PhD student in Animal and Plant Sciences


This page has information for you about PhD opportunities currently available in Animal and Plant Sciences. Most funded PhD opportunities in Animal and Plant Sciences are available through one of the Centres for Doctoral Training that our staff contribute to. Visit the webpages given below to find out more about each Centre's projects.

Other PhD projects that are not part of a Centre for Doctoral Training are also listed below. Click on a project title to find out more. Some of these projects come with funding to cover your tuition fees and living expenses, but they may not be available to students from outside the UK or the European Union.

If you are from outside the UK or the EU and you are interested in a PhD in Animal and Plant Sciences, please fill in our postgraduate enquiry form for international students.

Postgraduate enquiry form

If you are applying for a project that does not come with funding, there may be other ways for you to fund your PhD. We also accept applications from students who are able to fund themselves.

Funding your PhD

It is a good idea to contact the supervisor of any PhD opportunity you want to apply for, before you submit your application. If the project you want to apply for does not come with funding, they may also be able to advise you on other sources of funding.

Once you have identified a project, a supervisor and a source of funding, you can complete the University's Postgraduate online application form.

Postgraduate online application form

Centres for Doctoral Training

Adapting to the Challenges of a Changing Environment
– UK and EU applicants only

Grantham Centre for Sustainable Futures
– UK, EU and international applicants

Leverhulme Centre for Advanced Biological Modelling
– UK, EU and international applicants

Leverhulme Centre for Climate Change Mitigation – coming soon

Do you have your own idea for a project?

To find a potential supervisor, visit our research grouping's webpage. Contact a member of academic staff to find out about PhD opportunities in their area.

Research groupings

Effects of sludge-rainfall interactions on soil quality and wheat production

Supervisors: Professor Jonathan Leake; Dr James Chong, University of York

Closing Date for Applications - 2nd January 2017

To determine the effects of sludge application to agricultural land interacting with heavy rainfall on the subsequent physical, chemical and biological functions of soil and its quality as determined by drought-resilience and productivity of winter wheat.

Novelty and timeliness
Loss of soil organic matter and degraded soil structure as a result of long-term arable farming practices in the UK have reduced the soil capacity to store water and nutrients, and has led to the crop yield plateaux seen over the past decade. Biosolid sludges can to help to increase soil organic matter content, sustainably recycle nutrients and increase the biological activity and functioning of soil organisms involved in generating improved soil structure. With increasing use of no-tillage versus conventional tillage in arable farming, there is an urgent need to better understand how surface applied sludge interacts with tillage systems under normal and excessive rainfall events. This project will determine how sludge applications and field management interact with effects of ambient versus excessive rainfall in determining the properties of arable soil, the productivity of wheat and its resilience to early summer drought. A particular focus of the work will be on the effects of sludge on organisms involved in generating macroaggregates in arable soils which are important for water, nutrient and carbon storage and good drainage.


  1. To compare winter wheat growth and crop health in response to sludge additions to plots from different tillage systems and exposed to simulated extreme rainfall events compared to control plots with ambient rainfall.
  2. To determine how simulated extreme rainfall events impact on the effects of surface-applied sludge in terms of soil water and nutrient-holding, water-stable aggregate size distributions, organic matter, microbial populations and other soil qualities that effect plant performance and soil functioning.
  3. To determine how sludge applications to land under no tillage and conventional tillage affect soil water-holding capacity during the growing season and how excess rainfall impacts the incorporation of sludge into soil and the crop resilience to spring/ summer dry periods.

Resource and facilities available
The student will be based in the Department of Animal and Plant Sciences (APS) at the University of Sheffield where there are excellent facilities for analysis of crop and soil samples, including ball-mills, vegetation mills, wet chemistry and elemental analysis (CN). Complementary facilities at the University of York include microbial community analyses and high-throughput next generation Illumina MiSeq and nanopore (MinION) sequencing, etc. The field component of the work will involve sampling from several farms that have used no-tillage for at least 3 years and at Leeds University Farm, which is near Tadcaster and where Prof. Leake has two major projects currently running involving the White Rose Sustainable Agriculture Consortium. There are basic laboratory and toilet facilities close to the fields used for the research, and a full time field technician to oversee experimental work.

