CHAPTER 12. REFERENCES - Delta REvision · 2020-01-16 · References Chapter 12 Bay Delta...

References Chapter 12

Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page i

CHAPTER 12. REFERENCES

Chapter 1 Introduction ......................................................................................................... 12-1 1 Chapter 2 Existing Ecological Conditions ........................................................................... 12-1 2 Chapter 3 Conservation Strategy ....................................................................................... 12-30 3 Chapter 4 Description of Covered Activities and Associated Federal Actions ................. 12-77 4 Chapter 5 Overview of the Effects Analysis ...................................................................... 12-78 5 Chapter 6 Plan Implementation .......................................................................................... 12-81 6 Chapter 7 Implementation Structure .................................................................................. 12-81 7 Chapter 8 Implementation Costs and Funding Sources ..................................................... 12-81 8 Chapter 9 Alternatives to Take .......................................................................................... 12-84 9 Chapter 10 Integration of Independent Science in BDCP Development ............................. 12-84 10


Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page 12-1

CHAPTER 12. REFERENCES

CHAPTER 1. INTRODUCTION 1

Regulatory citations are provided in the footnotes within the chapter. 2

CHAPTER 2. EXISTING ECOLOGICAL CONDITIONS 3

Adams, P.N., R.L. Slingerland, and N.D. Smith. 2004. Variations in natural levee morphology in 4 anastomosed channel flood plain complexes. Geomorphology 61:127-142. 5

Alexander, D.G. 1976. Ecological aspects of temporary pool fauna. In: S. Jain, editor. Vernal 6 pools: their ecology and conservation. Institute of Ecology Publication Number 9, Davis, 7 California. 8

Alt, D. and D.W. Hyndman. 2000. Roadside geology of northern and central California. 9 Mountain Press Publishing Company, Missoula. 10

Anderson, D.M., P.M. Glibert, and J.M. Burkholder. 2002. Harmful algal blooms and 11 eutrophication: Nutrient sources, composition, and consequences. Estuaries. 25(4B): 704-12 726. 13

Andrew, M.E. and S.L. Ustin. 2009. Habitat suitability modelling of an invasive plant with 14 advanced remote sensing data. Diversity and Distributions 15:627-640. 15

Andrews, W.F. 1970. Soil Survey of Yolo County, California. United States Department of 16 Agriculture and University of California Agricultural Experiment Station. 17

Anonymous. 1870. The Western Shore Gazetteer, Yolo County. Sprague and Atwell, Woodland, 18 CA. 19

Argus, D.F. and R.G. Gordon. 2001. Present tectonic motion across the Coast Ranges and San 20 Andreas fault system in central California. Geological Society of America Bulletin 21 113:1580-1592. 22

Armstong, W.P. 1979. A marriage between a fern and an alga. Environment Southwest. No. 500: 23 20-24. 24

Arnold, R. A. 1983. Ecological studies of six endangered butterflies (Lepidoptera, Lycaenidae): 25 island biogeography, patch dynamics, and the design of habitat preserves. University of 26 California Press, Berkeley, CA. 27



Atwater, B.F. 1979. Ancient processes at the site of southern San Francisco Bay: movement of 1 the crust and changes in sea level. In: T. J. Conomos, ed., San Francisco: The Urbanized 2 Estuary. Pacific Division of the American Association for the Advancement of Science, 3 San Francisco, CA. pp. 143-174. 4

Atwater, B.F. 1980. Distribution of vascular plant species in six remnants of intertidal wetlands 5 of the Sacramento-San Joaquin Delta, California. USGS Open-File report 80-883. 51 pp. 6

Atwater, B.F. and D.F. Belknap. 1980. Tidal-wetland deposits of the Sacramento-San Joaquin 7 Delta, California. In: W.E. Field, A.H. Bouma, I.P. Colburn, R.G. Douglas, and J.C. 8 Ingle, eds., Quaternary depositional environments of the pacific coast: pacific coast 9 paleogeography symposium 4. Proceedings of the Society of Economic Paleontologists 10 and Mineralogists. Los Angeles (CA): Society of Economic Paleontologists and 11 Mineralogists. 12

Atwater, B.F., S.C. Conard, I.N. Dowden, C.W. Hedel, R.L. MacDonald, and W. Savage. 1979. 13 History, landforms, and vegetation of the estuary’s tidal marshes. In: T.J. Conomos, ed., 14 San Francisco Bay: The Urbanized Estuary. Proceedings of the 58th Annual Meeting of 15 the Pacific Division of the American Association for the Advancement of Science, 16 Golden Gate Park, San Francisco, CA. pp. 347-385. 17

Baraona, M., T. Ippolito, and W. Renz. 2007. Post-project appraisals of constructed vernal pools 18 in Solano, County, California. Water Resources Center Archives, University of 19 California. Berkeley, CA. 20

Barbour, M.G., A.I. Solomeshch, J.J. Buck, R.F. Holland, C.W. Witham, S.L. Starr, and K.A. 21 Lazar. 2007. Classification, ecological characterization, and presence of listed plant taxa 22 of vernal pool associations in California. U. S. Fish & Wildlife Service, Sacramento. 23

Barbour, M.G., A.I. Solomeshch, R.F. Holland, C.W. Witham, R.L. MacDonald, S. Cilliers, J.A. 24 Molina, J.J. Buck, and J.M. Hillman. 2005. Vernal pool vegetation of California: 25 communities of long-innundation habitats. Phytocoenologia 35:177-200. 26

Barbour, M.G., A.I. Solomeshch, C.W. Witham, R.F. Holland, R.L. MacDonald, S. Cilliers, J.A. 27 Molina, J.J. Buck, and J.M. Hillman. 2003. Vernal pool vegetation in California: 28 variation within pools. Madroño 50:129-146. 29

Barclay, W.R. and A.W. Knight. 1981. Physiochemical processes affecting production in a 30 turbid vernal pool. Pages 126-142 in Vernal pools and intermittent streams. Institute of 31 Ecology, Davis, California. 32

Barry, S. 1995. Rangeland oasis. University of California Cooperative Extension. Leaflet No. 33 21531. 34



Bartolome, J.W., M.C. Stroud, and H.F. Heady. 1980. Influence of natural mulch on forage 1 production on differing California annual range sites. Journal of Range Management. 33: 2 4-8. 3

Batcher, M.S. 2000. Element Stewardship Abstract for Eichhornia crassipes (Martius) Solms, 4 water hyacinth. The Nature Conservancy, Wildland Invasive Species Team. Arlington, 5 VA. Accessed 7/5/07. Available at: http://tncweeds.ucdavis.edu/esadocs/eichcras.html. 6

The Bay Institute. 1998. From the Sierra to the sea: the ecological history of the San Francisco 7 Bay-Delta Watershed. The Bay Institute of San Francisco, Novato, CA, USA. Available 8 at: http://www.bay.org/sierra_to_the_sea.htm. 9

Belitz, K. 1988. Character and evolution of the ground-water flow system in the central part of 10 the western San Joaquin Valley, California. USGS Open-file Report 87-573, Sacramento 11 California. 12

Bennett, W.A. 2005. Critical assessment of the delta smelt population in the San Francisco 13 Estuary, California. San Francisco Estuary and Watershed Science [online serial]. 14 Volume 3, Issue 2 (September 2005), Article 1. 15

Blum, M.D. and T.E. Tornqvist. 2000. Fluvial responses to climate and sea-level change: a 16 review and look forward. Sedimentology 47 (Supp. 1):2-48. 17

Boul, P. and T. Keeler-Wolf. 2008. 2006 Vegetation map update for Suisun Marsh, Solano 18 County, California. California Department of Water Resources, Sacramento. 19

Brown, R.L. 2004. Summary of the 2004 workshop: making science work for Suisun Marsh. San 20 Francisco Bay-Delta Science Consortium, Sacramento. 21

Brown, L.R. and D. Michniuk. 2007. Littoral fish assemblages of the alien-dominated 22 Sacramento-San Joaquin Delta, California, 1980-1983 and 2001-2003. Estuaries and 23 Coasts. 30: 186-200. 24

Brown, K.J. and G.B. Pasternack. 2005. A paleoenvironmental reconstruction to aid in the 25 restoration of floodplain and wetland habitat on an upper deltaic plain, California, USA. 26 Environmental Conservation 32:103-116 27

Bryan, K. 1923. Geology and ground-water resources of Sacramento Valley, California. USGS 28 Water-Supply Paper 495. 29 30

Burau, J. 2004. Transport in Suisun Marsh - why do we care and what do we know? Making 31 Science Work for Suisun Marsh. San Francisco Bay - Delta Science Consortium. 32



Byrne, R., B.L. Ingram, S. Starratt, and F. Malamud-Roam. 2001. Carbon-isotope, diatom, and 1 pollen evidence for late Holocene salinity change in a brackish marsh in the San 2 Francisco estuary. Quaternary Research 55:66-76. 3

CALFED Bay-Delta Program. 1998. Technical Report, Affected Environment, Vegetation and 4 Wildlife, Draft. March 1998. Available at: http://www.calwater.ca.gov/Admin_Record/C-5 009083.pdf 6

CALFED Bay-Delta Program, 2000. Multi-Species Conservation Strategy, Final Programmatic 7 EIS/EIR, Final. July 2000. Available at: 8 http://www.calwater.ca.gov/calfed/library/library_archive_EIS.html. 9

CalFlora. 2007. Accessed June 2007-January 2008. Available at: 10 http://www.calflora.org/species/index.html 11

California Climate Change Center. 2006. Accessed 6/18/2007. Available at: 12 http://calclimate.berkeley.edu. 13

California Data Exchange Center. 2007. Accessed on 11/22/2007. Available at: 14 http://cdec.water.ca.gov/. 15

California State Mining Bureau. 1918. Quicksilver resources of California. Page 389. California 16 State Printing Office, Sacramento. 17

Cappiella, K., C. Malzone, R. Smith, and B. Jaffe. 1999. Sedimentation and bathymetry changes 18 in Suisun Bay: 1867-1990. USGS ( U. S. Geological Survey), Menlo Park. 19

Carpenter, E.J. and S.W. Cosby. 1939. Soil survey of Contra Costa County, California. United 20 States Department of Agriculture, Berkeley, CA. 21

Cayan, D., M. Tyree, M. Dettinger, H. Hidalgo, T. Das, E. Maurer, P. Bromirski, N. Graham, 22 and R. Flick. 2009. Climate Change Scenarios and Sea Level Rise Estimates for the 23 California 2009 Climate Change Scenarios Assessment. California Energy Commission 24 PIER Program Report, CEC-500-2009-014-F. Sacramento, CA. 25

Center for Biological Diversity. 2007. Delta smelt. Accessed 6/18/2007. Available at: 26 http://www.biologicaldiversity.org/swcbd/species/deltasmelt/index.html. 27

CVRWQCB (Central Valley Regional Water Quality Control Board). 2008. Sacramento-San 28 Joaquin Delta TMDL for Methylmercury, draft report for public review. Sacramento, Ca. 29

CVRWQCB (Central Valley Regional Water Quality Control Board). 2009. Clean Water Act 30 Sections 305(b) and 303(d) integrated report for the Central Valley Region. Final Staff 31 Report. September 2009. Available at: 32 http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/impaired_waters_list/303d_list.shtml 33



Cheatham, N.H. and R. Haller. 1975. An annotated list of California habitat types. University of 1 California Natural Reserves System. Berkeley, CA, USA. 80 pp. 2

Cohen, A.N. and J.T. Carlton. 1995. Nonindigenous aquatic species in a United States estuary: A 3 case study of the biological invasions of the San Francisco Bay and Delta, University of 4 California Berkeley, Williams College-Mystic Seaport. Available at: 5 http://www.sgnis.org/publicat/cc1.htm. 6

Cole B.E. and J.E. Cloern. 1984. Significance of biomass and light availability to phytoplankton 7 productivity in San Francisco Bay. Marine Ecology Progress Series. 17: 15-24. 8

Conomos, T.J., R.E. Smith, and J.W. Gartner. 1985. Environmental setting of San Francisco 9 Bay. Hydrobiologia 129:1-12. 10

CCWD (Contra Costa Water District). 2010. Historical Fresh Water and Salinity Conditions in 11 the Western Sacramento-San Joaquin Delta and Suisun Bay. Technical Memorandum 12 WR10-001, February 2010. 13

Collins. J.N. and R.M. Grossinger. 2004. Synthesis of scientific knowledge concerning estuarine 14 landscapes and related habitats of the South Bay Ecosystem. Technical report of the 15 South Bay Salt Pond Restoration Project. San Francisco Estuary Institute, Oakland, CA. 16

Cowardin, L.M., V. Carter, F.C. Golet, and E.T. LaRoe. 1979. Classification of wetlands and 17 deepwater habitats of the United States, Version 04DEC98. U. S. Department of the 18 Interior, Fish and Wildlife Service, Washington, D.C. Jamestown, ND: Northern Prairie 19 Wildlife Research Center Online. Accessed 7/2/2007. Available at: 20 http://www.npwrc.usgs.gov/resource/1 998/classwet/classwet.htm. 21

Culberson, S.D. 2001. The interaction of physical and biological determinants producing 22 vegetation zonation in tidal marshes of the San Francisco Bay Estuary, California, USA. 23 Ph.D. dissertation, University of California, Davis. 24

Culberson, S.D., T.C. Foin, and J.N. Collins. 2004. The role of sedimentation in estuarine marsh 25 development within the San Francisco Estuary, California, USA. Journal of Coastal 26 Research. 20: 970-979. 27

Curtis, J.A., L.E. Flint, C.N. Alpers, and S.M. Yarnell. 2005. Conceptual model of sediment 28 processes inthe upper Yuba River watershed, Sierra Nevada. Geomorphology 68:149-29 166. 30

D’Antonio, C.M., C. Malmstrom, S.A. Reynolds, and J.D. Gerlach. 2007. Ecology of invasive 31 non-native species in California’s grassland. Pp. 67-83, in: M.R. Stromberg, J.D. Corbin, 32 C.M. D’Antonio, eds., California’s grasslands: ecology and management. University of 33 California Press, Berkeley, CA. 34



Davidson, C. 1995. Determining habitat conservation priorities for neotropical migrant birds in 1 California. Draft report, U.S. Forest Service, Pacific Southwest Research Station, San 2 Francisco, CA, USA. 3

Davis, S.D., V.H. Heywood, O. Herrera-MacBryde, J. Villa-Lobos, and A.C. Hamilton, editors. 4 1997. Centres of Plant Diversity: a Guide and Strategy for their Conservation. Volume 3: 5 The Americas. Cambridge, UK: The World Wildlife Fund for Nature and IUCN-the 6 World Conservation Union. 7

Davisson, M.L., T.S. Presser, and R.E. Criss. 1994. Geochemistry of tectonically expelled fluids 8 from the northern Coast ranges, Rumsey Hills, California, USA. Geochimica et 9 Cosmochimica Acta 58:1687-1699. 10

Dawson, K., K. Veblen, and T. Young. 2007. Experimental evidence for an alkali ecotype of 11 Lolium multiflorum, an exotic invasive annual grass in the Central Valley, CA, USA. 12 Biological Invasions. 9: 327-334. 13

Dayflow. 2007. Accessed on: October-December 2007. Available at: 14 http://iep.water.ca.gov/dayflow/index.html. 15

DBW (California Department of Boating and Waterways). 2006. Egeria densa Control Program 16 second addendum to 2001 environmental impact report with five-year program review 17 and future operations plan. United States Department of Agriculture, Sacramento, CA. 18

DBW (California Department of Boating and Waterways). 2008. California Department of 19 Boating and Waterways Egeria densa Control Program anual report 2007 application 20 season. United States Department of Agriculture, Sadramento, CA. 21

Dettinger, M.D. 2005. From climate-change spaghetti to climate-change distributions for 21st 22 Century California. San Francisco Estuary and Watershed Science [online serial]. 23 Volume 3, Issue 1 (March 2005), Article 4. Available at: 24 http://repositories.cdlib.org/jmie/sfews/ vol3/iss1/art4. 25

Dettinger, M., K. Redmond, and D.R. Cayan. 2004. Winter orographic precipitation ratios in the 26 Sierra Nevada - large-scale atmospheric circulations and hydrological consequences. 27 Journal of Hydrometerology 5:1102-1116. 28

Deverel, S.J. and S.K. Gallanthine. 1989. Relation of salinity and selenium in shallow 29 groundwater to hydrologic and geochemical processes, western San Joaquin Valley, 30 California. Journal of Hydrology 109: 125-149. 31

Deverel, S.J. and D.A. Leighton. 2010. Historic, recent, and future subsidence, Sacramento-San 32 Joaquin Delta, California, USA. San Francisco Estuary and Watershed Science [online 33 serial]. Volume 8, Issue 2 (August 2010). Available at: 34 http://www.escholarship.org/uc/item/7xd4x0xw. 35

http://iep.water.ca.gov/dayflow/index.html



DFG (California Department of Fish and Game). 2003. Atlas of the Biodiversity of California. 1 Sacramento, CA. 2

DFG (California Department of Fish and Game) - California Interagency Wildlife Task Group. 3 2005. California Wildlife Habitat Relationships Database version 8.1. Software and 4 updated database. Sacramento, CA. Accessed June 2007-January 2008. Available at: 5 http://www.dfg.ca.gov/whdab/html/wildlife_habitats.html. 6

