PhD student in Animal and Plant Sciences

Projects

On this page you can find out about PhD opportunities currently available in Animal and Plant Sciences. Click on a project title below to find out more, or view funded PhD opportunities that are available through one of the Centres for Doctoral Training that our staff contribute to.

Some of the projects in the list below come with specific funding (eg, from a research council or Centre for Doctoral Training) to cover your tuition fees and living expenses. If you successfully apply for one of these projects, and you meet the eligibility requirements, you will be automatically awarded the funding. These projects are marked 'FUNDED' in the list below.

If a project does not come with specific funding, that does not mean that there is no funding available. You may be awarded a scholarship after you have submitted your application – let us know if you wish to be considered for a scholarship by including this in your application form. We also accept applications from students who are applying for funding separately, or have funding in place already.

You can find out about scholarships on the following webpage:

Once you have identified a potential project and supervisor, please complete the University's postgraduate online application form to apply. If you wish to be considered for a scholarship, you should state this in the form. You should also include any information you have about funding that you are applying for separately, or that you have in place already. It is a good idea to contact the supervisor of any PhD opportunity you want to apply for, before you submit your application.

Postgraduate online application form

Centres for Doctoral Training

Many funded PhD opportunities are available through the Centres for Doctoral Training or Doctoral Training Partnerships that our staff contribute to. Visit the webpages for these centres to find out more about their projects.

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?

Find a potential supervisor by visiting our research webpages. Contact a member of academic staff to find out about PhD opportunities in their area.

Research


Current projects:

The biogeographic consequences of sexual and natural selection - FUNDED

Supervisors: Dr Gavin Thomas (lead), Dr Nicola Nadeau, Dr Chris Cooney

Closing Date for Applications: 23rd February 2018

Start date: PhD may commence between 1st April and 30th September 2018

Funded by The Royal Society

Project Description: We are looking for an enthusiastic and motivated PhD student for a project The biogeographic consequences of sexual and natural selection. Ever since the 18th Century naturalist and explorer Alexander von Humboldt observed that the number of different species increased as he travelled towards the tropics, biologists and geographers have tried to explain the latitudinal diversity gradient. With increasing numbers of species, we also see a greater diversity of form and function. Why are there so many species in the tropics and how have they become so diverse in form and function? This PhD will address these questions from an evolutionary perspective and ask how the two Darwinian processes of natural and sexual selection can lead to tropical hotspots of biodiversity. Species traits that are under natural and sexual selection can directly affect how fast new species form (speciation, as seen in Darwin’s finches on the Galapagos). The same traits can also determine which species can live together in the same place: when competing for resources (food, habitats, mates) being too similar to other organisms can be a disadvantage. If species evolve different forms they are more likely to be able to co-occur. The key to understanding the diversity of species in the tropics might then be to understand if, how and why species traits evolve at different rates in different parts of the world. Possible directions of research include (i) mapping global distributions of diversity and rates of evolution of ecological and sexually selected traits, (ii) modelling geographic variation in the tempo and mode of divergence within geographic assemblages of species, and (iii) modelling the global variation in alpha and gamma diversity as a function of the rate and diversity of ecological and sexually selected traits

The project will combine macroevolutionary and macroecological analyses of citizen science generated global trait data bases for birds with computer-based modelling. The student will also become familiar with the use of natural history museum collection, and will acquire important computer and communication skills that are highly transferable. We welcome applications from all candidates with broad interests in ecology and evolution particularly from a “tree of life” perspective.

The project is funded by a Royal Society grant, and covers fees for UK or EU students, in addition to the stipend and research and travel costs.

Our research group at the University of Sheffield offers a vibrant scientific environment:
http://macroevolution.group.shef.ac.uk
http://nadeau-lab.group.shef.ac.uk
https://www.christophercooney.co.uk
http://www.projectplumage.org
http://www.markmybird.org

For informal inquiries, please contact Gavin Thomas (mailto:gavin.thomas@sheffield.ac.uk)

Next-generation comparative genomics of grasses - FUNDED

Supervisor: Dr Pascal- Antoine Cristin

Closing Date for Applications: 31st January 2018

Start date: 1st April 2018 or as soon as possible after that

Funded by The Royal Society

Project Description: We are looking for an enthusiastic PhD student for a project analysing the genomes of a number of grass species to address fundamental questions in evolutionary biology. Grasses are incredibly important, covering over 40% of Earth's terrestrial area and including many key economic crops. They are distributed from the tropics to the Arctic and dominate many of the ecosystems they are found in. However, little is known about the genomic mechanisms responsible for their diversity and success. We propose to generate genomic datasets for several species representing key evolutionary transitions, and analyse them with those publicly available, to study the drivers of genomic diversification and how these relate to adaptive phenotype shifts. There is an array of questions that can be addressed with this type of data, and the interests of the student will be taken into account. Possible research directions include (i) the long term dynamics of gene retention and losses following whole genome duplications, (ii) the role of positive selection during the adaptive diversification of grasses, (iii) the impact of hybridization on the spread of functional traits, and (iv) the genomic origins of novel physiological traits, such as C4 photosynthesis and cold tolerance.

The project will combine lab work with computer-based analyses of large genomic datasets, providing the student with key skills in genome analyses and evolutionary biology. The student will also become familiar with grasses, and will acquire important computer and communication skills that are highly transferable. Fieldwork to collect important taxa is possible. We welcome applications from all candidates interested to understand the impact of genomic processes on the evolution of organisms.

The project is funded by a Royal Society grant, and covers fees for UK or EU students, in addition to the stipend and research and travel costs.