BIOSAS White Rose Studentship Network (
This studentship is one of three linked studentships that form part of the Sustainable Agriculture: BIOchemical-physical-biological function of Sludge in Agriculture Soils (BIOSAS) programme funded by the White Rose Studentship Network. The other two studentships, based in Leeds and York respectively focus on 'Effects of sludge-rainfall interactions on soil quality and crop production' and 'Earthworms and water drainage – impacts of floods and sewage sludge amendments'. This network will provide the opportunity to understand the broader context of the individual projects and promote applications of this work. The network will meet frequently to allow cross-fertilisation of ideas between the individual projects.

This three-year studentship will be fully funded at Home/EU or international rates. All tuition fees will be paid together with an annual tax-free stipend at the standard RCUK rate (£14,296 for 2016/17, to be confirmed for future years but typically increases annually in line with inflation) and research costs. Applicants should hold at least an upper second UK honours degree or equivalent in any relevant science discipline.

BBSRC iCASE PhD: The Mechanism of Cell Cycle Repression in Tubers

Supervisors:  Prof Andrew Fleming; Dr Lisa Smith

Closing Date for Applications - 4th January 2017

To allow potato storage and supply throughout the year, sprouting of tubers post-harvest must be suppressed. Sprouting is controlled predominantly through application of chloropropham (CIPC), however despite its commercial use for over fifty years remarkably little is known about how CIPC actually works. Disruption of the cell cycle is thought to result in abnormal placement of new cell walls, therefore stopping growth of the sprouts. Although cell division in plants and animals clearly share commonalities, a portion of the accessory machinery is kingdom specific. CIPC presumably targets some aspect of plant-specific cytokinesis (since CIPC effects on animal cells are minimal). Identification of these target processes will provide an insight into the plant cell cycle and how CIPC works, as well as identifying the part of the plant cell division machinery that is amenable to targeting for novel sprout suppressors. The use of CIPC is becoming seriously restricted as a result of new government guidelines. Consequently, the characterisation of alternative sprouting inhibitors is of existential importance for this industry. This project aims to provide fundamental knowledge on the mechanism of how CIPC influences the plant cell cycle and, as a result, identify potential new targets for controlling tuber sprouting.

The project will combine targeted RNAseq analysis of meristems (van Campen et al (2016) Plant Physiology 170:1655-1674) with the use of a functional screen to identify mutants with abnormal cellular responses to CIPC. Target validation will involve both analysis of tubers with known differential response to sprout suppressors and the testing of gene function in tubers.
The iCase partner, AHDB Potatoes, is a division of the Agriculture & Horticulture Development Board and is committed to making the potato industry (which has UK farm gate value c £1bn, c £4bn consumer value) more competitive and sustainable through factual, evidence-based advice, information and activity ( The student will undergo training with AHDB during the studentship, gaining an insight into the research and advisory role that the body plays in supporting a key sector of the UK food industry. In addition, the student will have access to the broad scope of training possibilities of the BBSRC White Rose DTP (, providing a fantastic opportunity to complement the specific skills developed in the research project.

The successful candidate will have a strong background in plant molecular, cell and developmental biology, preferably combined with an interest in the translation of this knowledge to agriculture. Sheffield provides an outstanding environment for the project (ranked in top 5 for Biological Sciences in REF2014), with one of the largest and most vibrant university-based plant science research communities in the UK. You will join an integrated group working on various aspects of cell division, growth and development with a supervisory team consisting of Andrew Fleming and Lisa Smith.
See our lab pages for an overview of what we do:
For further information, contact Andrew Fleming ( or Lisa Smith (

Funding Notes
This iCASE PhD project has been approved for funding by the BBSRC-White Rose Doctoral Training Program on “Mechanistic Biology”. It is a 4 yr PhD studentship with full funding for UK students and those who fulfill residency requirements, with part-funding possible for other EU nationals. Candidates will be invited for interview on a rolling basis until the position is filled.

BBSRC White Rose DTP- The Mechanism of Stomatal Function

Supervisors: Prof Andrew Fleming; Prof Julie Gray

Closing Date for Applications - 4th January 2017

Stomata consist of pairs of guard cells which change their shape as a result of altered internal pressure, leading to the opening/closing of pores to allow gas exchange essential for plant life. The dynamics of this shape change depend upon mechanical interaction of the guard cells with the surrounding epidermis, however most work in this area has focussed on guard cells, ignoring the adjacent cells. The overall aim of the project is to investigate the role of the epidermis in setting the mechanics of stomatal opening/closure.