DFG (California Department of Fish and Game). 2007. California Natural Diversity Database 7 (CNDDB). Accessed May 2007- January 2008. Available at: 8 http://www.dfg.ca.gov/bdb/html/cndd b.html. 9

Domagalski, J.L., C.A. Alpers, D.G. Slotton, T.H. Scchanek, and S.M. Ayers. 2004a. Mercury 10 and methlymercury concentrations and loads in the Cache Creek watershed, California. 11 Science of the Total Environment 327:215-237. 12

Domagalski, J.L., C.N. Alpers, C.N. Slotton, T.H. Scuhanek, and S.M. Ayers. 2004b. Mercury 13 and methylmercury concentration an dloads in Cache Creek Basin, California, January 14 2000 through May 2001. Page 56. USGS (United States Geological Survey), Denver. 15

Donnelly-Nolan, J.M., M.G. Burns, F.E. Geoff, E.K. Peters, and J.M. Thompson. 1993. The 16 Geysers-Clear Lake area, California; thermal waters, mineralization, volcanism, and 17 geothermal potential. Economic Geology 88:301-316. 18

Drexler, J.Z., C.S. de Fontaine, and T.A. Brown. 2009a. Peat accretion histories during the past 19 6,000 years in marshes of the Sacramento-San Joaquin Delta, CA, USA. Estuaries and 20 Coasts 32:871-892. 21

Drexler, J.Z., C.S. De Fontaine, and S.J. Deverel. 2009b. The legacy of wetland drainage on the 22 remaining peat in the Sacramento-San Joaquin Delta, California, USA. Wetlands 29:372-23 386. 24

Dudek. 2007. Final Water and Wastewater Services Municipal Services Review for East Contra 25 Costa County. Report prepared for Contra Costa Local Agency Formation Commission. 26 Martinez, CA. 27

Dudley, T. 2000. Arundo donax. In: C. Bossard, J. Randall, M. Hoshovsky, eds., Invasive Plants 28 of California’s Wildlands. University of California Press, Berkeley, CA. 29

Dugdale, R.C., F.P. Wilkerson, V.E. Hogue, and A. Marchi. 2007. The role of ammonium and 30 nitrate in spring bloom development in San Francisco Bay. Estuarine Coastal and Shelf 31 Science. 73: 17-29. 32

Dugdale, R.C. 2008. Effects of ammonium on phytoplankton growth and consequences for the 33 POD. 5th Beinnial CALFED Science Conference. October 22-24, 2008. Sacramento, CA. 34



Dukes, J.S. and M.R. Shaw. 2007. Responses to changing atmosphere and climate. Pp. 218-229, 1 in: M.R. Stromberg, J.D. Corbin, C.M. D’Antonio, eds., California grasslands: ecology 2 and management. University of California Press, Berkeley, CA. 3

DWR (California Department of Water Resources). 1931. Variation and control of salinity in 4 Sacramento-San Joaquin Delta and upper San Francisco Bay. DWR Bulletin No. 27. 5

DWR (California Department of Water Resources). 1993. Dams within the jurisdiction of the 6 State of California. DWR Bulletin 17-93. 7

DWR (California Department of Water Resources). 2005. California Water Plan Update 2005. 8 Volume 3. Regional Reports. Chapter 12. Sacramento-San Joaquin Delta. 21 pp. 9

DWR (California Department of Water Resources). 2006. Sacramento-San Joaquin Delta 10 Overview. Available at: http://baydeltaoffice.water.ca.gov/sdb/tbp/deltaoverview. 11

DWR (California Department of Water Resources). 2007a. California Data Exchange Center 12 web site. Accessed 5/17/2007. Available at:http//cdec.water.ca.gov. EDAW. 2005. 13 Flooded Island feasibility study baseline report. Prepared for: California Department of 14 Water Resources. Accessed 7/2/2007. Available at: 15 http://baydeltaoffice.water.ca.gov/ndelta/frankstract/documents/(4)Flooded%20Islands%16 20Baseline%20Report.pdf. 17

DWR (California Department of Water Resources). 2007b. Past and Present Land Uses in the 18 Sacramento-San Joaquin Delta and Suisun Marsh. Report to the Delta Vision Blue 19 Ribbon Task Force. November 21. Sacramento, CA. 20

EDAW (Eckbo, Dean, Austin, and Williams). 2007a. Yolo Bypass Wildlife Area Management 21 Plan. Prepared for: California Department of Fish and Game, Sacramento, CA. 22

EDAW (Eckbo, Dean, Austin, and Williams). 2007b. Lower Sherman Island Wildlife Area land 23 management plan. Prepared for DFG. April 2007. 24

Edwards, R. 2006. Sea levels: change and variability during warm intervals. Progress in Physical 25 Geography 30:785-796. 26

Ellison, J. 1983. Estuaries, California aquatic community abstract. California Department of Fish 27 and Game, Sacramento, CA. 28

ESA (Environmental Science Associates and Yolo County Planning & Public Works 29 Department). 2005. CALFED at-risk plant species, habitat restoration and recovery, and 30 non-native species management ERP-02-P46: final conservation and management plan. 31 CALFED Ecosystem Restoration Program, Sacramento. 32



ESA (Environmental Science Associates). 2007. Distribution and ecology of Lepidium latifolium 1 in Bay-Delta wetlands ERP 02-P09: final report. CALFED Ecosystem Restoration 2 Program, Sacramento. 3

Estep, J.A. In prep. Ecology of the Swainson’s Hawk in the Central Valley of California. 4

Eviner, V.T. and M.T. Firestone. 2007. Mechanisms determining patterns of nutrient dynamics. 5 Pages 94-106 in M.R. Stromberg, J. D. Corbin, and C. M. D’Antonio, editors. California 6 grasslands: ecology and management. University of California Press, Berkeley. 7

Fay, N.P. and E.D. Humphreys. 2008. Forces acting on the Sierra Nevada block and implications 8 for the strength of the San Andreas fault system and the dynamics of continental 9 deformation in the western United States. Journal of Geophysical Research 113:B12415. 10

Feyrer, F.V. 1999. Food habits of common Suisun Marsh fishes in the Sacramento-San Joaquin 11 estuary, California. M.S. Thesis, California State University, Sacramento. 53 pp. 12

Feyrer, F., T. Sommer, and W. Harrell. 2006. Managing floodplain inundation for native fish: 13 production dynamics of age-0 splitail (Pogonichthys macrolepidotus) in California’s 14 Yolo Bypass. Hydrobiologia 573:213-226. 15

Fiedler, P.L., M.E. Keever, B.J. Grewell, and D.J. Partridge. 2007. Rare plants in the Golden 16 Gate Estuary (California): the relationship between scale and understanding. Australian 17 Journal of Botany 55:206-220. 18

Fiedler, P. and R. Zebell. 1993. Restoration and recovery of Mason’s lilaeopsis: Phase I. Final 19 Report, submitted to the California Department of Fish and Game. 47 pp. plus 20 appendices. 21

Field, C.B., G.C. Daily, F.W. Davis, S. Gaines, P.A. Matson, J. Melack, and N.L. Miller. 1999 22 Confronting climate change in California: ecological impacts on the Golden State. 23 November 1999. A report of the Union of Concerned Scientists and the Ecological 24 Society of America. Available at: www.ucsusa.org. 25

Fleskes, J.P., J.L. Yee, M.L. Casazza, M.R. Miller, J.Y. Takekawa, and D.L. Orthmeyer. 2005. 26 Waterfowl distribution, movements, and habitat use relative to recent habitat changes in 27 the Central Valley of California. Report, U. S. Geological Survey, Dixon, CA. 28

Florsheim, J.L. and J.F. Mount 2003. Changes in lowland floodplain sedimentation processes: 29 pre-disturbance to post-rehabilitation, Cosumnes River, CA. Geomorphology 56:305-30 323. 31

Fredrickson, L.H. and T.S. Taylor. 1982. Management of seasonally flooded impoundments for 32 wildlife. U.S. Fish and Wildlife Service Resource Publication 148. 33



Ganju, N.K. and D,H, Schoellhamer. 2010. Decadal-timescale estuarine geomorphic change 1 under future scenarios of climate and sediment supply. Estuaries and Coasts. 33: 15-29. 2

Garrison, G.A., A.J. Bjugstad, D.A. Duncan, M.E. Lewis, and D.R. Smith. 1977. Vegetation and 3 environmental features of forest and range ecosystems. U.S. Department of Agriculture, 4 Forest Service, Handbook No. 475. 5

Gerlach, J.D., B.S. Bushman, J.K. McKay, and H. Meimberg. 2009. Taxonomic confusion 6 permits the unchecked invasion of vernal pools in California by low mannagrass 7 (Glyceria declinata).. Invasive Plant Science and Management. 2:92-97. 8

Gewant, D.S., S.M. Bollens. 2005. Macrozooplankton and micronekton of the lower San 9 Francisco Estuary: seasonal, interannual, and regional variation in relation to 10 environmental conditions. Estuaries 28:473-485. 11

Gilbert, G.K. 1917. Hydraulic mining in the Sierra Nevada. U.S. Geological Survey Professional 12 Paper. No. 105. 13

Gilmer, D.S., M.L. Miller, R.B. Bauer, and J.R. LeDonne. 1982. California's Central Valley 14 wintering waterfowl: concerns and challenges. Transactions of the North American 15 Wildlife and Natural Research Conference. 47: 441-452. 16

Glibert, P. In press. Long-term changes in nutrient loading and stoichiometry and their 17 relationships with changes in the food web and dominant pelagic fish species in the San 18 Francisco Estuary, California. Reviews in Fisheries Science. 19

Golden, M. and P. Fiedler. 1991. Characterization of the habitat for Lilaeopsis masonii 20 (Umbelliferae): a California state listed rare plant species. Final report to the California 21 Department of Fish and Game, Endangered Plant Program. 72 pp. plus appendices. 22

Goman, M. and L. Wells. 2000. Trends in river flow affecting the northeastern reach of the San 23 Francisco Bay Estuary over the past 7000 years. Quaternary Research 54:206-217. 24

Google. 2009. Google Earth ver 5.0. Google Inc., Mountain View, CA. 25

Governor’s Delta Vision Blue Ribbon Task Force. 2008. Our vision of the California Delta. 26 Report to Governor Schwarzenegger January 17. Sacramento, CA.12 pp. Available at: 27 http://deltavision.ca.gov/BlueRibbonTaskForce/FinalVision/ 28 Vision_12_Page_Summary.pdf. 29

Graham, R.C., A.M. Rossi, and K.R. Hubbert. 2010. Rock to regolith conversion: producing 30 hospitable substrates for terrestrial ecosystems. GSA Today 20:4-9. 31



Graymer, D.L., D.L. Jones, and E.E. Brabb. 2002. Geologic map and map database of 1 northeastern San Francisco Bay Region, California. Misc. Field Studies Map MF-2403 2 ver. 1.0. USGS. 3

Graymer, R.W., D.L. Jones, and E.E. Brabb. 1994. Preliminary geologic map emphasizing 4 bedrock formations in Contra Costa County, California. Open_file Report 94-622. USGS. 5

Grenfell, W.E., Jr. 2007. Valley Foothill Riparian habitat description. In: California Wildlife 6 Habitat Relationships database. Accessed 6/30/07. Available at: 7 http://www.dfg.ca.gov/bdb/html/cwhr.html. 8

Grewell, B. 2005. Population census and status of the endangered soft bird's beak (Cordylanthus 9 mollis ssp. mollis) at Benecia State Recreation Area and Rush Ranch in Solano County, 10 California. Final Report. Solano County Water Agency, Sacramento, CA. 11

Grewell, B., J. Callaway, and W. Ferren Jr. 2007. Estuarine wetlands. Pages 124-179. In, 12 Terrestrial vegetation of California. M. Barbour, T. Keeler-Wolf, and A. Schoenherr eds.. 13 University of California Press, Berkeley, CA. 14

Griggs, F.T., V. Morris, and E. Denny. 1993. Five years of valley oak riparian forest restoration. 15 Fremontia 22(2): 13-17. 16

Griggs, F.T. 2000. Vina Plains Preserve: eighteen years of adaptive management. Fremontia 17 27(4):48-51. 18

Griggs, F.T., and G.H. Golet. 2002. Riparian valley oak (Quercus lobata) forest restoration on 19 the middle Sacramento River, California. USDA Forest Service General Technical 20 Report. PSW-GTR-184. 21

Grimaldo L. and Z. Hymanson. 1999. What is the impact of the introduced waterweed Egeria 22 densa to the Delta Ecosystem? Interagency Ecological Program Newsletter 12(1): 43-45. 23

Grinnell, J., J.S. Dixon, and J.M. Linsdale. 1937. Fur bearing mammals of California, their 24 natural history, systematic status, and relations to man, Vol. I and II. University of 25 California Press, Berkeley, CA. 26

Grossinger, R. 2004. What does the history of Suisun Marsh tell us about its future management? 27 Making Science Work for Suisun Marsh. San Francisco Bay - Delta Science Consortium. 28

Grossinger, R., A. Whipple, and C. Wilcox. 2008. Pre-modification habitat mosaics of the Delta: 29 looking to the past to envision the future. CalFed Conference, Sacramento. 30

Grossman, D.H., K. Goodin, M. Anderson, P. Bourgeron, M.T. Bryer, R. Crawford, L. 31 Engelking, D. Faber-Langendoen, M. Gallyoun, S. Landaal, K. Metzler, K.D. Patterson, 32 M. Pyne, M. Reid., L. Sneddon, and A.S. Weakley. 1998. International classification of 33



ecological commununities: Terrestrial vegetation of the United States. The Nature 1 Conservancy. Arlington, VA. 2

Harrell W.C. and T.R. Sommer. 2003. Patterns of Adult Fish Use on California’s Yolo Bypass 3 Floodplain. In: P. M. Faber, ed., California riparian systems: Processes and floodplain 4 management, ecology, and restoration. 2001 Riparian Habitat and Floodplains 5 Conference Proceedings, Riparian Habitat Joint Venture, Sacramento, California. pp. 88-6 93. 7

Hayes, M.P. and M.R. Jennings. 1986. Decline of ranid frog species in western North America: 8 are bullfrogs (Rana catesbeiana) responsible? Journal of Herpetology. 20: 490-509. 9

Hayhoe, K., D. Cayan, C.B. Field, P.C. Frumhoff, E.P. Maurer, N.L. Miller, S.C. Moser, S.H. 10 Schneider, K.N. Cahill, E.E. Cleland, L. Dale, R. Drapek, R.M. Hanemann, L.S. 11 Kalkstein, J. Lenihan, C.K. Lunch, R.P. Neilson, S.C. Sheridan, and J.H. Verville. 2004. 12 Emissions pathways, climate change, and impacts on California. Proceedings of the 13 National Academy of Sciences. 101(34): 12422-12427. 14

Hecnar, S.J. and R.T. M'Closkey. 1997. Changes in the composition of a ranid frog community 15 following bullfrog extinction. American Midland Naturalist. 137(1): 145-50. 16

Helley, E.J. and D.D. Harwood. 1985. Geographic map of the late Cenozoic deposits of the 17 Sacramento Valley and northern Sierran foothills, California. Miscellaneous Field 18 Studies Map MF-1790. USGS (U. S. Geological Survey). 19

Hennessey, A. and K. Hieb. 2007. Zooplankton monitoring 2006. Interagency Ecological 20 Program Newsletter. 20(2): 10-14. 21

Herren, J.R. and S.S. Kawasaki. 2001. Inventory of water diversions in four geographic areas in 22 California’s Central Valley. In: R.L. Brown, ed., Contributions to the Biology of Central 23 Valley Salmonids. Volume 2. California Department of Fish and Game. Fish Bulletin 24 179. pp. 343-355. 25

Hickson, D. and T. Keeler-Wolf. 2007. Vegetation and land-use classification and map of the 26 Sacramento-San Joaquin River Delta. Report to the Bay Delta Region of the California 27 Dept. of Fish and Game. Sacramento, CA, USA. Available at: 28 http://dfg.ca.gov/biogeodata/vegcamp/veg_classification_reports_maps.asp. 29

Hitchcock, C.S., E.J. Helley, and R.W. Givler. 2005. Geomorphic and geologic mapping for 30 restoration planning, Sacramento-San Joaquin Delta region. Final report submitted to 31 CALFED, Sacramento. June 2005. 32

Hogle, I., J.H. Viers, and J.F. Quinn. 2006. Perennial Pepperweed Infestation on the Cosumnes 33 River Experimental Floodplain. Report to the Bay Delta Authority. Davis, CA, USA. 34



Holland, V.L. and D.J. Keil. 1995. California Vegetation. Kendall/Hunt Publishing Company, 1 Dubuque, IA, USA. 2

Hopkinson, P., M. Stevenson, M. Hammond, S. Gennet, D. Rao, and J.W. Bartolome. 2008. 3 Italian ryegrass: a new central California dominant? Fremontia 36(1):20-24. 4

