeated evolution of herbivorous crocodyliforms during the age of dinosaurs. Curr. Biol. 29, 2389–2395.e3 (2019).
Wilberg, E. W., Turner, A. H. & Brochu, C. A. Evolutionary structure and timing of major habitat shifts in Crocodylomorpha. Sci. Rep. 9, 514 (2019).
State of the World’s Birds: Taking the Pulse of the Planet (BirdLife International, 2018).
Pigot, A. L. et al. Macroevolutionary convergence connects morphological form to ecological function in birds. Nat. Ecol. Evol. 4, 230–239 (2020).
Hoffman, A. Mass extinctions, diversification, and the nature of paleontology. Rev. Esp. Paleontol. 1, 101–107 (1986).
von Reumont, B. M. et al. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol. Biol. Evol. 29, 1031–1045 (2012).
Laurent, S., Robinson-Rechavi, M. & Salamin, N. Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions. BMC Evol. Biol. 15, 157 (2015).
Davis, K. E., De Grave, S., Delmer, C. & Wills, M. A. Freshwater transitions and symbioses shaped the evolution and extant diversity of caridean shrimps. Commun. Biol. 1, 16 (2018).
Crouch, N. M. A. & Clarke, J. A. Body size evolution in palaeognath birds is consistent with Neogene cooling-linked gigantism. Palaeogeogr. Palaeoclimatol. Palaeoecol. 532, 109224 (2019).
Clavel, J. & Morlon, H. Accelerated body size evolution during cold climatic periods in the Cenozoic. Proc. Natl Acad. Sci. USA 114, 4183–4188 (2017).
Quintero, I. & Jetz, W. Global elevational diversity and diversification of birds. Nature 555, 246–250 (2018).
Markwick, P. J. Crocodilian diversity in space and time: the role of climate in paleoecology and its implication for understanding K/T extinctions. Paleobiology 24, 470–497 (1998).
Vasse, D. & Hua, S. Diversité des crocodiliens du Crétacé Supérieur et du Paléogene. Influneces et limites de la crise Maastrichtien-Paléocene et des ‘Terminal Eocene Events’. Oryctos 1, 65–77 (1998).
de Souza Carvalho, I., de Gasparini, Z. B., Salgado, L., de Vasconcellos, F. M. & da Silva Marinho, T. Climate’s role in the distribution of the Cretaceous terrestrial Crocodyliformes throughout Gondwana. Palaeogeogr. Palaeoclimatol. Palaeoecol. 297, 252–262 (2010).
Claramunt, S. & Cracraft, J. A new time tree reveals Earth history’s imprint on the evolution of modern birds. Sci. Adv. 1, e1501005 (2015).
Martin, J. E., Amiot, R., Lécuyer, C. & Benton, M. J. Sea surface temperature contributes to marine crocodylomorph evolution. Nat. Commun. 5, 4658 (2014).
Tennant, J., Mannion, P. D. & Upchurch, P. Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition. Proc. R. Soc. B. 283, 20152840 (2016).
De Celis, A., Narváez, I. & Ortega, F. Spatiotemporal palaeodiversity patterns of modern crocodiles (Crocodyliformes: Eusuchia). Zool. J. Linn. Soc. 189, 635–656 (2020).
Feduccia, A. ‘Big bang’ for tertiary birds? Trends Ecol. Evol. 18, 172–176 (2003).
Prum, R. O. et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573 (2015).
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448 (2012).
Mudelsee, M., Bickert, T., Lear, C. H. & Lohmann, G. Cenozoic climate changes: a review based on time series analysis of marine benthic δ18O records. Rev. Geophys. 52, 333–374 (2014).
Solórzano, A., Núñez-Flores, M., Inostroza-Michael, O. & Hernández, C. E. Biotic and abiotic factors driving the diversification dynamics of Crocodylia. Palaeontology 63, 415–429 (2020).
Groh, S. S., Upchurch, P., Barrett, P. M. & Day, J. J. How to date a crocodile: estimation of neosuchian clade ages and a comparison of four time-scaling methods. Palaeontology 65, e12589 (2022).
Darlim, G., Lee, M. S. Y., Walter, J. & Rabi, M. The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade. Biol. Lett. 18, 20210603 (2022).
