Publications

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Book Chapter
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.
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.
Viers, S.. D., Opler P.. A., Gilmer D.. S., Graber D.. M., Graham T.., Huckaby L.. S., et al. (1998).  California. (Mac, M.. J., Opler P.. A., Haecker C.. E. Puckett, & Doran P.. D., Ed.).Status and trends of the nation’s biological resources. 1 & 2, 593-603.
Johnson, RC., Lindley TC., Spence BC., Boughton DA., Crozier LG., Mantua NJ., et al. (2016).  Central Valley Domain. (Williams, TH., Ed.).Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act: Southwest. NOAA Technical Memorandum NMFS-SWFSC-564, PDF icon NOAA-TM-NMFS-SWFSC-564.pdf (6.23 MB)
Hobson, K., Cerling T., & Johnson RC. (2010).  Isotope tracking of terrestrial and freshwater vertebrates. (Bowen, G., Dawson T., & Tu K., Ed.).Isoscapes: Understanding movement patterns and processes on earth through isotope mapping.
Moyle, P. B., & Leidy R. A. (1992).  Loss of Biodiversity in Aquatic Ecosystems: Evidence from Fish Faunas. (Fiedler, P. L., & Jain S. K., Ed.).Conservation Biology: The Theory and Practice of Nature Conservation, Preservation, and Management. 128-169.
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. (2012).  Writing review papers. (Jennings, C. A., Lauer T. E., & Vondracek B., Ed.).Scientific Communication for Natural Resource Professionals. 155-162.
Conference Paper
Medellín-Azuara, J., Rosenstock T. S., Howitt R., Harter T., Jessoe K., Dzurella K. N., et al. (2012).  Economic Analysis of Crop Nitrate Source Reductions. International Water Resources: Challenges for the 2151 Century and Water Resources Education.
Harou, J., Medellín-Azuara J., Zhu T., Tanaka S., Lund J. R., Stine S., et al. (2006).  Extreme Drought and Water Supply Management in California. World Environmental and Water Resource Congress 2006. 1-10.
Gailey, R., & Jones D.E.. (1987).  The Use of Sediment Permeability Variations in the Performance of Petroleum Recovery from Glacial Sediments. Proc. of the Focus on Eastern Regional Groundwater Issues.
Journal Article
Medellín-Azuara, J., Harou J. J., Olivares M., Madani K., Lund J. R., Tanaka S., et al. (2008).  Adaptability and Adaptations of California's Water Supply System to Dry Climate Warming. Climatic Change. 87(S1), 
Medellín-Azuara, J., Rosenstock T. S., Howitt R., Harter T., Jessoe K., Dzurella K. N., et al. (2013).  Agro-Economic Analysis of Nitrate Crop Source Reductions. Journal of Water Resources Management and Planning ASCE. 139(5), 11.
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.
Harou, J. J., Medellín-Azuara J., Zhu T., Tanaka S., Lund J. R., Stine S., et al. (2010).  Economic consequences of optimized water management for a prolonged, severe drought in California. Water Resources Research. 46(W05522), PDF icon UC Davis Mega-drought study (531.61 KB)
Oxman, DS., Barnett-Johnson R., Smith M., Coffin SM., Miller D., Josephson R., et al. (2007).  The effect of vaterite deposition on sound reception, otolith morphology, and inner ear sensory epithelia in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences. 64,
Phillis, C.C.., Sturrock A.M.., Johnson RC., & Weber P.K.. (2018).  Endangered winter-run Chinook salmon rely on diverse rearing habitats in a highly altered landscape.. Biological Conservation. 217, PDF icon Phillis_et_al_2017_Biological_Conservation.pdf (907.84 KB)
Jeffres, C., Opperman J.J.., & Moyle P. B. (2008).  Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river. Environmental Biology of Fishes. 83(4), 
Jett, S. C., & Moyle P. B. (1986).  The Exotic Origins of Fishes Depicted on Prehistoric Mimbres Pottery from New Mexico. American Antiquity. 51(4), 688-720.
Grimaldo, L. F., Sommer T., Van Ark N., Jones G., Holland E., Moyle P. B., et al. (2009).  Factors Affecting Fish Entrainment into Massive Water Diversions in a Tidal Freshwater Estuary: Can Fish Losses be Managed?. North American Journal of Fisheries Management. 29(5), 1253-1270.
Schaefer, M. M., Doyle L. A., Fleenor W. E., & Johnson M. L. (2013).  Fate and Transport of Three Pharmaceuticals in the Sacramento-San Joaquin Delta. Fate and Transport of Three Pharmaceuticals in the Sacramento-San Joaquin Delta. 11(2), PDF icon SFEW Science Nine 2013 (650.98 KB)
Willmes, M., Hobbs J. A., Sturrock A.M.., Bess Z., Lewis L.S., Glessner JG., et al. (2018).  Fishery collapse, recovery, and the cryptic decline of wild salmon on a major California River. Canadian Journal of Fisheries and Aquatic Sciences. PDF icon cjfas-2017-0273.pdf (7.7 MB)
Katz, J., Jeffres C., Conrad L., Sommer T., Martinex J.., Brumbaugh S., et al. (2017).  Floodplain farm fields provide novel rearing habitat for Chinook salmon. PLoS ONE. 12(6), 
Quiñones, R. M., Johnson M. L., & Moyle P. B. (2014).  Hatchery practices may result in replacement of wild salmonids: adult trends in the Klamath basin, California. Environmental biology of fishes. 97, 233–246.