You will: characterise epidermal support cells to identify genes encoding cell wall modifying proteins expressed in these cells; create transgenic plants in which expression of these genes is altered to modulate support cell mechanics; investigate the outcome of altered support cell mechanics on stomatal function and its consequence for plant water use efficiency. Using this knowledge, is it possible to engineer stomatal complexes to improve plant performance under future climate conditions of elevated carbon dioxide and restricted water availability?

The project brings together molecular genetics, mechanics and physiology in the investigation of a specialised plant cell type. It is timely and novel, building on recent advances made by our group (Amsbury et al. 2016 Current Biology, in press). You will gain knowledge from three different research areas (stomatal biology, cell wall structure/function and mechanics), providing an excellent PhD training opportunity in an interdisciplinary project.

The successful candidate will have a strong background in plant molecular, cell and developmental biology, preferably combined with an interest in plant cell walls and mechanics. Sheffield provides an outstanding environment for research (ranked in top 5 for Biological Sciences in REF2014), with one of the largest and most vibrant university-based plant science research communities in the UK. You will join a group working on various aspects of leaf/stomata structure/function with a supervisory team consisting of Andrew Fleming and Julie Gray. We have a strong track record of PhD publication in this area (Plant Physiology (2016) 170: 1655-1674; Development (2016) 143: 3306-3314; Current Biology (2016) in press) and seek an excellent student to join our team.
See our lab pages for an overview of what we do:
For further information, contact Andrew Fleming ( or Julie Gray (

Funding Notes
This PhD project has been approved for funding by the BBSRC-White Rose Doctoral Training Program on “Mechanistic Biology” and is available now. It is a 4 yr PhD studentship with full funding for UK students and those who fulfill residency requirements, with part-funding possible for other EU nationals. The DTP provides a range of excellent training activities, as well as the opportunity for placements during the PhD ( Candidates will be invited for interview on a rolling basis until the position is filled.

 Linking metabolomics and metagenomics to resolve plant-microbial interactions involved in soil aggregation and carbon storage

BBSRC White Rose Mechanistic Biology DTP

Supervisors; Professor Jonathan Leake, University of Sheffield; Dr Thorunn Helgason, University of York

Closing date for Applications: 9 January 2017

Four year PhD on plant-microbe-soil interactions: Maintaining healthy and productive soils is essential for global food security. Plant-microbial interactions play a major role in the formation of soil macroaggregates (>500 µm diameter soil crumbs) that store carbon, nutrients and water and are essential components of most high quality arable soils. Conventional intensive arable cropping has decreased the abundance of macroaggregates, increasing the risks of crop yields being limited by drought and flooding, and soil being eroded (Blankinship et al.,2016, Geoderma). Crops and their associated soil microbial populations differ in the extent to which they support soil aggregation, amongst the best being short-term grassland (leys) containing a mixture of grass and clover. Although soil aggregation is known to involve interactions between plant roots, soil microorganisms, and organic molecules, the mechanisms remain poorly understood, constraining our abilities to restore these degraded but critical components of arable soil structure through targeted crop-breeding and changes to land management.

Objectives: Using grass-clover ley plots planted in 2015 in replicated arable fields that continue to be conventionally managed, the research student will combine the use of metagenomic analyses of soil microbial communities with metabolomic ‘fingerprinting’ and total organic carbon measurements in soil aggregates of different sizes. These studies will seek to simultaneously resolve the co-dependence of root-associated microbial communities and metabolites increasing macroaggregate formation and soil carbon storage in leys compared to arable fields. Our proof-of concept studies reveal important differences in metabolites in soil aggregates from arable land compared to unploughed field margins, and our leys improve soil aggregation, and increase soil water storage by 10%.

