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Simulating species: investigating the impact of biodiversity on the biosphere through deep time
Supervisor: Emily Mitchell, Department of Zoology
Co-supervisor: Euan Furness, Department of Zoology

Research proposal

The number of species of animal on Earth has changed extensively over the Phanerozoic (the last 539 million years). However, the mechanisms controlling this change are still debated, with a key hypothesis being that macroevolutionary patterns tend towards equilibria (a phenomenon called “density dependent diversification”), with perturbations from these equilibria (e.g. mass extinctions) being counteracted by changes in rates of speciation and/or extinction in the aftermath (Benson et al. 2016). However, an alternative hypothesis posits that these equilibria do not exist, or at the very least that they are not impactful, and that global species richness shows a pattern of gradual exponential growth (“density independent diversification”), dampened by extinction events (Benton & Emerson 2007, Cermeño et al. 2022). Density-dependence has usually been proposed to arise as a product of a negative relationship between population size and extinction risk (MacArthur & Wilson 1963). However, ecosystem engineering (the modification of the environment by organisms) also presents a plausible source of density dependence, as the extinction of ecosystem engineers could result in losses of other species that were dependent upon the engineered environment (Erwin 2008). 

Neither density-dependent nor density-independent diversification relies upon specific biological properties of the species that it models, and both make relatively few base assumptions. Consequently, these mechanisms are highly amenable to analysis using computer simulation systems. However, with relatively few exceptions (Alroy 2008), simulation studies have tended to simulate models at one extreme or the other of density dependence when, in reality, a variety of intermediate models, combining aspects of the two extremes, are plausible and, arguably, more likely. 

The LCLU internship student will construct a simulation model of biodiversity in the coding language of their choice, in the vein of the model of Alroy (2008). This model will include a number of parameters describing the degree and mechanisms of density dependence within the model, including the impact of density on abiotic factors (i.e. ecosystem engineering effects) and their feedbacks on diversity. The student will investigate how varying these parameters leads to variations in simulated biodiversity, speciation and extinction rates, and how these impact the abiotic environment. These variations will be compared with data drawn from the empirical fossil and geological record. 

The host team is experienced with programming in C++ and Python, and with using these programs to both handle data and model a range of biological phenomena, including change in diversity over geological time. Both hosts are members of the Department of Zoology, and are familiar with the biological underpinnings of the questions to be studied. 

The applicant must have a strong understanding of and interest in programming in at least one coding language, ideally python (although other languages are viable). The hosts will guide the student through any unfamiliar biological concepts; no previous biology experience is required. 


Alroy (2008) - Dynamics of origination and extinction in the marine fossil record. (See SI for model). 
Benson et al. (2016) - Near-stasis in the long-term diversification of Mesozoic tetrapods. 
Benton & Emerson (2007) - How did life become so diverse? The dynamics of diversification according to the fossil record and molecular phylogenetics. 
Cermeño et al. (2022) - Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots. 
Erwin (2008) - Macroevolution of ecosystem engineering, niche construction and diversity. 
MacArthur & Wilson (1963) – An equilibrium theory of insular zoogeography.