Rio, J. P. & Mannion, P. D. Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem. PeerJ 9, e12094 (2021).
Lee, M. S. Y. & Yates, A. M. Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record. Proc. Biol. Sci. 285, 20181071 (2018).
Toljagić, O. & Butler, R. J. Triassic–Jurassic mass extinction as trigger for the Mesozoic radiation of crocodylomorphs. Biol. Lett. 9, 20130095 (2013).
Pol, D. & Leardi, J. M. Diversity patterns of Notosuchia (Crocodyliformes, Mesoeucrocodylia) during the Cretaceous of Gondwana. Publ. Electron. Asoc. Paleontol. Argent. 15, 172–186 (2015).
Kellner, A. W. A., Pinheiro, A. E. P. & Campos, D. A. A new Sebecid from the Paleogene of Brazil and the crocodyliform radiation after the K–Pg boundary. PLoS ONE 9, e81386 (2014).
Paolillo, A. & Linares, O. J. Nuevos cocodrilos sebecosuchia del cenozoico suramericano (Mesosuchia: Crocodylia). Paleobiologia Neotropical 3, 1–25 (2007).
Salisbury, S. W. & Willis, P. M. A. A new crocodylian from the Early Eocene of south-eastern Queensland and a preliminary investigation of the phylogenetic relationships of crocodyloids. Alcheringa 20, 179–226 (1996).
Mead, J. I. et al. New extinct Mekosuchine crocodile from Vanuatu, South Pacific. Copeia 2002, 632–641 (2002).
Scheyer, T. M. et al. Crocodylian diversity peak and extinction in the late Cenozoic of the northern Neotropics. Nat. Commun. 4, 1907 (2013).
Salas-Gismondi, R. et al. A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands. Proc. Biol. Sci. 282, 20142490 (2015).
Young, M. T., Bell, M. A., de Andrade, M. B. & Brusatte, S. L. Body size estimation and evolution in metriorhynchid crocodylomorphs: implications for species diversification and niche partitioning. Zool. J. Linn. Soc. 163, 1199–1216 (2011).
Johnson, M. M., Young, M. T. & Brusatte, S. L. The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution. PeerJ 8, e9808 (2020).
Brochu, C. A. A new Late Cretaceous gavialoid crocodylian from eastern North America and the phylogenetic relationships of thoracosaurs. J. Vert. Paleontol. 24, 610–633 (2004).
Jouve, S. et al. The oldest African crocodylian: phylogeny, paleobiogeography, and differential survivorship of marine reptiles through the Cretaceous–Tertiary boundary. J. Vert. Paleontol. 28, 409–421 (2008).
Vermeij, G. J. Biogeography and Adaptation: Patterns of Marine Life (Harvard Univ. Press, 1978).
Vrba, E. S. Evolution, species and fossils: how does life evolve. S. Afr. J. Sci. 76, 61–84 (1980).
Kozak, K. H. & Wiens, J. J. Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecol. Lett. 13, 1378–1389 (2010).
Stockdale, M. T. & Benton, M. J. Environmental drivers of body size evolution in crocodile-line archosaurs. Commun. Biol. 4, 38 (2021).
Colbert, E. H., Cowles, R. B. & Cowles, R. B. Temperature tolerances in the American alligator and their bearing on the habits, evolution, and extinction of the dinosaurs. Bull. Am. Mus. Nat. Hist. 86, 7 (1946).
Markwick, P. J. Fossil crocodilians as indicators of Late Cretaceous and Cenozoic climates: implications for using palaeontological data in reconstructing palaeoclimate. Palaeogeogr. Palaeoclimatol. Palaeoecol. 137, 205–271 (1998).
Legendre, L. J., Guénard, G., Botha-Brink, J. & Cubo, J. Palaeohistological evidence for ancestral high metabolic rate in archosaurs. Syst. Biol. 65, 989–996 (2016).
Cubo, J. et al. Were Notosuchia (Pseudosuchia: Crocodylomorpha) warm-blooded? A palaeohistological analysis suggests ectothermy. Biol. J. Linn. Soc. Lond. 131, 154–162 (2020).
Estes, R. & Howard Hutchison, J. Eocene lower vertebrates from Ellesmere Island, Canadian Arctic Archipelago. Palaeogeogr. Palaeoclimatol. Palaeoecol. 30, 325–347 (1980).
