Bambach, R. K. Phanerozoic biodiversity mass extinctions. Annu. Rev. Earth Planet. Sci. 34, 127–155 (2006).
Ward, B. A. et al. EcoGEnIE 1.0: plankton ecology in the cGEnIE Earth system model. Geosci. Model Dev. 11, 4241–4267 (2018).
Ying, R., Monteiro, F. M., Wilson, J. D. & Schmidt, D. N. ForamEcoGEnIE 2.0: incorporating symbiosis and spine traits into a trait-based global planktic foraminiferal model. Geosci. Model Dev. 16, 813–832 (2023).
Gibbs, S. J. et al. Algal plankton turn to hunting to survive and recover from end-Cretaceous impact darkness. Sci. Adv. 6, eabc9123 (2020).
Bralower, T. J. et al. Origin of a global carbonate layer deposited in the aftermath of the Cretaceous–Paleogene boundary impact. Earth Planet. Sci. Lett. 548, 116476 (2020).
Lowery, C. M. et al. Early Paleocene paleoceanography and export productivity in the Chicxulub crater. Paleoceanogr. Paleoclimatol. 36, e2021PA004241.
Jiang, S., Bralower, T. J., Patzkowsky, M. E., Kump, L. R. & Schueth, J. D. Geographic controls on nannoplankton extinction across the Cretaceous/Palaeogene boundary. Nat. Geosci. 3, 280–285 (2010).
Schoene, B. et al. U-Pb constraints on pulsed eruption of the Deccan Traps across the end-Cretaceous mass extinction. Science 363, 862–866 (2019).
Morgan, J. V., Bralower, T. J., Brugger, J. & Wünnemann, K. The Chicxulub impact and its environmental consequences. Nat. Rev. Earth Environ. 3, 338–354 (2022).
Hull, P. M. et al. On impact and volcanism across the Cretaceous–Paleogene boundary. Science 367, 266–272 (2020).
Senel, C. B. et al. Chicxulub impact winter sustained by fine silicate dust. Nat. Geosci. 16, 1033–1040 (2023).
Henehan, M. J. et al. Rapid ocean acidification and protracted Earth system recovery followed the end-Cretaceous Chicxulub impact. Proc. Natl Acad. Sci USA 116, 22500–22504 (2019).
D’Hondt, S. Consequences of the Cretaceous/Paleogene mass extinction for marine ecosystems. Annu. Rev. Ecol. Evol. Syst. 36, 295–317 (2005).
Schulte, P. et al. The Chicxulub asteroid impact and mass extinction at the Cretaceous–Paleogene boundary. Science 327, 1214–1218 (2010).
Bown, P. Selective calcareous nannoplankton survivorship at the Cretaceous-Tertiary boundary. Geology 33, 653–656 (2005).
Fraass, A. J., Kelly, D. C. & Peters, S. E. Macroevolutionary history of the planktic foraminifera. Annu. Rev. Earth Planet. Sci. 43, 139–166 (2015).
Sims, P. A., Mann, D. G. & Medlin, L. K. Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 45, 361–402 (2006).
Thomas, E. in Large Ecosystem Perturbations: Causes and Consequences Vol. 424 (eds Monechi, S., Coccioni, R. & Rampino, M.) 1–24 (Geological Society of America, 2007).
Huber, B. T. in The Cretaceous-Tertiary Event and Other Catastrophes in Earth History (eds Ryder, G., Fastovsky, D. E. & Gartner, S.) 319–334 (Geological Society of America, 1996).
Witts, J. D. et al. Macrofossil evidence for a rapid and severe Cretaceous–Paleogene mass extinction in Antarctica. Nat. Commun. 7, 11738 (2016).
Birch, H., Schmidt, D. N., Coxall, H. K., Kroon, D. & Ridgwell, A. Ecosystem function after the K/Pg extinction: decoupling of marine carbon pump and diversity. Proc. R. Soc. B Biol. Sci. 288, 20210863 (2021).
Jablonski, D. Extinction and the spatial dynamics of biodiversity. Proc. Natl Acad. Sci. USA 105, 11528–11535 (2008).
Alvarez, L. W., Alvarez, W., Asaro, F. & Michel, H. V. Extraterrestrial cause for the Cretaceous-Tertiary extinction. Science 208, 1095–1108 (1980).
Alegret, L., Thomas, E. & Lohmann, K. C. End-Cretaceous marine mass extinction not caused by productivity collapse. Proc. Natl Acad. Sci. USA 109, 728–732 (2012).
