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Moyle, P. B., Daniels R. A., Herbold B., & Baltz D. M. (1986).  Patterns in distribution and abundance of a noncoevolved assemblage of estuarine fishes in California. Fishery Bulletin. 84, 105-117.
Moyle, P. B., Crain P. K., & Whitener K. (2007).  Patterns In The Use Of A Restored California Floodplain By Native And Alien Fishes. San Francisco Estuary and Watershed Science. 5(3), 
Howard, J., Klausmeyer K., Furnish J., Gardali T., Grantham T. E., Katz J., et al. (2015).  Patterns of Freshwater Species Richness, Endemism, and Vulnerability in California. PLoS ONE. 10(7), PDF icon Read full study (3.16 MB)
Moyle, P. B., & Vondracek B. (1985).  Persistence and Structure of the Fish Assemblage in a Small California Stream. Ecology. 66(1), 1-13.
Durand, J. R., Fleenor W. E., McElreath R., Santos M., & Moyle P. B. (2016).  Physical controls on the distribution of the submersed aquatic weed Egeria densa in the Sacramento-San Joaquin Delta and implcations for habitat.. San Francisco Estuary and Watershed Science. 14(1), 
Skiles, T. D., Yoshiyama R. M., & Moyle P. B. (2013).  Pink salmon (Oncorhynchus gorbuscha) in the Salinas River, California: a new record and historical perspectives. California Fish and Game. 99(1), 55-59.
Moyle, P. B. (1964).  Populations of peritrichs on the pond snail, Physa gyrina Say. Journal of the Minnesota Academy of Science . 31, 125-130.
Moyle, P. B. (1996).  Potential aquatic diversity management areas. Sierra Nevada Ecosystem Project: Final report to Congress Vol. II, assessments, commissioned reports, and background information. 2, 1493-1503.
Moyle, P. B., Randall P. J., & Yoshiyama R. M. (1996).  Potential aquatic diversity management areas in the Sierra Nevada. Sierra Nevada Ecosystem Project: Final report to Congress , Vol. III, assessments, commissioned reports, and background information. 3, 409-478.
Quiñones, R. M., Holyoak M., Johnson M. L., & Moyle P. B. (2014).  Potential factors affecting survival differ by run-timing and location: linear mixed-effects models of Pacific salmonids (Oncorhynchus spp.) in the Klamath River, California. PDF icon Quinones et al 2014 survival linear mixed-effects models.pdf (689.29 KB)
Quiñones, R. M., Holyoak M., Johnson M. L., & Moyle P. B. (2014).  Potential Factors Affecting Survival Differ by Run-Timing and Location: Linear Mixed-Effects Models of Pacific Salmonids (Oncorhynchus spp.) in the Klamath River, California. PLOS One. 9(5), PDF icon journal.pone_.0098392.pdf (702.76 KB)
Moyle, P. B., & Marchetti M. P. (2006).  Predicting Invasion Success: Freshwater Fishes in California as a Model. BioScience. 56(6), 515-524.
Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G. (1996).  Preface. (Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G., Ed.).Biological Conservation, Invasion biology. 78, 1 - 2.
Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G. (1996).  Preface. (Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G., Ed.).Biological Conservation, Invasion biology. 78, 1 - 2.
Santos, N. R., Katz J. V. E., Moyle P. B., & Viers J. H. (2014).  A programmable information system for management and analysis of aquatic species range data in California. Environmental Modelling & Software. 53, 13 - 26.PDF icon Santos_et_al_PISCES-2014.pdf (2.98 MB)
Moyle, P. B., Kiernan J. D., Crain P. K., & Quiñones R. M. (2012).  Projected Effects of Future Climates on Freshwater Fishes of California. Our Changing Climate.
Kondolf, G.M., Angermeier P. L., Cummins K., Dunne T., Healey M., Kimmerer W., et al. (2008).  Projecting Cumulative Benefits of Multiple River Restoration Projects: An Example from the Sacramento-San Joaquin River System in California. Environmental Management. 42(6), 933-945.
Marchetti, M. P., & Moyle P. B. (2010).  Protecting Life on Earth: An Introduction to the Science of Conservation. 232.
Moyle, P. B. (2008).  Protecting migration routes. Issues in Science and Technology. 24 (summer)(4), 
Moyle, P. B., & Yoshiyama R. M. (1994).  Protection of Aquatic Biodiversity in California: A Five-tiered Approach. Fisheries. 19(2), 6-18.
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Moyle, P. B., & F Senanayake R. (1981).  Rainforest fishes of Sri Lanka. Loris . 15, 341-344.
Moyle, P. B., Katz J. V. E., & Quiñones R. M. (2011).  Rapid decline of California’s native inland fishes: A status assessment. Biological Conservation. 144(10), 
Moyle, P. B., Katz J. V. E., & Quiñones R. M. (2011).  Rapid decline of California's native inland fishes: a status assessment.