Hothem, R.L., D.R. Bergen, M.L. Bauer, J.J. Crayon, and A.N. Meckstroth. 2007. Mercury and 5 trace elements in crayfish from northern California. Bulletin Environmental 6 Contamination and Toxicology 79:628-632. 7

Howard, A.Q. and R.A. Arnold. 1980. The Antioch Dunes - safe at last? Fremontia. 8:3-12. 8

Intergovernmental Panel on Climate Change. 2007. Climate Change 2007: Synthesis Report. 9 Contribution of Working Groups I, II and III to the Fourth Assessment Report of the 10 Intergovernmental Panel on Climate Change [Core Writing Team, Pachauri, R.K and 11 Reisinger, A. (eds.)]. IPCC, Geneva, Switzerland, 104 pp. Available at: 12 http://www.ipcc.ch/pdf/assessment-report/ar4/syr/ar4_syr.pdf. 13

Jackson, L.E., M. Potthoff, K.L. Steenwerth, A.T. O'Geen, M.R. Stromberg, and K.M. Scow. 14 2007. Soil biology and carbon sequestration in grasslands. Pages 107-118 in M.R. 15 Stromberg, J.D. Corbin, and C.M. D’Antonio, editors. California grasslands: ecology and 16 management. University of California Press, Berkeley. 17

Jackson, L.E., F. Santos-Martin, A.D. Hollander, W.R. Horwath, R.E. Howitt, J.B. Kramer, A.T. 18 O’Geen, B.S. Orlove, J.W. Six, S.K. Sokolow, D.A. Sumner, T.P. Tomich, and S.M. 19 Wheeler. 2009. Potential for adaptation to climate change in an agricultural landscape in 20 the Central Valley of California. California Energy Commission PIER Program Report, 21 CEC-500-2009-044-F. Sacramento, CA. 22

Jackson, R.D. and J.W. Bartolome. 2007. Grazing ecology of California grasslands. Pages 197-23 206 in M.R. Stromberg, J.D. Corbin, and C.M. D’Antonio, editors. California grasslands: 24 ecology and management. University of California Press, Berkeley. 25

Jackson, W.T. and A.M. Paterson. 1977. The Sacramento-San Joaquin Delta the evolution and 26 implementation of water policy: an historical perspective. Technical Completion Report, 27 Contribution No. 163. California Water Resources Center, Davis, CA. 28

Jain, S. 1979. Some biogeographic aspects of plant communities in vernal pools. In: S. Jain, ed., 29 Vernal pools: their ecology and conservation. Institute of Ecology Publication No. 9. 30 University of California. Davis, CA. pp. 15-21. 31

James, A. 1999. Time and the persistence of alluvium: river engineering, fluvial geomorphology, 32 and mining sediment in California. Geomorphology 31:265-290. 33



James, L.A. 2003. Glacial erosion and geomorphology in the northwest Sierra Nevada, CA. 1 Geomorphology 55:283-303. 2

James, L.A. 2004a. Decreasing sediment yields in northern California: vestiges of hydraulic 3 gold-mining and reservoir trapping. Pages 225-244 in Sediment transfer through the 4 fluvial system. IAHS, Moscow. 5

James, L.A. 2004b. Tailings fans and valley-spur cutoffs created by hydraulic mining. Earth 6 Surface Processes and Landforms 29:869-882. 7

James, L.A. 2006. Bed waves at the basin scale: implications for river management and storage. 8 Earth Surface Processes and Landforms 31:1692-1706. 9

James, L.A. and M.B. Singer. 2008. Development of the lower Sacramento Valley flood-control 10 system: historical perspective. Natural Hazards Review 9:125-135. 11

James, L.A., J. Harbor, D. Fabel, D. Dahms, and D. Elmore. 2002. Late Pleistocene glaciations 12 in the northwestern Sierra Nevada, California. Quaternary Research 57:409-419. 13

James, L.A., M.B. Singer, S. Ghoshat, and M. Megison. 2009. Historical channel changes in the 14 lower Yuba and Feather rivers, California: long-term effects of contrasting river-15 management systems. Pages 57-81 in L. A. James, S. L. Rathburn, and G. R. Whittecar, 16 editors. Management and restoration of fluvial systems with broad historical changes and 17 human impacts. 18

Jassby, A. 2008. Phytoplankton in the upper San Francisco Estuary: recent biomass trends, their 19 causes and their trophic significance. San Francisco Estuary & Watershed Science 6:1-20 24. 21

Jassby, A.D., W.J. Kimmerer, S.G. Monismith, C. Armor, J.E. Cloern, T.M. Powell, J.R. 22 Schubel, and T.J. Vendlinski. 1995. Isohaline position as a habitat indicator for estuarine 23 populations. Ecological Applications. 5: 272-289. 24

Jassby, A.D. and J.E. Cloern. 2000. Organic matter sources and rehabilitation of the Sacramento-25 San Joaquin Delta (California, USA). Aquatic Conservation: Marine and Freshwater 26 Ecosystems. 10: 323-352. 27

Jassby, A.D., J.E. Cloern, and B.E. Cole. 2002. Annual primary production: patterns and 28 mechanisms of change in a nutrient-rich tidal ecosystem. Limnology and Oceanography. 29 47: 698-712. 30

Jassby, A.D., J.E. Cloern, and A.B. Mueller-Solger. 2003. Phytoplankton fuels Delta food web. 31 California Agriculture. 57(4): 104-109. 32



Jassby, A.D., and E.E. Van Nieuwenhuyse. 2005. Low dissolved oxygen in an estuarine channel 1 (San Joaquin River, California): mechanisms and models based on long-term time series. 2 San Francisco Estuary and Watershed Science [online serial]. Vol. 3, Issue 2, (September 3 2005), Article 2. 4

Jennings, C.W., R.G. Strand, and T.H. Rogers. 1977. Geologic map of California. California 5 Division of Mines, Sacramento. 6

Jones and Stokes Associates, Inc. 1990. Sacramento County vernal pools: their distribution, 7 classification, ecology, and management. (JSA 89-303) Sacramento, CA. Prepared for 8 the Sacramento County Planning and Community Development Department, Sacramento, 9 CA. 10

Kapnick, S. and A. Hall. 2009. Observed Changes in the Sierra Nevada Snowpack: Potential 11 Causes and Concerns. California Energy Commission PIER Program Report, CEC-500-12 2009-016-F. Sacramento, CA. 13

Katibah, E.F. 1984. A brief history of riparian forest in the Central Valley of California. Pp. 23-14 29, in: M.N. Kochert, K. Steenhof, C.L. McIntyre, E.H. Craig, eds., The Birds of North 15 America. The Academy of Natural Sciences, Philadelphia, PA, USA. 16

Keeler-Wolf, T. and M. Vaghti. 2000. Vegetation Mapping of Suisun Marsh, Solano County 17 California. California Department of Fish and Game, Sacramento. 18

Keeler-Wolf, T., J.M. Evens, A.I. Solomeshch, V.L. Holland, and M.G. Barbour. 2007. 19 Community classification and nomenclature. Pp. 21-34, in: M.R. Stromberg, J.D. Corbin, 20 C.M. D’Antonio, eds., California grasslands ecology and management. University of 21 California Press, Berkeley, CA. 22

Keeley, J.E. and P.H. Zedler. 1998. Characterization and Global Distribution of Vernal Pools. 23 Pages 1-14 in: C.W. Witham, E.T. Bauder, D. Belk, W.R. Ferren Jr., and R. Ornduff 24 (Editors). Ecology, Conservation, and Management of Vernal Pool Ecosystems – 25 Proceedings from a 1996 Conference. California Native Plant Society, Sacramento, CA. 26 1998. 27

Keller, B.R. 2009. Literature review of unconsolidated sediment in the San Francisco Bay and 28 nearby Pacific Ocean Coast. San Francisco Estuary & Watershed Science 7:article 2. 29

Kelley, R. 1989. Battling the Inland Sea. University of California Press, Berkeley and Los 30 Angeles, California. 31

Kim, W., A. Dai, T. Muto, and G. Parker. 2009. Delta progradation driven by an advancing 32 sediment sourse: coupled theory and experiment describing the evolution of elongated 33 deltas. Water Resources Research 45:W06428. 34



Kimmerer, W.J. and J.J. Orsi. 1996. Changes in the zooplankton of the San Francisco Bay 1 estuary since the introduction of the clam Potamacorbula amurensis. In: J.T. Hollibaugh, 2 ed., San Francisco Bay: the ecosystem. San Francisco, CA: Pacific Division, American 3 Association for the Advancement of Science. pp. 403-424. 4

Kimmerer, W.J. 2002. Physical, biological, and management responses to variable freshwater 5 flow into the San Francisco Estuary. Estuaries. 25(6B): 1275-1290. 6

Kimmerer, W.J. 2004. Open water processes of the San Francisco Estuary: from physical forcing 7 to biological responses. San Francisco Estuary and Watershed Science [online serial]. 8 Volume 2, Issue 1 (February 2004), Article 1. 9

Kimmerer, W.J. 2008. Organic carbon, nutrients, and algae. Presentation to California Bay-Delta 10 Public Advisory Committee, Meeting of the Water Quality Subcommittee. CALFED, 11 Sacramento, CA. January 24, 2008. 12

Kleinschmidt Associates. 2008. Cosumnes River Preserve Management Plan. Prepared for: The 13 Nature Conservancy, Galt, CA. 14

Knowles, N. and D. Cayan. 2002. Potential effects of global warming on the Sacramento/San 15 Joaquin watershed and the San Francisco estuary. Geophysical Research Letters. 29: 38-16 1-38-4. 17

Knowles, N. and D.R. Cayan. 2004. Elevational dependence of projected hydrologic changes in 18 the San Francisco Estuary and watershed. Climatic Change. 62:319-336. 19

Knowles, N. 2006. Projecting inundation due to sea level rise in the San Francisco Bay and 20 Delta. Third Annual Climate Change Research Conference. September 13-15, 2006. 21 Available at: 22 http://www.climatechange.ca.gov/events/2006_conference/presentations/2006-09-23 14/2006-09-14_KNOWLES.PDF. 24

Kwasny, D.C., M. Wolder, and C.R. Isola. 2004. Central Valley Habitat Joint Venture, Technical 25 Guide to Best Management Practices for Mosquito Control in Managed Wetlands. 26

Larsen, E., E. Anderson, E. Avery, and K. Dole. 2002. The controls on and evolution of channel 27 morphology of the Sacramento River, as case study of river miles 201-185. The Nature 28 Conservancy, Davis. 29

Lee, G.F. and A. Jones-Lee. 2002. Synthesis of findings on the causes and factors influencing 30 low DO in the San Joaquin River Deep Water Ship Channel near Stockton, CA. Report. 31 SJR DO TMDL Steering Committee. El Macero, CA. 32

Lehman, P.W. 2000. Phytoplankton biomass, cell diameter, and species composition in the low 33 salinity zone of northern San Francisco Bay Estuary. Estuaries 23(2): 216-230. 34



Lehman, P.W., G. Boyer, C. Hall, S. Waller, and K. Gehrts. 2005. Distribution and toxicity of a 1 new colonial Microcystis aeruginosa bloom in the San Francisco Bay Estuary, California. 2 Hydrobiologia 541:87-99. 3

Lehman, P.W., G. Boyer, M. Satchwell, and S. Waller. 2008. The influence of environmental 4 conditions on the seasonal variation of Microcystis cell density and microcystins 5 concentration in San Francisco Estuary. Hydrobiologia 600:187-204. 6

Leigh Fisher Associates. 2005. Byron Airport Master Plan: Final Report. Contra Costa Public 7 Works Department. Concord, CA. 8

Lindley, S.T., R.S. Schick, E. Mora, P.B. Adams, J.J. Anderson, S. Greene, C. Hanson, B.P. 9 May, D.R. McEwan, R.B. MacFarlane, C. Swanson, and J.G. Williams. 2007. 10 Framework for assessing viability of threatened and endangered Chinook salmon and 11 steelhead in the Sacramento-San Joaquin Basin. San Francisco Estuary and Watershed 12 Science (online serial). Volume 5, Issue 1 [February 2007]. Article 4. 13

Loredo, I. and D. Van Vuren. 1996. Reproductive ecology of a population of the California tiger 14 salamander. Copeia 1996:895-901. 15

Loudeback, G.D. 1951. Geologic history of the San Francisco Bay. Pages 75-94 in O. P. Jenkins, 16 editor. Bulletin 154: geologic guidebook of the San Francisco Bay counties. Division of 17 Mines, Sacramento. 18

Lucas, L.V., J.E. Cloern, J.K. Thompson, and N.E. Monsen. 2002. Functional variability of 19 habitats within the Sacramento-San Joaquin Delta: restoration implications. Ecological 20 Applications. 12: 1528-1547. 21

Lund, J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle. 2007. Envisioning futures 22 for the Sacramento-San Joaquin Delta. Public Policy Institute of California. 324 pp. 23

Luoma, S.N. and T.S. Presser. 2000. Forecasting Selenium Discharges to the San Francisco Bay-24 Delta Estuary: Ecological Effects of a Proposed San Luis Drain Extension. OFR 00-416, 25 U.S. Geological Survey, Menlo Park, CA. 26

Lydon, P.A. 1968. Geology and lahars of the Tuscan Formation, northern California.in R. L. 27 Coats, R. L. Hay, and C. A. Anderson, editors. Volcanology: a memoir in honor of 28 Howel Williams. Geological Society of America, Boulder. 29

Malamud-Roam, F., M. Dettinger, B.L. Ingram, M.K. Hughes, and J.L. Florsheim. 2007. 30 Holocene climates and connections between the San Francisco Bay Estuary and its 31 watershed: a review. San Francisco Estuary & Watershed Science 5:article 3. 32



Malamud-Roam, F. and B.L. Ingram. 2004. Late holocene δ13C and pollen records of 1 paleosalinity from tidal marshes in the San Francisco Bay estuary, California. Quaternary 2 Research 62:134-145. 3

Malamud-Roam, F., B.L. Ingram, M.K. Hughes, and J.L. Florsheim. 2006. Holocene 4 paleoclimate records from a large California estuarine system and its watershed region: 5 linking watershed climate and bay conditions. Quaternary Science Reviews 25:1570-6 1598. 7

Manly P. and C. Davidson. 1993. A risk analysis of neotropical migrant birds in California. U.S. 8 Forest Service Report, Region 5, San Francisco, CA, USA. 9

Mann, C.W., J.F. Warner, H.L. Westover, and J.E. Ferguson. 1911. Soil survey of the Woodland 10 area, California. Government Printing Office, Washington, D.C. 11

Marchandt, D.E. and A. Allwardt. 1981. Late Cenozoic stratigraphic units, northeastern San 12 Joaquin Valley, California. Page 70. USGS ( U. S. Geological Survey. 13

Marty, J.T. 2005. Effects of cattle grazing on diversity in ephemeral wetlands. Conservation 14 Biology 19:1626-1632. 15

McKee, L.J., N.K. Ganju, and D.H. Schoellhamer. 2006. Estimates of suspended sediment 16 entering San Francisco Bay from the Sacramento and San Joaquin Delta, San Francisco 17 Bay, California. Journal of Hydrology 323:335-352. 18

McKnight, T.L. and D. Hess. 2005. Physical Geography: A Landscape Appreciation, 8th Edition. 19 Pearson Prentice Hall, Upper Saddle River, New Jersey. 640 pp. 20

Medeiros, J.L. 1976. Vernal pools and vernal lakes in the eastern Central Valley of California.in 21 S. Jain, editor. Vernal pools: their ecology and conservation. Institute of Ecology 22 Publication Number 9, Davis, California. 23

Meisler, J.A. 2002. Site Conservation Plan for the Jepson Prairie-Prospect Island Corridor. 24 Prepared for the Solano County Land Trust. 27 pp. plus appendices. 25

Mikhailov, V.O., T. Parsons, R.W. Simpson, E.P. Timoshkina, and C. Williams. 2006. Why the 26 Sacramento Delta area differes from other parts of the Great Valley: numberical 27 modeling of thermal structure and thermal subsidence of forearc basins. Physics of the 28 Solid Earth 43:75-90. 29

Moss, B. 1998. Ecology of fresh waters. 3rd edition. Blackwell Science Ltd., Victoria. 30

Mount, J.F. 1995. California Rivers and Streams: the conflict between fluvial process and land 31 use. University of California Press, Berkeley, CA. 359 pp. 32



Mount, J. and R. Twiss. 2005. Subsidence, sea level rise, seismicity in the Sacramento-San 1 Joaquin Delta. San Francisco Estuary and Watershed Science [online serial]. Volume 3, 2 Issue 1 (March 2005), Article 5. 3

Moyle, P.B. 2002. Inland Fishes of California, Revised and Expanded. University of California 4 Press, Berkeley, California. 502 pp. 5

Moyle, P.B., P.K. Crain, and K. Whitener. 2007. Patterns in the use of a restored California 6 floodplain by native and alien fishes. San Francisco Estuary and Watershed Science 7 [online serial]. Volume 5, Issue 3 (July 2007), Article 1. 8

Myers, N.R., A. Mittermeier, C.G. Mittermeier, G.A.B. da Fonseca, and J. Kent. 2000. 9 Biodiversity hot spots for conservation priorities. Nature. 403: 853-858. 10

