What were the trophic consequences of the extinction of the largest apex predator of all time?


We know the decline of apex predators can lead to catastrophic impacts on ecosystems which have severe knock-on effects for society (O’Bryan et al. 2018). That is because apex predators feed upon dominant species, thereby reducing consumer pressure on organisms at the base of the food web (Bruno & O’Connor 2005). As such, apex predators can influence community structure via cascading effects. Although the effects of the decline of apex predators on food webs have been observed and studied on current timescales (e.g. Estes et al. 2011), it is currently unknown how their actual extinctions will influence community structure in the world’s oceans. This lack of knowledge is due to the fact that we have not yet experienced the complete extinction of any marine top predator. As such, the only way we can study the trophic consequences of the extinction of apex predators is by the the fossil record. For instance, the largest marine predator ever to swim the ocean, the Megalodon, became extinct in the Pliocene epoch, around 3 million years ago. How did this extinction affect marine community structure and how these effects were dispersed amongst different trophic levels?

During the Pliocene, the giant shark Megalodon became extinct along with 36% of the marine “megafauna”, which included species of sharks, marine mammals and sea turtles (Pimiento et al. 2017). These extinctions have been associated with increase climatic variability and sea-level oscillations as the Earth plunged into the glacial cyclity of the Pleistocene ice ages, leading to the loss of productive coastal habitats. The extinction was felt most keenly amongst large, homeothermic megafauna (e.g. “Megalodon” and ancient whales) with high energy requirements as competition for resources within broad ecological guilds increased has habitat space contracted (Pimiento et al. 2017) although losses have also been noted amongst the zooplankton and phytoplankton.

The project

This project will investigate the effects of this previously overlooked global extinction event on marine food webs using a cutting-edge combination of macro- and microfossil data and ecological modelling techniques. The student will ask the following questions:

Was the megafaunal extinction at the end of the Pliocene driven by a “top-down” or “bottom up” trophic cascades?

It is not evident from observing diversity patterns of extinction rates through time whether extinction events are “top down” events, where top predators are victims of primary extinctions caused by environmental stressors, or “bottom up” events where primary extinctions, or population crashes, at the bottom of food webs cause cascading secondary extinction up through the trophic network. By reconstructing ancient food webs from fossil data, we can model various extinction scenarios which we can then compare to empirical data in the fossil record.

What were the short and long term effects of apex predator extinction in the Plio- Pleistocene oceans?

By comparing the trophic structure of marine communities from pre- and post-extinction intervals we can discover what the immediate effects of apex predator extinction were on ecosystem structure and stability. We can then track the ecological recovery of marine ecosystems through the subsequent Pleistocene and uncover whether any changes in ecosystem structure represent brief periods of instability in the immediate aftermath of the extinction event or whether the extinction resulted in a permanent regime shift in the marine realm.


The student will assemble meta-community assemblage data for marine macrofossil taxa for ecosystems either side of the Pliocene extinction event and then at intervals spanning into the Pleistocene. This will then be combined with detailed core records of phytoplanton (coccolithophores and diatoms) and zooplankton (planktic foraminifera) along with geochemical proxies which will provide abundance and productivity data to form the bottom two levels of the marine trophic ecosystem.


Plio-Pleistocene marine metacommunity food webs will be modelled using a combination of techniques, from inferential modelling using well defined palaeoecological traits (Fortune et al. 2020) to mechanistic foraging models (Beckerman et al. 2006; Petchey et al. 2009) that are highly effective at reconstructing the interactions between organisms and ecosystem structure in modern marine ecosystems (O’Gorman et al. 2019). The student will then employ well established techniques to instigate cascading secondary extinctions by triggering primary extinctions and/or population/productivity crashes at different levels of the trophic ecosystem.

Impact and Publications

This project will pioneer the use of well-developed ecological modelling techniques to address a long standing answered question in palaeobiology – are mass extinction largely top-down or bottom-up events? The project will also answer questions relevant to modern day ecology and conservation biology by detailing the short and long-term effects of apex predator loss in marine ecosystems. The work is easily divisible into publications that form consecutive chapters of the PhD thesis.

An excellent training and research environment

This interdisciplinary project will provide the successful PhD candidate with highly valued and sought-after tools for investigating macroecological and macroevolutionary processes. The student will gain experience and expertise in database construction, ecological modelling, and macroevolutionary modelling. This will equip the student with the necessary expertise to become the next generation of palaeontological and ecological scientist, ready to carry out their own programme of innovative scientific research. The student will be based within the Earth Surface Science Institute (https://environment.leeds.ac.uk/earth-surface-science-institute) in the School of Earth and Environment at the University of Leeds and will benefit from working within and collaborating with dynamic scientists within the multidisciplinary Palaeo@Leeds (https://environment.leeds.ac.uk/earth-surface-science-institute/doc/palaeoleeds) group (Paul Wignall, Alan Haywood, Fiona Gill, Benjamin Mills) as well as the Pimiento Research Group (https://www.catalinapimiento.com) with members in the University of Zurich and Swansea University, and the quantitative evolutionary ecology group at Sheffield (Dylan Childs, Gavin Thomas, Phil Warren, Tom Webb). There will be opportunities to present results at major, international conferences, e.g. BES, GSA, PalAss, and attend residential summer-schools (e.g. in USA, UK) and in-house workshops and courses. CASE partner the Santa Fe Institute will provide funding for the student to travel to Santa Fe to attend the summer-school in complexity science and for residential trips to work with supervisor Jennifer Dunne.

Student profile

A good first degree (1 or high 2i), or a good Master’s degree in physical or biological sciences, mathematics or computer science with a focus towards ecology, palaeobiology, or evolutionary biology, experience in programming (e.g. R) is an advantage but not essential.


Beckerman AP, Petchey OL, and Warren PH. 2006. Foraging biology predicts food web complexity. Proceedings of the National Academy of Sciences 103:13745-13749.

Bruno JF, and O’Connor MI. 2005. Cascading effects of predator diversity and omnivory in a marine food web. Ecology Letters 8:1048-1056.

Fortune, IG, Allen, BJ, Shaw, JP, Pavey, T. Wignall, PB, Beckerman, AP and Dunhill, AM A marine meta-community food web reconstruction from the Kimmeridge Clay Formation (Upper Jurassic, Dorset, United Kingdom). In prep.

Estes, JE et al. 2011. Trophic Downgrading of Planet Earth. Science 333:301-306.

O’Bryan CJ, Braczkowski AR, Beyer HL, Carter NH, Watson JEM, and McDonald-Madden E. 2018. The contribution of predators and scavengers to human well-being. Nature Ecology & Evolution 2:229-236.

O’Gorman EJ, Petchey OL, Faulkner KJ, Gallo B, Gordon TAC, Neto-Cerejeira J, Ólafsson JS, Pichler DE, Thompson MSA, and Woodward G. 2019. A simple model predicts how warming simplifies wild food webs. Nature Climate Change 9:611-616.

Petchey OL, Beckerman AP, Riede JO, and Warren PH. 2008. Size, foraging, and food web structure. Proceedings of the National Academy of Sciences 105:4191-4196.

Pimiento C, Griffin JN, Clements CF, Silvestro D, Varela S, Uhen MD, and Jaramillo C. 2017. The Pliocene marine megafauna extinction and its impact on functional diversity. Nature Ecology & Evolution 1:1100-1106.