Pinceel, T. et al. Environmental change as a driver of diversification in temporary aquatic habitats: does the genetic structure of extant fairy shrimp populations reflect historic aridification? Freshw. Biol. 58, 1556–1572 (2013).
Dorn, A., Musilová, Z., Platzer, M., Reichwald, K. & Cellerino, A. The strange case of East African annual fishes: aridification correlates with diversification for a savannah aquatic group? BMC Evol. Biol. 14, 210 (2014).
Tennant, J. P., Mannion, P. D. & Upchurch, P. Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval. Nat. Commun. 7, 12737 (2016).
van Hengstum, P. J., Cresswell, J. N., Milne, G. A. & Iliffe, T. M. Development of anchialine cave habitats and karst subterranean estuaries since the last ice age. Sci. Rep. 9, 11907 (2019).
Klausen, T. G., Paterson, N. W. & Benton, M. J. Geological control on dinosaurs’ rise to dominance: Late Triassic ecosystem stress by relative sea level change. Terra Nova 32, 434–441 (2020).
Benson, R. B. J. & Butler, R. J. Uncovering the diversification history of marine tetrapods: ecology influences the effect of geological sampling biases. Geol. Soc. Spec. Publ. 358, 191–208 (2011).
Jones, L. A. & Eichenseer, K. Uneven spatial sampling distorts reconstructions of Phanerozoic seawater temperature. Geology 50, 238–242 (2022).
Wellborn, G. A. & Langerhans, R. B. Ecological opportunity and the adaptive diversification of lineages. Ecol. Evol. 5, 176–195 (2015).
Losos, J. B. Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E. O. Wilson award address. Am. Nat. 175, 623–639 (2010).
Aristide, L. & Morlon, H. Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification. Ecol. Lett. 22, 2006–2017 (2019).
Gamisch, A. & Comes, H. P. Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae). BMC Evol. Biol. 19, 93 (2019).
Greenberg, D. A. & Mooers, A. Ø. Linking speciation to extinction: diversification raises contemporary extinction risk in amphibians. Evol. Lett. 1, 40–48 (2017).
Jouve, S., Bouya, B. & Amaghzaz, M. A long-snouted dyrosaurid (crocodyliformes, mesoeucrocodylia) from the Paleocene of Morocco: phylogenetic and palaeobiogeographic implications. Palaeontology 51, 281–294 (2008).
Spiridonov, A. & Lovejoy, S. Life rather than climate influences diversity at scales greater than 40 million years. Nature 607, 307–312 (2022).
Lewitus, E., Bittner, L., Malviya, S., Bowler, C. & Morlon, H. Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nat. Ecol. Evol. 2, 1715–1723 (2018).
Valente, L. M., Savolainen, V. & Vargas, P. Unparalleled rates of species diversification in Europe. Proc. Biol. Sci. 277, 1489–1496 (2010).
Davis, K. E., Hill, J., Astrop, T. I. & Wills, M. A. Global cooling as a driver of diversification in a major marine clade. Nat. Commun. 7, 13003 (2016).
Tang, C., Davis, K. E., Delmer, C., Yang, D. & Wills, M. A. Elevated atmospheric CO2 promoted speciation in mosquitoes (Diptera, Culicidae). Commun. Biol. 1, 182 (2018).
Thomson, R. C., Spinks, P. Q. & Shaffer, H. B. A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc. Natl Acad. Sci. USA 118, e2012215118 (2021).
Rose, J. P. et al. Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Mol. Phylogenet. Evol. 122, 59–79 (2018).
Davis, K. E. et al. Ecological transitions and the shape of the decapod tree of life. Integr. Comp. Biol. 62, 332–344 (2022).
Thompson, J. B., Davis, K. E., Dodd, H. O., Wills, M. A. & Priest, N. K. Speciation across the Earth driven by global cooling in terrestrial orchids. Proc. Natl Acad. Sci. USA 120, e2102408120 (2022).
Lloyd, G. T., Bapst, D. W., Friedman, M. & Davis, K. E. Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds. Biol. Lett. 12, 20160609 (2016).
Wright, A. M., Lloyd, G. T. & Hillis, D. M. Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors. Syst. Biol. 65, 602–611 (2016).