National Atlas of the United States. 2009. http://nationalatlas.gov. 11

NMFS (National Marine Fisheries Service). 2004. Biological Opinion on the Long-Term Central 12 Valley Project and State Water Project Operations Criteria and Plan. National Marine 13 Fisheries Service, Southwest Region, Long Beach, California. October 2004. 14

Natural Heritage Institute. 2003. The past and present condition of the Marsh Creek watershed. 15 The Natural Heritage Institute, Berkeley. 16

National Research Council. 2002. Riparian Areas: Functions and Strategies for Management. 17 Committee on Riparian Zone Functioning and Strategies for Management, Water 18 Science, and Technology Board. Washington, DC, USA. 19

Naylor, L.W. 2002. Evaluating moist-soil seed production and management in Central Valley 20 wetlands to determine habitat needs for waterfowl. M.S. Thesis, University of California, 21 Davis, CA. 22

Nicholls, R.J., F.M.J. Hoozemans, and M. Marchand. 1999. Increasing flood risk and wetland 23 losses due to global sea-level rise: regional and global analyses. Global Climate Change. 24 9:S69-S87. 25

Norris, R. 1851. General land office survey notes. October 1851. 26

NRCS (Natural Resources Conservation Service). 2009. Soil Survey Geographic (SSURGO) 27 Database. 28

Olmsted, F.H. and G.H. Davis. 1961. Geologic features and ground-water storage capacity of the 29 Sacramento Valley, California. Page 241. USGS (U. S. Geological Survey). 30

Opperman, J.J. 2005. Large woody debris and land management in California’s hardwood-31 dominated watersheds. Environmental Management. 35(3): 266-277. 32

http://nationalatlas.gov/



Orr M., S. Crooks, and P.B. Williams. 2003. Will restored tidal marshes be sustainable? San 1 Francisco Estuary and Watershed Science [online serial]. Volume 1, Issue 1 (October 2 2003), Article 5. 3

Page, R.W. 1985. Geology of the fresh ground-water basin of the Central Valley, California, 4 with texture maps and sections. USGS Technical Paper 1401-C. 5

Parker, A., A. Machi, J. Davidson-Drexel, R. Dugdale, and F. Wilkerson. 2010. Effect of 6 ammonium and wastewater effluent on riverine phytoplankton on the Sacramento River, 7 CA. Final Report to the State Water Resources Control Board, 73 pp. 8

Parker, G., T. Muto, Y. Akamatsu, W.D. Dietrichs, and W. Lauer. 2008. Unravelling the 9 conundrum of river response to rising sea-level from laboratory to field. Part II. The Fly-10 Strickland River system, Papua New Guinea. Sedimentology 55:1657-1686. 11

Parker, I. and W.J. Matyas. 1981. CALVEG: a classification of Californian vegetation. U.S. 12 Department of Agriculture, Forestry Service, Reg. Ecology Group, San Francisco. 13

Pearce, S. 2004. Analysis of reference tidal channel plan form for the Montezuma Wetlands 14 restoration project. San Francisco Estuary Institute, Oakland. 15

Peltier, W.R. and R.G. Fairbanks. 2006. Global glacial ice volume and Last Glacial Maximum 16 duration from an extended Barbados sea level record. Quaternary Science Reviews 25: 17 3322-3337. 18

Peters, E.K. 1991. Gold-bearing hot spring systems of the northern California Coast Ranges, 19 California. Economic Geology 86:1519-1528. 20

Petranka, J.W. 1998. Salamanders of the United States and Canada. Smithsonian Institution 21 Press, Washington, D. C. xvi +587 pp. 22

Pierce, D.W. and D. Gaushell. 2005. The California delta breeze: characteristics and sub-daily 23 forecasting. Abstract from the Sixth Conference on Coastal Atmospheric and Oceanic 24 Prediction and Processes, San Diego, CA. 25

Planty-Tabacchi, A., E. Tabacchi, R.J. Naiman, C. Deferrari, and H. Décamps. 1996. Invasibility 26 of species-rich communities in riparian zones. Conservation Biology. 10: 598-607. 27

Pollack, O. and T. Kan. 1998. The use of prescribed fire to control invasive exotic weeds at 28 Jepson Prairie Preserve. Pages 241-249 in C. W. Witham, E. T. Bauder, D. Belk, W. R. 29 Ferren, and R. Ornduff, editors. Ecology, conservation, and management of vernal pool 30 ecosystems. Sacramento, CA. California Native Plant Society, Sacramento, CA. 31



Power, M.E. and W.E. Rainey. 2000. Food webs and resource sheds: towards spatially delimiting 1 trophic interactions. Pages 291-314 in 40th Symposium of the British Ecological Society. 2 Cambridge University Press, University of Sussex. 3

Rains, M.C., R.A. Dahlgren, R.J. Williamson, G.E. Fogg, and T. Harter. 2008. Geological 4 control of physical and chemical hydrology in vernal pools, Central Valley, California. 5 Wetlands. 28:347-362. 6

Rains, M.C., G.E. Fogg, T. Harter, R.A. Dahlgren, and R.J. Williamson. 2006. The role of 7 perched aquifers in hydrological connectivity and biogeochemical processes in vernal 8 pool landscapes. Hydrological Processes. 20:1157-1175. 9

Rahmstorf, S. 2007. A semi-empirical approach to projecting future sea level. Science. 10 315(5810):368-370. 11

Reed, D., J. Anderson, E. Fleishman, D. Freyberg, W. Kimmerer, K. Rose, M. Stacey, S. Ustin, 12 I. Werner, B. DiGennaro, and W. Spencer. 2007. Bay Delta Conservation Plan 13 Independent Science Advisors Report. Available at: 14 http://www.baydeltaconservationplan.com/Libraries/Background_Documents/BDCP_IS15 A_Report_11-16-07.sflb.ashx 16

Reever-Morghan, K., J.D. Corbin, and J.D. Gerlach. 2007. Water relations. Pages 87-93 in M.R. 17 Stromberg, J.D. Corbin, and C.M. D’Antonio, editors. California grasslands: ecology and 18 management. University of California Press, Berkeley. 19

Reiner, R.J. and R. Swenson. 2000. Saving vernal pools in the Cosumnes River watershed. 20 Fremontia 28:33-37. 21

Resources Agency, DWR, and DFG. 2007. Pelagic Fish Action Plan, March 2007. 84 pp. 22 Available at: http://www.water.ca.gov/deltainit/docs/030507pod.pdf. 23

Riparian Habitat Joint Venture. 2004. The riparian bird conservation plan: a strategy for 24 reversing the decline of riparian associated birds in California. Version 2.0 California 25 Partners in Flight. Available at: http://www.prbo.org/calpif/pdfs/riparian_v-2.pdf. 26

Robertson, K.G. 1987. Paleochannels and recent evolution of Sacramento River, California. MS 27 thesis. University of California, Davis. 28

Rogers, D.C. 1998. Aquatic macroinvertebrate occurrences and population trends in constructed 29 and natural vernal pools in Folsom, California. Pages 224-235 in C.W. Witham, E.T. 30 Bauder, D. Belk, W.R.J. Ferren, and R. Ornduff, editors. Ecology, Conservation, and 31 Management of Vernal Pool Ecosystems. California Native Plant Society, Sacramento. 32

Roos, M. 2006. Flood management practice in northern California. Irrigation and Drainage 55: 33 S93-S99. 34

http://www.baydeltaconservationplan.com/Libraries/Background_Documents/BDCP_ISA_Report_11-16-07.sflb.ashx

http://www.baydeltaconservationplan.com/Libraries/Background_Documents/BDCP_ISA_Report_11-16-07.sflb.ashx



Rosatti ed., T. 2010. The Jepson manual: vascular plants of California. University of California 1 Press, Berkeley, CA. 2

Rowland, J.C., W.E. Dietrich, G. Day, and G. Parker. 2009. Formation and maintenance of 3 single-thread tie channels entering floodplain lakes: observations from three diverse river 4 systems. Journal of Geophysical Research 114:F02013. 5

Ruhl, C.A. and D.H. Schoellhamer. 2004. Spatial and temporal variability of suspended-6 sediment concentration in a shallow estuarine environment. San Francisco Estuary & 7 Watershed Science 2:article 1. 8

Rutter, C. 1908. The Fishes of the Sacramento-San Joaquin basin, with a study of their 9 distribution and variation. U.S. Bureau of Fisheries, Document No. 637. 10

Saleeby, J. and Z. Foster. 2004. Topographic response to mantle lithosphere removal in the 11 southern Sierra Nevada region, California. Geology 32:245-248. 12

Sanderson, E.W., S.L. Ustin, and T.C. Foin. 2000. The influence of tidal channels on the 13 distribution of salt marsh plant species in Petaluma Marsh, CA, USA. Plant Ecology 14 146:29-41. 15

SFEI (San Francisco Estuary Institute). 1998. EcoAtlas version 1.50b4. (Updated 2007). 16 Oakland, CA. 17

SFEI (San Francisco Estuary Institute). 2003. Practical Guidebook for the Identification and 18 Control of Invasive Aquatic and Wetland plants in the San Francisco Bay-Delta Region. 19 Available at: http://www.sfei.org/nis. 20

SFEI (San Francisco Estuary Institute). 2004. Second annual report Montezuma Wetlands 21 Restoration Project Technical Review Team. Oakland. 22

SFEI (San Francisco Estuary Institute). 2006. Second annual report Montezuma Wetlands 23 Restoration Project Technical Review Team. Oakland. 24

SFEI (San Francisco Estuary Institute). 2010. Draft East Contra Costa Historical Ecology Study. 25 Contra Costa County and the Contra Costa County Watershed Forum, Oakland, CA. 26

San Joaquin County Planning Division. 2008. San Joaquin County Mountain House New 27 Community Master Plan amended July 2008. Stockton, CA. Available at: 28 http://www.sjgov.org/commdev/cgi-bin/cdyn.exe?grp=planning&htm=mhmasterplan. 29

Sarna-Wojcicki, A.M., C.E. Meyer, H.R. Bowman, N.T. Hall, P.C. Russell, M.J. Woodward, and 30 J.L. Slate. 1985. Correlation of the Rockland Ash Bed, a 400,000-year-old stratigraphic 31 marker in northern California and western Nevada, and implications of middle Plistocene 32 paleogeography of central California. Quaternary Research 23:236-257. 33

http://www.sjgov.org/commdev/cgi-bin/cdyn.exe?grp=planning&htm=mhmasterplan



Sawyer, J.O. and T. Keeler-Wolf. 1995. A manual of California vegetation. California Native 1 Plant Society, Sacramento, CA, USA. 2

Sawyer, J.O., T. Keeler-Wolf, and J.M. Evens. 2009. A manual of California vegetation. 2nd 3 edition. California Native Plant Society, Sacramento. 4

Scheffer, M. 2004. Ecology of shallow lakes. Kluwer Academic Publishers, Boston, 5 Massachusetts. 6

Schulz, P.D. and D.D. Simons. 1973. Fish species diversity in a prehistoric central California 7 indian midden. California Fish and Game 59(2):107-118. 8

Sculthorpe, C.D. 1967. The biology of aquatic vascular plants. Edward Arnold Ltd., London. 9

Shelmon, R.J. 1971. The quaternary deltaic and channel system in the Central Great Valley, 10 California. Annals of the Association of American Geographers 61:427-440. 11

Showers, M.T. 1996. Cordylanthus palmatus habitat survey, mitigation potential, and 12 management recommendations. PAR Environmental Services, Inc, Sacramento, CA. 13

Shuford, W.D., G.W. Page, and J.E. Kjelmyr. 1998. Patterns and dynamics of shorebird use of 14 California's Central Valley. Condor. 100: 227-244. 15

Shvidchenko, A.B., R.C. MacArthur, and B.R. Hall. 2004. Historic sedimentation in 16 Sacramento-San Joaquin Delta. IEP Newsletter 17:21-29. 17

Siegel S. 2007. Determinism, chaos, and randomness: restoring Delta ecosystems. 8th Biennial 18 State of the San Francisco Estuary Conference presentation. 10/18/07. 19

Silveira, J.G. 1998. Avian uses of vernal pools and implications for conservation practice. Pp. 20 92-106 In: C.W. Witham et al. (eds.). Ecology, conservation, and management of vernal 21 pool ecosystems—proceedings from a 1996 conference. California Native Plant Society, 22 Sacramento, CA. 23

Simenstad, C., J. Toft, H. Higgins, J. Cordell, M. Orr, P. Williams, L. Grimaldo, and Z. 24 Hymanson. Sacramento/ San Joaquin Delta Breached Levee Wetland Study (BREACH) 25 Preliminary Report. 2000. Wetland Ecosysteam Team, University of Washington School 26 of Fisheries. Seattle, WA. February 2000. 27

Singer, M.B. 2008. Downstream patterns of bed material grain size in a large, lowland alluvial 28 river subject to low sediment supply. Water Resources Research 44:W12202. 29

Singer, M.B. and T. Dunne. 2001. Identifying eroding and depositional reaches of valley by 30 analysis of suspended sediment transport in the Sacramento River, California. Water 31 Resources Research 37:3371-3381. 32



Singer, M.B. and R. Aalto. 2009. Floodplain development in an engineered setting. Earth 1 Science Process and Landforms 34:291-304. 2

Singer, M.B., R. Aalto, and L.A. James. 2008. Status of the lower Sacramento Valley flood-3 control system within the context of its natural geomorphic setting. Natural Hazards 4 Review 9:104-115. 5

Skinner, M.W. and B.M. Pavlik. 1994. Inventory of rare and endangered vascular plants in 6 California. 5th edition. (Special Publication No. 1.) California Native Plant Society. 7 Sacramento, CA. 8

Smith, R.L. 1974. Ecology and field biology. Harper and Row, New York. 9

Solomeshch, A.I., M.J. Barbour, and R.F. Holland. 2007. Vernal pools. In: M.J. Barbour, T. 10 Keeler-Wolf, A. A. Schoenherr eds., Terrestrial vegetation of California. Berkeley, CA: 11 pp. 394-424. 12

Sommer T. 2007. The Decline of Pelagic Fishes in the San Francisco Estuary: An Update. 13 Presented to the State Water Resources Control Board, Sacramento, CA. 3/22/2007. 14 Available at: http://www.waterrights.ca.gov/baydelta/docs/pelagicorganism/ 15 dwr_032207sommer.pdf. 16

Sommer, T., R. Baxter, and F. Feyrer. 2007. Splittail “delisting”: a review of recent population 17 trends and restoration activities. American Fishing Symposium. 53:25-38. 18

Sommer, T., R. Baxter, and B. Herbold. 1997. Resilience of splittail in the Sacramento-San 19 Joaquin Estuary. Transactions of the American Fisheries Society. 126:961-976. 20

Sommer, T., B. Harrell, M. Nobriga, R. Brown, W. Kimmerer, and L. Schemel. 2001a. 21 California’s Yolo Bypass: evidence that flood control can be compatible with fisheries, 22 wetlands, wildlife, and agriculture. Fisheries. 26(8): 6-16. 23

Sommer, T.R., W.C. Harrell, and T.J. Swift. 2008. Extreme hydrologic banding in a large-river 24 floodplain, California, U.S.A. Hydrobiologia 598:409-415. 25

Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. Batham, and W.J. Kimmerer. 2001b. Floodplain 26 rearing of juvenile Chinook salmon: Evidence of enhanced growth and survival. 27 Canadian Journal of Fisheries and Aquatic Sciences. 58(2): 325-333. 28

Stainstreet, I.G. and T.S. McCarthy. 1993. The Okavango Fan and the classification of subaerial 29 fan systems. Sedimentary Geology 85:115-133. 30

State of California. 1987. A proposal to the U.S. Department of Energy for siting the super 31 conducting super collider in California, Davis site: Vol. 3 Geology and tunneling. 32



State Water Resources Control Board. 1999. Water Right Decision 1641. Available at: 1 http://www.waterrights.ca.gov/Decisions/D1641rev.pdf. 2

Stein, B.A. 2002. States of the Union: Ranking America’s Biodiversity. Arlington, VA: 3 NatureServe. National Research Council. Washington, D.C. Accessed on December 2006 4 Available at: http://www.natureserve.org/Reports/stateofunions.pdf 5

Stein, B.A., L.S. Kutner, and J.S. Adams. 2000. Precious Heritage: The Status of Biodiversity in 6 the United States. Oxford University Press, New York, NY. 7

Storer, T.I. 1925. A synopsis of the amphibia of California. University of California Publications 8 in Zoology 27:60-71. 9

Strahan, J. 1984. Regeneration of riparian forests of the Central Valley. In: R.E. Warner and K. 10 Hendrix, eds., California riparian systems: ecology, conservation and productive 11 management. University of California Press, Berkeley, CA. pp. 58-67. 12

Suisun Ecological Workgroup. 1997. Suisun Ecological Workgroup brackish marsh vegetation 13 subcommittee report. California Department of Water Resources Control Board, 14 Sacramento. 15

Suisun Ecological Workgroup. 2001. Suisun Ecological Workgroup final report to the State 16 Water Resources Control Board. State Water Resources Control Board, Sacramento. 17