Novelty and Timeliness: The project seeks to resolve the mechanistic basis of plant-microbial community and interactions and effects of their metabolites driving soil aggregation and how leys differ from arable land in these processes and outcomes. The project benefits from access to a new portable mass-spectrometer, enabling rapid analysis of metabolites immediately on soil sampling, complemented by a wide range of specialist mass-spectrometry facilities including stable isotope (13C, 15N) and high throughput lipid analysis using Ultra Performance Convergence Chromatography (UPC2). These are complemented by the high-throughput next generation Illumina MiSeq and nanopore (MinION) sequencing facilities at the University of York, together with bioinformatics pipelines for analysis developed in Dr Helgason’s lab. The project couples the application of these state-of-the-art ‘omics’ technologies from the scale of different sized soil aggregates through to the effects of changes in land management and crop rotations at field-scales to gain mechanistic understanding of how leys improve soil quality. The studentship will include a 3 month Professional Internship Placement away from the lab.

Agriculture, ecology and evolution

Supervisor: Professor Colin Osborne

Research in my group is broadly concerned with the evolution and ecological effects of physiological processes, with emphases on photosynthesis, water relations and growth. Applications for PhD study are welcomed in three particular research areas:

1) Evolution and ecology of C4 plants. Which genes are required for C4 photosynthesis and how have they evolved? Does C4 photosynthesis protect the hydraulic system from failure under water deficits and atmospheric CO2 depletion? How does C4 photosynthesis interact with plant adaptations to fire and drought? How have grasses from C3 and C4 lineages come to dominate ecosystems?

2) Diversity of physiological traits in wild plants. Why do some species grow faster than others? To what extent is growth influenced by physiological innovation, ecological adaptation and evolutionary history? What mechanisms underpin physiological trade-offs between photosynthesis and leaf morphology, and between plant growth and survival?

3) Crop domestication and weed evolution. Which characteristics differentiate crop progenitors from other wild species that were gathered during the Mesolithic but never domesticated? What role did unconscious selection play in crop domestication? How did have weeds evolved? Which physiological and morphological traits trade off against growth in crops, and to what extent has commercial breeding escaped these trade-offs?

Climate change and ecology

Supervisor: Dr Gareth Phoenix

PhD projects can be undertaken in the areas of ecosystem and plant responses to climate change in the UK and the Arctic, impacts of climate change on ecosystem carbon and nutrient cycling, and plant (including crop) nutrient acquisition.

Topics include the impacts of acute (extreme) climate change events, such as drought and heat waves, on UK upland and Arctic ecosystems, and comparing these impacts with those of chronic (trend) climate change. Such projects will include understanding inter-specific differences in plant response, and how individual species responses drive ecosystem responses. Such studies may lead to determining the direct and indirect (i.e. through changes in biodiversity) impacts on the capacity of ecosystems to sequester carbon or cycle nutrients. Impacts of pollutant atmospheric nitrogen deposition, as a single factor or as a modifying factor in climate change responses can also be studied.

Projects can also be undertaken in plant nutrient acquisition. Such studies may focus on how plants acquire non-inorganic nutrients (e.g. organic and mineral bound forms) from soils and how species differences in ability to acquire these nutrients may control biodiversity. Projects may also seek to understand how crop plants acquire natural soil sources of nutrients to reduce reliance on fertilizers.

Dangerous liaisons in the soil: how do orchids parasitise fungi?

Supervisor: Professor Duncan Cameron

Around 80 genera representing 10% of plant species, most of which are orchids, produce seeds that are so small that they do not have sufficient reserves to germinate underground unaided. Instead, these plants parasitise soil fungi which supply the developing seedling with carbon (C) and much of their mineral nutrient requirements (mycoheterotrophy). Mycoheterotrophy is essential for establishment of gametophytes and seedlings of many “lower” and “higher” land plants. Although a widespread and common strategy for recruitment employed by many of the worlds’ most rare and threatened plant species, including most orchids, virtually nothing is known about the mechanisms through which evolutionarily divergent plant taxa are able to parasitise fungi and how this strategy has evolved.

This PhD aims to resolve the identity of the main metabolites passing from fungus-to-plant in mycoheterotrophy, identify whether the major groups of mycoheterotrophic orchids exploit different metabolic pathways which are constrained by the biochemistry of C and N transport and metabolism and to resolve whether the abandonment of autotrophy completely in those species that retain the fully mycoheterotrophic condition beyond the seedling stage is underpinned by switching to fungal partners with a superior ability to supply carbohydrates rather than amino-compounds as C sources.

