All animals shed cells containing their DNA, and (sort of amazingly) we can use this genetic information to survey whole ecological communities.  We aim to move these techniques toward being quantitative tools for ecology, conservation biology, and management.

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Brandão-Dias, P.F., Shaffer, M., Guri, G. et al. (2025).Differential decay of multiple environmental nucleic acid components. Sci Rep 15, 26791

Shaffer, M.R., Andruszkiewicz Allan, E., Van Cise, A.M., Parsons, K.M., Shelton, A.O. and Kelly, R.P. (2025). Observation Bias in Metabarcoding. Mol Ecol Resour e14119. 

Keller, A. G., &  Kelly, R. P.  eDNAjoint: An R package for interpreting paired or semi-paired environmental DNA and traditional survey data in a Bayesian framework. (2025). Methods in Ecology and Evolution, 16,  886–894. 

Xiong, J., MacCready, P., Brasseale, E., Andruszkiewicz Allan, E, Ramón-Laca, A., Parsons, K. M., Shaffer, M., Kelly, R. P.(2025). Advective Transport Drives Environmental DNA Dispersal in an Estuary. Environmental Science & Technology, 59 (15), 7506-7516

Brasseale, E.,  Adams, N.,  Allan, E. A.,  Jacobson, E. K.,  Kelly, R. P.,  Liu, O. R., et al. (2025).  Marine eDNA production and loss mechanisms. Journal of Geophysical Research: Oceans,  130, e2024JC021643. 

Guri, G., Ray, J.L., Shelton, A.O., Kelly, R.P., Præbel, K., Andruszkiewicz Allan, E., Yoccoz, N., Johansen, T., Wangensteen, O.S., Hanebrekke, T. and Westgaard, J.-I. (2024), Quantifying the Detection Sensitivity and Precision of qPCR and ddPCR Mechanisms for eDNA Samples. Ecol Evol, 14: e70678.

Guri, G., Shelton, A.O., Kelly, R.P., Yoccoz, N., Johansen, T., Præbel, K. Hanebrekke, T., Ray, J.L., Johanna Fall, Westgaard, J.I. (2024). Predicting trawl catches using environmental DNA, ICES Journal of Marine Science, Volume 81, Issue 8, Pages 1536–1548

Hirsch, S., Acharya-Patel, N., Amamoo, P. A., Borrero-Pérez, G.,H., Ni Kadek, D. C., Joape, G. M. G., . . . Ryan, K. (2024). Centering accessibility, increasing capacity, and fostering innovation in the development of international eDNA standards. MBMG Metabarcoding and Metagenomics, 8, 2089-2121.

Fisher M.C., Grason E.W., Stote A., Kelly R.P., Litle K., et al. (2024). Invasive European green crab (Carcinus maenas) predation in a Washington State estuary revealed with DNA metabarcoding. PLOS ONE 19(5): e0302518.

Guri, G., Westgaard, J.I., Yoccoz, N., Wangensteen, O.S., Præbel, K., Ray, J.L., Kelly, R.P., Shelton, A.O., Hane- brekke, T. and Johansen, T. (2023). Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords. Environmental DNA.

Gold, Z., R.P. Kelly, A.O. Shelton, A. Thompson, K.D. Goodwin, R. Gallego, K. Parsons, L.R. Thompson, D. Kacev, and P.H. Barber. (2023). Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages. Environmental DNA.


Gold, Z., Shelton, A.O., Casendino, H.R., Duprey, J., Gallego, R., Van Cise, A., Fisher, M., Jensen, A.J., D’Agnese, E., Allan, E.A. and Ramon-Laca, A., (2023). Signal and Noise in Metabarcoding Data. PlosOne.

Shelton, A.O., Gold, Z., A.J. Jensen, E. D’Agnese, E. Allan, A. Van Cise, R. Gallego, A. Ramón-Laca, M. Garber- Yonts, K. Parsons, R.P. Kelly. (2022). Toward Quantitative Metabarcoding. Ecology, e3906.

