Publications
Regional Applications of an Index of Biotic Integrity for Use in Water Resource Management.
Fisheries. 13(5), 12-20.
(1988).
(2007). 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.
(2013).
(1996).
(2007). Recent changes in the fish fauna of the San Joaquin River system.
Cal-Neva Wildlife. 1973, 60–63.
(1973). The Rebirth of California Fish & Game Code Section 5937: Water for Fish.
UC Davis Law Review. 45, 105.
The Rebirth of California Fish & Game Code Section 5937: Water for Fish (495.38 KB)
(2012).
(2011). 
Rapid decline of California’s native inland fishes: A status assessment.
Biological Conservation. 144(10),
(2011). Rainforest fishes of Sri Lanka.
Loris . 15, 341-344.
(1981). 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),
(2009). Protection of Aquatic Biodiversity in California: A Five-tiered Approach.
Fisheries. 19(2), 6-18.
(1994). Protecting migration routes.
Issues in Science and Technology. 24 (summer)(4),
(2008).
(2010). 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.
(2008). Projected Effects of Future Climates on Freshwater Fishes of California.
Our Changing Climate.
(2012). A programmable information system for management and analysis of aquatic species range data in California.
Environmental Modelling & Software. 53, 13 - 26.
Santos_et_al_PISCES-2014.pdf (2.98 MB)
(2014). 
Preface.
(Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G., Ed.).Biological Conservation, Invasion biology. 78, 1 - 2.
(1996). Preface.
(Carey, J.R., Moyle P. B., Rejmánek M., & Vermeij G., Ed.).Biological Conservation, Invasion biology. 78, 1 - 2.
(1996). Predicting Invasion Success: Freshwater Fishes in California as a Model.
BioScience. 56(6), 515-524.
(2006). Potential factors affecting survival differ by run-timing and location: linear mixed-effects models of Pacific salmonids (Oncorhynchus spp.) in the Klamath River, California.
Quinones et al 2014 survival linear mixed-effects models.pdf (689.29 KB)
(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),
journal.pone_.0098392.pdf (702.76 KB)
(2014). 
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.
(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.
(1996). Populations of peritrichs on the pond snail, Physa gyrina Say.
Journal of the Minnesota Academy of Science . 31, 125-130.
(1964). Pink salmon (Oncorhynchus gorbuscha) in the Salinas River, California: a new record and historical perspectives.
California Fish and Game. 99(1), 55-59.
(2013). 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),
(2016). Persistence and Structure of the Fish Assemblage in a Small California Stream.
Ecology. 66(1), 1-13.
(1985). Patterns of Freshwater Species Richness, Endemism, and Vulnerability in California.
PLoS ONE. 10(7),
Read full study (3.16 MB)
(2015). 
Patterns In The Use Of A Restored California Floodplain By Native And Alien Fishes.
San Francisco Estuary and Watershed Science. 5(3),
(2007). Patterns in distribution and abundance of a noncoevolved assemblage of estuarine fishes in California.
Fishery Bulletin. 84, 105-117.
(1986). Occurrence of king (chinook) salmon in the Kings River, Fresno County.
California Fish and Game . 56, 314-315.
(1970). Nuisance essay: good report but should go much farther.
Fisheries. 19, 22-23.
(1994).
(2011). Novel Aquatic Ecosystems: The New Reality For Streams In California And Other Mediterranean Climate Regions.
River Research and Applications.
Novel aquatic ecosystems (2.62 MB)
(2013). 
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.
(2009). 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.
(1992). 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.
(2005). 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.
(2002). Myths of California water: implications and reality.
West Northwest. 3-73.
(2010). A multidisciplinary approach to vector ecology at Clear Lake, California.
Bulletin of the Society of Vector Ecologists . 2, 21-31.
(1975).
(2009). Morphometric Analysis of Tule Perch (Hysterocarpus traski) Populations in Three Isolated Drainages.
Copeia. 1981(2), 305-311.
(1981). More on Nile perch.
SFI Bulletin . 281, 7.
(1977). Montane meadows in the Sierra Nevada: comparing terrestrial and aquatic assessment methods.
Environmental Monitoring and Assessment. 184(11), 6967-6986.
(2012). Molecular evidence for multiple paternity in a population of the viviparous tule perch, Hysterocarpus traski.
Journal of Heredity. 104(2),
(2013). Molecular Evidence for Multiple Paternity in a Population of the Viviparous Tule Perch Hysterocarpus traski.
Journal of Heredity. 104(2), 217-222.
(2012). Mississippi Silversides and Logperch In Sacramento San-Joaquin River System.
California Fish and Game . 60, 144-149.
(1974). Missing the Boat on Freshwater Fish Conservation in California.
Missing the Boat on Freshwater Fish Conservation in California (1.35 MB)
(2016). 
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.
(1985).