Dr Lara Urban1
1University Of Otago, Dunedin, New Zealand
We used environmental DNA to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We established a barcoding protocol to identify the distribution of the species in a highly localised manner based on soil samples. Leveraging nanopore sequencing, adaptive sampling and the high-quality kākāpō reference genome, we then extracted species-specific DNA from these samples. We combined read-based haplotype phasing with known individual genetic variation in the kākāpō population to predict the presence of individuals, and were able to confirm these predictions based on in-depth metadata describing the kākāpō territories. This study shows that individual identification is feasible through adaptive sampling of environmental DNA, with important implications for in-depth monitoring of rare and elusive species, potentially expanding the application of environmental DNA research from monitoring species distribution to inferring fitness-related parameters such as genetic structure and inbreeding.
Biography:
Lara did her PhD at the University of Cambridge, UK, and the EMBL – European Bioinformatics Institute, where she applied and developed methodology in the fields of statistical genomics, deep learning and single-cell genetics. As a Humboldt Research Fellow in New Zealand, she now studies how genomic and environmental DNA research can benefit and be incorporated into the conservation of nature, and how specifically portable DNA sequencing can be leveraged to revolutionise our understanding of planetary health.