Eco-evolutionary dynamics

Supervisor: Dr Patrik Nosil

Research in the lab focuses on the interplay between ecology and evolution. For example, ecological factors such as habitat type, competition, predation, and community composition might affect the evolution of a species. However, evolution itself might affect the ecological properties of populations and communities, particularly if evolution affects key parameters such as the size of populations. Such associations between ecology and evolution have recently been brought under the umbrella of ‘eco-evolutionary dynamics’, and work in the lab can involve any type of research along these themes. Most work has focused on stick insects (genus Timema) in California, but other study systems are possible. A wide range of work is conducted in the lab, including fieldwork in California, field and lab experiments, cutting edge genomic methodologies, computational biology and theoretical modeling. The lab is funded by a European Research Council Grant and we work with multiple collaborating labs, ensuring all lab members are exposed to a wide range of techniques and expertise. The collective work conducted in the lab helps increase understanding of the role of ecology and evolution in affecting patterns of biological diversity.

Ecosystem services and urban ecology

Supervisor: Professor Philip Warren

Current research opportunities exist for projects on the landscape-scale determinants of biodiversity and ecosystem services, particularly in urban or wetland habitats. Topics of particular interest include: the use of ponds to increase ecosystem services, the potential for restoration of wetlands in managed landscapes, the visual and aesthetic benefits of urban greenspace, dispersal processes and biodiversity in urban areas, river restoration and management. These opportunities focus primarily on UK landscapes, but aim to develop general principles applicable to other situations. Projects may be field-based, use existing data sources, or could also involve using laboratory model ecosystems to test ideas experimentally.

Environmental change, biodiversity and ecosystems

Supervisor: Dr Karl Evans

Climate change and urban development are amongst the most important drivers of environmental change. There is insufficient understanding of their impacts on biodiversity and ecosystem services, and the precise mechanisms through which these impacts arise. Developing this mechanistic understanding is essential for predicting future impacts, assessing species’ vulnerability and designing effective conservation action to mitigate these impacts. My research group explores these issues using avian and botanical case studies with a combination of large scale (macro-ecological) techniques and intensive fieldwork that includes experimental manipulations. I welcome applications to tackle these issues as a PhD student within my research group, which currently consists of five PhD students and three post-docs.

Evolutionary biology

Supervisor: Dr Rhonda Snook

I am an evolutionary biologist working in two areas of research. Most of my work has addressed how interactions between the sexes influences the evolution of genes, cells (i.e. gametes), and behaviour, morphology and physiology of males and females. Such changes may impact how populations interact with each other and therefore this work is also relevant to speciation. I primarily use experimental evolution to study how changes in the interactions between sexes impacts evolutionary trajectories of populations. This assessment is made using a mix of traditional phenotypic assessments of evolutionary change with modern next generation sequencing projects to link the phenotype and genotype. New research areas include how genome structure may influence local adaptation, particularly along environmental gradients, and how such effects may impact response to climate change. In particular, I am interested in how chromosome inversion polymorphisms contribute to both local adaptation and speciation. Like my work on sexual selection, a variety of methods are employed to address these issues, including physiological performance tests and next generations sequencing. I welcome queries from motivated students who are passionate about evolutionary biology and I am open to discussing potential projects to identify shared research interests.

Evolutionary developmental biology

Supervisor: Dr Gareth Fraser

Dr Fraser's research is primarily focused on the developmental basis of craniofacial morphology. He is involved in a number of projects that are interested in understanding the expression and regulation of essential genetic components during the development of teeth and related structures. Dr. Fraser uses non-conventional vertebrate models to study novelty of form and development, he is particularly interested in models that provide alternative methods of discovering general insights into vertebrate biology. Currently he studies the formation and continued development of teeth in teleost (Lake Malawi cichlids and pufferfish) and cartilaginous fishes (i.e. sharks) in an attempt to provide a comparative framework to associate evolutionary changes among divergent vertebrate groups.

Freshwater ecology, pollution biology and ecotoxicology

Supervisor: Professor Lorraine Maltby

The human global population is predicted to reach 9 billion by 2050 and managing landscapes to provide the food, water, fuel, housing and other resources required by this growing population, whilst protecting the ecosystems that provide them, is a major challenge. In order to address this challenge we need to understand the impact of anthropogenic activities on freshwater ecosystems and their catchments. A major research aim is therefore to gain a mechanistic understanding of key ecosystem services and the ecological processes that underpin them, and to investigate how they are affected by anthropogenic inputs (e.g. pollution) and activities (e.g. land use). The output from this research is used to inform environmental decision making and to influence policy development and implementation.

