Modeling Stratigraphic Paleobiology in R

Introduction

Stratigraphic paleobiology is a methodological framework that applies physical stratigraphy - which includes event deposition, sequence-stratigraphic architecture, and sedimentary basin analysis - to the interpretation of the fossil record (Patzkowsky and Holland 2012; Holland, Patzkowsky, and Loughney 2024). The discipline is founded on the principle that the fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes, meaning that fossil occurrences are controlled not only by where organisms lived and when they evolved, but also by when and where sediment capable of preserving them accumulated (Holland and Patzkowsky 2015; Holland, Patzkowsky, and Loughney 2024). Because species are distributed along environmental gradients such as water depth, and because sequence-stratigraphic architecture systematically controls sediment deposition, first and last occurrences of fossil taxa cluster predictably at sequence boundaries, flooding surfaces, and surfaces of forced regression, even when no change in extinction or origination rate has occurred (Holland 2020, 1995).

Stratigraphic paleobiology has changed our understanding of mass extinctions: simulation studies and field tests (e.g. Italy’s Po Plain) demonstrated that what appeared to be sudden, stepwise extinction events may actually reflect long intervals of elevated extinction rate compressed by stratigraphic architecture into apparent clusters of last occurrences (Holland 2020; Holland and Patzkowsky 2015).

What do you need to do stratigraphic paleobiology?

The first studies focused on first and last occurrence data (e.g. Holland and Patzkowsky (2015); Nawrot et al. (2018); Hohmann (2021)), but subsequent research extended it to occurrences in bin (Jarochowska et al. 2018), diversity (Loughney et al. 2021), abundance (Danise and Holland 2017), trait value measurements (Hannisdal 2006; Hohmann et al. 2024) and assemblage composition (Belanger and Bapst 2023) - all types of data representing fossils or other variables stored in the physical geological record are potentially subject to stratigraphic paleobiology. Secondly, a representation of the stratigraphy is needed. This can be: lithofacies, systems tracts, estimates of depositional rate, or another class. Here we advocate for using an age-depth model and show how they can be used even when no data on absolute age is available.

Depositional systems

All depositional systems have their defining physical, chemical and biological processes; the same biological event will be preserved differently on a clastic shelf than on a carbonate shelf or in a river delta (Holland 2023). Much previous work focused on siliciclastic marine settings (Hannisdal 2006; Holland and Patzkowsky 1999, 2015) and some on terrestrial (Holland 2021, 2022) and mixed, cool-water carbonates (Scarponi et al. 2017; Nawrot et al. 2018). Also a transition between systems will have a strong effect on fossil preservation (Danise and Holland 2017). Here we will use tropical carbonate platforms (Hohmann et al. 2024), because the effects in them have been largely predicted, but not well tested yet. If you are interested in modeling a different depositional setting, please discuss with us and we may be able to point you to a suitable model.

Learning Objectives

By the end of this workshop, you will be able to

  1. build age-depth models to quantify stratigraphic incompleteness and hiatus distributions across depositional environments,

  2. simulate and analyze different modes of trait evolution (stasis, random walk, and Ornstein-Uhlenbeck processes) and identify how stratigraphy affects their expression in the fossil record,

  3. model ecological niche preferences and understand how environmental gradients control fossil abundance patterns, and

  4. simulate last occurrence data to recognize how stratigraphic phenomena like hiatuses and condensation surfaces can create artifactual “mass extinction” signals.

You will develop proficiency in using R’s pipe operator |> to build reproducible, modular analysis workflows that combine the StratPal and admtools packages.

Structure

The webpage and workshop is structured as follows:

  • Getting Started covers software dependencies, package installation and loading, and a brief introduction to the pipe operator in base R (10 min).

  • Stratigraphic Architectures provides an overview of the example stratigraphic architecture used in the workshop, and introduces age-depth models (45 min).

  • Trait Evolution explores how stratigraphic effects changes patterns of phenotypic evolution (45 min).

  • Event Data discusses how data such as fossil abundance or last occurrences are modified by ecological, taphonomic, and stratigraphic effects (45 min).

  • Advanced Topics covers miscellaneous topics, e.g., combining niche models with trait evolution, and modification of phylogenetic trees.

Contributing

Did you find a typo, a mistake, or do you thing some topics are not sufficiently covered? Please post your issue in the GitHub repo.

