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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. (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), 
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. (2000).  Restoring aquatic ecosystems is a matter of values. California Agriculture. 54(2), 16–25.
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.
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.
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. (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.
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), 
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), 
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.
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., & 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. (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.
Moyle, P. B. (1970).  Occurrence of king (chinook) salmon in the Kings River, Fresno County. California Fish and Game . 56, 314-315.
Moyle, P. B., & Li H.W. (1994).  Nuisance essay: good report but should go much farther. Fisheries. 19, 22-23.
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.
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.
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.
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., 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.
Liu, J-X., Taternkov A., O'Rear T., Moyle P. B., & Avise J. (2012).  Molecular evidence for multiple paternity in a population of the viviparous tule perch, Hysterocarpus traski. Journal of Heredity. 104(2), 
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.
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.
Bunn, D. A., Moyle P. B., & Johnson C. K. (2014).  Maximizing the ecological contribution of conservation banks. Wildlife Society Bulletin. 38(2), 377–385.
Herbold, B. (2018).  Managing for salmon resilience in California’s variable and changing climate. (Carlson, SM., Henery R., Johnson RC., Mantua N., Moyle P. B., & Sommer T., Ed.).San Francisco Estuary and Watershed Sciences. 16(2), PDF icon SFEWS_Herbold_0818_final.pdf (6.85 MB)
Noss, R. F., Franklin J. F., Baker W. L., Schoennagel T., & Moyle P. B. (2006).  Managing Fire-Prone Forests in the Western United States. Frontiers in Ecology and the Environment. 4(9), pp. 481-487.
Mount, JF., Gray B., Chappelle C., Gartrell G., Grantham T. E., Moyle P. B., et al. (2017).  Managing California's Freshwater Ecosystems: Lessons from the 2012-16 Drought.. Public Policy Institute of California.
Bugg, RL., & Moyle P. B. (2006).  Making a precarious perch more secure: Central Valley farm ponds for native fish conservation. Sustainable Agriculture . 18(3), 
Baumsteiger, J., Schroeter R., O'Rear T., Cook J., & Moyle P. B. (2017).  Long-term surveys show invasive overbite clams (Potamocorbula amurensis) are spatially limited in Suisun Marsh. San Francisco Estuary and Watershed Science. 15(1), 
Carmona-Catot, G., Moyle P. B., & Simmons R. E. (2012).  Long-term captive breeding does not necessarily prevent reestablishment: lessons learned from Eagle Lake rainbow trout. Reviews in Fish Biology and Fisheries. 22(1), 325-342.
O'Rear, T., & Moyle P. B. (2010).  Long term and recent trends in fishes and invertebrates in Suisun Marsh. Interagency Ecological Program Newsletter. 23(2), 
Moyle, P. B. (1991).  Livebearing fish in evolutionary research. Review of G. K. Meffe and F. F. Snelson (Editors), Ecology and Evolution of Livebearing Fishes (Poeciliidae). Prentice Hall, Englewood Cliffs, New Jersey. Evolution. 45, 453pp.
Moyle, P. B., & Davis L. H. (2001).  A list of freshwater, anadromous, and euryhaline fishes of California. California Fish and Game. 86(4), 244–258.