Keller, A., E. Grason, P.S. McDonald, A. Ramon-Laca, R.P. Kelly. Tracking an Invasion Front with Environmental DNA. (In Press, Ecological Applications).

Jacobs-Palmer, E., Gallego, R., Cribari, K., Keller, A., & Kelly, R. P. (2021). Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae. Frontiers in Ecology and Evolution 9:262.

Gallego, R., Jacobs-Palmer, E., Cribari, K. J., & Kelly, R. P. (2020). Environmental DNA Metabarcoding Reveals Winners and Losers of Global Change in Coastal Waters. Proceedings of the Royal Society, Series B.

Djurhuus, A., Closek, C.J., Kelly, R.P. et al. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nature Communications 11, 254 (2020)

Kelly, R.P., A.O. Shelton, and R. Gallego. 2019. Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies (formerly: Understanding eDNA.) Scientific Reports 9: 1-14. [Supplemental Info here].

Shelton, A.O., R.P. Kelly, J.L. O'Donnell, L. Park, P. Schwenke, C. Greene, R.A. Henderson, and E.M. Beamer. Environmental DNA provides quantitative estimates of a threatened salmon species. Biological Conservation 237 (2019): 383-391.

Kelly, R.P., R. Gallego, and E. Jacobs-Palmer. 2018. The Effect of Tides on Nearshore Environmental DNA. PeerJ: 6:e4521.

Tillotson, M.D., R.P. Kelly, J.J. Duda, M. Hoy, J. Kralj, and T.P. Quinn. 2018. Concentrations of Environmental DNA (eDNA) Reflect Spawning Salmon Abundance at Fine Spatial and Temporal Scales. Biological Conservation 220:1-11.

O’Donnell, J.L., R.P. Kelly, A.O. Shelton, J.F. Samhouri, N.C. Lowell, G.D. Williams. 2017. Spatial Distribution of Environmental DNA in a Nearshore Marine Habitat. PeerJ 5:e3044 https://doi.org/10.7717/peerj.3044.

Kelly, R.P.,  C.J. Closek, J.L. O’Donnell, J.E. Kralj, A.O. Shelton, and J.F. Samhouri. 2017. Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem. Frontiers in Marine Science 3:283.

Kelly, R.P.,  J.L. O’Donnell, N.C. Lowell, A.O. Shelton, J.F. Samhouri, S.M. Hennessey, B.E. Feist, and G.D. Williams. 2016. Genetic Signatures of Ecological Diversity Along an Urbanization Gradient. PeerJ 4:e2444.

Kelly, R.P. 2016. Making Environmental DNA Count. Molecular Ecology Resources 16: 10-12.

J.L. O'Donnell, R.P. Kelly, N. Lowell, and J.A. Port. 2016. Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies.11(3): e0148698. doi:10.1371/journal.pone.0148698.

Port, J.A., J.L. O'Donnell, O. Romero-Maraccini, P.R. Leary, S.Y. Litvin, K.J. Nickols, and R.P. Kelly (2016, Molecular Ecology), Assessing Vertebrate Biodiversity of a Kelp Forest Ecosystem Using Environmental DNA.

Shelton, A.O., J. L. O'Donnell, J.F. Samhouri, N. Lowell, G.D. Williams, and R.P. Kelly. 2016. A Framework for Inferring Biological Communities from Environmental DNA. 26: 1645-1659.

Kelly, R.P., J.A. Port, K.M. Yamahara, R.G. Martone, N. Lowell, P.F. Thomsen, M.E. Mach, E. Prahler, M.R. Caldwell, and L.B. Crowder. 2014. Harnessing DNA to Improve Environmental Management, Science 344 (6191): 1455-1456. doi:10.1126/science.1251156 

Kelly, R.P., J.A. Port, K.M. Yamahara, and L. Crowder.  2014.  Using Environmental DNA to Census Marine Fishes in a Large Mesocosm.  PLoS ONE 9(1): e86175. doi:10.1371/journal.pone.0086175.

Kelly, R.P.  2014. Will More, Better, Cheaper, and Faster Monitoring Improve Environmental Management? 44 Environmental Law 1111.