Börk, K. S., Krovoza J. F., Katz J. V. E., & Moyle P. B. (2012).  The Rebirth of California Fish & Game Code Section 5937: Water for Fish. UC Davis Law Review. 45, 105.PDF icon The Rebirth of California Fish & Game Code Section 5937: Water for Fish (495.38 KB)
Moyle, P. B. (1973).  Recent changes in the fish fauna of the San Joaquin River system. Cal-Neva Wildlife. 1973, 60–63.
Hanson, C., Landis P., Luce B., McBain S., Mitchell D., Moyle P. B., et al. (2007).  Recommendations on Restoring Spring-run Chinook Salmon to the Upper San Joaquin River. 34.
Moyle, P. B., Pine R., Brown L. R., Hanson C.H., Herbold B., Lentz K.M., et al. (1996).  Recovery plan for the Sacramento-San Joaquin Delta native fishes. 193.
Carmona-Catot, G., & Moyle P. B. (2013).  Re-establishment of the natural life histories of Eagle Lake rainbow trout, USA. (Soorae, P. S., Ed.).Global Re-introduction Perspectives: 2013. Further case studies from around the globe. 21-25.
Mount, JF., Moyle P. B., Lund J. R., & Doremus H. (2007).  Regional Agreements, Adaptation, and Climate Change: New Approaches to FERC Licensing in the Sierra Nevada, California.
Miller, D. L., Leonard P. M., Hughes R. M., Karr J. R., Moyle P. B., Schrader L. H., et al. (1988).  Regional Applications of an Index of Biotic Integrity for Use in Water Resource Management. Fisheries. 13(5), 12-20.
Moyle, P. B., Andrews RE., Jenkins RM., Noble R. L., Saila S. B., & Wick W. O. (1979).  Research needs in fisheries. Transactions of the 44th North American Wildlife and Natural Resources Conference. 176-187.
Moyle, P. B., & F. Senayake R. (1984).  Resource partitioning among the fishes of rainforest streams in Sri Lanka. Journal of Zoology. 202(2), 195–223.
Moyle, P. B., Herbold B., & Daniels R. A. (1982).  Resource partitioning in a non-coevolved assemblage of estuarine fishes. (Caillet, G. M., & Simenstad C. A., Ed.).Proceedings of the Third Pacific Workshop on Fish Food Habit Studies. 178-184.
Moyle, P. B., Vondracek B., & Grossman G. D. (1983).  Responses of Fish Populations in the North Fork of the Feather River, California, to Treatments with Fish Toxicants. North American Journal of Fisheries Management. 3(1), 48-60.
Crain, P. K., Moyle P. B., Woodley C., Cech J. J., Schwartz R., & May B. (2007).  Restoration of Sacramento perch to the San Francisco Estuary.
Moyle, P. B. (2000).  Restoring aquatic ecosystems is a matter of values. California Agriculture. 54(2), 16–25.
Kiernan, J. D., Moyle P. B., & Crain P. K. (2012).  Restoring native fish assemblages to a regulated California stream using the natural flow regime concept. Ecological Applications. 22(5), 10.PDF icon Kiernan et al. 2012, Ecological Applications (560.77 KB)
Moyle, P. B., Smith J. J., & Baltz D. M. (1982).  A Review. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 255-256.
Moyle, P. B., Smith J. J., & Baltz D. M. (1982).  A Review. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 255-256.
Moyle, P. B. (2012).  Review of An entirely synthetic fish: how rainbow trout beguiled America and overran the world by Anders Halverson. Quarterly Review of Biology . 87(168), 
Moyle, P. B. (2008).  Review of: Analysis and interpretation of freshwater fisheries data. (Guy, CS., & Brown ML., Ed.).Quarterly Review of Biology. 83, 203-204.
Moyle, P. B. (1987).  Review of C. H. Hocutt and E. O. Wiley, The Zoogeography of North American Freshwater Fishes. Aquaculture . 62, 171-172.
Moyle, P. B. (2003).  Review of Candiru: life and legend of bloodsucking catfishes by Stephen Spotte. Fisheries . 28(1), 
Moyle, P. B. (2011).  Review of Community ecology of stream fishes: concepts, approaches, and techniques, edited by K.B. Gido and D. A. Jackson. Quarterly Review of Biology . 86(339), 
Moyle, P. B. (1980).  Review of D. L. Soltz and R. J. Naiman, The Natural History of Native Fishes in the Death Valley System. Natural History Museum of Los Angeles County Science Series 30. . Environmental Biology of Fishes . 5(1), 96.
Moyle, P. B. (1981).  Review of E. K. Balon (Editor), Charrs, salmonid fishes of the Genus Salvelinus. Transactions of the American Fisheries Society . 110, 313-316.