Rothstein, A. P., R. A. Knapp, G. Bradburd, D. M. Boiano, C. J. Briggs, and E. B. Rosenblum. 2020. Stepping into the past to conserve the future: Archived skin swabs from extant and extirpated populations inform genetic management of an endangered amphibian. Molecular Ecology, in press. [PDF]


Ellison, S., R. A. Knapp, W. Sparagon, A. Swei, and V. T. Vredenburg. 2019. Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host. Molecular Ecology 28: 127-140. [PDF]


Joseph, M. B., and R. A. Knapp. 2018. Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian. Ecosphere 9:e02499. [link]


Jani, A. J., R. A. Knapp, and C. J. Briggs. 2017. Epidemic and endemic pathogen dynamics correspond to distinct host population microbiomes at a landscape scale. Proceedings of the Royal Society B: Biological Sciences 284: 20170944. [link]

Poorten, T. J., R. A. Knapp, and E. B. Rosenblum. 2017. Population genetic structure of the endangered Sierra Nevada yellow-legged frog (Rana sierrae) in Yosemite National Park based on multi-locus nuclear data from swab samples. Conservation Genetics 18: 731–744. [PDF]

Smith, T. C., A. M. Picco, and R. Knapp. 2017. Ranaviruses infect mountain yellow-legged frogs (Rana muscosa and Rana sierrae) threatened by Batrachochytrium dendrobatidis. Herpetological Conservation and Biology 12: 149–159. [link]

Wilber, M. Q., R. A. Knapp, M. Toothman, and C. J. Briggs. 2017. Resistance, tolerance and environmental transmission dynamics determine host extinction risk in a load-dependent amphibian disease. Ecology Letters 20: 1169–1181. [PDF]


Knapp, R. A., G. M. Fellers, P. M. Kleeman, D. A. W. Miller, V. T. Vredenburg, E. B. Rosenblum, and C. J. Briggs. 2016. Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors. Proceedings of the National Academy of Sciences USA 113: 11889–11894. [link]

Piovia-Scott, J., S. Sadro, R. A. Knapp, J. Sickman, K. L. Pope, and S. Chandra. 2016. Variation in reciprocal subsidies between lakes and land: perspectives from the mountains of California. Canadian Journal of Fisheries and Aquatic Sciences 73: 1691–1701. [link]

Smith, T. C., R. A. Knapp, and C. J. Briggs. 2016. Declines and extinctions of mountain yellow-legged frogs have small effects on benthic macroinvertebrate communities. Ecosphere 7: e01327. [link]


Matchett, J. R., P. B. Stark, S. M. Ostoja, R. A. Knapp, H. C. McKenny, M. L. Brooks, W. T. Langford, L. N. Joppa, and E. L. Berlow. 2015. Detecting the influence of rare stressors on rare species in Yosemite National Park using a novel stratified permutation test. Scientific Reports 5: 10702. [link]

Zhou, H., T. Hanson, and R. Knapp. 2015. Marginal Bayesian nonparametric model for time to disease arrival of threatened amphibian populations. Biometrics 71: 1101–1110. [PDF]


Berlow, E. L., R. A. Knapp, S. M. Ostoja, R. J. Williams, H. McKenny, J. R. Matchett, Q. Guo, G. M. Fellers, P. Kleeman, M. L. Brooks, and L. Joppa. 2013. A network extension of species occupancy models in a patchy environment applied to the Yosemite toad (Anaxyrus canorus). PLoS ONE 8: e72200. [link]

Bradford, D. F., K. A. Stanley, N. G. Tallent, D. W. Sparling, M. S. Nash, R. A. Knapp, L. L. McConnell, and S. L. Massey Simonich. 2013. Temporal and spatial variation of atmospherically deposited organic contaminants at high elevation in Yosemite National Park, California, USA. Environmental Toxicology and Chemistry 32: 517-525. [link]

Deiner, K., R. A. Knapp, D. M. Boiano, and B. May. 2013. Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens. Molecular Ecology Resources 13: 820-831. [PDF]

Garwood, J. M., R. A. Knapp, K. L. Pope, R. L. Grasso, M. L. Magnuson, and J. R. Maurer. Use of historically fishless high-mountain lakes and streams by neartic River Otters (Lontra canadensis) in California. 2013. Northwestern Naturalist 94: 51-66. [PDF]

Miner, B. E., R. A. Knapp, J. K. Colbourne, and M. E. Pfrender. 2013. Evolutionary history of alpine and subalpine Daphnia in western North America. Freshwater Biology 58: 1512-1522. [PDF]


