Ecology and Evolution PhD research projects

Supervisor: Mayhew, Dr Peter J

The evolution of insect life histories and their effect on diversification (2015-16)

Our understanding of macroevolution forms the background against which current biodiversity change is assessed. The insects make up over half of all described macroscopic species, but most of our knowledge on comparative life history evolution, and its effect on diversification, comes from vertebrates. We aim to elucidate the broad pattern of evolutionary change in basic insect life history traits, their interactions with key innovations such as metamorphosis, and their effect on diversification, to help understand their diversity. We will:  develop a database of insect life history parameters and to populate it with published and original information from representatives of all major insect taxa; test, using recent Bayesian phylogenetic & comparative techniques, if the origin of metamorphosis is associated with directional shifts or changes in the rate of evolution in traits such as development time, body size, and fecundity; reveal the patterns of covariation among life history traits; test the association between life history traits and diversification across taxa in the insects. This will be the first broad assessment of life history evolution across the whole of the insects. The project is suitable for students with an interest in evolutionary ecology, insect biology and comparative biology.

Co directors - Rob Freckleton (Sheffield) and Nick Isaac (CEH)

Supervisor: Fogg, Dr Paul

PhD project that's currently available - The impact of gene transfer agents on bacterial evolution.

Supervisor: Jeffares, Dr Daniel

Self-funded PhD applications are welcome.


Supervisor: Ferrari, Dr Julia

Multiple beneficial symbionts – too much of a good thing? (2015-16)

All organisms face a multitude of environmental threats and have to adapt to overcome these challenges.  Many insects get help from an unexpected source – bacterial symbionts that live in their bodies.  These endosymbionts affect their host’s biology, from allowing the host insect to feed on unbalanced diets to protecting from extreme temperatures or natural enemies.  A newly acquired symbiont can rapidly spread through a population and alter the insects’ interactions with other species and the environment under suitable conditions. This can have undesirable consequences if the host insect is an agricultural pest.

Endosymbionts that confer ecologically important benefits are particularly well studied in aphids, where phenotypic effects are fairly well understood.  However, often multiple species of symbionts occur in the same aphid individual.  It is likely that these species compete for resources and the host might be overexploited as a consequence.  This project will elucidate how single and multiple infections of beneficial symbionts differ in their effect on the host’s ecology.  The student will have the opportunity to develop this project according to his/her interests; this might include investigating the competitive interactions within the aphid, assessing the effects on the wider ecological community, or a mechanistic understanding of the interactions.

Supervisor: Wood, Dr Jamie

Computational investigation of microbial communities involved in methane production (2015-16)

The overall goal is to better understand microbial fermentation technology with a view to developing a sustainable approach for producing energy and other valuable products from waste biomass. The project will use mathematical modelling and computational approaches to investigate the complex interactions that occur in complex microbial communities, especially metabolite cross-feeding. The long term goal is to optimise the breakdown of variable or defined feedstocks in anaerobic digestion (AD) systems and to be able to manipulate the yield of particular fermentation end products (eg. alcohols, acids, gases).

Applicants should have a good first degree in a relevant physical/mathematical science, some experience in computer programming and an interest in the application of mathematical approaches to biological systems.




Supervisor: Helgason, Dr Thorunn

Microbes and environmental change: the importance of interactions in maintaining ecosystem function (2015-16)

Applicants can develop projects based on communities of microbes relevant to ecology and ecosystem function. Many ecosystem processes, such as nutrient cycling, productivity and maintenance of biodiversity depend upon interactions with microbial populations. It is increasingly important that we understand the structure and function of microbial communities and how they respond to environmental change. The project will focus on one group of microbes which may include soil prokaryotes (e.g. methanogens) or arbuscular mycorrhizal fungi Using a combination of field sampling, manipulated experiments and advanced molecular ecology/bioinformatic techniques including next generation sequencing, the student will develop hypotheses and tests to further our understanding of these important processes.‌

Supervisor: Beale, Dr Colin

Modelling the abundance - distribution relationships (2015-16)

As global change impacts species a pressing question is how distribution shifts translate to abundance changes, yet complexities in the relationship between abundance and distribution make this difficult. Some species show abundance peaks at the range centre and a gradual decline towards the edge, others are abundant right up to their distribution limits. If we can understand these fundamental differences we should be able to make more accurate projections of the impacts of global change on abundance on biodiversity. Although we currently lack an understanding of these fundamental patterns, preliminary models suggest that a mechanistic approach linking birth and death rates to environmental variables can explain many of the observed patterns.

In this PhD you will use data on bird abundance and distribution in a variety of countries from UK to Tanzania to undertake statistical and theoretical models of abundance and distribution relationships at a range of spatial scales. This project will involve training in advanced Bayesian, spatially-explicit modelling methods, joining a team of graduates students and researcher at York that leads the field of spatial ecology and has a strong focus on conservation biology.

This opportunity is only available as a self-funded project and will appeal to numerate biologists.



Supervisor: Hartley, Professor Sue

Plant defence vs Insect defence: impacts of plant quality on insect immune systems (2015-16)

Insects defend themselves against pathogens and parasites with an immune system, but key aspects of insect immunity remain unknown, including how immune function is affected by diet. Insect herbivores often consume a diet low in protein and high in plant toxins; such a diet may compromise their immune system by reducing the resources that can be allocated to it. Many grasses, including vital crops such as rice and wheat, use silicon as a defence. Silicon reduces the ability of herbivores to digest protein, but the effect of this on their immune systems has not been tested. Silicon also increases the development time of insects, increasing their exposure to invasive enemies at a time when their immune systems may less effective.

This project aims to:

(i) Assess the impacts of silicon in the diet on the immune function of insect herbivores by rearing them on plants containing different amounts/types of silicon defences and their immune function.

(ii) Understand how silicon affects the vulnerability of different types of insect herbivores to parasitoid attack.

Strategies for compromising insect immunity could lead to the development of novel sustainable pest control methods, vital when climate change may increase the frequency and severity of pest outbreaks

Supervisor: Young, Professor J Peter W

Bioinformatic analysis of bacterial genome evolution (2015-16)

Bacterial genomes are relatively small in size but very varied in content and composition.  Public databases provide a huge and growing resource of bacterial genome data that has barely been mined to date, and we also have access to our own new data that require analysis before publication.  This opens up numerous possibilities for projects that use or develop bioinformatic tools for sequence analysis.  One possibility would be to seek to identify the highways for bacterial gene traffic by tracking the distribution of genes that have spread across many bacterial groups.  By comparing sequences, the pathways of transfer can be reconstructed, and evidence for selection may be detected.  A different project might explore the functional classes of genes in different locations in the genome – the core genome, genomic islands, plasmids, etc. – in order to understand how bacterial genomes are constructed and maintained in the face of constant rearrangement and environmental challenges.  Such projects require familiarity with computer programming and analysis languages such as Python and R, so a Masters degree in bioinformatics, or similar relevant experience, is normally a prerequisite.