Publications

Fisher MC, Grason EW, Stote A, Kelly RP, 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.

Kelly, R.P., T. Klinger, P.J. Krug, and J. Meyer. 2024. Between the Tides in California: Exploring Beaches and Tidepools. University of Washington Press.

Lee, K. N., Kelly, R. P., Demir-Hilton, E., Laschever, E., & Allan, E. A. (2023). Adoption of environmental DNA in public agency practice. Environmental DNA, 6, e470.

Kelly, R.P., David M. Lodge, Kai N. Lee, and 34 coauthors. 2023. Toward a National eDNA Strategy for the United States. Environmental DNA.


Laschever, E., R.P. Kelly, Michelle Hoge, and Kai N. Lee. The Next Generation of Environmental Monitoring:

Environmental DNA in Federal Agency Practice. 2023. 48 Columbia Environmental Law Journal 260-310.


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.

Samhouri, J.F., Shelton, A.O., Williams, G.D., Feist, B.E., Hennessey, S.M., Bartz, K., Kelly, R.P., O’Donnell, J.L., Sheer, M., Stier, A.C. and Levin, P.S., 2022. How much city is too much city? Biodiversity and ecosystem functioning along an urban gradient at the interface of land and sea. Frontiers in Marine Science, 9.

Crosman, K.M., Allison, E.H., Ota, Y. et al. Social Equity is Key to Sustainable Ocean Governance. npj Ocean Sustainability 1, 4 (2022).

Kelly, R.P., T. Klinger, and J. Meyer. 2022. Between the Tides in Washington and Oregon: Exploring Beaches and Tidepools. University of Washington Press.

Shelton, A.O., A. Ramón-Laca, A. Wells, J. Clemons, D. Chu, B.E. Feist, R.P. Kelly, S.L. Parker-Stetter, R. Thomas, K.M. Nichols, and L. Park. 2022. Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean. Proceedings of the Royal Society B 289: 20212613.

Keller, A., E. Grason, P.S. McDonald, A. Ramón-Laca, R.P. Kelly. 2022. Tracking an Invasion Front with Environmental DNA. Ecological Applications, e2561.

A.J. Jensen, R.P. Kelly, E.C. Anderson, W.H. Satterthwaite, A.O. Shelton, and E.J. Ward. Introducing ‘zoid‘: A Mixture Model (and R Package) for Modeling Proportional Data with 0s and 1s in Ecology. Ecology, e3804.

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 287:20202424.

Gold, Z., AR Wall, EE Curd, RP Kelly, ND Pentcheff, L Ripma, PH Barber, and R Wetzer. eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genetic Resources 12, 685–690 (2020).

Jacobs-Palmer E, Gallego R, Ramón-Laca A, Kunselman E, Cribari K, Horwith M, Kelly RP. 2020. A Halo of Reduced Dinoflagellate Abundances in and Around Eelgrass Beds. PeerJ 8:e8869

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.

Lebon, K.M., and R.P. Kelly. Evaluating alternatives to reduce whale entanglements in commercial Dungeness Crab fishing gear. Global Ecology and Conservation 18 (2019): e00608.

Battista, W., R.P. Kelly, A. Erickson, and R. Fujita. Fisheries Governance Affecting Conservation Outcomes in the United States and European Union. Coastal Management 46, no. 5 (2018): 388-452.

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

Hart, C.J., R.P. Kelly, and S.F. Peterson. 2018. Will the California Current Lose its Nesting Tufted Puffins? PeerJ: 6:e4519.

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.

Lee, T.S., J.D. Toft, J. Cordell, M.N. Dethier, J. Adams, and R.P. Kelly. 2018. Quantifying the Effectiveness of Shoreline Armoring Removal on Coastal Biota of Puget Sound. PeerJ 6:e4275.

Kelly, R.P. 2017. Ocean Acidification Policy: Applying the Lessons of Washington to California and Beyond. 7 Washington Journal of Environmental Law and Policy 1-34.

Mossler, M.V., A. Bostrom, R.P. Kelly, K.M. Crosman, and P. Moy. 2017. How Does Framing Affect Policy Support for Emissions Mitigation? Testing the Effect of Ocean Acidification and Other Frames. Global Environmental Change 45: 63-78.

