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Book Chapter
Podolak, K., & Yarnell S. M. (2015).  Adaptive management in Federal Energy Regulatory Commission relicensing. The Water Sustainability Reader: Lessons from California for the 21st Century. 193-211.
Taylor, T. L., Moyle P. B., & Price DG. (1982).  Fishes of the Clear Lake Basin. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 171–224.
Lund, J. R., Hui R., Escriva-Bou A., Porse E., Adams L., Connaughton J., et al. (2017).  Reservoir Operation Design. The Handbook of Applied Hydrology.
Journal Article
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.
Steel, A. E., Peek R. A., Lusardi R. A., & Yarnell S. M. (2018).  Associating metrics of hydrologic variability with benthic macroinvertebrate communities in regulated and unregulated snowmelt-dominated rivers. Freshwater Biology. 63(8), 844-858.
Wilkinson, G. M., Walter J. A., Fleck R., & Pace M. L. (2020).  Beyond the trends: the need to understand multiannual dynamics in aquatic ecosystems. Limnology and Oceanography Letters. 5,
Power, M. E., R. Stout J., Cushing C. E., Harper P. P., F. Hauer R., Matthews W. J., et al. (1988).  Biotic and Abiotic Controls in River and Stream Communities. Journal of the North American Benthological Society. 7(4), 456-479.
Willis, A. D., Peek R. A., & Rypel A. L. (2021).  Classifying California’s stream thermal regimes for cold-water conservation. PloS one. 16, e0256286.
Baird, I., Hogan Z., Phylaivanh B., & Moyle P. B. (2001).  A Communal Fishery for the Migratory Catfish Pangasius macronemain the Mekong River. Asian Fisheries Science. 14, 25–41.
Tassone, S. J., Besterman A. F., Buelo C. D., Walter J. A., & Pace M. L. (2021).  Co-occurrence of Aquatic Heatwaves with Atmospheric Heatwaves, Low Dissolved Oxygen, and Low pH Events in Estuarine Ecosystems. Estuaries and Coasts. 1–14.
Medellín-Azuara, J., Durand J. R., Fleenor W. E., Hanak E., Lund J. R., Moyle P. B., et al. (2013).  Costs of Ecosystem Management Actions for the Sacramento-San Joaquin Delta.
Milner, V., Yarnell S. M., & Peek R. A. (2018).  The ecological importance of unregulated tributaries to macroinvertebrate diversity and community composition in a regulated river. Hydrobiologia. 829, 291-305.
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)
Perales, M., Rowan J., & Moyle P. B. (2015).  Evidence of Landlocked Chinook Salmon Populations in California. North American Journal of Fisheries Management. 35(6), PDF icon Perales_Salmon.pdf (498.87 KB)
Young, M., Perales M., Durand J. R., & Moyle P. B. (2016).  Fish distribution in the cache slough complex of the Sacramento-San Joaquin Delta during a drought. IEP Newsletter.
Mosepele, K., Moyle P. B., Merron G. S., Purkey D. R., & Mosepele B. (2009).  Fish, Floods, and Ecosystem Engineers: Aquatic Conservation in the Okavango Delta, Botswana. BioScience. 59(1), 53-64.
Peek, R. A., O'Rourke S. M., & Miller M. R. (2021).  Flow modification associated with reduced genetic health of a river‐breeding frog, Rana boylii. Ecosphere. 12(5), 
Howard, J. K., Fesenmyer K., Grantham T. E., Viers J. H., Ode P., Moyle P. B., et al. (2018).  A Freshwater Conservation Blueprint for California: Prioritizing Watersheds for Freshwater Biodiversity. Freshwater Science. 37(2), 
Yarnell, S. M., Stein E. D., Webb J.A., Grantham T. E., Lusardi R. A., Zimmerman J., et al. (2020).  A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications. River Research and Applications. 36(2), 318–324.PDF icon Yarnell et al. 2020 RRA (759.84 KB)
Yarnell, S. M., Petts G., Schmidt J., Whipple A., Beller E., Dahm C., et al. (2015).  Functional Flows in Modified Riverscapes: Hydrographs, Habitats and Opportunities. BioScience. 65(9), PDF icon BioScience-2015-Yarnell-biosci_biv102.pdf (327.28 KB)
Brown, K., & Pasternack G. (2004).  The geomorphic dynamics of an upper deltaic floodplain tract in the Sacramento-San Joaquin Delta, California, USA. Earth Surface Processes and Landforms. 29,
Rypel, A. L., Vaughn C. C., Nesper L., O’Reilly K., Parisek C. A., Miller M. L., et al. (2021).  Goodbye to “Rough Fish”: Paradigm Shift in the Conservation of Native Fishes. (Saffarinia, P., Ed.).Fisheries.
