Publications

2019

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]

2018

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]

2017

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]

2016

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]

2015

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]

2013

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]

2011

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]

2010

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]

2008

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]

2007

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]

2006

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]

2005

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]

2004

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]

2003

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]

2002

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]

2001

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]

2000

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]

1999

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]

1998

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]

1996

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]