2025-L10 Multigenerational epigenetic consequences of pollution exposure in wild fish populations

Project highlights

Fieldwork to sample wild/semi-wild populations of freshwater fish

State-of-the-art epigenetic sequencing using Nanopore technology

“Real-world” application of findings through collaboration with the Angling Trust

Overview

Environmental insults such as pollution can cause transgenerational negative health outcomes in wild animal populations. Of particular concern are freshwater ecosystems, where 76% of species have experienced a decline since 1970 (WWF Living Planet Report 2014). Whilst mitigation strategies and policies are being put in place to reduce the impact of pollution, the consequences across generations have largely been ignored.

Epigenetic mechanisms, such as DNA methylation, can act as the causative agents, driving transgenerational health outcomes and/or act as a biomarker which can predict transgenerational health (Fig.1). Current research on pollution-induced epigenetic inheritance has focused on lab model systems – with limited applicability to “real-world” scenarios. This project will create a significant leap in this field by combining molecular epigenetics with natural population studies to understand the multigenerational impact of pollution exposure.

Specifically, this PhD will examine DNA methylation differences between fish populations from high and low pollution environments. Fish will then be reared for multiple generations in a controlled un-polluted environment to determine if there are heritable DNA methylation marks associated with historic pollution exposure. This will provide evidence for multigenerational effects of pollution exposure (or lack thereof) which will feed into regulatory policy.

Questions this project will address:

What is the epigenetic signature of high pollution exposure within individuals?

Can this signature be erased within individuals, if pollution is removed?

Is this signature heritable across generations even if the pollution is removed?

Fig.1: stress exposure in one individual may cause molecular changes which can be passed on to subsequent generations (Beal et al. 2018).

CENTA Flagship

This is a CENTA Flagship Project

Case funding

This project is suitable for CASE funding

Host

University of Leicester

Theme

Organisms and Ecosystems

Supervisors

Project investigator

Dr Hollie Marshall (Uni of Leicester: [email protected])

Co-investigators

Dr Emily Smith (Angling Trust: [email protected])

How to apply

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Methodology

Fieldwork: Fieldwork will be carried out with the Angling Trust and the Environment Agency to sample semi-wild populations of common roach (Rutilus rutilus) from high and low pollution lakes west of London. Non-invasive fin clips will be taken as tissue samples.

Experimental rearing: Captured individuals will be reared in semi-wild controlled conditions free of pollution. Post-acclimation fin clips will be taken and fin clips will also be taken from 1-2 subsequent generations.

Molecular lab work: DNA will be extracted from tissue samples and sequenced in-house using Nanopore technology. This will give both the genome and epigenome for all samples.

Bioinformatics: Genetic and epigenetic data will be analysed using custom pipelines to explore population genetics, population epigenetics and multigenerational epigenetics.

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.

You will also receive training in all aspects of the project. Specifically, partners from the Angling Trust and the Environment Agency will provide fieldwork and fish handling skills. The UoL supervisor is an expert in ecological epigenetics and will provide in-house training in the molecular wet-lab work and the bioinformatic analysis of data.

You will also be a member of the Centre for Environmental Health and Sustainability at UoL as well as the Applied Population Genomics group within the Department of Genetics, Genomics and Cancer Sciences. These groups offer a welcoming and positive research environment with opportunities for cross-disciplinary learning.

Partners and collaboration

You will work directly with the Angling Trust and the Environment Agency to carry out the fieldwork and experimental-rearing components of this project. In addition to this, you will carry out a 3-month placement with the Angling Trust towards the end of your PhD where you will have the opportunity to produce a White Paper on your findings. This document can be used to inform policy decisions around the impact of pollution on wild fish populations.

Further details

For any enquiries related to this project please contact Dr Hollie Marshall (Uni of Leicester: [email protected]). 

To apply to this project: 

You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2025.

You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.

Please submit your application and complete the host institution application process via: CENTA PhD Studentships | Postgraduate research | University of Leicester.  Please scroll to the bottom of the page and click on the “Apply Now” button.  The “How to apply” tab at the bottom of the page gives instructions on how to submit your completed CENTA Studentship Application Form 2025, your CV and your other supporting documents to your University of Leicester application. Please quote CENTA 2025-L10  when completing the application form.

Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025. 

Possible timeline

Year 1

What are the DNA methylation differences between populations exposed to high and low pollution? (Fieldwork to collect samples, molecular wet-lab work, bioinformatic analysis).

Year 2

Are these DNA methylation differences maintained within individuals when moved to unpolluted conditions? (Experimental hatchery rearing, molecular wet-lab work, bioinformatics).

Year 3

Are these DNA methylation differences maintained in subsequent generations even when the parents were moved to unpolluted conditions? (Experimental hatchery rearing, molecular wet-lab work, bioinformatics).