Developing non-invasive DNA sampling methods in African savannah elephants
Funded by Revive and Restore under the Catalyst Science Fund, I have spent the last three years developing a SNP based approach to provide an estimate for the number of elephants living in Arabuko Sokoke Forest on Kenya’s east coast.
Using ancient sedimentary DNA to examine Ireland’s lost biodiversity.
Ireland is presently one of the most nature depleted regions on Earth, with native forest cover (once the dominant ecosystem) dropping to 1% by the 19th century, as a result of a variety of factors, such as rapid population growth in the 18th and 19th centuries, and colonial overexploitation of Irelands natural resources. This loss of nature was accompanied by the loss of our native Irish as the dominant language in Ireland, and with it a rich oral tradition that had maintained ancient stories about the plants and animals of Ireland for centuries. It is from this baseline that scientists began to characterise what was left of Ireland’s biodiversity in the late 19th and early 20th centuries, cementing a narrative that Ireland’s suite of flora and fauna is a lesser subset compared to the rest of Europe.
By sequencing sedimentary DNA from a lake core taken in the West of Ireland, we have uncovered a DNA record of the ecosystems surrounding Lough Feeagh for the last 10,000 years. Our results show how in the Mesolithic, this region in the West of Ireland was dominated by hazel and oak, but also had a much broader suite of mammals present, namely red deer, reindeer, wild boar and aurochs. Our results also add a new species to the short list of native Irish trees, hornbeam, and lend evidence to previous theories that pike may be a native Irish fish. The finding of aurochs presence in the Mesolithic however, may be the most important as it resolves both the prey gap paradox and explains how light demanding trees were able to regenerate.
Versatile Amplicon Metabarcoding Pipeline (VAMP)
VAMP is a BASH script which streamlines the analysis of metabarcoding sequence data, which automates the entire process from demultiplexing raw sequences, generating actual sequence variants, and taxonomically assigning reads.
Other projects
Uncovering the origins of Britains midwife toad population using DNA
I have been working with researchers from the UK on a project now nearing completion where we’ve taken non-invasive DNA samples in order to determine the origin of non-native midwife toads in England.
Using ancient manuscripts to explore Ireland’s lost biodiversity
I believe that many records of Ireland’s lost biodiversity remain undiscovered in ancient manuscripts, such as the image below, drawn by the Norman scholar Gerald of Wales, as part of his description of Irish storks 800 years ago. Both his description and drawing match to black storks, which had not previously been considered a native Irish species.
Viruses in aquaculture
My PhD was focused on developing novel techniques to track viral outbreaks in aquaculture, and led to the identification of new strains of various viruses.