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

Illegal trading in animal products ranges from food substitution (e.g. the 2013 horse meat scandal), through to trafficking of high-value, CITES-protected, endangered species. Once stripped of species-specific morphological characters many products can only be identified by DNA testing. However, until recently this been costly and time-consuming, making it impractical for application in the field. Recent developments in third-generation DNA sequencing, the Oxford Nanopore Technologies (ONT) MinION, offer the possibility of affordable and portable DNA sequencing at a food processing plant or customs post, providing rapid confirmation of species of origin and the option to seize illegal products and detain traders. This project will ask if a universal species ID test suitable for field use can be developed and validated, in partnership with Twycross Zoo and collaborators at the Zoological Society of London (ZSL). Experiments will focus initially on preferential sequencing of mitochondrial DNA (mtDNA; molecular barcoding), using comparison with the BOLD & GenBank databases that already cover many species affected by illegal trade. Geographically, the focus will be on Mongolia, a key source and transit country for IWT, which is driving catastrophic declines across a broad spectrum of its wildlife populations. The student will gain a deep understanding of nanopore sequencing, novel targeted sequencing approaches and the development of sample preparation methods, as well as phylogenetic and evolutionary frameworks for data interpretation. They will learn about the role of science in conservation policy and the scenarios where a species identification test can play a vital role. The project will provide an opportunity to establish protocols that can be used as routine practice by non-scientists and to validate a test within a typical working environment.