Peek, R. A., Bedwell M., O'Rourke S. M., Goldberg C., Wengert G. M., & Miller M. R. (2019).  Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA. Molecular ecology. 28, 4636–4647.
Harou, J. J., Pulido-Velazquez M., Rosemberg D., Medellín-Azuara J., Lund J. R., & Howitt R. (2009).  Hydro-economic models: Concepts, design, applications, and future prospects. Journal of Hydrology. 375(3-4), 
Parker, I.M., Simberloff D., Lonsdale W.M., Goodell K., Wonham M., Kareiva P.M., et al. (1999).  Impact: Toward a Framework for Understanding the Ecological Effects of Invaders. Biological Invasions. 1(1), 3-19.
Katz, J. V. E., Moyle P. B., Quiñones R. M., Israel J. A., & Purdy S. (2012).  Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes.
Katz, J. V. E., Moyle P. B., Quiñones R. M., Israel J. A., & Purdy S. (2013).  Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes. 96, 1169-1186.PDF icon Katz_et_al._2013 salmonids in CA.pdf (517.46 KB)
Forni, L. G., Medellín-Azuara J., Tansey M., Young C., Purkey D., & Howitt R. (2016).  Integrating Complex Economic and Hydrologic Planning Models: An Application for Drought Under Climate Change Analysis. Water Resources and Economics.
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,
Fangue, N. A., Cocherell D. E., Maudult F., Poletto J. B., Carr K., O'Rear T., et al. (2021).  Juvenile Chinook salmon use of sandbar willows in a large-scale, simulated riparian floodplain: microhabitat and energetics. Environmental Biology of Fishes.
Yarnell, S. M., Peek R. A., Keung N., Todd B. D., Lawler S., & Brown C. (2019).  A lentic breeder in lotic waters: Sierra Nevada Yellow-Legged Frog (Rana sierrae) habitat suitability in northern Sierra Nevada streams. Copeia.
Yarnell, S. M., Peek R. A., Epke G., & Lind A. J. (2016).  Management of the Spring Snowmelt Recession in Regulated Systems. JAWRA Journal of the American Water Resources Association. 52, 723-736.
Grantham, T. E., Perrée I., Cañedo-Argüelles M., Rieradevall M., & Prat N. (2012).  A mesocosm approach for detecting stream invertebrate community responses to treated wastewater effluent. Environmental Pollution. 160, 95-102.
Grantham, T. E., Perrée I., Cañedo-Argüelles M., Rieradevall M., & Prat N. (2012).  A mesocosm approach for detecting stream invertebrate community responses to treated wastewater effluent. Environmental Pollution. 160, 95-102.
Pinter, N., Huthoff F., Dierauer J., Remo W.F., & Damptz A. (2016).  Modeling residual flood risk behind levees, Upper Mississippi River, USA. Environmental Science & Policy. 58(131-140), PDF icon PinterEtAl2016.pdf (517.19 KB)
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), 
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.
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.
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.
Brown, K., & Pasternack G. (2005).  Natural and anthropogenic geochemical signatures of floodplain and deltaic sedimentary strata, Sacramento Delta, CA. Environmental Pollution. 141(2), 
Wilkinson, G. M., Walter J. A., Buelo C. D., & Pace M. L. (2021).  No evidence of widespread algal bloom intensification in hundreds of lakes. Frontiers in Ecology and the Environment.