Our research group at the University of Sheffield offers a vibrant scientific environment:

http://christinlab.group.shef.ac.uk/

For informal inquiries, please contact Pascal-Antoine Christin (p.christin@sheffield.ac.uk)

Identification and functional validation of effector genes in the parasitic weed Striga – FUNDED

Supervisors: Professors Julie Scholes and Roger Butlin (Department of Animal and Plant Sciences) and Dr Roy Chaudhuri (Department of Molecular Biology and Biotechnology) University of Sheffield.

Closing Date for Applications: 5th January 2018

4 year BBSRC studentship

Project Description: Striga species are root-invading parasitic weeds that devastate the yields of rain-fed rice, maize and sorghum across sub Saharan Africa. The UN considers Striga to be the major biotic constraint to cereal production, causing yield losses in excess of U$ 1 B annually and a major threat to food security. The use of crop cultivars resistant to these parasites is an important control strategy but their use is compromised by the potential for rapid evolution of virulence in the parasite.

In order to breed crops with durable resistance to Striga we need to understand the molecular genetic basis of host-parasite specificity, in particular, the nature of effector proteins secreted by the parasite that are recognised by the host, eliciting a resistant response or which suppress host defences leading to susceptibility. As part of ongoing BBSRC projects we have sequenced the genomes of S. hermonthica and S. asiatica and carried out an in silico prediction of secreted effectors. As part of a new GCRF project we are currently re-sequencing the genomes of many individuals of S. asiatica collected from rice cultivars in different regions of Madagascar. Together these resources open the way for an analysis of effector proteins in S. asiatica.

The aim of this studentship is to use a combination of bioinformatics, comparative genomic and molecular techniques, to identify and functionally validate, candidate effector genes in relation to their differing virulence profiles on rice cultivar from Madagascar. S/he will benefit from training in a variety of bioinformatics, genomics, comparative genomics and molecular analyses that are in considerable demand by academic and industrial employers.

Requirements: We welcome applications from students with first degrees (2.1 or higher) in Biology, Molecular Biology or Genetics. The applicant should have an interest in bioinformatics and a willingness to learn comparative genetic analyses.

To apply online see: https://www.sheffield.ac.uk/postgraduate/research/apply/applying

For further information contact Prof. Julie Scholes (j.scholes@sheffield.ac.uk)

Promoting microbial nitrogen cycling to improve crop nitrogen availability – FUNDED

Supervisors: Tim Daniell, Julie Gray and Duncan Cameron

Closing Date for Applications: 5 January 2018

Funding covers:
(i) a tax-free stipend at the standard Research Council rate (~£14-£15K, to be confirmed for 2018) for up to 4 years
(ii) research costs, and
(iii) tuition fees at the UK/EU rate for up to 4 years

Studentships are available to UK and EU students who meet the UK residency requirements. Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award. Further information on eligibility http://www.bbsrc.ac.uk/documents/studentship-eligibility-pdf/

Requirements: At least a 2:1 honours degree, or equivalent. There are language requirements for international students.

Modern agriculture relies on substantial additions of nitrogen fertilisers. Rising energy costs and downstream environmental damage, including greenhouse gas emissions, mean that to improve agricultural sustainability we need to find ways to use this resource more efficiently reducing environmental impacts. Recent work demonstrates an opportunity to use the crop plant to manipulate soil nitrogen cycling although the underlying biochemical mechanisms remain largely obscure. This exciting project aims to use stomatal mutants that vary in their preference for ammonium and nitrate update to dissect the fine scale mechanisms driving the plants manipulation of the soil community. The project will develop skills in plant and microbiological molecular biology as well as metabolomics skills required for exudate chemistry analysis. This will place the student in an enviable position to aid the development of the growing area of science exploring agricultural sustainability.

The project is a competitive studentship based at the University of Sheffield funded as part of the BBSRC DTP White Rose Studentship Network in Agri-tech / Agri-science which builds on the excellent track records of the Universities of Leeds (The Faculties of Biological Sciences and Maths and Physical Science), Sheffield (Faculty of Science) and York (Departments of Biology and Chemistry) as leading centres of research and training in molecular and cellular biosciences.

Informal enquiries to Tim Daniell t.j.daniell@sheffield.ac.uk

Application process: Please apply using the University of Sheffield's online application form http://www.shef.ac.uk/postgraduate/research/apply/applying

Diet and mTor signalling in ageing-related neurodegenerative disease – FUNDING PENDING

Supervisors: Dr Mirre Simons; Dr Sean Sweeney, University of York

Closing Date for Applications: 5 February 2018

Open to Home and EU applicants who meet residency requirements.

Please note that funding is pending.

Reducing food intake robustly increases lifespan in model organisms. When this data is extrapolated to humans, the predicted gain in healthy lifespan beats curing all stroke, diabetes, cancer and cardiac disease. Unfortunately, mechanisms of this diet effect have remained highly elusive. The mTor signalling network, able to also reliably extend longevity, is strongly modulated by diet. Yet, the longevity benefits of diet have so far been shown to be largely independent of mTor.

We have now identified in a Drosophila model of frontal temporal dementia that downregulation of a specific mTor signalling component negates any effect of diet on the disease phenotype. This opens up an exciting opportunity to investigate the intricate and important relationships between diet, ageing and mTor signalling using this in vivo disease-relevant model. You will use a wide range of genetic tools using powerful genetic high-throughput models to understand these intricate relationships. You will further integrate your findings into neuroscience by spending time in the Sweeney lab (York).

The work is multidisciplinary as it crosses boundaries between nutritional science, neuroscience and ageing research. The research environment is an ambitious group with a strong team spirit and with widely divergent skill sets from which you will benefit.

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 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 (www.sheffieldmeme.org) 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.