Hull, P. M. & Norris, R. D. Diverse patterns of ocean export productivity change across the Cretaceous–Paleogene boundary: new insights from biogenic barium. Paleoceanography 26, PA3205 (2011).
Prinn, R. G. & Fegley, B. Bolide impacts, acid rain, and biospheric traumas at the Cretaceous–Tertiary boundary. Earth Planet. Sci. Lett. 83, 1–15 (1987).
Trudgill, M. et al. Pulses of ocean acidification at the Triassic–Jurassic boundary. Nat. Commun. 16, 6471 (2025).
Gibbs, S. J., Bown, P. R., Sessa, J. A., Bralower, T. J. & Wilson, P. A. Nannoplankton extinction and origination across the Paleocene–Eocene thermal maximum. Science 314, 1770–1773 (2006).
Brugger, J., Feulner, G., Hofmann, M. & Petri, S. A pronounced spike in ocean productivity triggered by the Chicxulub impact. Geophys. Res. Lett. 48, e2020GL092260 (2021).
Lowery, C. M., Bown, P. R., Fraass, A. J. & Hull, P. M. Ecological response of plankton to environmental change: thresholds for extinction. Annu. Rev. Earth Planet. Sci. 48, 403–429 (2020).
Malanoski, C. M., Farnsworth, A., Lunt, D. J., Valdes, P. J. & Saupe, E. E. Climate change is an important predictor of extinction risk on macroevolutionary timescales. Science 383, 1130–1134 (2024).
Solan, M. et al. Extinction and ecosystem function in the marine benthos. Science 306, 1177–1180 (2004).
Monarrez, P. M., Heim, N. A. & Payne, J. L. Mass extinctions alter extinction and origination dynamics with respect to body size. Proc. R. Soc. B Biol. Sci. 288, 20211681 (2021).
Follows, M. J., Dutkiewicz, S., Grant, S. & Chisholm, S. W. Emergent biogeography of microbial communities in a model ocean. Science 315, 1843–1846 (2007).
Ying, R., Monteiro, F. M., Wilson, J. D., Ödalen, M. & Schmidt, D. N. Past foraminiferal acclimatization capacity is limited during future warming. Nature 636, 385–389 (2024).
Zhang, L., Hay, W. W., Wang, C. & Gu, X. The evolution of latitudinal temperature gradients from the latest Cretaceous through the present. Earth Sci. Rev. 189, 147–158 (2019).
Huber, B. T., Norris, R. D. & MacLeod, K. G. Deep-sea paleotemperature record of extreme warmth during the Cretaceous. Geology 30, 123–126 (2002).
Niezgodzki, I., Knorr, G., Lohmann, G., Tyszka, J. & Markwick, P. J. Late Cretaceous climate simulations with different CO2 levels and subarctic gateway configurations: a model–data comparison. Paleoceanography 32, 980–998 (2017).
Ward, B. A., Dutkiewicz, S. & Follows, M. J. Modelling spatial and temporal patterns in size-structured marine plankton communities: top-down and bottom-up controls. J. Plankton Res. 36, 31–47 (2014).
Dutkiewicz, S. et al. Dimensions of marine phytoplankton diversity. Biogeosciences 17, 609–634 (2020).
Brugger, J., Feulner, G. & Petri, S. Baby, it’s cold outside: climate model simulations of the effects of the asteroid impact at the end of the Cretaceous. Geophys. Res. Lett. 44, 419–427 (2017).
Sepúlveda, J., Wendler, J. E., Summons, R. E. & Hinrichs, K.-U. Rapid resurgence of marine productivity after the Cretaceous-Paleogene mass extinction. Science 326, 129–132 (2009).
Lowery, C. M. & Bralower, T. J. Elevated post K-Pg export productivity in the Gulf of Mexico and Caribbean. Paleoceanogr. Paleoclimatol. 37, e2021PA004400 (2022).
Schaefer, B. et al. Microbial life in the nascent Chicxulub crater. Geology 48, 328–332 (2020).
Henehan, M. J., Hull, P. M., Penman, D. E., Rae, J. W. B. & Schmidt, D. N. Biogeochemical significance of pelagic ecosystem function: an End-Cretaceous case study. Phil. Trans. R. Soc. B 371, 20150510 (2016).
Tyrrell, T., Merico, A. & McKay, D. I. A. Severity of ocean acidification following the End-Cretaceous asteroid impact. Proc. Natl Acad. Sci. USA 112, 6556–6561 (2015).
