Environmental DNA (eDNA) is a powerful tool that allows us to survey biodiversity in high resolution and across wide swathes of the tree of life without the need to directly sample or observe organisms in their habitat. All aquatic organisms shed material (mucus, feces, skin cells, etc.) into the surrounding environment. This material contains DNA, which can be used to identify the original organism that shed it. In theory, we can sample a volume of seawater, filter it, extract the DNA, and sequence it and the resulting sequences will allow us to reconstruct the original biological community. In practice, this all actually works surprisingly well, but there are limitations. These limitations and mitigating factors include DNA residence times, water movement, and perhaps most importantly the availability of accurately-identified reference sequences.
In my research, I use eDNA for applications such as biogeography (both on local and ocean-wide scales), community ecology, and conservation. I particularly interested in the potential for something we’ve decided to call “molecular biogeography,” in which we can use eDNA surveys across a wide geographic area to understand patterns of species distributions across the tree of life. In addition, it has exciting potential for investigating and discovering biodiversity patterns in remote and hard-to-reach habitats such as mesophotic reefs and the deep sea.
I am also involved in building out accurate and well-curated reference libraries using genome skimming and museum collections. One current goal is to skim the complete mitochondrial genomes of all fishes from the United States’ exclusive economic zone (EEZ).
Relevant Publications
Wishingrad, V., M. L.Hoban, C. A. J.Walsh, et al. 2025. “Metabarcoding Primers for Indo-Pacific Fishes.” Environmental DNA7, no. 5: e70205. https://doi.org/10.1002/edn3.70205.
Timmers, M. A., Viehl, K., Angulo, C., Hoban, M. L., Toonen, R. J., Walsh, C. A. J., Wishingrad, V., & Bowen, B. W. (2024). Proteinase K is not essential for marine eDNA metabarcoding. Environmental DNA, 6, e523. https://doi.org/10.1002/edn3.523
Hoban, M. L., Bunce, M., & Bowen, B. W. (2023). Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45–60 m on mesophotic coral reefs. Molecular Ecology, 32, 5590–5608. https://doi.org/10.1111/mec.17140
Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. 2022. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 10:e13790 https://doi.org/10.7717/peerj.13790