Dr Aden Ip1, Dr. Elizabeth Allan1, Professor Ryan Kelly1
1eDNA Collaborative, University of Washington, Seattle, United States of American
Biography:
Aden Ip is a staff scientist at The eDNA Collaborative, specializing in environmental genomics to monitor biodiversity and ecological health. His research focuses on practical eDNA applications for conservation and management, developing portable detection and sequencing methods for rapid biodiversity assessments. Aden’s work aims to make eDNA analysis more accessible, efficient, and reliable for a wide range of stakeholders. Outside the lab, Aden enjoys scuba diving, hiking, and photography, and is always eager to engage with fellow researchers and practitioners in environmental science.
Abstract:
Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, but the complexity and resource demands of current workflows often limit its accessibility for researchers in remote or resource-constrained areas. This study aims to streamline key parts of the eDNA workflow—from environmental sampling to sequence analysis—to make it more accessible to a broader range of end users. We term this approach “cutting corners,” focusing on simplifying both wet laboratory processes and bioinformatic analyses while assessing whether significant reductions in cost, time, and logistical demands can be achieved without compromising the accuracy of eDNA results. In the wet lab, we evaluated five DNA extraction methods, including the widely used Qiagen Blood and Tissue Kit, which is considered the gold standard for high-quality eDNA extractions. We compared this with four alternative methods, including direct PCR, that are more field-ready, featuring shorter protocol times, minimal equipment requirements, and no need for a cold chain, making them suitable for remote settings. On the bioinformatics side, we explored the basecalling of raw nanopore sequences, testing fast, high accuracy, and super accuracy models to assess whether quicker, less computationally demanding methods could still accurately recover animal DNA signals from aquarium seawater samples. By benchmarking these methods against the gold standard, we assessed how closely the “cut corners” approach can replicate the same level of accuracy. This work has the potential to democratize eDNA use, extending its reach to researchers in remote and underserved regions worldwide.