Peters, S. E. & McClennen, M. The Paleobiology Database application programming interface. Paleobiology 42, 1–7 (2016).
Baum, B. R. & Ragan, M. A. The MRP method. In Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (ed. Bininda-Emonds, O. R. P.) 17–34 (Springer, 2004).
Oaks, J. R. A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles. Evolution 65, 3285–3297 (2011).
Goloboff, P. A. & Catalano, S. A. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32, 221–238 (2016).
Swofford, D. L. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 b8 (Sinauer, 2001).
Walker, J. D., Geissman, J. W., Bowring, S. A. & Babcock, L. E. Geologic Time Scale v. 5.0 (Geological Society of America, 2018).
Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).
Irmis, R. B., Nesbitt, S. J. & Sues, H.-D. Early Crocodylomorpha. Geol. Soc. Spec. Publ. 379, 275–302 (2013).
Turner, A. H., Pritchard, A. C. & Matzke, N. J. Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades. PLoS ONE 12, e0169885 (2017).
Mitchell, J. S., Etienne, R. S. & Rabosky, D. L. Inferring diversification rate variation from phylogenies with fossils. Syst. Biol. 68, 1–18 (2019).
Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9, e89543 (2014).
Rabosky, D. L. et al. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014).
Veizer, J. et al. 87Sr/86Sr, δ13C and δ18O evolution of Phanerozoic seawater. Chem. Geol. 161, 59–88 (1999).
Zachos, J., Pagani, M., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001).
Haq, B. U., Hardenbol, J. & Vail, P. R. Chronology of fluctuating sea levels since the Triassic. Science 235, 1156–1167 (1987).
Miller, K. G. et al. The Phanerozoic record of global sea-level change. Science 310, 1293–1298 (2005).
Prokoph, A., Shields, G. A. & Veizer, J. Compilation and time-series analysis of a marine carbonate δ18O, δ13C, 87Sr/86Sr and δ34S database through Earth history. Earth Sci. Rev. 87, 113–133 (2008).
Kristoufek, L. Measuring correlations between non-stationary series with DCCA coefficient. Physica A 402, 291–298 (2014).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
R Core Team R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2015).
Koehn, C. R., Petrie, M. D., Bradford, J. B., Litvak, M. E. & Strachan, S. Seasonal precipitation and soil moisture relationships across forests and woodlands in the southwestern United States. J. Geophys. Res. Biogeosci. 126, e2020JG005986 (2021).
Dunhill, A. M., Hannisdal, B. & Benton, M. J. Disentangling rock record bias and common-cause from redundancy in the British fossil record. Nat. Commun. 5, 4818 (2014).
Liow, L. H., Reitan, T. & Harnik, P. G. Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night. Ecol. Lett. 18, 1030–1039 (2015).
Schreiber, T. Measuring information transfer. Phys. Rev. Lett. 85, 461–464 (2000).
Steeg, G. V., Ver Steeg, G. & Galstyan, A. Information transfer in social media. In Proceedings of the 21st International conference on World Wide Web, 509–518 (2012).
Lungarella, M., Pitti, A. & Kuniyoshi, Y. Information transfer at multiple scales. Phys. Rev. E 76, 056117 (2007).
Behrendt, S., Dimpfl, T., Peter, F. J. & Zimmermann, D. J. RTransferEntropy—quantifying information flow between different time series using effective transfer entropy. SoftwareX 10, 100265 (2019).
Visser, I. & Speekenbrink, M. depmixS4: an R package for hidden Markov models. J. Stat. Softw. 36, 1–21 (2010). Others.
Title, P. O. & Rabosky, D. L. Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles. Syst. Biol. 66, 843–856 (2017).
Wilberg, E. W. What’s in an outgroup? The impact of outgroup choice on the phylogenetic position of Thalattosuchia (Crocodylomorpha) and the origin of Crocodyliformes. Syst. Biol. 64, 621–637 (2015).
Jones, A. S. & Butler, R. J. A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding. PeerJ 6, e5901 (2018).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Bell, M. A. & Lloyd, G. T. strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology 58, 379–389 (2015).
Dr. Thomas Hughes is a UK-based scientist and science communicator who makes complex topics accessible to readers. His articles explore breakthroughs in various scientific disciplines, from space exploration to cutting-edge research.
