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Disentangling ecological and taphonomic signals in ancient food webs


Shaw, Jack et al. (2020), Disentangling ecological and taphonomic signals in ancient food webs, Dryad, Dataset,


Analyses of ancient food webs reveal important paleoecological processes and responses to a range of perturbations throughout Earth’s history, such as climate change. These responses can inform our forecasts of future biotic responses to similar perturbations. However, previous analyses of ancient food webs rarely accounted for key differences between modern and ancient community data, particularly selective loss of soft-bodied taxa during fossilization. To consider how fossilization impacts inferences of ancient community structure we (1) analyzed node-level attributes to identify correlations between ecological roles and fossilization potential and (2) applied selective information loss procedures to food web data for extant systems. We found that selective loss of soft-bodied organisms has predictable effects on the trophic structure of “artificially fossilized” food webs, because these organisms occupy unique, consistent food web positions. Fossilized food webs misleadingly appear less stable (i.e., more prone to trophic cascades), with less predation and an overrepresentation of generalist consumers. We also found that ecological differences between soft- and hard-bodied taxa—indicated by distinct positions in modern food webs—are recorded in an Early Eocene web, but not in Cambrian webs. This suggests that ecological differences between the groups have existed for ≥ 48 million years. Our results indicate that accounting for soft-bodied taxa is vital for accurate depictions of ancient food webs. However, the consistency of information loss trends across the analyzed food webs means it is possible to predict how the selective loss of soft-bodied taxa affects food web metrics, which can permit better modeling of ancient communities.


We analyzed food webs for four modern marine systems, one modern freshwater system, two ancient marine systems, and one ancient lake system from previous publications. All webs have similar, broad higher-rank taxonomic compositions and contain at least 85 nodes (the size of the smallest ancient network considered). For comparisons with ancient diversity, we downloaded fossil occurrences from the Paleobiology Database (PBDB) on 17th January 2020. 

Usage Notes

Repository Contents:

Supplementary Information: Containing Supplementary Text, Figures, Tables, and Data descriptions.  

Supplementary Data 1: Food web data (adjacency matrices and metadata; see publication; see Related Works).

Supplementary Data 2: Additional references consulted for preservation group assignments.

Supplementary Data 3: Data and R scripts to recreate analyses from this study.

  • S3_AllWebTaxonomy_updated_200903.csv: Taxonomy data for all food web nodes.
  • S3_AnalysisOfTaxonomicRanks.csv: Lowest taxonomic rank for each node.
  • S3_MainFigures_CaimanComparison.R: Compare the three food webs contained in (Roopnarine and Hertog 2013).
  • S3_MainFigures_ComparisonFunctions.R: Functions for calculating metrics and generating trophic species webs.
  • S3_MainFigures_FossilizationFunctions.R: Functions for artificially fossilizing networks.
  • S3_MainFigures_Setup_200826.R: Setup to import food webs.
  • S3_MainFigures_Code.R: Code to apply functions.
  • S3_pbdb_data_200504.csv: Data from the Paleobiology Database, excluding Lagerstätten (see publication).

S3_PresGrAssignments_updated_200902.csv: Preservation group assignments for all nodes.

Fossil faunal lists were downloaded from the PBDB on 17th January 2020. Any data processing steps are shown in R Scripts and described in publication. Paleobiology Database is licensed under a CC BY 4.0 International License.


National Science Foundation, Award: DGE-1632976