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Sturgess, J. A., & Moyle P. B. (1978).  Biology of rainbow trout (Salmo gairdneri), brown trout (S. trutta), and interior Dolly Varden (Salvelinus confluentus) in the McCloud River, California, in relation to management. Cal-Neva Wildlife . 1978, 239-250.
Brown, L. R., Chase S., Mesa M., Beamish R., & Moyle P. B. (2010).  Biology, management, and conservation of lampreys in North America. American Fisheries Society Symposium . 72, 321.
Crain, P. K., & Moyle P. B. (2011).  Biology, History, Status, and Conservation of Sacramento Perch, Archoplites interruptus: A Review . San Francisco Estuary and Watershed Science. 9(1), 
Daniels, R. A., & Moyle P. B. (1978).  Biology, Distribution and Status of Cottus asperrimus in the Pit River Drainage, Northeastern California. Copeia. 1978(4), 673-679.
Moyle, P. B., Baxter R. D., Sommer T., Foin T. C., & Matern S. A. (2004).  Biology and Population Dynamics of Sacramento Splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: A Review. San Francisco Estuary and Watershed Science. 2(2), 1-47.
Lodge, D. M., Williams S., Isaac H. J. Mac, Hayes K. R., Leung B., Reichard S., et al. (2006).  Biological Invasions: Recommendations for U.S. Policy and Management. Ecological Applications. 16(6), 2035-2054.
Moyle, P. B., & Light T. (1996).  Biological invasions of fresh water: Empirical rules and assembly theory. Biological Conservation. 78(1-2), 149 - 161.
Moyle, P. B., & Williams J. E. (1990).  Biodiversity Loss in the Temperate Zone: Decline of the Native Fish Fauna of California. Conservation Biology. 4(3), pp. 275-284.
Jr, WR. Courtenay, & Moyle P. B. (1996).  Biodiversity, fishes, and the introduction paradigm. (Szaro, R. C., & Johnston D. W., Ed.).Biodiversity in Managed Landscapes. 239–252.
Moyle, P. B. (1994).  Biodiversity, biomonitoring, and the structure of stream fish communities. (Loeb, S., & Spacie A., Ed.).Biological monitoring of aquatic systems. 171–186.
Trenham, P. C., H. Shaffer B., & Moyle P. B. (1998).  Biochemical Identification and Assessment of Population Subdivision in Morphologically Similar Native and Invading Smelt Species (Hypomesus) in the Sacramento-San Joaquin Estuary, California. Transactions of the American Fisheries Society. 127(3), 417-424.
Jeffres, C., Mount JF., Moyle P. B., Deas M., Buckland E., Hammock B., et al. (2007).  Baseline Assessment of Salmonid Habitat and Aquatic Ecology of the Nelson Ranch, Shasta River, California Water Year 2007. PDF icon Read full report (1.9 MB)
Jeffres, C., Dahlgren R. A., Kiernan J. D., King A. M., Lusardi R. A., Nichols A., et al. (2009).  Baseline Assessment of Physical and Biological Conditions Within Waterways on Big Springs Ranch, Siskiyou County, California. PDF icon Read full study (9.11 MB)
Moyle, P. B. (1991).  Ballast water introductions. Fisheries. 16, 4–6.
Jeffres, C., Nichols A., Willis A., Mount JF., Moyle P. B., & Deas M. (2010).  Assessment of Restoration Actions on Big Springs Creek, Shasta River, California 2009-2010.
Grantham, T. E., & Moyle P. B. (2014).  Assessing flows for fish below dams: A systematic approach to evaluate compliance with California Fish and Game Code 5937. Center for Watershed Sciences Technical Reports. 1-136.PDF icon Download complete report (5.64 MB)
Baumsteiger, J., & Moyle P. B. (2017).  Assessing Extinction. Bioscience. 67,
Light, T., Moyle P. B., & J Clode C. (2015).  Assembly rules and novel assemblages in aquatic ecosystems. Biological Invasions in Changing Ecosystems Vectors, Ecological Impacts, Management and Predictions.