Funding

Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. European Union and European Research Council logos

References

Belanger, Christina, and David Bapst. 2023. “Simulating Our Ability to Accurately Detect Abrupt Changes in Assemblage-Based Paleoenvironmental Proxies.” Palaeontologia Electronica. https://doi.org/10.26879/1282.
Danise, Silvia, and Steven M. Holland. 2017. “Faunal Response to Sea-Level and Climate Change in a Short-Lived Seaway: Jurassic of the Western Interior, USA.” Edited by Roger Benson. Palaeontology 60 (2): 213–32. https://doi.org/10.1111/pala.12278.
Hannisdal, Bjarte. 2006. “Phenotypic Evolution in the Fossil Record: Numerical Experiments.” The Journal of Geology 114 (2): 133–53. https://doi.org/10.1086/499569.
Hohmann, Niklas. 2021. “Incorporating Information on Varying Sedimentation Rates into Paleontological Analyses.” PALAIOS 36 (2): 53–67. https://doi.org/10.2110/palo.2020.038.
Hohmann, Niklas, Joël R. Koelewijn, Peter Burgess, and Emilia Jarochowska. 2024. “Identification of the Mode of Evolution in Incomplete Carbonate Successions.” BMC Ecology and Evolution 24 (1): 113. https://doi.org/10.1186/s12862-024-02287-2.
Holland, Steven M. 1995. “The Stratigraphic Distribution of Fossils.” Paleobiology 21 (1): 92–109. https://doi.org/10.1017/s0094837300013099.
———. 2020. “The Stratigraphy of Mass Extinctions and Recoveries.” Annual Review of Earth and Planetary Sciences 48 (1): 75–97. https://doi.org/10.1146/annurev-earth-071719-054827.
———. 2021. “The Stratigraphic Paleobiology of Nonmarine Systems,” January. https://doi.org/10.1017/9781108881869.
———. 2022. “The Structure of the Nonmarine Fossil Record: Predictions from a Coupled Stratigraphicpaleoecological Model of a Coastal Basin.” Paleobiology 48 (3): 372–96. https://doi.org/10.1017/pab.2022.5.
———. 2023. “The contrasting controls on the occurrence of fossils in marine and nonmarine systems.” Bollettino della Società Paleontologica Italiana 62 (1): 125. https://doi.org/10.4435/BSPI.2023.02.
Holland, Steven M., and Mark E. Patzkowsky. 1999. “Models for Simulating the Fossil Record.” Geology 27 (6): 491. https://doi.org/10.1130/0091-7613(1999)027<0491:mfstfr>2.3.co;2.
———. 2015. “The Stratigraphy of Mass Extinction.” Edited by Roger Benson. Palaeontology 58 (5): 903–24. https://doi.org/10.1111/pala.12188.
Holland, Steven M., Mark E. Patzkowsky, and Katharine M. Loughney. 2024. “Stratigraphic Paleobiology.” Paleobiology 51 (1): 44–61. https://doi.org/10.1017/pab.2024.2.
Jarochowska, Emilia, David C. Ray, Philipp Röstel, Graham Worton, and Axel Munnecke. 2018. “Harnessing Stratigraphic Bias at the Section Scale: Conodont Diversity in the Homerian (Silurian) of the Midland Platform, England.” Palaeontology 61 (1): 57–76. https://doi.org/10.1111/pala.12326.
Loughney, Katharine M., Catherine Badgley, Alireza Bahadori, William E. Holt, and E. Troy Rasbury. 2021. “Tectonic Influence on Cenozoic Mammal Richness and Sedimentation History of the Basin and Range, Western North America.” Science Advances 7 (45). https://doi.org/10.1126/sciadv.abh4470.
Nawrot, Rafał, Daniele Scarponi, Michele Azzarone, Troy A. Dexter, Kristopher M. Kusnerik, Jacalyn M. Wittmer, Alessandro Amorosi, and Michał Kowalewski. 2018. “Stratigraphic Signatures of Mass Extinctions: Ecological and Sedimentary Determinants.” Proceedings of the Royal Society B: Biological Sciences 285 (1886): 20181191. https://doi.org/10.1098/rspb.2018.1191.
Patzkowsky, Mark E, and Steven M. Holland. 2012. Stratigraphic Paleobiology: Understanding the Distribution of Fossil Taxa in Time and Space. University of Chicago Press.
Scarponi, Daniele, Michele Azzarone, Kristopher Kusnerik, Alessandro Amorosi, Kevin M. Bohacs, Tina M. Drexler, and Michał Kowalewski. 2017. “Systematic Vertical and Lateral Changes in Quality and Time Resolution of the Macrofossil Record: Insights from Holocene Transgressive Deposits, Po Coastal Plain, Italy.” Marine and Petroleum Geology 87 (November): 128–36. https://doi.org/10.1016/j.marpetgeo.2017.03.031.