PhD Opportunities
This page details PhD projects of which we are aware. This list is by no means exhaustive and the institutions listed, and others, may well be offering additional projects. Further details for many of these projects are already available on institutional websites. For UK PhD programmes, note that application deadlines can be as early as January, and interviews usually take place during the period January-April.
This list relies on supervisors submitting details of their projects. If you are advertising a PhD currently, please submit it using the form linked below:
Early Miocene Atlantic–Mediterranean marine ecosystem change investigated through fossil fish remains and ecological modeling
The Early Miocene (23–17 Ma) was a period of global marine biotic change. However, many of its aspects remain unknown and understudied. The objectives of this thesis will be to: a) reconstruct the Atlantic and Mediterranean fish communities; b) place the detected fish biodiversity and fish paleoecological changes within the dynamic Early Miocene paleoclimatic, paleoceanographic and paleogeographic context; and c) investigate potential impacts on marine ecosystem structure.
The PhD student will be trained in paleontological, geochemical and ecological modelling methods. They will be incorporated in the iMARES research group of ICM-CSIC, and will collaborate closely with the Science Team of the IODP3 Expedition 505S ENIGMA.
The impact of death and decay on the early animal biosphere
The Ediacaran Period (~635–539 Ma) represents one of Earth's most crucial biosphere transitions, culminating in the emergence of complex animal life. Carbon cycling during this interval was markedly unstable, characterised by extreme isotopic excursions whose drivers remain poorly constrained. The emergence of widespread animal life, found in the fossil record as the Avalon assemblage would almost certainly influence organic carbon burial and carbon cycling. However, little is known about the extent and strength of the mechanistic biological processes that contributed to carbon cycling on a community level, and its this community level that biological and ecological processes act on, then scale up to macroecological levels. Understanding how these animals processed, exported, and/or changed organic matter type, distribution and cycling has direct bearing on our interpretation of the early animal biosphere, and on the interpretation of the atmospheric spectra of exoplanets.
This project will transform our understanding of Ediacaran carbon cycling by quantifying the influence of early animals on carbon flow, particularly the neglected ivesheadiomorphs of the Avalon assemblage. While understanding early animals is hampered by the paucity of analogues with modern animals, the exceptional, in-situ, census preservation of thousands of specimens enables robust quantitative community analyses, rarely applicable in the fossil record, to be used to test hypotheses about early animal life. Drawing on exceptional Newfoundland and southern England fossil localities, the student will focus on quantify the different ways that Avalonian animals could have changed carbon cycling, both when alive and when dead.
The student will conduct systematic fieldwork at key Avalon assemblage localities in Newfoundland (Mistaken Point, Ferryland) and Charnwood Forest, UK, to document ivesheadiomorph occurrences within their palaeocommunity context. Using high-resolution laser-scanning, photogrammetry and image analysis, they will produce quantitative census data on ivesheadiomorph morphology, size-frequency distributions, and spatial relationships with co-occurring Ediacaran taxa. These empirical data will then be used to build carbon flow models of the ecosystems, using agent based models to reconstruct how ivesheadiomorphs decomposed and what proportion of their biomass would have entered the sedimentary organic carbon pool. Together, this palaeobiological framework will allow robust estimates of standing biomass and carbon flux attributable to ivesheadiomorphs, forming the biological foundation from which their broader impact on Ediacaran carbon cycling can be evaluated.
Eco-evolutionary dynamics of early animals
Life has existed on Earth for more than 3.5 billion years, but it is only around 600 million years ago, during the Ediacaran time period (635 – 541 Ma), that animals appear in the rock record. It is during the Ediacaran animals evolved some of their most important traits: most obviously large body-size but also tissue-differentiation, mobility, bilateral symmetry and ecosystem engineering (reef-building). Over the last ten years, mathematical ecological approaches have demonstrated how previously elusive biological details can be extracted from the Ediacaran fossil record. This proposal will tap into the exceptionally rich biological information captured in the Ediacaran fossil record and use using mathematical models to investigate the underlying processes that drive the evolution of early animals.
