I am a bioinformatician and evolutionary biologist whose primary interests lie at the intersection of transposable elements (TEs), adaptation, comparative genomics, and big data.

TEs are DNA sequences with the ability to change their position within a host genome through a process called transposition. Through this, large blocks of DNA can be repositioned, or copied and relocated, within a host genome. This can profoundly alter host genomes, and it is likely that TEs have had significant impacts, with several examples of adaptive TEs being discovered across diverse species. For example, TEs are implicated in the evolution of the mammalian placenta, adaptive colour change in the peppered moth, and the evolution of insecticide resistance in aphid pests.

The dynamic nature of TEs can also lead to differences in TE content between individuals from the same species. This enables us to explore the potential adaptive roles of TEs by comparing populations of the same species found, for example, in different environments. Further, we can also explore TE evolutionary dynamics in this system to understand how they have persisted in host genomes over long evolutionary timescales, particularly as TE insertions are often deleterious and considered genomic parasites.

I am interested in exploring and characterising TE-host evolutionary dynamics across diverse species to evaluate the role of TEs as fundamental drivers of genome evolution. In essence, how important are TEs as a source of variation for their hosts? This is then broken down into several core questions that form the basis of my research:

i) What roles do TEs play in host adaptation to diverse environmental and evolutionary pressures?

ii) What factors govern the rate of successful TE insertion, and can the evolutionary outcomes of this activity be predicted?

iii) How often does TE activity provide a source of adaptive variation, and in which contexts is this potential likely to be recognised?

iv) What new tools and approaches can support the exploration of TE diversity and their evolutionary roles?

v) How can community-driven initiatives enhance the study of TEs and provide resources for researchers globally?

Currently, I am using Zymoseptoria tritici as a model to investigate TE variation among populations, with the aim of determining the impact of TEs on the rapid adaptation of Z. tritici during its spread across the globe, including the emergence of resistant phenotypes and changes enabling the pathogen to cope with climate challenges.

I am interested in the TE-host evolutionary dynamics that enable TEs to persist throughout evolution by characterising the factors that govern their success rates, including transposition activity, TE-host interactions, and subsequent impacts on host fitness. My interests in this area include uncovering the life-history traits that influence the TE landscape, the emergence and spread of adaptive TE insertions, and the frequency and success of horizontal TE transfer (HTT) as a mechanism of persistence.

Currently, I am using Zymoseptoria tritici as a model to investigate TE variation among populations, and to determine how TEs drive rapid adaptation in Z. tritici, particularly in the context of resistance evolution and climate resilience. As the amount of genomic data increases exponentially, big data approaches to its management and interrogation are required. I am leveraging large amounts of new sequencing data to develop methodologies to systematically explore TE-host evolutionary dynamics across the fungal kingdom, including determining rates of HTT and investigating how lifestyle influences TE content and vice versa. As information on the TE diversity in Fungi is also sparse, this dataset will provide a source of TE knowledge for the wider community. Beyond this, the approaches being developed will be developed in a flexible manner to be adopted in investigations concerned with other branches of the eukaryotic tree of life.

I continue to develop innovative bioinformatics tools, such as the Earl Grey TE annotation pipeline, designed to improve user-friendliness for non-specialists, as well as approaches to facilitate the study of adaptive TEs. I am invested in improving TE annotation and classification. Beyond providing new consensus sequences for a broad selection of non-model species, I am actively developing novel approaches to solve this widely-applicable problem leveraging emerging technologies including large language models (LLMs), and associated ML approaches. As an active member of the TEhub consortium, I contribute to developing tools, resources, and best practices for the global TE research community.

I am currently an SNSF postdoctoral fellow working with Prof. Daniel Croll in the Laboratory of Evolutionary Genetics at Université de Neuchâtel, Switzerland. I received my PhD in Evolutionary Genetics with Dr. Alex Hayward at the University of Exeter in 2022, where I was supported by the BBSRC SWBio Doctoral Training Partnership.

For more information on TEs, the TE community, and tools to facilitate studies on TEs, check out the TE Hub.

Current Appointments

Editorial Board Member - BMC Genomics