Bradford, D. F., R. A. Knapp, D. W. Sparling, M. S. Nash, K. A. Stanley, N. G. Tallent-Halsell, L. L. McConnell, and S. M. Simonich. 2011. Pesticide distributions and population declines of California, USA, alpine frogs, Rana muscosa and Rana sierrae. Environmental Toxicology and Chemistry 30: 682-691. [PDF]

Knapp, R. A., C. J. Briggs, T. C. Smith, and J. R. Maurer. 2011. Nowhere to hide: impact of a temperature-sensitive amphibian pathogen along an elevation gradient in the temperate zone. Ecosphere 2: art93. [link]


Briggs, C. J., R. A. Knapp, and V. T. Vredenburg. 2010. Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians. Proceedings of the National Academy of Sciences 107: 9695-9700. [link]

Epanchin, P. N., R. A. Knapp, and S. P. Lawler. 2010. Nonnative trout impact an alpine-nesting bird by altering aquatic insect subsidies. Ecology 91: 2406-2415. [PDF]

Latta, L. C., Fisk, D. L., R. A. Knapp, and M. E. Pfrender. 2010. Genetic resilience of Daphnia populations following experimental removal of introduced fish. Conservation Genetics 11: 1737-1745. [PDF]

Vredenburg, V. T., R. A. Knapp, T. S. Tunstall, and C. J. Briggs. 2010. Dynamics of an emerging disease drive large-scale amphibian extinctions. Proceedings of the National Academy of Sciences, 107: 9689-9694. [link]


Knapp, R. A., and O. Sarnelle. 2008. Recovery after local extinction: factors affecting re-establishment of alpine lake zooplankton. Ecological Applications 18: 1850-1859. [PDF]

Kramer, A. M., O. Sarnelle, and R. A. Knapp. 2008. Allee effect limits colonization success of sexually reproducing zooplankton. Ecology 89: 2760-2769. [PDF]


Davidson, C., and R. A. Knapp. 2007. Multiple stressors and amphibian declines: dual impacts of pesticides and fish on yellow-legged frogs. Ecological Applications 17: 587-597. [PDF]

Fisk, D. L., L. C. Latta, R. A. Knapp, and M. E. Pfrender. 2007. Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence. BMC Evolutionary Biology 7: 22. [link]

Knapp, R. A., D. M. Boiano, and V. T. Vredenburg. 2007. Removal of nonnative fish results in population expansion of a declining amphibian (mountain yellow-legged frog, Rana muscosa). Biological Conservation 135: 11-20. [PDF]

Latta, L. C., J. W. Bakelar, R. A. Knapp, and M. E. Pfrender. 2007. Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity. BMC Evolutionary Biology 7: 21. [link]

Morgan, J. A. T., V. T. Vredenburg, L. J. Rachowicz, R. A. Knapp, M. J. Stice, T. Tunstall, R. E. Bingham, J. M. Parker, J. E. Longcore, C. Moritz, C. J. Briggs, and J. W. Taylor. 2007. Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis. Proceedings of the National Academy of Sciences, USA 104: 13845–13850. [link]

Vredenburg, V. T., R. Bingham, R. Knapp, J. A. T. Morgan, C. Moritz, and D. Wake. 2007. Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog. Journal of Zoology 271: 361-374. [PDF]


Knapp, R. A., and J. A. T. Morgan. 2006. Tadpole mouthpart depigmentation as an accurate indicator of chytridiomycosis, an emerging disease of amphibians. Copeia 2006: 188–197. [PDF]

Rachowicz, L. J., R. A. Knapp, J. A. T. Morgan, M. J. Stice, V. T. Vredenburg, J. M. Parker, and C. J. Briggs. 2006. Emerging infectious disease as a proximate cause of amphibian mass mortality. Ecology 87: 1671–1683. [PDF]


Adams, M. J., B. R. Hossack, R. A. Knapp, P. S. Corn, S. A. Diamond, P. C. Trenham, and D. B. Fagre. 2005. Distribution patterns of lentic-breeding amphibians in relation to ultraviolet radiation exposure in western North America. Ecosystems 8: 488-500. [PDF]

Briggs, C. J., V. T. Vredenburg, R. A. Knapp, and L. J. Rachowicz. 2005. Investigating the population-level effects of chytridiomycosis: an emerging infectious disease of amphibians. Ecology 86: 3149–3159. [PDF]