Broadway, J. E., & Moyle P. B. (1978).  Aspects of the ecology of the prickly sculpin,Cottus asper Richardson, a persistent native species in Clear Lake, Lake County, California. Environmental Biology of Fishes. 3(4), 337-343.
R. Geary, E., & Moyle P. B. (1980).  Aspects of the Ecology of the Hitch, Lavinia exilicauda (Cyprinidae), a Persistent Native Cyprinid in Clear Lake, California. The Southwestern Naturalist. 25(3), 385-390.
Moyle, P. B. (1977).  Are coarse fish a curse? . Fly Fisherman, Early Season . 8, 35-39.
Schroeter, RE., O'Rear T., Young M., & Moyle P. B. (2015).  The aquatic trophic ecology of Suisun Marsh, San Francisco Estuary, California, during autumn in a wet year. San Francisco Estuary and Watershed Science. 13(3), 
Kimmerer, W., Brown L. R., Culberson S., Moyle P. B., Nobriga M., & Thompson J. (2008).  Aquatic ecosystems. (Healey, M., Dettinger M., & Norgaard R., Ed.).The State of Bay-Delta Science 2008. 55-72.
Mount, JF., Bennett W. A., Durand J. R., Fleenor W. E., Hanak E., Lund J. R., et al. (2012).  Aquatic Ecosystem Stressors in the Sacramento–San Joaquin Delta. 22.
Moyle, P. B., & Marchetti M. P. (1999).  Applications of indices of biotic integrity to California streams and watersheds. (Simon, T. P., & Hughes R., Ed.).Assessing the sustainability and biological integrity of water resources using fish communities. 367–380.
Moyle, P. B. (1984).  America's carp. Natural History. 93(9), 42-51.
Jr, J. J. Cech, & Moyle P. B. (1983).  ALTERNATIVE FISH SPECIES AS PREDATORS FOR RICE FIELD MOSQUITOS IN CALIFORNIA'. Bulletin of the Society of Vector Ecologists. 8(2), 107–110.
Stanley, S. E., Moyle P. B., & H. Shaffer B. (1995).  Allozyme Analysis of Delta Smelt, Hypomesus transpacificus and Longfin Smelt, Spirinchus thaleichthys in the Sacramento-San Joaquin Estuary, California. Copeia. 1995(2), 390-396.
Moyle, P. B. (2000).  Aliens in fresh water. Review of R. Claudi and J. H. Leach, eds. 2000. Non-indigenous freshwater organisms: vectors, biology, and impacts. . Ecology . 81, 2945-2946.
Moyle, P. B., Crain P. K., Whitener K., & Mount JF. (2003).  Alien Fishes in Natural Streams: Fish Distribution, Assemblage Structure, and Conservation in the Cosumnes River, California, U.S.A.. Environmental Biology of Fishes. 68(2), 143-162.
Marchetti, M. P., Moyle P. B., & Levine R. (2004).  Alien Fishes in California Watersheds: Characteristics of Successful and Failed Invaders. Ecological Applications. 14(2), 587-596.
Schroeter, RE., & Moyle P. B. (2005).  Alien fishes in California’s marine environments. (Allen, L. G., & Horn M. H., Ed.).Ecology of California marine fishes. . 611–620.
Lund, J. R., & Moyle P. B. (2013).  Adaptive Management and Science for the Delta Ecosystem. San Francisco Estuary and Watershed Science. 11(3), 
Chornesky, E. A., Ackerly D. D., Beier P., Davis F. W., Flint L. E., Lawler J. J., et al. (2015).  Adapting California's Ecosystems to a Changing Climate. BioScience. 65(3), 247–262.
Wintzer, A. P., Meek M. H., & Moyle P. B. (2013).  Abundance, size, and diel feeding ecology of Blackfordia virginica (Mayer, 1910), a non-native hydrozoan in the lower Napa and Petaluma Rivers, California (USA). Aquatic Invasions. 8(2), 147–156.