This project will use theoretical models of Ediacaran communities to investigate taxa life-history traits and use these traits to develop dynamic models of Ediacaran eco-evolutionary dynamics to investigate how difference processes influence Ediacaran evolution. In contrast to modern marine systems, the oldest Ediacaran benthic organisms do not interact much with each other, i.e. resource competition, facilitation and mutualisms are relatively limited. Instead, reproductive dynamics appears key to Ediacaran life. Mechanistic models can be used to investigate these different processes, with the outputs compared to the available data to determine which models best reflect observed diversity patterns, and so which processes are key.
The student will have access to an extensive photographic and laser-scan data dataset of Ediacaran communities and use this data alongside existing analyses to document life-history traits such as reproductive modes and the strength and extent of environmental and competitive interactions within and between species within these communities. They will use this information to parameterise different types of models, and explore how changing different variables, such as the proportion of sexual to asexual reproduction, or the extent of resource competition, impacts speciation rates. The impact of these different processes on the origins of evolutionary innovations throughout the Ediacaran can also be explored.
How did the closure of the Tethys Ocean impact global marine biodiversity?
The closure of the Tethys Ocean during the Miocene represents one of the most profound reorganisations of Earth’s surface systems in the Cenozoic. Once a vast marine corridor linking the Indo-Pacific with the Atlantic and Mediterranean, the progressive narrowing and final disappearance of the Tethys dramatically altered ocean circulation, climate, and the dispersal opportunities available to marine organisms. While the geological processes of closure are increasingly well understood, its ecological and biogeographic consequences for global biodiversity remain less clearly resolved.
This PhD project will investigate how the restriction and closure of the Tethys Seaway shaped global marine biodiversity patterns, with a particular focus on dispersal and diversification dynamics. The research will ask: (1) How did changing gateway geometries influence dispersal pathways and connectivity among marine provinces? (2) Did diversification events coincided with key phases of seaway restriction? (3) Did biodiversity hotspots shift in response to declining connectivity? (4) How did coral assemblages reorganise ecologically in response to declining dispersal opportunities and habitat fragmentation?
Synthesis of fossil occurrence records will track how marine biodiversity changed through space and time in response to the closure of the Tethys Ocean. Dispersal modelling using palaeogeographic reconstructions and ocean circulation simulations will quantify potential connectivity between regions. Macroevolutionary analyses will test for links between seaway restriction and diversification pulses. Ecological comparisons across the Indo-Pacific, Mediterranean, Paratethys, and Atlantic will reveal how communities reorganised under declining connectivity. This research will provide new insights into how large-scale earth system changes reshape marine biodiversity.
Reducing uncertainty in the impact of climate on biodiversity
Background
Species distribution models (SDMs) aim to constrain the response and distribution of organisms to climate change. However, these models are built on ecological monitoring records spanning decades rather than the hundreds of thousands of years and broader climatic landscapes that species have persisted in. This means any model based on these records is highly overfit and the predicted response is biased to the current climatic window. SDM predictions therefore have previously unrecognised and unaccounted for uncertainties.
Palaeontology and historical ecology can address this, using fossil records, museum collections and archival data to extend baselines far beyond living memory. Advances in digitisation and AI-driven data extraction are now unlocking vast amounts of previously inaccessible “dark data”, enabling richer, longer-term ecological datasets. These deeper records can feed into ecological models to capture and reduce uncertainty in SDM predictions.
PhD Project
Marine ecosystems face escalating pressure from climate change, yet our ability to forecast their future is fundamentally limited by short-term datasets. This introduces unaccounted-for uncertainties into ecological models and limits their usefulness for informing policy.
This PhD will tackle this challenge by applying data mining to ‘dark data’, generating long-term datasets for two important marine groups, arthropods and corals. This will quantify and address unaccounted-for uncertainties in present ecological modelling approaches.