Sweeney, B.W., T.L. Bott, J.K. Jackson, L.A. Kaplan, J.D. Newbold, L.J. Standley, W.C. 18 Hession, and R.J. Horowitz. 2004. Riparian deforestation, stream narrowing, and loss of 19 stream ecosystem services. Proceedings of the National Academy of Sciences U.S.A. 20 101: 14132-14137. 21

Swiecki, T.J. and E. Bernhardt. 2002. Exotic and native plant monitoring at Jepson Prairie 22 Preserve, 2002. Solano Land Trust, Fairfield. 23

Takekawa, J.Y., I. Woo, H. Spautz, N. Nur, J.L. Grenier, K. Malmud-Roam, J.C. Nordby, A.N. 24 Cohen, F. Malamud-Roam, and S.E. Wainwright-De La Cruz. 2006. Environmental 25 threats to tidal-marsh vertebrates of the San Francisco Bay estuary. Studies in Avian 26 Biology 32:176-197. 27

TAIC 2008 (Technology Associates International Corporation). 2008. Unpublished Material, 28 YoloCounty_Regional Vegetation_July08. Online 29 Links:http://www.yoloconservationplan.org/yolo_data/YoloCounty_RegionalVegetation_30 July08.shp 31

Thomasson, H.G., Jr., F.H. Olmsted, and E.F. LeRoux. 1960. Geology, water resources and 32 usable ground-water storage capacity of part of Solano County, California. USGS Water-33 Supply Paper 1464. 34

http://www.natureserve.org/Reports/stateofunions.pdf



Thompson, J. 1957. The settlement geography of the Sacramento-San Joaquin Delta, California. 1 Dissertation. Stanford University, Palo Alto, CA. 2

Thompson, J. 1965. Reclamation sequence in the Sacramento-San Joaquin Delta. California 3 Geographer 1965: 29-35. 4

Thompson, K. 1960. Historic flooding in the Sacramento Valley. Pacific Historical Review 29: 5 349-360. 6

Thompson, K. 1961. Riparian forests of the Sacramento Valley, California. Annals of the 7 Association of American Geographers 51: 294-315. 8

Trenham, P.C. 1998. Radio tracking information. Unpublished manuscript. 6 pp. 9

Trowbridge, W.B. 2002. The influence of restored flooding on floodplain plant distributions. 10 Ph.D. dissertation. University of California, Davis.Trowbridge, W.B. 2005. The role of 11 stochasticity and priority effects in floodplain restoration. Ecological Applications 12 17:1312-1324. 13

Trowbridge, W.B. 2005. The role of stochasticity and priority effects in floodplain restoration. 14 Ecological Applications 17:1312-1324. 15

Trowbridge, W.B., S. Kalmanovitz, and M.W. Schwartz. 2005. Growth of valley oak (Quercus 16 lobata Nee) in four floodplain environments in the Central Valley of California. Plant 17 Ecology 176:157-164. 18

Tu, I.M. 2000. Vegetation patterns and processes of natural regeneration in periodically flooded 19 riparian forests in the Central Valley of California. Ph.D. dissertation. University of 20 California, Davis. 21

Twidale, C.R. and J.R. Vidal Romaní. 2005. Landforms and geology of granitic terrains. A.A. 22 Balkema Publishers, Leiden, Netherlands. 23

Unruh, J.R. and S.T. Hector. 1999. Subsurface characterization of the Potrero-Ryer Island thrust 24 system, western Sacramento-San Joaquin Delta, northern California: final technical 25 report. USGS National Earthquake Hazards Program. 26

Unruh, J.R. and C.S. Hitchcock. 2009. Characterization of potential seismic sources in the 27 Sacramento-San Joaquin Delta, California. Final Technical Report submitted to the 28 USGS National Earthquake Hazards Reduction Program. November, 2009. 29

URS Corporation. 2007. Status and trends of Delta-Suisun Services. Prepared for California 30 Department of Water Resources. May 2007. Available at: 31 http://deltavision.ca.gov/DeltaVisionStatusTrends.shtml. 32



URS Corporation and Jack R. Benjamin & Associates, Inc. 2006. Delta Risk Management 1 Strategy, Initial Technical Framework Paper, Geomorphic Response to Levee Failure. 2 Prepared for Department of Water Resources. 3

USACE (U.S. Army Corps of Engineers). 1978. Preliminary guide to wetlands of the West Coast 4 states. U.S. Army Engineer Waterways Experiment Staation Technical Repeport Y-78-4. 5

USACE (U.S. Army Corps of Engineers). 2009. Water Resources Policies and Authorities 6 Incorporating Sea Level Change Considerations in Civil Works Programs. Circular No. 7 1165-2-211. July. 8

U. S. Bureau of Soils. 1909. Alkali map, Woodland sheet, CA. 9

USDA (U.S. Department of Agriculture). 1999. Soil taxonomy a basic system of soil 10 classification for making and interpreting soil surveys, 2nd ed.. U.S. Department of 11 Agriculture, Agriculture Handbook Number 436. 12

USDA-FSA (U.S. Department of Agriculture-Farm Service Agency). 2005. Downloaded July 3, 13 2007 from CaSIL mirror site hosted by California EPA at: 14 ftp://casil.calepa.ca.gov/casil/remote_sensing/naip_2005. 15

USFWS (United States Fish & Wildlife Service). 1984. Revised recovery plan for three 16 endangered species endemic to Antioch Dunes, California. USFWS, Portland, OR. 17

USFWS (United States Fish & Wildlife Service). 2001. Antioch Dunes National Wildlife Refuge 18 Draft comprehensive conservation plan: plan and environmental assessment. USFWS, 19 Sacramento, CA. 20

USFWS (U.S. Fish and Wildlife Service). 2002. Antioch Dunes National Wildlife Refuge 21 Comprehensive Conservation Plan. July. Sacramento, CA. 22

USFWS (U.S. Fish and Wildlife Service). 2004. 5-year review Hypomesus transpacificus (delta 23 smelt). Sacramento, CA. 50 pp. 24

USFWS (U.S. Fish and Wildlife Service). 2005. Reinitiation of Formal and Early Section 7 25 Endangered Species Consultation on the Coordinated Operations of the Central Valley 26 Project and State Water project and the Operational Criteria and Plan to Address 27 Potential Critical Habitat Issues. February 24, 2005. Sacramento, CA. Available at: 28 http://www.fws.gov/sacramento/es/biological_opinions.htm 29

USFWS (U.S. Fish and Wildlife Service). 2007. Stone Lakes National Wildlife Refuge 30 Comprehensive Conservation Plan. January, Sacramento, CA. 31

USFWS (United States Fish & Wildlife Service). 2008. Lange's metalmark butterfly (Apodemia 32 mormo langei), Antioch Dunes evening-primrose, (Oenothera deltoides subsp. howellii), 33

http://www.fws.gov/sacramento/es/biological_opinions.htm



Contra Costa wallflower (Erysimum capitatum var. angustatum) - Five-year review: 1 summary and evaluation. USFWS, Sacramento, CA. 2

USFWS. 2009a. Cirsium hydrophilum var. hydrophilum (Suisun thistle) 5-year review: summary 3 and evaluation. Sacramento. 4

USFWS. 2009b. Cordylanthus mollis ssp. mollis (soft bird’s-beak) 5-year review: summary and 5 evaluation. Sacramento. 6

USGS. 2005. Preliminary integrated geological map databases for the United States - western 7 states: California, Nevada, Arizona, Washington, Oregon, Idaho, and Utah. Open-File 8 Report 2005-1305. USGS. 9

Vaghti, M.G. and S.E. Greco. 2007. Riparian vegetation of the Great Valley. In: M. Barbour, T. 10 Keeler-Wolf, and A. Schoenherr (eds), Terrestrial vegetation of California. University of 11 California Press, Berkeley, CA. pp 425-455. 12

Vaghti, M. and T. Keeler-Wolf. 2004. Suisun Marsh vegetation mapping change detection 2003. 13 California Department of Water Resources, Sacramento. 14

Van Dijk, M., G. Postma, and M.G. Kleinhans. 2009. Autocyclic behavior of fan deltas: an 15 analogue experimental study. Sedimentology 56:1569-1589. 16

Wahrhaftig, C. 1965. Stepped topography of the southern Sierra Nevada, California. Geological 17 Society of America Bulletin 76:1165-1190. 18

Wakabayashi, J. and T.L. Sawyer. 2001. Stream incision, tectonics, uplift, and evolution of 19 topography of the Sierra Nevada, California. Journal of Geology 109:539-562. 20

Water Resources & Information Management Engineering Inc. 2006. Yolo County integrated 21 groundwater and surface water model. Yolo County Flood Control and Water Conservation 22 District and Water Resources Association of Yolo County, Woodland. 23

Watson, E.B. 2006. Environmental change in San Francisco Estuary Tidal Marshes. Ph.D. 24 dissertation, University of California, Berkeley, CA. 25

Watson, E.B. and R. Byrne. 2009. Abundance and diversity of tidal marsh plants along the 26 salinity gradient of the San Francisco Estuary: implications for global change ecology. 27 Plant Ecology 205:113-228. 28

Weber-Band, J. 1998. Neotectonics of the Sacramento-San Joaquin Delta area, east-central Coast 29 Ranges, California. PhD thesis, Department of Geology/Geophysics, University of 30 California, Berkeley. 31



Weissmann, G.S., G.L. Bennett, and A.L. Lansdale. 2005. Factors controlling sequence 1 development on Quaternary fluvial fans, San Joaquin Basin, California.in A. M. Harvey, 2 A. E. Mather, and M. Stokes, editors. Alluvial fans: geomorphology, sedimentology, 3 dynamics. Geological Society of London, London. 4

Welch, P.S. 1952. Limnology, 2nd ed. McGraw-Hill, New York. 5

Wentz, W.A. 1981. Wetlands values and management. U.S. Government Printing Office, 6 Washington, D.C. 7

Werner, I. 2007. Pyrethroids in the water column – is there reason for concern? Seminar, 8 University of California, Davis, November 8, 2007. 9

Winder, M. and A.D. Jassby. In press. Shifts in zooplankton community structure: implications 10 for food-web processes in the upper San Francisco Estuary. Estuaries and Coasts. 11

Wildlands Inc. 2005. Mitigation banks: performance standards and credit release. 12

William Lettis & Associates. 2005. Geomorphic and Geologic Mapping for Restoration 13 Planning, Sacramento-San Joaquin Delta Region. Final Report CALFED Ecosystem 14 Restoration Program. June 2005. 15

Williams, D.D. 2006. The biology of temporary waters. Oxford University Press, New York. 16

Williamson, R., G. Fogg, M. Rains, and T. Harter. 2005. Hydrology of vernal pools at three sites, 17 southern Sacramento Valley. Final technical report to the California Department of 18 Transportation, Sacramento, CA. 19

Witham, C.W. 2003. Tule Ranch vernal pools botanical resources survey report. Davis, CA: 20 Yolo Basin Foundation. 21

Witham, C.W. 2006. Greater Jepson Prairie ecosystem regional management plan. Fairfield: 22 Solano Land Trust. 23

Witham, C.W. and G.A. Kareofelas. 1994. Botanical resources inventory at Calhoun Cut 24 Ecological Reserve following California’s recent drought. California Department of Fish 25 and Game, Sacramento, California. 26

Wright, S.A. and D.H. Schoellhamer. 2004. Trends in the sediment yield of the Sacramento 27 River, California, 1957 - 2001. San Francisco Estuary and Watershed Science. Volume 2, 28 Issue 2 (May 2004), Article 2. 29

Young, J.A., C.E. Turner, and L.F. James. 1995. Perennial Pepperweed. Rangelands. 17(4): 121-30 123. 31



Zebell, R. and P. Fiedler. 1996. Restoration and recovery of Mason's lilaeopsis: Phase II. Final 1 report to the California Department of Fish and Game, Plant Conservation Program. 50 2 pp. 3

Zedler, P.H. 1987. The ecology of southern California vernal pools: a community profile. U. S. 4 Fish & Wildlife Service. 5

Zedler, P.H. 1990. Life histories of vernal pool vascular plants.in D.H. Ikeda and R.A. Schlising, 6 editors. Vernal pools: their habitat and biology. Herbarium, California State University 7 Chico, Number 8, Chico, California. 8

Personal Communications 9

January 5, 2007. C. Simenstad (Associate Professor, University of Washington), phone 10 conversation with Rick Wilder about tidal marsh formation in the northern Delta. 11

April 2, 2009. T. Keeler-Wolf, T. (CDFG Senior Vegetation Ecologist), email response with 12 Chris McColl concerning Suisun Marsh GIS dataset registration issues. 13

CHAPTER 3. CONSERVATION STRATEGY 14

A. Munevar, Hydrologist, CH2M Hill. Presentation to the BDCP Conveyance Working Group 15 on Hydrodynamic effects of Delta-wide tidal marsh restoration: initial evaluation. 16 9/26/08. 17

Ackerman J., C. Eagles-Smith, J. Takekawa, J. Bluso, and T. Adelsback. 2008. Mercury 18 concentrations in blood and feathers of prebreeding Forster’s Terns in relation to space 19 use of San Francisco Bay, California, USA, habitats. Environmental Toxicology and 20 Chemistry. 27:897-908. 21

AFS (American Fisheries Society California-Nevada Chapter). 2009. Policy statement 22 supporting total (100%) marking of all California hatchery produced fall run chinook 23 salmon. January 13, 2009. 24

Albers, P.H., M.T. Koterba, R. Rossmann, W.A. Link, J.B. French, R.S. Bennett, and W.C. 25 Bauer. 2007. Methylmercury and reproduction in American kestrels. Environmental 26 Toxicology and Chemistry. 26(9):1856-1866. 27

Albertson, J.D. 1995. Ecology of the California clapper rail in South San Francisco Bay. M.S. 28 Thesis, San Francisco State University, San Francisco, CA, 200 pp. 29

Alexander, D.G. 1976. Ecological aspects of temporary pool fauna. In: S. Jain, editor. Vernal 30 pools: their ecology and conservation. Institute of Ecology Publication Number 9, Davis, 31 California. 32



Alexander, D.G. 2007. Thirty years research on vernal pool macroinvertebrates from Vina 1 plains. In: Schlising, R.A. and D.G. Alexander(eds.). Vernal pool landscapes − 2 proceedings from a 2006 conference. California State University, Chico, CA. pp. 89-110. 3

Alpers C.N., C. Eagles-Smith, C. Foe, S. Klasing, M.C. Marvin-DiPasquale, DG Slotton, and L 4 Windham-Myers. 2008. Mercury conceptual model. Sacramento(CA): Delta Regional 5 Ecosystem Restoration Implementation Plan. 6

Amweg E.L., D.P. Weston, J. You, and M. Lydy. 2006. Pyrethroid insecticides and sediment 7 toxicity in urban creeks from California and Tennessee. Environmental Science and 8 Technology. 40(5):1700-1706. 9

Anderson, C. and M. Rigney. 1980. California least tern breeding survey, South San Francisco 10 Bay – 1981. U.S. Department of the Interior, Fish and Wildlife Service, San Francisco 11 Bay National Wildlife Refuge Special Report, 16pp. 12

Araki, H., W. R. Ardren, E. Olsen, B. Cooper, and M. Blouin. 2006. Reproductive success of 13 captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the 14 Hood River. Conservation Biology 21:181–190. 15

Archibald Consulting, Richard Woodward Water Quality Consultants, and Palencia Consulting 16 Engineers. 2007. Watershed Sanitary Survey 2006 Update. Report prepared for State 17 Water Project Contractors Authority. June 2007. 18

Arnold, R. A. 1983. Ecological studies of six endangered butterflies (Lepidoptera, Lycaenidae): 19 island biogeography, patch dynamics, and the design of habitat preserves. University of 20 California Press, Berkeley, CA. 21

Arnold, R. A. 2005. Insect and invertebrates site assessment: Country Crossings development, 22 Antioch, Contra Costa, California. RCL Ecology, Clayton, CA. 23

Atwater, B.F. 1980. Distribution of vascular plants in six remnants of intertidal wetland of the 24 Sacramento-San Joaquin Delta, California. Menlo Park (CA) US. Geological Survey, 25 U.S. Geological Survey Open File Report 80-883. 26

B. Naslund, Captain, DBEEP, DFG. Written budget sent via email to R. Wilder, 7/14/09. 27

B.J. Miller, Private Consultant. Presentation to the Other Stressors Working Group on 28 monitoring for toxics in fish, 5/27/08. 29

Bailey S.A., I.C. Duggan, C.D.A .Van Overdijk, T.H. Johengen, D.F. Reid, and H.J. Macissaic. 30 2004. Salinity tolerance of diapausing eggs of freshwater zooplankton. Freshwater 31 Biology. 49: 286-295. 32

Baker, P. F., and J. E. Morhardt. 2001. Survival of Chinook salmon smolts in the Sacramento-33 San Joaquin Delta and Pacific Ocean. Pages 163-182 in R. L. Brown, editor. 34 Contributions to the biology of Central Valley salmonids. Fish Bulletin 179: Volume 2. 35 California Department of Fish and Game, Sacramento. 36



Bakir, F., S.F. Damluji, L. Amin-Zaki, M. Murtadha, A. Khalidi, N.Y. Al-Rawi, S. Tikriti, H.I. 1 Dhahir, T.W. Clarkson, J.C. Smith, and R.A. Doherty. 1973. Methylmercury poisoning in 2 Iraq. Science 181:230–241. 3