Brooks, P. D., C. M. O’Reilly, S. A. Diamond, D. H. Campbell, R. Knapp, D. Bradford, P. S. Corn, B. Hossack, and K. Tonnessen. 2005. Spatial and temporal variability in the amount and source of dissolved organic carbon: implications for ultraviolet exposure in amphibian habitats. Ecosystems 8: 478-487. [PDF]

Brose, U., L. Cushing, E. L. Berlow, T. Jonsson, C. Banasek-Richter, L.-F. Bersier, J. L. Blanchard, T. Brey, S. R. Carpenter, M.-F. C. Blandenier, J. E. Cohen, H. A. Dawah, T. Dell, F. Edwards, S. Harper-Smith, U. Jacob, R. A. Knapp, M. E. Ledger, J. Memmott, K. Mintenbeck, J. K. Pinnegar, B. C. Rall, T. Rayner, L. Ruess, W. Ulrich, P. Warren, R. J. Williams, G. Woodward, P. Yodzis, and N. D. Martinez. 2005. Body sizes of consumers and their resources. Ecology 86: 2545. [PDF]

Diamond, S. A., P. C. Trenham, M. J. Adams, B. R. Hossack, R. A. Knapp, S. L. Stark, D. Bradford, P. S. Corn, K. Czarnowski, P. D. Brooks, D. Fagre, B. Breen, N. E. Detenbeck, and K. Tonnessen. 2005. Estimated ultraviolet radiation doses in wetlands in six national parks. Ecosystems 8: 462-477. [PDF]

Harper-Smith, S., E. L. Berlow, R. A. Knapp, R. J. Williams, and N. D. Martinez. 2005. Communicating ecology through food webs: visualizing and quantifying the effects of stocking alpine lakes with trout. Pages 407-423 in P. C. de Ruiter, V. Wolters, and J. C. Moore, editors. Dynamic food webs – multispecies assemblages, ecosystem development and environmental change. Academic Press, Burlington, Massachusetts. [PDF]

Knapp, R. A. 2005. Effects of nonnative fish and habitat characteristics on lentic herpetofauna in Yosemite National Park, USA. Biological Conservation 121: 265-279. [PDF]

Knapp, R. A., C. P. Hawkins, J. Ladau, and J. G. McClory. 2005. Fauna of Yosemite National Park lakes has low resistance but high resilience to fish introductions. Ecological Applications 15: 835-847. [PDF]

Sarnelle, O., and R. A. Knapp. 2005. Nutrient recycling by fish versus zooplankton grazing as drivers of the trophic cascade in alpine lakes. Limnology and Oceanography 50: 2032-2042. [PDF]


Armstrong, T. W., and R. A. Knapp. 2004. Response by trout populations in alpine lakes to an experimental halt to stocking. Canadian Journal of Fisheries and Aquatic Sciences 61: 2025-2037. [PDF]

Sarnelle, O., and R. A. Knapp. 2004. Zooplankton recovery after fish removal: Limitations of the egg bank. Limnology and Oceanography 49: 1382-1392. [PDF]


Knapp, R. A., K. R. Matthews, H. K. Preisler, and R. Jellison. 2003. Developing probabilistic models to predict amphibian site occupancy in a patchy landscape. Ecological Applications 13: 1069-1082. [PDF]


Matthews, K. R., R. A. Knapp, and K. L. Pope. 2002. Garter snake distributions in high-elevation aquatic ecosystems: is there a link with declining amphibian populations and nonnative trout introductions? Journal of Herpetology 36: 16-22. [PDF]


Knapp, R. A., P. S. Corn, and D. E. Schindler. 2001. The introduction of nonnative fish into wilderness lakes: good intentions, conflicting mandates, and unintended consequences. Ecosystems 4: 275-278. [PDF]

Knapp, R. A., J. A. Garton, and O. Sarnelle. 2001. The use of egg shells to infer the historical presence of copepods in alpine lakes. Journal of Paleolimnology 25: 539-543. [PDF]

Knapp, R. A., K. R. Matthews, and O. Sarnelle. 2001. Resistance and resilience of alpine lake fauna to fish introductions. Ecological Monographs 71: 401-421. [PDF]

Matthews, K. R., K. L. Pope, H. K. Preisler, and R. A. Knapp. 2001. Effects of nonnative trout on Pacific treefrogs (Hyla regilla) in the Sierra Nevada. Copeia 101: 1130-1137. [PDF]