AI-based methods (e.g. text and image mining) will be developed and applied to extract ecological data from diverse sources at scale. This will be used to build robust ecological baselines spanning the Quaternary (last 2.5 million years), giving a long-term view of how these groups have responded to past environmental changes. This record exists scattered across historical survey reports, museum collections, and fossil archives but it is largely inaccessible, undigitised, or unstructured.
Uncertainty will be quantified by comparing predictions for datasets with and without long-term records. Evaluation of differences in prediction interval, extrapolation error, and hindcast skill against known climate transitions will validate the method and provide a framework that can be applied to risk projections for marine biodiversity and the ecosystem services they underpin across a range of taxonomic groups.
These baselines will feed into the development of new species distribution models, incorporating both taxonomic and functional ecology data, to generate improved, more confident predictions of how arthropods and corals will respond to future climate scenarios.
This project will be co-supervised by Dr Lewis A. Jones at the Natural History Museum, London, an expert in corals and ecological modelling, and provide access to large collections of material including modern, historical and fossil.
Applicant Profile
This project would suit students with a strong quantitative and computational background in a field such as environmental/Earth science, ecology, biology, palaeontology, computer science, or a related discipline. The student should be comfortable working with data in R or Python and keen to develop these skills further in an interdisciplinary research setting.
Essential is a genuine interest in applying data science and machine learning approaches to ecological and palaeontological questions. Prior experience in data analysis, statistics, or coding is highly desirable, as much of the project involves developing AI-driven tools to extract and analyse large, complex datasets.
No prior experience with fossils is required, though an interest in using the fossil record and deep-time perspectives to understand present-day biodiversity change would be an advantage. Similarly, a background in ecology (marine or otherwise) is welcome but not essential. What matters most is enthusiasm for combining ecological thinking with modern computational methods to answer questions about how species and ecosystems respond to environmental change over long timescales.
Bridging the taphonomic gap between the lab and the real world: Experimental Insights into Fossilization and Preservation
The fossil record provides the primary evidence for the evolutionary history of life, yet it is fundamentally shaped by post-mortem decay and preservation processes. Constrained experimental investigations of the processes of decay and decomposition have significantly advanced our understanding of fossilization and preservation. Making direct connections to interpretations of the fossil record can be challenging however because we don’t know how representative laboratory experiments are to real world conditions. Do the closed and rarefied conditions of in vitro decay experiments reflect the complexity of open, in vivo environments? This project will include a series of experiments to compare the anatomical and microbial processes of decay and decomposition observed in the laboratory and in the field. The results will inform interpretations and hypothesis of fossil preservation, provide a framework for scaling laboratory experiments to natural systems, and improve our understanding of how exceptional fossil deposits form. Together this will enable us to build of a general model of the processes of decay and fossilization and constrain experimentally informed interpretations of the fossil record and palaeontology. This inter disciplinary project will involve a combination of biological experiments, fieldwork, microbial and genetic techniques, and palaeontology. This project will make use of the dedicated taphonomy, microbial and analytical facilities and the University of Manchester and bring together expertise and training from palaeontology, archaeology and environmental microbiology.
More information about this opportunityThe early evolution of crocodylians and extinction selectivity across the end-Cretaceous mass extinction
Living crocodylians (alligators, caimans, gavials, true crocodiles) are the remnants of a diverse radiation, first appearing 100 million years ago. However, our understanding of their initial diversification is obscured by uncertainty in reconstructions of their early evolutionary relationships. For example, a recent study suggested that the Cretaceous giant, Deinosuchus, and the Cenozoic hyper-diverse genus, Diplocynodon, long-thought to represent early alligatoroids, in fact lie outside of Crocodylia. However, existing trees do not sufficiently sample taxa unequivocally outside of Crocodylia to robustly test the position of enigmatic taxa. Such uncertainty also affects assessments of extinction selectivity across the end-Cretaceous mass extinction, i.e. which lineages survived and what factors differentiated them from the victims.
