Abstract
Clade extinction is a crucial process that contributes to the loss of evolutionary history. The extinction of abundant and diverse clades has been linked to a range of abiotic and biotic factors, but their relative contributions and importance remain debated. Here, by analysing the fossil record of 12 major extinct marine clades, we show a consistent extinction trajectory comprising two phases: a slow, age-dependent decline followed by a fast, environment-triggered wipe-out. In the first phase, the clade proportional diversity (the diversity of a clade relative to the combined diversity of its ecologically similar taxa) steadily declined, largely independent of environmental factors such as temperature, dissolved oxygen, sea level and carbon-cycle variations, and instead reflecting biotic drivers such as competition and niche contraction. Once proportional diversity fell below a critical threshold (mean of approximately 0.13), major abiotic perturbations acted as the ‘last straw’, causing the clade extinction. Simulation and analytical models corroborate this pattern, showing near-zero extinction risk at high proportional diversity, but a steep risk rise once thresholds are crossed owing to reduced ecological dominance and narrowed functional roles. These findings reveal additive effects of biotic–abiotic factors in driving clade extinction, providing a predictive hypothesis for assessing future extinction risk among modern clades.
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Data availability
Fossil occurrence data are available via PBDB at http://www.paleobiodb.org. All processed data are available via GitHub at https://github.com/haijunsong/Clade-extinction.
Code availability
All codes used to conduct analyses are available via GitHub at https://github.com/haijunsong/Clade-extinction.
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Acknowledgements
We thank J. M. McArthur, B. J. W. Mills and G. A. Shields for providing paleoenvironmental data. We also thank all contributors to the PBDB. This is PBDB contribution number 545.
Funding
Haijun Song discloses support for the research of this work from the National Natural Science Foundation of China (grant nos. 42325202 and 92155201), the Natural Science Foundation of Hubei (grant no. 2023AFA006) and the Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan). D.S. discloses support for the research of this work from ETH Zurich, the Swedish Research Council (grant no. VR: 2024-04303) and the Swedish Foundation for Strategic Environmental Research MISTRA within the framework of the research programme BIOPATH (grant no. F 2022/1448).
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Haijun Song designed the research. Haijun Song, X.L. and D.S. carried out data processing and analyses. Haijun Song, J.D.C. and D.S. wrote the paper. X.L., D.C., X.D., L.T., Huyue Song, Y.W. and F.W. participated in interpreting the results and refining the paper.
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Extended data
Extended Data Fig. 1 Generic range through diversity (PyRate) of extinct clades and their competitors.
a, Generic diversity. b, Epoch box. The shaded areas represent 95% credible intervals. The colorful boxes on the x-axis represent the stratigraphic framework; see details in the International Chronostratigraphic Chart, www.stratigraphy.org. Green lines represent extinct clades; orange lines represent their competitors. Or, Ordovician; S, Silurian; Pg, Paleogene; N, Neogene; Q, Quaternary.
Extended Data Fig. 2 Generalized additive model (GAM) fitting curves of proportional diversity (SQS-derived diversity) of extinct clades.
Proportional diversity values are presented as mean values ± 95% confidence intervals, calculated from 50 independent SQS subsampling iterations for each time bin. N, the number of proportional diversity data points in the time series. Blue curves represent the GAM fitting curves.
Extended Data Fig. 3 Generalized additive model (GAM) fitting curves of proportional diversity (PyRate-corrected diversity) of extinct clades.
Proportional diversity values are presented as mean values ± 95% highest posterior density intervals, calculated from 500 independent replications for each time bin. Blue curves represent the GAM fitting curves. N, the number of proportional diversity data points in the time series.
Extended Data Fig. 4 Correlation plot of genus or proportional diversity (PyRate-corrected diversity) versus abiotic variables.
Analyses were performed using two-sided Spearman tests. No multiple testing correction was applied. Number and exact p values see Supplementary Tables 5, 6. Stars * represent p < Bonferroni limit 0.004, respectively. GAT, global average temperature; DO, dissolved oxygen in surface seawater. |ρ | > 0.7 means that the correlation is strong and therefore selected for statistical analysis. Age (absolute diversity) and age (proportional diversity) represent the correlations between age and absolute diversity/proportional diversity.
Extended Data Fig. 5 Results of meta-analysis of correlations from PyRate-corrected diversity.
Combined Bayesian ρ values are presented as mean values ± 95% confidence intervals. Number = 12 independent marine clades. Stars *, **and *** represent posterior probability of non-zero effect < 0.05, < 0.01 and < 0.001, respectively. AD, absolute diversity; PD, proportional diversity.
Extended Data Fig. 6 Simulation results of extinction probability of clades under background and mass extinction scenarios.
a, The clade maintains a stable ecological breadth as proportional diversity decreases. b, The clade’s ecological breadth narrows as proportional diversity decreases. The lines represent the average values of 1000 independent simulations. Shadows represent 95% confidence intervals.
Extended Data Fig. 7 Origination rates of marine clades from the PyRate analyses.
Origination rates are presented as mean values (blue lines) ± 95% highest posterior density intervals (shaded areas), calculated from 100 independent replications.
Extended Data Fig. 8 Extinction rates of marine clades from the PyRate analyses.
Extinction rates are presented as mean values (blue lines) ± 95% highest posterior density intervals (shaded areas), calculated from 100 independent replications.
Extended Data Fig. 9 The average rates of extinction and speciation from the PyRate analyses during the rise and decline phases of marine clades.
a, Speciation rate. b, Extinction rate. Diversification rates are presented as mean values (column) ± 95% confidence intervals (bars). N = number of data points representing extinction or speciation rates.
Extended Data Fig. 10 Sensitivity analysis of the diversity-dependent extinction model with respect to the initial number of species.
a, Number of species is 50. b, Number of species is 100. c, Number of species is 200. The lines represent the average values of 1000 independent simulations. Shadows represent 95% confidence intervals.
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Song, H., Liu, X., Dal Corso, J. et al. Identifying biotic and abiotic roles in marine clade extinction.
Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-026-03134-x
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DOI: https://doi.org/10.1038/s41559-026-03134-x
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