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A modeling approach to quantify ecological dynamics and functional structures of paleocommunities

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Abstract

Fossils preserve crucial information about the underlying biological and ecological processes of past ecosystems. Models built on paleontological and paleoecological data can help to elucidate the factors influencing ecosystem health, stability, resilience and function, offering a unique perspective on the long-term ecological impacts of the ongoing human-induced biodiversity crisis and ecosystem degradation. Substantial advances have been made in quantifying the ecological dynamics and functional structures of paleocommunities. However, the effective reconstruction of paleo-food webs and the quantitative evaluation of paleocommunity dynamics are still challenging tasks. Here we present a detailed protocol for reconstructing paleo-food webs using fossil data and for modeling the stability and structures of these paleocommunities using the cascading extinction on graphs model. The procedure includes (1) selecting an appropriate geological time range and geographic scope, collecting fossil data and reconstructing paleocommunities; (2) assigning species to guilds on the basis of shared prey–predator relationships and connecting the guilds that interacted trophically; (3) measuring the functional structures and modeling their dynamics using species-level networks and cascading extinction on graphs models; and (4) analyzing the results to understand the community evolution and identify tipping points that predict ecosystem collapse. Organismal expertise is needed in the reconstruction of paleo-food webs. The resulting comparisons of the paleocommunity stability and structure can help calibrate the timing and patterns of ecological changes during critical intervals in Earth history. This Protocol aims to enhance the utilization of ecological modeling in understanding the evolution of ancient ecosystems. The time required for the protocol is community size dependent — for example, ~5 months for communities containing ~1,000 species.

Key points

  • This Protocol provides detailed steps for reconstructing paleo-food webs using fossil data and modeling the stability and structures of these food webs to environmental disturbances using the cascading extinction on graphs model.

  • This approach can be used to identify tipping points of ecosystem collapse and is applicable to both events from the distant past and those from the present.

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Fig. 1: An overview of the food web modeling pipeline.
Fig. 2: Examples of metanetworks (guild-level food webs).
Fig. 3: Rarefaction analysis of number of species against number of guilds.
Fig. 4: NMDS ordinations of paleocommunities using Jaccard and Bray–Curtis distances.
Fig. 5: Trophic space variations of the PTB1, PTB2 and PTB3 mega-communities.
Fig. 6: Expected and observed losses of taxa of the PTB1, PTB2 and PTB3 paleocommunities.
Fig. 7: NTPs.
Fig. 8: Structural food web properties.
Fig. 9: Variation in nestedness among different communities.
Fig. 10: Variation in modularity among different communities.
Fig. 11: The CEG program data input screen and example plots showing perturbation magnitude versus secondary extinction.
Fig. 12: SELP and collapse threshold variations of 27 communities across the Permian–Triassic boundary in South China.

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Data availability

All the data52 used in this protocol are available via Open Science Framework (OSF) at: https://osf.io/fqg37/.

Code availability

All the code used in this protocol is available via Open Science Framework (OSF) at: https://proc.io/fqg37/. The code in this protocol has been peer-reviewed.

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Acknowledgements

This work was supported by grants from the National Key R&D Program of China (grant nos. 2022YFF0802900 and 2023YFF0806200), the National Natural Science Foundation of China (grant nos. 42377205, 41930322 and 92055212), and the US National Science Foundation (grant nos. 1714898, 1629776, 1336986 and 0530825). This is a contribution to the Theory of Hydrocarbon Enrichment under Multi-Spheric Interactions of the Earth (grant no. THEMSIE04010101).

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Authors and Affiliations

  1. State Key Laboratory of Geomicrobiology and Environmental Changes, China University of Geosciences, Wuhan, China

    Yuangeng Huang & Zhong-Qiang Chen

  2. Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, CA, USA

    Peter D. Roopnarine

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  1. Yuangeng Huang
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  2. Peter D. Roopnarine
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Contributions

Y.H. and P.R. developed the protocol. Y.H. and P.R. tested the protocol and provided feedback on improvements. Y.H. wrote an initial draft, which was then revised by all coauthors. P.R. and Z.-Q.C. supervised the software development process, manuscript writing and testing of the protocol and secured funding to support the project.

Corresponding author

Correspondence to Yuangeng Huang.

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Competing interests

The authors declare no competing interests.

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Peer review information

Nature Protocols thanks Kenneth Angielczyk, William Foster, Alycia Stigall and Carrie Tyler for their contribution to the peer review of this work.

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Key references

Huang, Y. et al. Curr. Biol. 33, 1059–1070 (2023): https://doi.org/10.1016/j.cub.2023.02.007

Huang, Y. et al. Proc. Roy. Soc. B. Biol. Sci. 288, 20210148 (2021): https://doi.org/10.1098/rspb.2021.0148

Roopnarine, P. et al. J. Vertebr. Paleontol. 37, 254–272 (2018): https://doi.org/10.1080/02724634.2018.1424714

Supplementary information

Supplementary Data 1

Fossil occurrences with their stratigraphic information.

Supplementary Data 2

The guild richness data for all communities.

Supplementary Data 3

Metanetwork matrix.

Supplementary Data 4

The matrix data used to generate the food web diagrams.

Supplementary Data 5

The data used for hypergeometric probability analysis.

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Huang, Y., Roopnarine, P.D. & Chen, ZQ. A modeling approach to quantify ecological dynamics and functional structures of paleocommunities. Nat Protoc (2025). https://doi.org/10.1038/s41596-025-01201-4

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