Through first-hand study of specimens and the literature, the PhD student will produce an expanded phylogenetic dataset, improving sampling of early-diverging crocodylians and neosuchian crocodyliform species outside of this radiation. This dataset will be analysed to produce a new evolutionary tree that clarifies the relationships at the base of Crocodylia, including a more robust assessment of the placement of enigmatic taxa. The newly assembled tree will then be utilised to test for phylogenetic clustering of extinction and to determine whether ecomorphological and abiotic differences were key to survival versus extinction of crocodyliform lineages across the end-Cretaceous mass extinction. As part of this, the PhD student will test the hypothesis that traits associated with low survivorship at mass extinctions are not associated with higher extinction rates at other times, i.e. the ‘rules’ of extinction are not always the same.
The PhD candidate will join a diverse group of palaeontologists at UCL, with a large number of academic staff, postdoctoral researchers, and PhD students. They will receive training in vertebrate anatomy, virtual reconstruction of CT scan data, and phylogenetic and macroevolutionary analyses. They will also receive training in scientific writing, presentation, and open research practices. The PhD candidate will also be encouraged to attend external palaeontological/macroevolutionary training workshops.
The Rise of Vertebrate Apex Predators and the Ecological Origins of the Devonian Nekton Revolution
Project Summary
The Silurian and Devonian saw the rise of vertebrate predators, including the first jawed fishes, and may represent one of the most important ecological transitions in Earth history. Innovations such as jaws, teeth, enhanced locomotion, and increasing body size allowed vertebrates to occupy new trophic roles and potentially transform marine food webs. This interval has been described as the Devonian Nekton Revolution, during which active swimmers expanded into the water column, increasing trophic complexity and ecological connectivity. However, it remains unclear whether this was a discrete Devonian event or part of a longer-term ecological reorganisation extending across much of the Palaeozoic.
Crucially, vertebrates entered ecosystems already inhabited by large predators such as orthocone cephalopods and eurypterids. The key question is therefore whether vertebrates simply replaced existing apex predators or introduced fundamentally new predatory strategies, trophic interactions, and ecosystem functions that reshaped marine communities.
This project will investigate the origins and ecological impacts of vertebrate predation from the Late Ordovician to Carboniferous by integrating macroevolutionary analyses, food-web reconstruction, and functional palaeoecology. It will evaluate whether the diversification of vertebrate predators contributed to ecological escalation, influenced prey evolution, altered food-web structure, and changed the organisation and stability of marine ecosystems. More broadly, the project will assess the role of vertebrate innovations in major evolutionary transitions, bridging ecological processes associated with the Great Ordovician Biodiversification Event and later ecosystem restructuring events such as the Mesozoic Marine Revolution.
Research Questions
Did the diversification of vertebrate apex predators drive ecological escalation, reflected in the diversification of prey groups with defensive adaptations and turnover among incumbent predator guilds?
How did marine food-web structure and trophic network properties change during the rise of major vertebrate groups?
Did innovations associated with jaws, teeth, and feeding systems expand vertebrate functional diversity and generate novel trophic roles within marine ecosystems?
Objective 1: Diversification Dynamics and Ecosystem Turnover
A comprehensive Silurian-Carboniferous database of vertebrates, predators, and prey groups will be assembled to investigate diversity dynamics, origination and extinction rates, sampling-standardised richness patterns, and guild turnover. These analyses will test whether vertebrate diversification coincided with the radiation of prey groups, decline of incumbent invertebrate predators, and major changes in benthic communities, providing evidence for ecological escalation and ecosystem restructuring.
Objective 2: Reconstruction of Palaeozoic Food Webs
Marine food webs will be reconstructed from the Late Ordovician to Carboniferous using functional traits, body size, feeding morphology, phylogeny, and palaeoenvironmental information. Ecological network metrics, including connectance, trophic level, food-chain length, vulnerability, generality, and motif structure, will be used to test whether vertebrate diversification was associated with increasing trophic complexity, novel feeding strategies, and stronger coupling of pelagic and benthic ecosystems. The analyses will determine whether ecosystem change occurred abruptly during the Devonian or more gradually throughout the Palaeozoic.