Quiñones, R. M., & Johnson M. L. (2014).  Hatchery practices may result in replacement of wild salmonids: adult trends in the Klamath basin, California. Environmental Biology of Fishes. 97(3), 233-246.PDF icon Quiñones et al 2013.pdf (486.04 KB)
Morais, P.., Dias E.., Cerveira I.., Carlson S.M.., Johnson R.C.., & Sturrock A.M.. (2018).  How Scientists Reveal The Secret Migrations of Fish. Frontiers for Young Minds. 6(67), PDF icon Morais et al 2018 secret migrations of fish frym-06-00067_small.pdf (536.93 KB)
Heublein, J., Bellmer R., Chase RD., Doukakis P., Gingras M., Hampton D., et al. (2017).  Improved fisheries management through life stage monitoring: the case for the Southern Distinct Population Segment of North American Green Sturgeon and the Sacramento-San Joaquin River White Sturgeon. NOAA Technical Memorandum . NMFS-SWFSC-588, PDF icon NOAA-TM-NMFS-SWFSC-588.pdf (1.53 MB)
Heublein, J., Bellmer R., Chase RD., Doukakis P., Gingras M., Hampton D., et al. (2017).  Improved fisheries management through life stage monitoring: the case for the Southern Distinct Population Segment of North American Green Sturgeon and the Sacramento-San Joaquin River White Sturgeon. NOAA Technical Memorandum . NMFS-SWFSC-588, PDF icon NOAA-TM-NMFS-SWFSC-588.pdf (1.53 MB)
Johnson, RC., Garza JC., MacFarlane RB., Phillis CC., Koch PL., Weber PK., et al. (2016).  Isotopes and genes reveal freshwater origins of Chinook salmon (Oncorhynchus tshawytscha) aggregations in California’s coastal ocean. Marine Ecology Progress Series. 548,
Heublein, J., Bellmer R., Chase RD., Doukakis P., Gingras M., Hampton D., et al. (2017).  Life history and current monitoring inventory of San Francisco Estuary sturgeon. NOAA Technical Memorandum . NMFS-SWFSC-589, PDF icon NOAA-TM-NMFS-SWFSC-589.pdf (420.07 KB)
Heublein, J., Bellmer R., Chase RD., Doukakis P., Gingras M., Hampton D., et al. (2017).  Life history and current monitoring inventory of San Francisco Estuary sturgeon. NOAA Technical Memorandum . NMFS-SWFSC-589, PDF icon NOAA-TM-NMFS-SWFSC-589.pdf (420.07 KB)
Heublein, J., Bellmer R., Chase RD., Doukakis P., Gingras M., Hampton D., et al. (2017).  Life history and current monitoring inventory of San Francisco Estuary sturgeon. NOAA Technical Memorandum . NMFS-SWFSC-589, PDF icon NOAA-TM-NMFS-SWFSC-589.pdf (420.07 KB)
Johnson, RC., Weber PK., Wikert JD., Workman M., MacFarlane RB., Grove MJ., et al. (2012).  Managed metapopulations: Do salmon hatchery ‘sources’ lead to in-river ‘sinks’ in conservation?. PLos ONE. 7(2), PDF icon 2012_Johnson_plosone.pdf (418.82 KB)
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)
Bunn, D. A., Moyle P. B., & Johnson C. K. (2014).  Maximizing the ecological contribution of conservation banks. Wildlife Society Bulletin. 38(2), 377–385.
Feyrer, FV., Hobbs J., Acuna S., Mahardja B., Grimaldo L., Baerwald B., et al. (2015).  Metapopulation structure of a semi-anadromous fish in a dynamic environment. Canadian Journal of Fisheries and Aquatic Sciences. 72(5), 
Young, C., Escobar M., Fernandes M., Joyce B., Kiparsky M., Mount JF., et al. (2009).  Modeling the Hydrology of Climate Change in California's Sierra Nevada for Subwatershed Scale Adaptation. Journal of the American Water Resources Association. 45(6), 
Jeffres, C. A., A Klimley P., Merz J. E., & Cech J. J. (2006).  Movement of Sacramento sucker, Catostomus occidentalis, and hitch, Lavinia exilicauda, during a spring release of water from Camanche Dam in the Mokelumne River, California. Environmental Biology of Fishes. 75, 365–373.
Jeffres, C. A., & Adams C. (2019).  Novel life history tactic observed in fall-run Chinook Salmon. Ecology. 100(10), 
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)
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)
Sturrock, A.M.., Hunter E., Milton AEIMF., Johnson RC., Waring CP., & Trueman CN. (2015).  Quantifying physiological influences on otolith microchemistry. Methods in Ecology and Evolution. 6, PDF icon Sturrock et al 2015 Quantifying physiological influences on otolith microchemistry MEE_small.pdf (918.81 KB)
Ali, O. A., O'Rourke S. M., Amish S. J., Meek M. H., Luikart G., Jeffres C., et al. (2016).  RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. Genetics. 202 (2),