Kelly, R.P., P. Levin, and K.N. Lee. 2017. Science, Policy, And Data-Driven Decisions in a Data Vacuum. 44 Ecology Law Quarterly 7-40.

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.

Hillier, A., R.P. Kelly, and T. Klinger. 2016. Narrative Style Influences Citation Frequency in Climate Change Science. PLoS One 11(12): e0167983.

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.

Freeman, M.C., L. Whiting, and R.P. Kelly. 2016. Assessing Potential Spatial and Temporal Conflicts in Washington's Marine Waters. Marine Policy 70: 137-144.

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

N. Lowell and R.P. Kelly. 2016. Evaluating Agency Use of “Best Available Science” Under the United States Endangered Species Act. Biological Conservation 196:53-59.

W. Battista, R.P. Kelly, A. Erickson, and R. Fujita. 2016. A Comprehensive Method for Assessing Marine Resource Governance: Case study in Kāne‘ohe Bay, Hawai‘i. Journal of Coastal Management 44: 295-332.

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

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. Ecological Applications 26: 1645-1659.

Port, J.A., J.L. O'Donnell, O. Romero-Maraccini, P.R. Leary, S.Y. Litvin, K.J. Nickols, and R.P. Kelly. 2016. Assessing Vertebrate Biodiversity of a Kelp Forest Ecosystem Using Environmental DNA. Molecular Ecology 25: 527-541.

Gattuso, J-P., A. Magnan, R. Billé, W.W.L. Cheung, E.L. Howes, F. Joos, D. Allemand, L. Bopp, S. Cooley, C.M. Eakin, O. Hoegh-Guldberg, R.P. Kelly, H-O. Pörtner, A.D. Rogers, J.M. Baxter, D. Laffoley, D. Osborn, A. Rankovic, J. Rochette, U.R. Sumaila, S. Treyer, C. Turley. 2015. Contrasting Futures for Ocean and Society from Different CO2 Emissions Scenarios. Science 349 (6243): aac4722.

Marshall, K., A. Stier, J. Samhouri, R.P. Kelly, E. Ward. 2016. Conservation Challenges of Predator Recovery. Conservation Letters 9:70-78.

Selkoe, K.A., T. Blenckner, M.R. Caldwell, L. Crowder, A. Erickson, T. Essington, J. Estes, R. Fujita, B.S. Halpern, M. Hunsicker, C.V. Kappel, R.P. Kelly, J.N. Kittinger, P.S. Levin, J. Lynham, M. Mach, R. Martone, L. Mease, A. Salomon, J. Samhouri, C. Scarborough, A. Stier, C. White, J. Zedler. 2015. Principles for Managing Marine Ecosystems Prone to Tipping Points. 2015. Ecosystem Health and Sustainability 1(5):17.

Kelly, R.P., A. Erickson, L. Mease, W. Battista, J. Kittinger, R. Fujita.  2015.  Embracing Thresholds for Better Environmental Management.  Philosophical Transactions of the Royal Society B 370: 20130276.

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., A.L. Erickson, and L.A. Mease. 2014. How Not to Fall Off a Cliff, or Using Tipping Points to Improve Environmental Management. 41 Ecology Law Quarterly 843.

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

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

A.L. Strong, K.J. Kroeker, L.T. Teneva, L.A. Mease, and R.P. Kelly.  2014.  Ocean Acidification 2.0: Managing Our Changing Coastal Ocean Chemistry.  BioScience: doi: 10.1093/biosci/biu072.

Kelly, R.P., T. Klinger, and S. Cooley.  2013.  Narratives Can Motivate Environmental Action: The Whiskey Creek Ocean Acidification Story.  AMBIO: 1-8.

Kelly, R.P. and M. Caldwell.  2013.  “Not Supported by Current Science” : The National Forest Management Act and the Lessons of Environmental Monitoring for the Future of Public Resources Management. 32 Stanford Environmental Law Journal 151. (Available at: http://ssrn.com/abstract=2265478).