Large-scale dynamics of marine biodiversity

Supervisor: Dr Tom Webb

Global databases of the occurrences, relationships, and biological characteristics of marine species offer us unprecedented opportunities to determine what structures patterns of marine biodiversity, and how stresses such as overexploitation and climate change are likely to affect marine ecosystems and the services we derive from them. Work in my group ( involves statistical and macroecological analysis of large marine biodiversity databases, in collaboration with various international data providers, to understand the fundamental dynamics of marine diversity in space and time. We are also very interested in how human activities, from fishing to renewable energy installations and designation of marine protected areas will affect these large-scale patterns.

Large scale patterns in diversity across the Tree of Life

Supervisor: Dr Gavin Thomas

My research addresses large-scale patterns in diversity across the Tree of Life, particularly (but not exclusively) in birds. Current works ask how natural and sexual selection influence the macroevolution of species traits and whether variation in the rate of trait evolution determines diversification (speciation minus extinction). This work frequently involves use of museum specimens coupled with building and analysing phylogenetic trees. I welcome enquiries from prospective students with interests in macroevolution and phylogenetic approaches to biodiversity science in any group of organisms.

Population biology

Supervisor: Dr Dylan Childs

Research in my lab addresses a diverse range of questions in population biology. We work with both plant and animal systems to tackle problems at the pure and applied ends of the spectrum. A core question that runs through much of this research is: How do environmental variation (e.g. climate) and among-individual differences shape population dynamics and natural selection? A range of quantitative methods (mathematical theory and statistics), long-term observational datasets and experimental microcosms underpin this research. Current questions that interest me include: What influences our ability to forecast population dynamics and extinction processes? Can we use dynamic energy budget theory to inform the development of more useful models of population processes? What determines the dynamics of weed populations and the evolution of herbicide resistance?

Students in my lab are trained in state-of-the-art methods of statistical analysis and modelling of populations. Projects can be undertaken in any area of theoretical or empirical population biology, and I am happy to support students interested in applied areas of research (e.g. developing data-informed management strategies of local populations). Students wishing to develop new field-studies in their home country should contact me to discuss their ideas before applying.

The biology of ageing

Supervisor: Dr Mirre Simons

One of the most intriguing and certain things about life is that it inevitably ends in death. Understanding how ageing causes physiological deterioration that leads to death and dysfunction has clear impact from a biomedical perspective: developing drugs or other interventions that can elongate healthy lifespan. From an evolutionary perspective ageing is interesting because it appears to reduce fitness, however multiple overlapping evolutionary theories of ageing can explain why ageing occurs. My lab studies ageing from both this biomedical, but also evolutionary perspective using the power of both approaches to understand the complex and physiological multifaceted nature of ageing. We use theory, meta-analysis, comparative work and empirical studies using the genetic toolkit available in fruit flies (Drosophila melanogaster). Our phenotype of choice is age-specific mortality rate, the chance an individual dies in the population at a specific age. Such demography of mortality is especially powerful because it reveals patterns of physiological ageing that are not apparent in conventional measures such as median lifespan. Death through ageing is as close to the elusive physiology of ageing as we can currently get, but close examination of high sample size demography of mortality is rarely exploited.

I encourage queries and applications from students with a quantitative mind-set and an interest in the biology of ageing. Practical experience with the model system we use is not a requirement. Please see below a range of specific topics, but note that I am always open to discuss other options.

Specific topics:

  • Evolutionary biology of ageing: developing and testing novel theory
  • The demography of cancer mortality towards a Drosophila model system
  • The functional genetics of the life extending effects of dietary restriction
  • TOR (target of rapamycin) signalling and lifespan: extending the signalling network using Drosophila
  • Testing Drosophila models of disease in an holistic ageing framework
The immunity of pest insects

Supervisor: Professor Michael Siva-Jothy

My laboratory has two decades experience of empirical studies of insect immune function in the context of their natural ecology. By examining how life-history and ecology impact on patterns of immune investment it is possible to identify ontogenetic stages, or ecological conditions that are associated with periods of vulnerability to natural pathogens. Our insect rearing facilities and laboratories are state-of-the-art and I am very happy to design research projects that meet the need of government-funded overseas PhD candidates in this broad general area.