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).
Hoppe, C. J. M. et al. Photosynthetic light requirement near the theoretical minimum detected in Arctic microalgae. Nat. Commun. 15, 7385 (2024).
Stanley, G. & Van De Schootbrugge, B. in Coral Bleaching Vol. 233 (eds Van Oppen, M. J. H. & Lough, J. M.) 9–26 (Springer International Publishing, 2018).
Behrenfeld, M. J. et al. Thoughts on the evolution and ecological niche of diatoms. Ecol. Monogr. 91, e01457 (2021).
Ribeiro, S. et al. Phytoplankton growth after a century of dormancy illuminates past resilience to catastrophic darkness. Nat. Commun. 2, 311 (2011).
Guinot, G. & Condamine, F. L. Global impact and selectivity of the Cretaceous–Paleogene mass extinction among sharks, skates, and rays. Science 379, 802–806 (2023).
Payne, J. L., Bush, A. M., Heim, N. A., Knope, M. L. & McCauley, D. J. Ecological selectivity of the emerging mass extinction in the oceans. Science 353, 1284–1286 (2016).
Feng, Y. et al. High extinction risk in large foraminifera during past and future mass extinctions. Sci. Adv. 10, eadj8223 (2024).
Alegret, L., Arreguín-Rodríguez, G. J., Trasviña-Moreno, C. A. & Thomas, E. Turnover and stability in the deep sea: Benthic foraminifera as tracers of Paleogene global change. Glob. Planetary Change 196, 103372 (2021).
Sibert, E. C., Hull, P. M. & Norris, R. D. Resilience of Pacific pelagic fish across the Cretaceous/Palaeogene mass extinction. Nat. Geosci. 7, 667–670 (2014).
Lowery, C. M. et al. Rapid recovery of life at ground zero of the end-Cretaceous mass extinction. Nature 558, 288–291 (2018).
Coxall, H. K., D’Hondt, S. & Zachos, J. C. Pelagic evolution and environmental recovery after the Cretaceous–Paleogene mass extinction. Geology 34, 297–300 (2006).
Sepúlveda, J. et al. Stable isotope constraints on marine productivity across the Cretaceous-Paleogene mass extinction. Paleoceanogr. Paleoclimatol. 34, 1195–1217 (2019).
Esmeray-Senlet, S. et al. Evidence for reduced export productivity following the Cretaceous/Paleogene mass extinction. Paleoceanography 30, 718–738 (2015).
Schmidt, A. et al. Selective environmental stress from sulphur emitted by continental flood basalt eruptions. Nat. Geosci. 9, 77–82 (2016).
Geider, R. J., Maclntyre, H. L. & Kana, T. M. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnol. Oceanogr. 43, 679–694 (1998).
Estrada, M. et al. Phytoplankton across tropical and subtropical regions of the Atlantic, Indian and Pacific Oceans. PLoS ONE 11, e0151699 (2016).
Malviya, S. et al. Insights into global diatom distribution and diversity in the world’s ocean. Proc. Natl Acad. Sci. USA 113, E1516–E1525 (2016).
Biard, T. et al. In situ imaging reveals the biomass of giant protists in the global ocean. Nature 532, 504–507 (2016).
Wilson, J. D., Monteiro, F. M., Schmidt, D. N., Ward, B. A. & Ridgwell, A. Linking marine plankton ecosystems and climate: a new modeling approach to the warm early Eocene climate. Paleoceanogr. Paleoclimatol. 33, 1439–1452 (2018).
Marañón, E. et al. Unimodal size scaling of phytoplankton growth and the size dependence of nutrient uptake and use. Ecol. Lett. 16, 371–379 (2013).
Hatton, I. A., Dobson, A. P., Storch, D., Galbraith, E. D. & Loreau, M. Linking scaling laws across eukaryotes. Proc. Natl Acad. Sci. USA 116, 21616–21622 (2019).
Ward, B. A., Cael, B. B., Collins, S. & Young, C. R. Selective constraints on global plankton dispersal. Proc. Natl Acad. Sci. USA 118, e2007388118 (2021).
Ying, R. cGENIE model output for ‘Darkness and body size shaped End-Cretaceous marine extinction patterns’. Zenodo https://doi.org/10.5281/zenodo.17742290 (2026).
Ying, R. cgeniepy: a Python package for analysing cGENIE Earth System Model output. J. Open Source Softw. 9, 6762 (2024).