Baldwin, D.H., J.A. Spromberg, T.K. Collier, and N.L. Scholz. 2009. A fish of many scales: 4 extrapolating sublethal pesticide exposures to the productivity of wild salmon 5 populations. Ecological Applications 19(8):2004-2015. 6

Ballard A., R. Breuer, F. Brewster, C. Dahm, C. Irvine, K. Larsen, A. Mueller-Solger, A. Vargas. 7 2009. Background/summary of ammonia investigations in the Sacramento-San Joaquin 8 Delta and Suisun Bay. March 2, 2009. Unpublished technical report for the CALFED 9 Science Program. Available at: http://www.science.calwater.ca.gov/pdf/workshops/ 10 workshop_ammonia_bckgrnd_paper_nh4-nh3_030209.pdf 11

Baraona, M., T. Ippolito, and W. Renz. 2007. Post-project appraisals of constructed vernal pools 12 in Solano, County, California. Water Resources Center Archives, University of 13 California. Berkeley, CA. 14

Barber L.B., K.E. Lee, D.L. Swackhamer, and H.L. Schoenfuss. 2007. Reproductive responses 15 of male fathead minnows exposed to wastewater treatment plant effluent, effluent treated 16 with XAD8 resin, and an environmentally relevant mixture of alkylphenol compounds. 17 Aquatic Toxicology. 82(1): 36-46. 18

Barbour, M.G., A.I. Solomeshch, C.W. Witham, R.F. Holland, R.L. MacDonald, S. Cilliers, J.A. 19 Molina, J.J. Buck, and J.M. Hillman. 2003. Vernal pool vegetation in California: 20 variation within pools. Madroño 50:129-146.Barbour, M.G., A.I. Solomeshch, R.F. 21 Holland, C.W. Witham, R.L. MacDonald, S. Cilliers, J.A. Molina, J.J. Buck, and J.M. 22 Hillman. 2005. Vernal pool vegetation of California: communities of long-innundation 23 habitats. Phytocoenologia 35:177-200. 24

Barbour, M.G., A.I. Solomeshch, J.J. Buck, R.F. Holland, C.W. Witham, S.L. Starr, and K.A. 25 Lazar. 2007b. Classification, ecological characterization, and presence of listed plant taxa 26 of vernal pool associations in California. U. S. Fish & Wildlife Service, Sacramento. 27

Barbour, Michael and Todd Keeler-Wolf, and Allan A. Schoenherr. 2007a. Terrestrial 28 Vegetation of California, 3rd edition. University of California Press, Berkeley and Los 29 Angeles, CA 30

Barclay, W.R. and A.W. Knight. 1981. Physiochemical processes affecting production in a 31 turbid vernal pool. Pages 126-142 in Vernal pools and intermittent streams. Institute of 32 Ecology, Davis, California. 33

Barko J.W. and R.M. Smart. 1981. Comparative influence of light and temperature on the growth 34 and metabolism of selected submersed freshwater macrophytes. Ecological Monographs. 35 51(2): 219-235. 36

http://www.science.calwater.ca.gov/pdf/workshops/%20workshop_ammonia_bckgrnd_paper_nh4-nh3_030209.pdf

http://www.science.calwater.ca.gov/pdf/workshops/%20workshop_ammonia_bckgrnd_paper_nh4-nh3_030209.pdf



Barr, C.B. 1991. The Distribution, Habitat, and Status of the Valley Elderberry Longhorn Beetle 1 Desmocerus californicus dimorphus Fisher (Insecta: Coleoptera: Cerambycidae). U.S. 2 Fish and Wildlife Service, Sacramento, CA. 3

Barry, S. 1995. Rangeland oasis. University of California Cooperative Extension. Leaflet No. 4 21531. 5

Barry, S.J. and H.B. Shaffer. 1994. The status of the California tiger salamander (Ambystoma 6 californiense) at Lagunita: a 50-year update. Journal of Herpetology 28:159-164. 7

Barry, W. J. (1972). The Central Valley Prairie Volume I. Sacramento, State of California- The 8 Resources Agency: 82. 9

Bartolome, J.W., Barry, W.J., Griggs, T., and P. Hopkinson. 2007. Valley Grassland. In: 10 Terrestrial Vegetation of California (eds. M.G. Barbour, T. Keeler-Wolf, and A.A. 11 Schoenherr), 3d Ed., pp: 367-393. University of California Press. 12

Baxter, R. D., K. Hieb, S. DeLeon, K. Fleming and J. Orsi. 1999. Report on 1980-1995 fish shrimp and 13 crab sampling in the San Francisco Estuary, California. Interagency Ecological Program for the 14 Sacramento-San Joaquin Estuary Technical Report 63. 503 pp. 15

Baxter, R., R. Breuer, L. Brown, M. Chotkowski, F. Feyrer, M. Gingras, B. Herbold, A. Mueller-16 Solger, M. Nobriga, T. Sommer, and K. Souza. 2008. Pelagic organism decline progress 17 report: 2007 synthesis of results. January 15, 2008. Available at: 18 http://www.fws.gov/sacramento/es/documents/POD_report_2007.pdf. 19

Bay, California: Concentration, speciation and mobility. U.S. Geological Survey, Open File 20 Report 2007-1240, 98 p. <http://pubs.usgs.gov/of/2007/1240/> 21

Bay, California: Concentration, speciation and mobility. U.S. Geological Survey, Open File 22 Report 2007-1240, 98 p. <http://pubs.usgs.gov/of/2007/1240/> 23

Bay-Delta Oversight Council. 1995. An introduction to harvest and its effects on selected species 24 of fish of the San Francisco Bay/Sacramento-San Joaquin Delta Estuary: Draft briefing 25 paper. California Resources Agency. Sacramento, CA. March 1995. 26

Beamesderfer R.C.P, M. L. Simpson, and G.L. Kopp. 2007. Use of life history information in a 27 population model of Saramento green sturgeon. Enironmental Biology of Fishes. 70:315-28 337. 29

Beedy, E.C. 2008. Tricolored Blackbird. In: Shuford W.D., T.Gardali (eds): California Bird 30 Species of Special Concern. Studies of Western Birds No. 1. Western Field 31 Ornithologists and California Department of Fish and Game and Game. Sacramento, CA. 32

Beedy, E.C. and W.J. Hamilton III. 1999. Tricolored Blackbird (Agelaius tricolor). In: The Birds 33 of North America, No. 423 (A. Poole and F. Gill [eds.]). The Birds of North America, 34 Inc., Philadelphia, PA. 35

http://www.fws.gov/sacramento/es/documents/POD_report_2007.pdf



Beedy, E.C. and W.J. Hamilton. 1997. Tricolored Blackbird Status Update and Management 1 Guidelines. (Jones & Stokes Associates, Inc. 97-099.) Sacramento, CA. Prepared for U.S. 2 Fish and Wildlife Service, Portland, OR and California Department of Fish and Game, 3 Sacramento, CA. 4

Beedy, E.C., S.D. Sanders, and D. Bloom. 1991. Breeding status, distribution, and habitat 5 associations of the Tricolored Blackbird (Agelaius tricolor) 1850-1989. (Jones & Stokes 6 Associates, Inc. 88-197). Prepared for U.S. Fish and Wildlife Serv. Sacramento, CA. 7

Begon, M, J. L. Harper, and C. R. Townsend. (1996) Ecology: individuals, populations and 8 communities. 3rd ed. Blackwell Scientific Publications, Oxford, UK. 9

Bell, H.M. 1994. Analysis of habitat characteristics of the San Joaquin kit fox in its northern 10 range. M.A. thesis, California State Univ., Hayward, CA, 90 pp. 11

Benigno G.M. and T.R. Sommer. 2008. Just add water: sources of chironomid drift in a large 12 river floodplain. Hydrobiologia. 600(1): 297-305. 13

Bennett W.A. 2005. Critical assessment of the delta smelt population in the San Francisco 14 Estuary, California. San Francisco Estuary and Watershed Science [online serial]. Vol. 15 3, Issue 2 (September 2005), Article 1. 16

Bent, A.C. 1940. Life histories of North American Cuckoos, Goastsuckers, Hummingbirds, and 17 their allies. United States Natural History Museum Bulletin 176. 18

Berntssen, M.H.G., A. Aatland, and R.D. Handy. 2003. Chronic dietary mercury exposure causes 19 oxidative stress, brain lesions, and altered behavior in Atlantic salmon (Salmo salar) parr. 20 Aquatic Toxicology. 65:55-72. 21

Bettaso, J. and D. H. Goodman. 2008. Mercury contamination in two long-lived filter feeders in 22 the Trinity River basin: a pilot project. U. S. Fish and Wildlife Service, Arcata Fish and 23 Wildlife Office, Arcata Fisheries Technical Report Number TR2008-09 Arcata, CA. 24

Boreman, J. 1997. Sensitivity of North American sturgeons and paddlefish to fishing mortality. 25 Enironmental Biology of Fishes. 48:399-405. 26

Boul, R and T. Keeler-Wolf. 2008. 2006 Vegetation Map Update For Suisun Marsh, Solano 27 County, California. A Report to the California Department of Water Resources 28 Vegetation Classification and Mapping Program, Biogeographic Data Branch, California 29 Department of Fish & Game. Available at: 30 http://nrm.dfg.ca.gov/documents/ContextDocs.aspx?cat=VegCAMP 31

Bowen MD, L Hanna, R. Bark, V. Maisonneuve, S. Hiebert. 2008. Non-physical barrier 32 evaluation, Physical Configuration I. US Department of the Interior, Bureau of 33 Reclamation. Technical Memorandum. Technical Service Center. Denver, CO. 34



Bowen, M.D., S. Hiebert, C. Hueth, V. Maisonneuve. 2009 effectiveness of a non-physical fish 1 barrier at the divergence of the Old and San Joaquin Rivers (CA). Reclamation. 2 Technical Memorandum 86-68290-09-05. 3

Brandes P.L. and J.S. McLain. 2001. Juvenile chinook salmon abundance, distribution, and 4 survival in the Sacramento-San Joaquin Estuary. In: Brown RL, editor. Contributions to 5 the Biology of Central Valley Salmonids. Fish Bulletin 179(2). Sacramento (CA): 6 California Department of Fish and Game. pp 39-136. 7

Brannon E., S. Brewer, A. Setter, H. Miller, F. Utter, and W. Hershberger. 1985. Columbia River 8 white sturgeon (Acipenser transmontanus) early life history and genetics study: final 9 report. Project No. 83-316. U. S. Department of Energy. December 1985. 10

Brown L.R. 2003. Will Tidal Wetland Restoration Enhance Populations of Native Fishes? In: 11 Larry R. Brown, editor. Issues in San Francisco Estuary Tidal Wetlands Restoration. San 12 Francisco Estuary and Watershed Science. Vol. 1, Issue 1 (October 2003), Article 2. 13 Available at: http://repositories.cdlib.org/jmie/sfews/vol1/iss1/art2 14

Brown L.R. and D. Michniuk. 2007. Littoral fish assemblages of the alien-dominated 15 Sacramento-San Joaquin Delta, California, 1980-1983 and 2001-2003. Estuaries and 16 Coasts 30:186-200. 17

Brown R.L. 1982. Screening agricultural diversions in the Sacramento-San Joaquin Delta. 18 Department of Water Resources. 19

Brown, R.J., R.L. Rudd. 1981. Chromosomal comparisons with the Sorex ornatus-S. vagrens 20 complex. Wassman Journal of Biology 39:30-35. 21

Brown, R.L. 2004. Summary of the 2004 workshop: making science work for Suisun Marsh. San 22 Francisco Bay-Delta Science Consortium, Sacramento. 23

Buddington, R.K. and J. P. Christofferson. 1985. Digestive and feeding characteristics of the 24 chondrosteans. Environmental Biology of Fishes 14:31–41. 25

Burkhard, Bill, Incident Commander, California Department of Water Resources (916-376-26 9761). Telephone conversation with J-L Cartron, July 22, 2010 regarding functioning of 27 Suisun Marsh salinity control gates and patterns of land use in Suisun Marsh. 28

Bury, R.B. and D.J. Germano. 2008. Actinemys marmorata (Baird and Girard 1852) – Western 29 Pond Turtle, Pacific Pond Turtle. Conservation of Freshwater Turtles and Tortoises: A 30 Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. 31 A.G.J. Rhodin, P.C.H. Pritchard, P.P. van Dijk, R.A. Samure, K.A. Buhlmann, and J.B. 32 Iverson, Eds. Chelonian Research Monographs No. 5. 33

C. Armor, Bay-Delta Regional Manager, DFG. Presentation to the Other Stressors Working 34 Group about proposed monitoring of non-project entrainment effects, 8/19/08. 35

http://repositories.cdlib.org/jmie/sfews/vol1/iss1/art2



C. Enright, Senior Engineer, DWR, Telephone conversation with R. Wilder about methyl-1 mercury and low dissolved oxygen in effluent from managed seasonal wetlands in Suisun 2 Marsh, 8/26/08. 3

C. Hanson, Environmental Consultant, Hanson Environmental. Presentation to BDCP Integration 4 Team about Hood Bypass flow effects on covered fish species, 12/9/08. 5

CALFED 2000. Final Environmental Impact Statement/Environmental Impact Report. CALFED Bay-6 Delta Program Available at http://calwater.ca.gov/calfed/library/Archive_EIS.html 7

CALFED Bay-Delta Program. 1998. Technical Report, Affected Environment, Vegetation and 8 Wildlife, Draft. March 1998. Available at: http://www.calwater.ca.gov/Admin_Record/C-9 009083.pdf 10

CALFED Bay-Delta Program. 2000. Ecosystem Restoration Program Plan. Volume II: 11 Ecological Management Zone Visions. Final Programmatic ESI/EIR Technical 12 Appendix. Available at: 13 http://www.delta.dfg.ca.gov/erp/docs/reports_docs/ERPP_Vol_2.pdf. 14

CALFED. 2001. Scrutinizing the Delta Cross-Channel. News from the CALFED Bay-Delta 15 Science Program. 16

Calflora. 2007. The Calflora Database (a non-profit organization). Available at: 17 http://www.calflora.org/. 18

California Academy of Sciences Herpetology Department. 2008. Available at: 19 Hhttp://www.research.calacademy.org/research/herpetology/catalog/H. 20

California Resources Agency. 2007. California Spatial Information Library (CaSIL)Available 21 at: http://casil.ucdavis.edu/casil/ 22

California Science Advisory Panel. 2007. California's response to the zebra/quagga mussel 23 invasion in the west: recommendations of the California Science Advisory Panel. 24 California Science Advisory Panel, Sacramento, CA. 25

California State Coastal Conservancy. 2003. Draft Programmatic Environmental Impact 26 Statement/Environmental Impact Report, San Francisco Estuary Invasive Spartina 27 Project: Spartina Control Program. Available at: http://www.spartina.org. 28

California State Parks - Delta Meadows Park Property website. http://www.parks.ca.gov/?p 29 age_id=492 30

Campbell C.G., S.E. Borglin, F.B. Green, A. Grayson, E. Wozei, and W.T. Stringfellow. 2006. 31 Biologically directed environmental monitoring, fate, and transport of estrogenic 32 endocrine disrupting compounds in water: A review. Chemosphere. 65(8): 1265-1280. 33

Carolsfeld J, Tester M, Kreiberg H, Sherwood NM (1997) Pheromone-induced spawning of pacific 34 herring. Horm Behav 31(3):256-268. 35

http://calwater.ca.gov/calfed/library/Archive_EIS.html

http://www.delta.dfg.ca.gov/erp/docs/reports_docs/ERPP_Vol_2.pdf

http://www.calflora.org/

http://www.research.calacademy.org/research/herpetology/catalog/

http://casil.ucdavis.edu/casil/

http://www.spartina.org/



Castillo G, Morinaka J, Lindberg J, Fujimura B, Hobbs J, Tigan G, Ellison L, Baskerville-Bridges B. An 1 Experimental Approach to Evaluate Entrainment Losses of Delta Smelt in the South Delta. 2009 2 State of the Estuary. 9/29-10/1/2009. Oakland, CA 3

CDFA (California Department of Food and Agriculture). 2009. California Border Protection 4 Stations: first line of defense in protecting our environment and resources from invasive 5 species. Accessed 6/12/09. Available at: 6 http://www.cdfa.ca.gov/phpps/PE/ExteriorExclusion/borders.html 7

Cech Jr., J. J. and C. E. Crocker. Physiology of sturgeon: effects of hypoxia and hypercapnia. 8 Journal of Applied Ichthyology. 18: 320-324. 9

Center for Biological Diversity. 2007. Delta smelt. Accessed 6/18/2007. Available at: 10 http://www.biologicaldiversity.org/swcbd/species/deltasmelt/index.html. 11

Chambers D.B. and T.J. Leiker. 2006. A reconnaissance for emerging contaminants in the South 12 Branch Potomac River, Cacapon River, and Williams River Basins, West Virginia, April-13 October 2004. U.S. Geological Survey Open-File Report 2006-1393, 23 p. Available at: 14 http://pubs.usgs.gov/of/2006/1393. 15

