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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.
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.
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.
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.
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. (1973).  Recent changes in the fish fauna of the San Joaquin River system. Cal-Neva Wildlife. 1973, 60–63.
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., Katz J. V. E., & Quiñones R. M. (2011).  Rapid decline of California's native inland fishes: a status assessment.
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., & F Senanayake R. (1981).  Rainforest fishes of Sri Lanka. Loris . 15, 341-344.
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Williams, P. B., Andrews E., Opperman J.J., Bozkurt S., & Moyle P. B. (2009).  Quantifying activated floodplains on a lowland regulated river: its application to floodplain restoration in the Sacramento Valley. San Francisco Estuary and Watershed Science. 7(1), 
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Moyle, P. B., & Yoshiyama R. M. (1994).  Protection of Aquatic Biodiversity in California: A Five-tiered Approach. Fisheries. 19(2), 6-18.
Moyle, P. B. (2008).  Protecting migration routes. Issues in Science and Technology. 24 (summer)(4), 
Marchetti, M. P., & Moyle P. B. (2010).  Protecting Life on Earth: An Introduction to the Science of Conservation. 232.
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.
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.
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)
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.
Moyle, P. B., & Marchetti M. P. (2006).  Predicting Invasion Success: Freshwater Fishes in California as a Model. BioScience. 56(6), 515-524.
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., 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.
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. (1964).  Populations of peritrichs on the pond snail, Physa gyrina Say. Journal of the Minnesota Academy of Science . 31, 125-130.
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.
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), 
Moyle, P. B., & Vondracek B. (1985).  Persistence and Structure of the Fish Assemblage in a Small California Stream. Ecology. 66(1), 1-13.
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., 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), 
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.
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Moyle, P. B. (1970).  Occurrence of king (chinook) salmon in the Kings River, Fresno County. California Fish and Game . 56, 314-315.
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Moyle, P. B., & Li H.W. (1994).  Nuisance essay: good report but should go much farther. Fisheries. 19, 22-23.
Durand, J. R., & Moyle P. B. (2011).  Novel ecosystems? Changes in the Kobuk River basin (AK) and the Sacramento-San Joaquin Delta (CA), USA.
Moyle, P. B. (2013).  Novel Aquatic Ecosystems: The New Reality For Streams In California And Other Mediterranean Climate Regions. River Research and Applications. PDF icon Novel aquatic ecosystems (2.62 MB)
Ribeiro, F., Collares-Pereira M. J., & Moyle P. B. (2009).  Non-native fish in the fresh waters of Portugal, Azores and Madeira Islands: a growing threat to aquatic biodiversity. Fisheries Management and Ecology. 16(4), 255–264.
Brown, L. R., & Moyle P. B. (1992).  Native fishes of the San Joaquin drainage: status of a remnant fauna and its habitats. (Williams, D. L., Byrne S., & Rado T. A., Ed.).Endangered and sensitive species of the San Joaquin Valley, California: their biology, management and conservation. 89–98.
Brown, L. R., & Moyle P. B. (2005).  Native Fishes of the Sacramento-San Joaquin Drainage, California: A History of Decline. (Rinne, J. N., Hughes R. M., & Calamusso B., Ed.).Historical Changes in Large River Fish Assemblages of the Americas. 45, 75-98.
Matern, S. A., Moyle P. B., & Pierce L. C. (2002).  Native and Alien Fishes in a California Estuarine Marsh: Twenty-One Years of Changing Assemblages. Transactions of the American Fisheries Society. 131(5), 797-816.
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Hanak, E., Lund J. R., Dinar A., Gray B. E., Howitt R., Mount JF., et al. (2010).  Myths of California water: implications and reality. West Northwest. 3-73.
Prine, J.E., Lawley G.E., & Moyle P. B. (1975).  A multidisciplinary approach to vector ecology at Clear Lake, California. Bulletin of the Society of Vector Ecologists . 2, 21-31.
Purdy, S., & Moyle P. B. (2009).  Mountain Meadows of the Sierra Nevada: An Integrated Means of Determining Ecological Condition in Mountain Meadows—Protocols and Results from 2006..
Baltz, D. M., & Moyle P. B. (1981).  Morphometric Analysis of Tule Perch (Hysterocarpus traski) Populations in Three Isolated Drainages. Copeia. 1981(2), 305-311.
Moyle, P. B. (1977).  More on Nile perch. SFI Bulletin . 281, 7.
Purdy, S. E., Moyle P. B., & Tate K. W. (2012).  Montane meadows in the Sierra Nevada: comparing terrestrial and aquatic assessment methods. Environmental Monitoring and Assessment. 184(11), 6967-6986.
Liu, J-X., Taternkov A., O'Rear T., Moyle P. B., & Avise J. (2013).  Molecular evidence for multiple paternity in a population of the viviparous tule perch, Hysterocarpus traski. Journal of Heredity. 104(2), 
Liu, J-X., Tatarenkov A., O’Rear T. A., Moyle P. B., & Avise J. C. (2012).  Molecular Evidence for Multiple Paternity in a Population of the Viviparous Tule Perch Hysterocarpus traski. Journal of Heredity. 104(2), 217-222.
Moyle, P. B., Fisher FW., & Li HW. (1974).  Mississippi Silversides and Logperch In Sacramento San-Joaquin River System. California Fish and Game . 60, 144-149.
Grantham, T. E., Fesenmyer K., Peek R. A., Holmes E., Quiñones R. M., Bell A., et al. (2016).  Missing the Boat on Freshwater Fish Conservation in California. PDF icon Missing the Boat on Freshwater Fish Conservation in California (1.35 MB)
Moyle, P. B., & Baltz D. M. (1985).  Microhabitat Use by an Assemblage of California Stream Fishes: Developing Criteria for Instream Flow Determinations. Transactions of the American Fisheries Society. 114(5), 695-704.