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Combating Illegal Trade in Animal Products by Rapid On-Site DNA Sequencing


Project Description

Illegal trading in animal products is commonplace, widespread and diverse, ranging from trafficking high-value, CITES-protected, endangered species between countries, fraudulent misidentification of by-catch fish filleted at sea (estimated at ~25%), through to substitution of low-value meat from one species into foodstuffs advertised as containing another (e.g. the 2013 horse meat scandal).

Once stripped of species-specific morphological characters many products can only be reliably identified by DNA testing, which has until now been costly and time-consuming, requiring both bulky specialist equipment and highly trained lab personnel. However, a recent development in third-generation DNA sequencing, the Oxford Nanopore Technologies (ONT) MinION, offers the possibility of affordable and portable DNA sequencing capacity at a customs post, quayside or food processing plant, providing rapid confirmation of species of origin and the option to seize illegal products and detain those trading in them on the spot.

We intend to develop and test a universal species ID test applicable to all these scenarios in partnership with the East Midlands Zoological Society (Twycross Zoo) and our collaborators at the Zoological Society of London (ZSL). ZSL has been working with the Mongolian Government to tackle the Illegal Wildlife Trade (IWT) since 2013, building law enforcement capacity and raising awareness within local communities. Mongolia is a key source and transit country for IWT, driving catastrophic declines across a broad spectrum of Mongolia’s wildlife populations, including most of their iconic medium and large-sized mammals. Unfortunately many of its frontline law enforcement officers are unable to identify seized wildlife products. This project will seek to trial the use of nanopore sequencing at key IWT border and market hotspots as a proof of concept to aid the rapid and accurate identification of (previously unidentifiable) wildlife products such as meat, fur and traditional medicine ingredients and in the long-term, establishing a chain-of-evidence to aid ultimate prosecution of illicit wildlife product smugglers. We will also explore the global issue of bushmeat, which threatens not only wild species but also human consumers exposed to pathogens borne by them (which can also be detected by nanopore sequencing).

The test will build upon methods we are currently developing with ONT to preferentially sequence mitochondrial DNA and compare results with the BOLD & GenBank databases of species-specific mtDNA sequences that already cover many species affected by illegal trade. The student will exploit a number of products planned for release next year to meet ONT’s declared aim of allowing “anyone to sequence anything, anywhere”. Twycross & ZSL will supply samples for DNA extraction and processing optimisation, and source reference samples from both the target and closely related species to evaluate accuracy in blind tests.

CAM, JHW & MAJ have expertise in the analysis of mitochondrial DNA, emerging sequencing technologies (including nanopore) and the application of fgenetics in forensic investigation. Twycross and ZSL have both contributed to scoping this proposal and their knowledge will be key to formulating the project plan, guiding the research and contributing to reports and publications arising from this project. ZSL will work with the student to trial the test in an enforcement setting in Mongolia (separate funding will be sought) and to develop awareness and training materials for their customs officials. We will publicise the research through outreach activities.

Entry requirements

Applicants are required to hold/or expect to obtain a UK Bachelor Degree 2:1 or better in a relevant subject. The University of Leicester English language requirements apply where applicable.

How to apply

Please refer to the CENTA Studentship application information on our website for details of how to apply.

As part of the application process you will need to:
• Complete a CENTA Funding form – to be uploaded to your PhD application
• Complete and submit your PhD application online. Indicate project CENTA2-GENE3-JOBL in the funding section.
• Complete an online project selection form Apply for CENTA2-GENE3-JOBL

Funding Notes

This studentship is one of a number of fully funded studentships available to the best UK and EU candidates available as part of the NERC DTP CENTA consortium. The award will provide tuition fees as the UK/EU rate and a stipend at the RCUK rates for a period of 3.5 years.

For more details of the CENTA consortium please see the CENTA website: View Website.

Applicants must meet requirements for both academic qualifications and residential eligibility: View Website

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