Champion P.D. and C.C. Tanner. 2000. Seasonality of macrophytes and interaction with flow in 16 a New Zealand lowland stream. Hydrobiologia 441: 1-12. 17

Chan S.Y., Y.F. Tsang, L.H. Cui, and H. Chua. 2008. Domestic wastewater treatment using 18 batch-fed constructed wetland and predictive model development for NH3-N removal. 19 Process Biochemistry. 43: 297-305. 20

Chan, Y. and P. Arcese. 2002. Subspecific differentiation and conservation of Song Sparrows 21 (Melospiza melodia) in the San Francisco Bay region inferred by microsatellite loci 22 analysis. Auk 119:641-657. 23

Clark K.W., M.D. Bowen, K.P. Zehfuss, and R.B. Mayfield. 2008. Pre-Screen Loss of Steelhead 24 within Clifton Court Forebay. Abstract for the 2008 CalFed Science Conference. 25

Clark KW, MD Bowen, RB Mayfield, KP Zehfuss, JD Taplin, CH Hanson. 2009. Quantification of Pre-26 Screen Loss of Juvenile Steelhead in Clifton Court Forebay. CA Department of Water Resources. 27 Available at: 28 http://baydeltaoffice.water.ca.gov/ndelta/fishery/documents/2009_clark_et_al_quantification_of_29 steelhead_pre-screen_loss.pdf 30

Clarke B. 2008. USFWS plans for captive propagation of delta smelt. CALFED Science Program 31 Workshop: The use of artificial propagation as a tool for Central Valley salmonid and 32 delta smelt conservation, Sacramento, CA, July 14, 2008. 33

Clifford, M.A., K.J. Eder, I. Werner, and R.P. Hedrick. 2005. Environmental toxicology – 34 synergistic effects of esfenvalerate and infectious hematopoietic necrosis virus on 35 juvenile Chinook salmon mortality. Environmental Toxicology and Chemistry. 36 24(7):1766-1772. 37

http://www.cdfa.ca.gov/phpps/PE/ExteriorExclusion/borders.html

http://www.biologicaldiversity.org/swcbd/species/deltasmelt/index.html

http://pubs.usgs.gov/of/2006/1393



CNDDB (California Natural Diversity Database RareFind). 2009. California Department of Fish 1 and Game, Sacramento, CA. Ver. 3.1.0. 2

CNPS (California Native Plant Society). 2009. Inventory of Rare and Endangered Plants (online 3 edition, v7-09a). California Native Plant Society. Sacramento, CA. Accessed on Thu, 4 Apr. 9, 2009 from http://www.cnps.org/inventory. 5

Cochlan W.P. and P.J. Harrison. 1991. Inhibition of nitrate uptake by ammonium and urea I nthe 6 eukaryotic picoflagellate Micromonas pusilla (Butcher) Manton et Parke. Journal of 7 Experimental Marine Biology and Ecology. 153: 143-152. 8

Cogswell, H.L. 1977. Water birds of California. University of California Press, Berkeley, 399 9 pp. 10

Cohen, A.N. and J.T. Carlton. 1995. Nonindigenous Aquatic Species in a United States Estuary: A Case 11 Study of the Biological Invasions of the San Francisco Bay and Delta. U.S. Fish and Wildlife 12 Service, Washington, DC (pp. 94-95). 13

Cole, B. E., Cloern, J. E. (1984). Significance of biomass and light availability to phytoplankton 14 productivity in San Francisco Bay. Mar. Ecol. Prog. Ser. 17: 15-24 15

Collinge, S.K., M. Holyoak, C.B. Barr, and J.T. Marty. 2001. Riparian habitat fragmentation and 16 population persistence of the threatened valley elderberry longhorn beetle in central 17 California. Biological Conservation 100:103-113. 18

Comrack, L. 2008. Yellow-breasted Chat (Icteria virens). In: D. Shuford and T. Gardali, eds. 19 Bird Species of Special Concern. California Department Fish and Game, Sacramento, 20 CA. 21

CCWD (Contra Costa Water District). 2010. Historical Freshwater and Salinity Conditions in the Western 22 Sacramento-San Joaquin Delta and Suisun Bay. Water Resources Department, Technical 23 Memorandum WR10-001. Available at http://www.ccwater.com\salt.asp 24

Conway H.L. 1977. Interactions of inorganic nitrogen in the uptake and assimilation by marine 25 phytoplankton. Marine Biology. 39: 221-232. 26

Cook, L. 1999. Tricolored Blackbird (Agelaius tricolor) conservation plan for southern 27 Sacramento County. Unpublished report submitted to Jones & Stokes, in cooperation 28 with the southern Sacramento County Habitat Conservation Plan. 29

Cook, L. and L. D. Buffaloe. 1998. Delta agricultural diversion evaluation summary report, 30 1993-1995. Interagency Ecological Program for the San Francisco Bay/Delta Estuary. 31 Technical Report Number 61. Sacramento, CA. 32

Cook, L.F. and C.A. Toft. 2005. Dynamics of extinction: Population decline in the colonially 33 nesting Tricolored Blackbird (Agelaius tricolor). Bird Conservation International 15: 73-34 88. 35



Crawford, H.S., R.G. Hooper, and R.W. Titterington. 1981. Song bird population response to 1 silvicultural practices in central Appalachian hardwoods. Journal of Wildlife 2 Management 45: 680-692. 3

Culberson, S.D., C.B. Harrison, C. Enright, and M.L. Nobriga. 2004. Sensitivity of larval fish 4 transport to location, timing, and behavior using a particle tracking model in Suisun 5 Marsh, California. Pages 257-267 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, 6 editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. 7 American Fisheries Society, Symposium 39, Bethesda, Maryland. 8

CRWQCB (California Regional Water Quality Control Board). 2005. Amendments to the Water 9 Quality Control Plan for the Sacramento River and San Joaquin River Basins for the 10 control program for factors contributing to the dissolved oxygen impairment in the 11 Stockton Deep Water Ship Channel. Final Staff Report. February 28, 2005. Available at: 12 http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_joaquin13 _oxygen/final_staff_report/do_tmdl_final_draft.pdf 14

CVRWQCB. 2007. The water quality control plan (Basin Plan) for the California Regional 15 Water Quality Control Board Central Valley Region. Fourth Edition, Revised October 16 2007 (with approved amendments). Available at: 17 www.waterboards.ca.gov/centralvalley/water_issues/basin_plans/sacsjr.pdf. 18

CVRWQCB. 2008. Sacramento-San Joaquin Delta TMDL for Methylmercury. Draft report for 19 public review. February 2008. Available at: http://www.swrcb.ca.gov/centralvalley/wa 20 ter_issues/tmdl/central_valley_projects/delta_hg/staff_report_feb08/tmdl_full_rpt.pdf. 21

CVRWQCB (California Regional Water Quality Control Board). 2010. A Review of 22 methylmercury and inorganic mercury discharges from NPDES facilities in California’s 23 Central Valley, staff report, final. March 2010. Sacramento, CA 24

D’Antonio C.M., C. Malmstrom, S.A. Reynolds, J. Gerlach. 2007. Ecology of invasive non-25 native species in California grassland. In: Stromberg MR, Corbin JD, D’Antonio CM, 26 editors. California Grasslands. Berkeley and Los Angeles: University of California Press. 27 pp. 67–83. 28

Davidson, C., H.B. Shaffer, and M.R. Jennings. 2002. Spatial tests of the pesticide drift, habitat 29 destruction, UV-B, and climate-change hypotheses for California amphibian declines. 30 Conservation Biology 16:1588-1601. 31

Dawson, K., K. Veblen, and T. Young. 2007. Experimental evidence for an alkali ecotype of 32 Lolium multiflorum, an exotic invasive annual grass in the Central Valley, CA, USA. 33 Biological Invasions 9:327-334. 34

DBEEP (DFG Delta Bay Enhanced Enforcement Project). 2007. Unpublished report. 35

http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_joaquin_oxygen/final_staff_report/do_tmdl_final_draft.pdf

http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/san_joaquin_oxygen/final_staff_report/do_tmdl_final_draft.pdf

http://www.waterboards.ca.gov/centralvalley/water_issues/basin_plans/sacsjr.pdf

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_hg/staff_report_feb08/tmdl_full_rpt.pdf

http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/delta_hg/staff_report_feb08/tmdl_full_rpt.pdf



DBW (Department of Boating and Waterways). 2006. Egeria densa Control Program Second 1 Addendum to 2001 Environmental Impact Report with Five-Year Program Review and 2 Future Operations Plan. December 8, 2006. Available at: 3 http://www.dbw.ca.gov/PDF/Egeria/EIR/eirAdd2.pdf. 4

DBW (Department of Boating and Waterways. 2008. California Department of Boating and 5 Waterways Egeria densa Control Program annual report 2007 application season. United 6 States Department of Agriculture, Sacramento, CA. 7

de Oliveira Ribeiro, C. A., L. Belger, E. Pelletier, C. Rouleau. 2002. Histopathological evidence 8 of inorganic mercury and methyl mercury toxicity in the arctic charr (Salvelinus alpinus). 9 Environmental Research 90:217-225. 10

Deblois, E.M. and W.C. Leggett. 1993. Importance of biotic and abiotic regulators of abundance of the 11 intertidal amphipod Calliopius laeviusculus (Amphipoda: Gammaridae) and assessment of the 12 accuracy and precision of sampling methods for detecting abundance changes. Marine Biology 13 115: 75-83. 14

Dedrick, K.G. 1989. San Francisco Bay tidal marshland acreages: recent and historic values. 15 Proceedings of the 6th Symposium in Coastal and Ocean Management (Coastal Zone 16 1989). American Society of Engineers. pp. 383-398. 17

DeHaven, R.W. 2000. Breeding Tricolored Blackbirds in the Central Valley, California: a 18 quarter century perspective. U.S. Fish and Wildlife Service white paper, 23 pp. 19

DeHaven, R.W., F.T. Crase, and P.D. Woronecki. 1975. Breeding status of the Tricolored 20 Blackbird, 1969–1972. California Fish and Game. 61: 166-180. 21

Del Rosario, R. and Y. Redler. 2009. Residence of Sacramento River Winter-Run Chinook Salmon in the 22 Sacramento-San Joaquin Delta: Outmigration Coincides with Pulse Flows and Floodplain 23 Drainage. Poster presented at the 9th Biennial State of the San Francisco Estuary Conference. 24 9/29-10/1/2009. Oakland, CA. 25

DeSante, D. F., E. D. Ruhlen, and R. Scalf. 2007. The distribution and relative abundance of 26 Burrowing Owls in California during 1991-1993: evidence for a declining population and 27 thoughts on its conservation. Pp. 1-41 in Barclay, J.H., K.W. Hunting, J.L. Lincer,, J. 28 Linthicum, and T.A. Roberts (eds.). Proceedings of the California Burrowing Owl 29 Symposium, November 2003. Bird Populations Monographs No.1. 30

Devlin, E.W. 2006. Acute toxicity, uptake and histopathology of aqueous methyl mercury to 31 fathead minnow embryos. Ecotoxicology. 15:97-110. 32

Devlin, E.W., and B. Clary. 1998. In vitro toxicity of methyl mercury to fathead minnow cells. 33 Bulletin of Environmental Contamination and Toxicology. 61:527-533. 34

DFG (California Department of Fish and Game). 2000. The status of rare, threatened, and 35 endangered animals and plants in California, California clapper rail, California 36 Department of Fish and Game, Sacramento, CA. 37

http://www.dbw.ca.gov/PDF/Egeria/EIR/eirAdd2.pdf



DFG (California Department of Fish and Game) and NMFS (National Marine Fisheries Service). 1 2001. Final report on anadromous salmonid fish hatcheries in California. Sacramento, 2 CA. December 3, 2001. 3

DFG (California Department of Fish and Game)up. 2005. California Wildlife Habitat 4 Relationships Database version 8.1. Software and updated database. Sacramento, CA. 5 Accessed June 2007-January 2008. Available at: 6 http://www.dfg.ca.gov/whdab/html/wildlife_habitats.html. 7

DFG (California Department of Fish and Game) 2007a. Delta vegetation and land use GIS 8 dataset cross-walked to SAIC natural community vegetation types. Sacramento, CA. 9

DFG (California Department of Fish and Game). 2007b. Delta-Bay enhanced enforcement 10 project: annual report July 2006-June2007. Sacramento, CA. 11

DFG(California Department of Fish and Game). 2007c. California steelhead fishing report-12 restoration card. Report to the Legislature. Sacramento, CA. July 2007. 13

DFG(California Department of Fish and Game). 2008a. California Aquatic Invasive Species 14 Management Plan. January 2008. 136 pp plus appendices. Accessed 5/29/08. Available 15 at: www.dfg.ca.gov/invasives/plan. 16

DFG (California Department of Fish and Game). 2008b. A guide to cleaning boats and 17 preventing mussel damage. Available at: http://www.dfg.ca.gov/invasives/quaggamussel/ 18

DFG (California Department of Fish and Game). 2008c. 2007 Sturgeon Fishing Report Card: 19 Preliminary Data Report. Sacramento, CA. 20

DFG (California Department of Fish and Game). 2008d. Central Valley Angler Survey. 21 Sacramento, CA. December 27, 2008. 22

DFG et al. (Department of Fish and Game) 2007.Wetlands and Water Resources, Suisun 23 Resource Conservation District, California Department of Water Resources Suisun Marsh 24 Branch, California Department of Fish and Game Moss Landing Marine Laboratory, U.S. 25 G, U.C. Davis Department of Wildlife, Fish, and Conservation Biology. 2007. Final 26 monitoring plan and GPS locations strategy for resolving MeHg and low dissolved 27 oxygen events in northern Suisun Marsh. State Water Resources Control Board. 28 Sacramento, CA. September 20, 2007. 29

DFG. 2009. Protocols for surveying and evaluating impacts to special status native plant 30 populations and natural communities. Available at: 31 http://www.dfg.ca.gov/biogeodata/cnddb/pdfs/Protocols_for_Surveying_and_Evaluating32 _Impacts.pdf 33

DiTomaso J.M. and E.A. Healy. 2003. Aquatic and riparian weeds of the west. University of 34 California Department of Natural Resources, Oakland, CA. 35

http://www.dfg.ca.gov/whdab/html/wildlife_habitats.html

http://www.dfg.ca.gov/invasives/plan

http://www.dfg.ca.gov/invasives/quaggamussel/



Domagalski, J.L., C.N. Alpers, D.G. Slotton, T.H. Suchanek, S.M. Ayers. 2004. Mercury and 1 methylmercury concentrations and loads in the Cache Creek watershed, California. 2 Science of the Total Environment. 327:215-237. 3

Drewes J.E., J. Hemming, S.J. Ladenburger, J. Schauer, and W. Sonzogni. 2005. An assessment 4 of endocrine disrupting activity changes during wastewater treatment through the use of 5 bioassays and chemical measurements. Water Environment Research. 77(1): 12-23. 6

Dugdale R.C. 2008. Effects of ammonium on phytoplankton growth and consequences for the 7 POD. 5th Biennial CALFED Science Conference. 10/22-10/24/08. Sacramento, CA. 8

Dugdale R.C. and J.J. MacIsaac. 1971. A computational model for the uptake of nitrate in the 9 Peru upwelling region. Investigacion Pesquera 35: 299-308. 10

Dugdale R.C. and T.S. Hopkins. 1978. Predicting the structure and dynamics of a pollution-11 driven marine ecosystem embedded in an oligotrophic sea. Thalassia Jugoslavica. 14: 12 107-126. 13

Dugdale R.C. and T.S. Hopkins. 1978. Predicting the structure and dynamics of a pollution-14 driven marine ecosystem embedded in an oligotrophic sea. Thalassia Jugoslavica. 14: 15 107-126. 16

Dugdale R.C., F.P. Wilkerson, V.E. Hogue, and A. Marchi. 2007. The role of ammonium and 17 nitrate in spring bloom development in San Francisco Bay. Estuarine Coastal and Shelf 18 Science. 73:17-29. 19

Dugdale, R.C., F.P. Wilkerson, A. Marchi, and V. Hogue. 2006. Nutrient controls on new 20 production in the Bodega Bay, California, upwelling plume. Deep-Sea Research II. 53: 21 3049-3062. 22

Dunk, J.R. 1995. White-tailed kite (Elanus leucurus). In The Birds of North America, No. 178 23 (A. Poole and F. Gill, eds.). The Academy of Natural Sciences, Philadelphia, and The 24 American Ornithologists’ Union, Washington, D.C. 25

Dussault E.B., V.K. Balakrishnan, E. Sverko, K.R. Solomon, and P.K. Sibley. 2008. Toxicity of 26 human pharmaceuticals and personal care products to benthic invertebrates. 27 Environmental Toxicology and Chemistry. 27(2): 425-432. 28

DWR (Department of Water Resources). 1994. Summary of sensitive plant and wildlife 29 resources in Suisun Marsh during water years 1984 – 1994. Environmental Services 30 Office, Department of Water Resources, Sacramento, CA. 31

DWR (Department of Water Resources). 1999. Biological Assessment: Suisun Marsh 32 Preservation Agreement as Modified by Amendment Three. 33