Kelly, R.P., and M. Caldwell.  2013.  Ten Ways States Can Fight Ocean Acidification (and Why They Should). 37 Harvard Environmental Law Review 57. (Available at: http://www3.law.harvard.edu/journals/elr/files/2013/05/Kelly-Caldwell.pdf).

R. Billé, J-P. Gattuso, R.P. Kelly, et al.  2013.  Taking Action Against Ocean Acidification: A Review of Management and Policy Options. Environmental Management 52: 761-779.

Caldwell, M. R., Hartge, E. H., Ewing, L. C., Griggs, G., Kelly, R. P., Moser, S. C., Newkirk, S. G., Smyth, R. A., & Woodson, C. B. (2013). Chapter 9: Coastal Issues. In: Garfin, G., Jardine, A., Merideth, R., Black, M., & LeRoy, S. (Eds.), Assessment of Climate Change in the Southwest United States: a Report Prepared for the National Climate Assessment. A report by the Southwest Climate Alliance. Washington, DC: Island Press. (Available at: this link).

Kelly, R.P., and M.R. Caldwell. 2012. The Limits of Water Quality Criteria. The Environmental Forum 29(6): 34-38.  (Available here).

Kelly, R.P. and J. Grote Stoutenburg. 2012. Washington State's Legal and Policy Options for Combating Ocean Acidification in State Waters. Center for Ocean Solutions. (Available at: http://www.ecy.wa.gov/water/marine/oa/2012report_app8.pdf).

Kelly, R.P., and M. Caldwell.  2012.  Why Ocean Acidification Matters to California, and What California Can Do About It. Center for Ocean Solutions.  (Available here).

Kelly, R.P., M.M. Foley, W. Fisher, R. Feely, B.S. Halpern, G.G. Waldbusser, and M.R. Caldwell. 2011.  Mitigating Local Causes of Ocean Acidification with Existing Laws.  Science 332: 1036-1037.  (Available at: http://www.sciencemag.org/cgi/content/full/332/6033/1036?ijkey=n2jTVQ81X...)

Kelly, R.P.  2011.  Spineless Wonders: How Listing Marine Invertebrates and their Larvae Challenges the US Endangered Species Act.  19 Penn State Environmental Law Review 1-53. (Available at: http://papers.ssrn.com/abstract=1676435).

D.J. Barshis, E.E. Sokta, R.P. Kelly, A. Sivasundar, B.A. Menge, J. Barth, and S.R. Palumbi.  2011. Coastal Upwelling May Drive Sweepstakes Recruitment in the Acorn Barnacle Balanus glandula. Marine Ecology Progress Series 439: 139-150.

Kelly, R.P.  2010.  The Use of Population Genetics in Endangered Species Act Listing Decisions.  37 Ecology Law Quarterly 1107-1159. (Available at: http://www.boalt.org/elq/documents/elq37_4_04_kelly_2011_0220.pdf).

Kelly, R.P., and S.R. Palumbi.  2010.  Genetic Structure Among 50 Species of the Northeastern Pacific Rocky Intertidal Community. PLoS ONE 5(1): e8594. doi:10.1371/journal.pone.0008594

Kelly, R.P., T.A. Oliver, A. Sivasundar, and S.R. Palumbi.  2010.  A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species.  Journal of Heredity 101(4): 423-436.

Kelly, R.P., and S.R. Palumbi.  2009. General-use polymerase chain reaction primers for amplification and direct sequencing of enolase, a single-copy nuclear gene, from different animal phyla.  Molecular Ecology Resources 9: 144-147.

Kelly, R.P., and D.J. Eernisse.  2008. Reconstructing a Radiation: The Chiton Genus Mopalia in the North Pacific.  Invertebrate Systematics 22: 17-28.

Kelly, R.P. and D.J. Eernisse.  2007.  Southern Hospitality: A Latitudinal Gradient in Gene Flow in the Marine Environment.  Evolution 61(3): 700-707.

Kelly, R.P., I.N. Sarkar, D.J. Eernisse, and R. Desalle.  2007.  DNA Barcoding Using Chitons (genus Mopalia).  Molecular Ecology Notes 7: 177-183.