Schindler, D. E., R. A. Knapp, and P. R. Leavitt. 2001. Alteration of nutrient cycles and algal production resulting from fish introductions into mountain lakes. Ecosystems 4: 308-321. [PDF]


Knapp, R. A., and K. R. Matthews. 2000. Non-native fish introductions and the decline of the mountain yellow-legged frog from within protected areas. Conservation Biology 14: 428-438. [PDF]

Knapp, R. A., and K. R. Matthews. 2000. Effects of nonnative fishes on wilderness lake ecosystems in the Sierra Nevada and recommendations for reducing impacts. Pages 312-317 in Proceedings: Wilderness Science in a Time of Change. Ogden, UT: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. [PDF]


Knapp, R. A., and H. K. Preisler. 1999. Is it possible to predict habitat use by spawning salmonids? A test using California golden trout (Oncorhynchus mykiss aguabonita). Canadian Journal of Fisheries and Aquatic Sciences 56: 1576-1584. [PDF]


Knapp, R. A., and K. R. Matthews. 1998. Eradication of nonnative fish by gill netting from a small mountain lake in California. Restoration Ecology 6: 207-213. [PDF]

Knapp, R. A., V. T. Vredenburg, and K. R. Matthews. 1998. Effects of stream channel morphology on golden trout spawning habitat and recruitment. Ecological Applications 8: 1104-1117. [PDF]


Knapp, R. A. 1996. Non-native trout in natural lakes of the Sierra Nevada: an analysis of their distribution and impacts on native aquatic biota. Pages 363-407 in Sierra Nevada Ecosystem Project: Final Report to Congress. Volume III: Assessments, Commissioned Reports, and Background Information. Davis: University of California, Centers for Water and Wildland Resources. [PDF]

Knapp, R. A., and K. R. Matthews. 1996. Livestock grazing, golden trout, and streams in the Golden Trout Wilderness, California: impacts and management implications. North American Journal of Fisheries Management 16: 805-820. [PDF]

Knapp, R. A., and V. T. Vredenburg. 1996. Spawning by California golden trout: characteristics of spawning fish, seasonal and daily timing, redd characteristics, and microhabitat preferences. Transactions of the American Fisheries Society 125: 519-531. [PDF]

Knapp, R. A., and V. T. Vredenburg. 1996. A field comparison of the substrate composition of California golden trout redds sampled with two devices. North American Journal of Fisheries Management 16: 674-681. [PDF]

Moyle, P. B., R. M. Yoshiyama, and R. A. Knapp. 1996. Status of fish and fisheries. Pages 953-973 in Sierra Nevada Ecosystem Project: Final Report to Congress. Vol. II: Assessments and scientific basis for management options. Davis: University of California, Centers for Water and Wildland Resources. [PDF]


Knapp, R. A. 1995. Influence of energy reserves on the expression of a secondary sexual trait in male bicolor damselfish, Stegastes partitus. Bulletin of Marine Science 57: 672-681. [PDF]

Knapp, R. A., P. C. Sikkel, and V. T. Vredenburg. 1995. Age of clutches in nests and the within-nest spawning site preferences of three damselfish species (Pomacentridae). Copeia 1995: 78-88. [PDF]


Knapp, R. A. 1993. The influence of egg survivorship on the subsequent nest fidelity of female bicolor damselfish, Stegastes partitus. Animal Behaviour 46: 111-121. [PDF]


Knapp, R. A., and R. R. Warner. 1991. Male parental care and female choice in the bicolor damselfish, Stegastes partitus: bigger is not always better. Animal Behaviour 41: 747-756. [PDF]

Knapp, R. A., and J. T. Kovach. 1991. Courtship as an honest indicator of male parental quality in the bicolor damselfish, Stegastes partitus. Behavioral Ecology 2: 295-300. [PDF]


Knapp, R. A., and T. L. Dudley. 1990. Growth and longevity of golden trout, Oncorhynchus aguabonita, in their native streams. California Fish and Game 76: 161-173. [PDF]


Knapp, R. A., and R. C. Sargent. Egg-mimicry as a male mating strategy in the fantail darter (Etheostoma flabellare): females prefer males with eggs. Behavioral Ecology and Sociobiology 25: 321-326. [PDF]


Wilzbach, M. A., K. W. Cummins, and R. A. Knapp. Toward a functional classification of stream invertebrate drift. Verhandlung Internationale Vereinigung für Theoretische und Angewandte Limnologie 23: 1244-1254. [PDF]