Objective 3: Functional Evolution of Vertebrate Predation
Morphological and functional datasets will be used to quantify changes in vertebrate ecological roles through time. Analyses of functional disparity, morphospace occupation, ecological guild structure, and feeding adaptations will assess whether innovations such as jaws and teeth expanded trophic diversity, created novel predatory roles, and contributed to ecosystem-wide ecological restructuring.
Broader Significance and Training Environment
By integrating vertebrate evolution, food-web ecology, and macroevolutionary theory, this project will move beyond traditional taxonomic approaches to understand how evolutionary innovations reshape ecosystems. It will test whether the rise of vertebrate predators represents a discrete ecological revolution or part of a longer-term pattern of marine ecosystem transformation.
The PhD student will receive interdisciplinary training in palaeobiology, macroevolution, ecological network analysis, functional morphology, database construction, and quantitative modelling. Based within the DeepBio@Leeds group and collaborating with researchers at Leeds and Sheffield, the student will benefit from a supportive research environment, opportunities to present at major international conferences, and participation in specialist workshops and summer schools. The project is suitable for students with backgrounds in biological, physical, or quantitative sciences, with programming experience advantageous but not essential.
References
Blanco, F., Lazagabaster, I.A., Sanisidro, Ó., Bibi, F., Heckeberg, N.S., Ríos, M., Mennecart, B., Alberdi, M.T., Prado, J.L., Saarinen, J., Silvestro, D., Müller, J., Calatayud, J., & Cantalapiedra, J. L. (2025). Two major ecological shifts shaped 60 million years of ungulate faunal evolution. Nature Communications, 16(1), 4648.
Dunhill, A. M., Zarzyczny, K., Shaw, J. O., Atkinson, J. W., Little, C. T., & Beckerman, A. P. (2024). Extinction cascades, community collapse, and recovery across a Mesozoic hyperthermal event. Nature Communications, 15(1), 8599.
Janvier, P. (1996). Early Vertebrates. Oxford University Press.
Long, J. A. (2011). The Rise of Fishes: 500 Million Years of Evolution (2nd ed.). Johns Hopkins University Press.
Shaw, J.O., Dunhill, A.M., Beckerman, A.P., Dunne, J.A., Hull, P.M. A framework for reconstructing ancient food webs using functional trait data, BioRxiv, doi:https://doi.org/10.1101/2024.01.30.578036
Whalen C.D. and Briggs D.E.G. (2018). The Palaeozoic colonization of the water column and the rise of global nekton. Proc R Soc B Biol Sci. 285(1883):20180883. doi:10.1098/rspb.2018.0883
The origin of animals: Building a precise timeline from the geological record
Moulting animals (ecdysozoans) comprise over half of living animal species. The radiation of their constituent phyla – including arthropods, nematodes and priapulid worms – is a key component of the Cambrian ‘explosion’ half a billion years ago. The developmental trajectories and body plans defined in this radiation persist to this day, but the evolutionary processes behind this burst of innovation remain obscure.
Exceptionally preserved Cambrian fossils provide a direct window on the evolutionary steps that underpin the group’s immense morphological and taxonomic diversity. However, many key taxa remain incompletely characterised, and are difficult to place amidst the uncertain relationships of early ecdysozoans, thus hindering the determination of the origin and diversification processes of this major group of animals.
This project will use X-ray tomographic investigation to characterize the internal morphology of fossils from the earliest Cambrian. Insights from evolutionary developmental biology will inform morphological phylogenetic analysis, and thus place these fossils in the context of early ecdysozoan evolution. By integrating developmental and genomic information from extant taxa with new fossil evidence, alongside embryo fossils such as Markuelia, the project will investigate how key body-plan innovations emerged during the Cambrian radiation. The project will ultimately resolve the evolutionary and developmental processes that gave rise to morphological complexity and diversity in one of the most successful animal groups on Earth.
OVERSEAS APPLICATIONS due Monday 7th December 2026.