DWR (Department of Water Resources). 2001. Suisun Ecological Workgroup; Wildlife of the 34 Suisun Marsh, California Black Rail Final Report to the State Water Resources Control 35



Board. Sacramento, CA. Available at: 1 http://www.iep.ca.gov/suisun_eco_workgroup/workplan/report/wildlife/blackrail.html. 2

DWR (Department of Water Resources). 2005. Collection, Handling, Transport, and Release 3 (CHTR) New Technologies Proposal: Phase 1 Baseline Conditions. May 2005. 72 pp 4 plus appendices. Accessed 5/29/08. Available at: 5 http://baydeltaoffice.water.ca.gov/ndelta/fishery/element3/index.cfm. 6

DWR (Department of Water Resources). 2007. Past and Present Land Uses in the Sacramento-7 San Joaquin Delta and Suisun Marsh. Report to the Delta Vision Blue Ribbon Task 8 Force. November 21. Sacramento, CA. 9

DWR. 2008. North/Central Delta Salmon Out-migration Study. Accessed on 10/16/2008. 10 http://baydeltaoffice.water.ca.gov/ndelta/salmon/index.cfm 11

DWR and DFG (Department of Water Resources and Department of Fish and Game). 2008. 12 Risks and options to reduce risks to fishery and water supply uses of the Sacramento/San 13 Joaquin Delta. A report pursuant to requirements of Assembly Bill 1200, Laird. Available 14 at: http://www.water.ca.gov/floodmgmt/dsmo/sab/drmsp/docs/AB1200_report.pdf. 15

DWR and SCC (Department of Water Resources and State Coastal Conservancy). 2008. Dutch Slough 16 Tidal Marsh Restoration Project Environmental Impact Report. Draft. November. (State 17 Clearinghouse No. 2006042009.) Sacramento, CA. Prepared by Grassetti Environmental 18 Consulting, Berkeley, CA. NEEDS A LETTER 19

DWR and BOR (U.S. Department of the Interior, Bureau of Reclamation). 2006. South Delta 20 Improvements Program Final Environmental Impact Statement/Environmental Impact 21 Report. 22

Ebbert J.C., S.S. Embrey, and J.A. Kelley. 2003. Concentrations and Loads of Suspended 23 Sediment and Nutrients in Surface Water of the Yakima River Basin, Washington, 1999-24 2000--With an Analysis of Trends in Concentrations. Water-Resources. Investigations 25 Report 03-4026. Available at: http://pubs.usgs.gov/wri/wri034026/pdf/wri034026.pdf. 26

EDAW. 2004. San Joaquin saltbush mitigation plan Yolo County Juvenile Detention Facility. 27 Sacramento: Yolo County Central Services. 28

EDAW. 2005. Flooded Islands: Pre-Feasibility Study Report. Prepared for: California 29 Department of Water Resources. 30

EDAW (Eckbo, Dean, Austin, and Williams). 2007. Lower Sherman Island Wildlife Area land 31 management plan. Prepared for DFG. April 2007. 32

EDAW. 2008. Update on fisheries-based modeling approach and results. Draft Memorandum – 33 Franks Tract Project from Chris Fitzer, EDAW to the Franks Tract Project Fisheries 34 Working Group. November 12, 2008. 35

http://www.iep.ca.gov/suisun_eco_workgroup/workplan/report/wildlife/blackrail.html

http://baydeltaoffice.water.ca.gov/ndelta/fishery/element3/index.cfm

http://baydeltaoffice.water.ca.gov/ndelta/salmon/index.cfm

http://www.water.ca.gov/floodmgmt/dsmo/sab/drmsp/docs/AB1200_report.pdf

http://pubs.usgs.gov/wri/wri034026/pdf/wri034026.pdf



Eddy, F.B. 2005. Ammonia in estuaries and effects on fish. Journal of Fish Biology 67:1495-1 1513. 2

Egoscue, H. J. 1975. Population dynamics of the kit fox in western Utah. Southern Calif. Acad. 3 Sci. 74:122-127. 4

Egoscue, H. J. 1975. Population dynamics of the kit fox in western Utah. Southern Calif. Acad. 5 Sci. 74:122-127. 6

Eng, L.L. 1984. Rare, threatened and endangered invertebrates in California riparian systems. In: 7 R.E. Warnter, K.M. Hendrix, eds., California riparian systems ecology, conservation, and 8 productive management. University of California Press, Berkeley, CA. 9

England, A.S., J.A. Estep, and W.R. Holt. 1995. Nest-site selection and reproductive 10 performance of urban-nesting Swainson’s Hawks in the Central Valley of California. 11 Journal of Raptor Research 29:179-186. 12

England, A.S., M.J. Bechard, and C.S. Houston. 1997. Swainson’s Hawk (Buteo swainsoni). In 13 Birds of North America no. 265 (A. Poole and F. Gill [eds.]). The Academy of Natural 14 Sciences, Philadelphia, PA, and The American Ornithologists’ Union, Washington, D.C. 15

Ernst, C.H., R.W. Barbour, and J.E. Lovich. 1994. Turtles of the United States and Canada. 16 Smithsonian Institution Press, Washington and London. xxxviii+578 pp. 17

ESA (Environmental Science Associates and Yolo County Planning & Public Works 18 Department). 2005. CALFED at-risk plant species, habitat restoration and recovery, and 19 non-native species management ERP-02-P46: final conservation and management plan. 20 CALFED Ecosystem Restoration Program, Sacramento, CA. 21

Estep, J.A. 1984. Diurnal Raptor Eyrie Monitoring Program. California Department of Fish and 22 Game, Nongame Wildlife Investigations. Project Report W-65-R-1, Job No. II-2.0. 23 Sacramento, CA. 24

Estep, J.A. 1989. Biology, movements, and habitat relationships of the Swainson’s Hawk in the 25 Central Valley of California, 1986-87. California Department of Fish and Game. 26 Unnumbered Report. 27

Estep, J.A. 2008. The Distribution, Abundance, and Habitat Associations of the Swainson’s 28 Hawk (Buteo swainsoni) in Yolo County. Prepared by Estep Environmental Consulting 29 for the Yolo Natural Heritage Program, Woodland, CA. 30

Evens, J.G., G.W. Page, S.A. Laymon, and R.W. Stallcup. 1991. Distribution, relative abundance 31 and status of the California black rail in western North America. Condor 93:952-966. 32

Evers, D.C., O.P. Lane, L. Savoy, and W. Goodale. 2004. Assessing the impacts of 33 methylmercury on piscivorous wildlife using a wildlife criterion value based on the 34 common loon, 1998-2003. Gorham (ME): BioDiversity Research Institute, rpt BRI 2004-35 2005; Maine Department of Environmental Protection. 36



Fahnenstiel G.L., G.A. Lang, T.F. Nalepa, and T.H. Johengen. 1995b. Effects of zebra mussel 1 (Dreissena polymorpha) colonization on water quality parameters in Saginaw Bay, Lake 2 Huron. Journal of Great Lakes Research. 21(4) 435-448. 3

Fahnenstiel G.L., T.B. Bridgeman, G.A. Lang, M.J. McCormick, and T.F. Nalepa. 1995a. 4 Phytoplankton productivity in Saginaw Bay, Lake Huron: effects of zebra mussel 5 (Dreissena polymorpha) colonization. Journal of Great Lakes Research. 21(4) 465-475. 6

Falconer I.R., H.F. Chapman, M.R. Moore, and G. Rammuthugala. 2006. Endocrine-disrupting 7 compounds: a review of their challenge to sustainable and safe water supply and water 8 reuse. Environmental Toxicology 21:181-191. 9

Falkner M., L. Takata, S. Gilmore, and N. Dobroski. 2007. 2007 Biennial Report on the 10 California Marine Invasive Species Program. California State Lands Commission. 11 February 2007. Available at: 12 http://www.slc.ca.gov/Spec_Pub/MFD/Ballast_Water/Documents/2007FinalBiennialRep13 ort.pdf. 14

Feyrer F., B. Herbold, S.A. Matern, P.B. Moyle. 2003. Dietary shifts in a stressed fish 15 assemblage: Consequences of a bivalve invasion in the San Francisco Estuary. 16 Environmental Biology of Fishes. 67: 277-288. 17

Feyrer, F., T. Sommer, and J. Hobbs, 2007a. Living in a dynamic environment: variability in life 18 history traits of age-0 splittail in tributaries of San Francisco Bay. Transactions of the 19 American Fisheries Society 136:1393-1405. 20

Feyrer F., M.L. Nobriga, and T.R. Sommer. 2007b. Multidecadal trends for three declining fish 21 species: habitat patterns and mechanisms in the San Francisco Estuary, California, USA . 22 Canadian Journal of Fisheries and Aquatic Sciences. 64(4): 723-734. 23

Feyrer, F., T. Sommer, and W. Harrell. 2006. Managing floodplain inundation for native fish: 24 production dynamics of age-0 splittail (Pogonichthys macrolepidotus) in California’s 25 Yolo Bypass. Hydrobiologia 573:213-226. 26

Fiedler, P. and R. Zebell. 1993. Restoration and recovery of Mason’s lilaeopsis: Phase I. Final Report, 27 submitted to the California Department of Fish and Game. 47 pp. plus appendices. 28

Fiedler, P. L, M. E. Keever, B. J. Grewell, and D. J. Partridge. 2007. Rare plants in the Golden 29 Gate Estuary (California): the relationship between scale and understanding. Australian J. 30 Botany 55:206-220. 31

Field, C. B., G. C. Daily, F. W. Davis, S. Gaines, P. A. Matson, J. Melack and N. L. Miller. 199932 Confronting Climate Change in California: Ecological Impacts on the Golden State. Unio33 n of Concerned Scientists and Ecological Society of America. Cambridge, MA and Wash34 ington, DC 35

http://www.slc.ca.gov/Spec_Pub/MFD/Ballast_Water/Documents/2007FinalBiennialReport.pdf

http://www.slc.ca.gov/Spec_Pub/MFD/Ballast_Water/Documents/2007FinalBiennialReport.pdf



Fisher, R.N. and H.B. Shaffer. 1996. The decline of amphibians in California’s Great Central Valley. 1 Conservation Biology 10:1387-1397Flagg, T. A., B. A. Berejikian, J. E. Colt, W. W. 2 Dickhoff, L. W. Harrell, D. J. Maynard, C. E. Nash, M. S. Strom, R. N. Iwamoto, and C. 3 V.W. Mahnken. 2000. Ecological and behavorial impacts of artificial production 4 strategies on the abundance of wild salmon populations: a Review of Practices in the 5 Pacific Northwest. NOAA Technical Memorandum NMFS-NWFSC-XX. Seattle, WA. 6

Fleming E.J., E.E. Mack, P.G. Green, D.C. Nelson. 2006. Mercury methylation from unexpected 7 sources: Molybdate-inhibited freshwater sediments and an iron-reducing bacterium. 8 Applications in Environmental Microbiology. 72: 457-464. 9

Fleskes, J.P., J.L. Yee, M.L. Casazza, M.R. Miller, J.Y. Takekawa, and D.L. Orthmeyer. 2005. 10 Waterfowl distribution, movements, and habitat use relative to recent habitat changes in 11 the Central Valley of California. Report, U. S. Geological Survey, Dixon, CA. 12

Foe, C.G., W. Croyle. 1999. Mercury concentrations and loads from the Sacramento River and 13 from Cache Creek to the Sacramento–San Joaquin Delta Estuary: California Regional 14 Water Quality Control Board, Central Valley Region, Sacramento, CA. 15

Foerster, K.S. and J.E. Takekawa. 1991. San Francisco Bay National Wildlife Refuge predator 16 management plan and environmental assessment. San Francisco Bay National Wildlife 17 Refuge, Fremont, CA. 54 pp. 18

Foss S.F., P.R. Ode, M. Sowby, and M. Ashe. 2007. Non-indigenous aquatic organisms in the 19 coastal waters of California. California Fish and Game 93:111-129. 20

Frayer, W.E., D.E. Peters, and H.R. Pywell. 1989. Wetlands of the California Central Valley: 21 status and trends, 1939 to mid- 1980’s. U.S. Fish and Wildlife Service, Portland, OR. 29 22 pp. 23

Friedmann AS, EK Costain, DL MacLatchy, W Stansley, EJ Washuta. 2002. Effect of mercury 24 on general and reproductive health of largemouth bass (Micropterus salmoides) from 25 three lakes in New Jersey. Ecotoxicological Environmental Safety 52:117-122. 26

Fujimura R.W., G. Edwards, D. Killam, T.M. Frink, and L. Millett. 2000. Evaluation of adult 27 salmon migration passage at the Suisun Marsh Salinity Control Gates in Montezuma 28 Slough, California. In: JH Eiler et al. (ed.). Biotelemetry 15: Proceedings of the 15th 29 International Symposium on Biotelemetry, Juneau, Alaska USA, May 9-14, 1999. pp. 68-30 75 31

Fujimura R.W., J. Morinaka, G. Aasen, and V. Afentoulis. 2008. CHTR program overview: six 32 years later. Abstract for the 2008 CalFed Science Conference. 33

Futuyma, D. J. 1998. Evolutionary biology. 3rd ed. Sinauer Associates. Sunderland, 34 MA.Gahnström G., P. Blomqvist, and S. Fleischer. 1993. Are key nitrogen fluxes 35 changed in the acidified aquatic ecosystem? Ambio. 22 (5): 318-324. 36



Gaines, D. and S. Laymon. 1984. Decline, Status, and Preservation of the Yellow-billed Cuckoo 1 in California. Western Birds 15:49-80. 2

Gallagher, S.P. 1996. Seasonal occurrence and habitat characteristics of some vernal pool 3 brachiopoda in northern Californai, U.S.A.. Journal of Crustacean Biology. 16: 323-329. 4

Gantes H.P. and A.S. Caro. Environmental heterogeneity and spatial distribution of macrophytes 5 in plain streams. Aquatic Botany. 70: 225-236. 6

Gantes HP, Caro AS. 2001. Environmental heterogeneity and spatial distribution of macrophytes in plain 7 streams. Aquatic Botany. 7: 225-236. 8

Ger K.A., S.J. Teh. 2008. Extent of acute, chronic, and nutritional impacts of Microcystis 9 blooms on the Delta's calanoid copepods. 5th Biennial CALFED Science Conference. 10 10/22-10/24/2008. Sacramento, CA. 11

Gerlach, J.D., B.S. Bushman, J.K. McKay, and H. Meimberg. 2009. Taxonomic confusion 12 permits the unchecked invasion of vernal pools in California by low mannagrass 13 (Glyceria declinata).. Invasive Plant Science and Management. 2:92-97. 14

Gilmer, D. S., M. R. Miller, R. D. Bauer, and J. R. LeDonne. 1982 California's Central Valley 15 Wintering Waterfowl: Concerns and Challenges . Transactions of the 47th North 16 American Wildlife and Natural Resources Conference, Wildlife Management Institute, 17 Washington, D.C. 18

Gilmer, D.S., M.L. Miller, R.B. Bauer, and J.R. LeDonne. 1982. California's Central Valley 19 wintering waterfowl: concerns and challenges. Transactions of the North American 20 Wildlife and Natural Research Conference. 47: 441-452. 21

Gilmour C.C., E.A. Henry, R. Mitchell. 1992. Sulfate stimulation of mercury methylation in 22 freshwater sediments. Environmental Science and Technology. 26: 2281-2287. 23

Gingras M. 1997. Mark/Recapture Experiments at Clifton Court Forebay to Estimate Pre-24 Screening Loss to Entrained Juvenile Fishes: 1976-1993. Interagency Ecological 25 Program Technical Report 55 (November 1997). 26

Goals Project. 2000. Baylands Ecosystem Species and Community Profiles: Life histories and 27 environmental requirements of key plants, fish and wildlife. Prepared by the San 28 Francisco Bay Area Wetlands Ecosystem Goals Project. P.R. Olofson, editor. San 29 Francisco Bay Regional Water QualityControl Board, Oakland, CA. 30

Golden, M. and P. Fiedler. 1991. Characterization of the habitat for Lilaeopsis masonii (Umbelliferae): a 31 California state listed rare plant species. Final report to the California Department of Fish and 32 Game, Endangered Plant Program. 72 pp. plus appendices 33

Goldwasser, S. 1981. Habitat requirements of the least Bell’s vireo. California Department of 34 Fish and Game, Job IV-38.1. 35



Goldwasser, S., D. Gaines, and S. Wilbur. 1980. The Least Bell’s Vireo in California: a de facto 1 endangered race. American Birds 34:742-745. 2

Gomes RL, Scrimshaw MD, Lester JN. 2003. Determination of endocrine disrupters in sewage 3 treatment and receiving waters. Trends in Analytical Chemistry. 22(10): 697-707. 4

Goodman D. 2005. Selection equilibrium for hatchery and wild spawning fitness in integrated 5 breeding programs. Canadian Journal of Fisheries and Aquatic Sciences 62: 374-389. 6

Gray J.L., D.L. Sedlak. 2005. The fate of estrogenic hormones in an engineered treatment 7 wetland with dense macrophytes. Water Environment Research 77(1): 24-31. 8

Gray, M.V. and J. Greaves. 1981. The riparian forest as habitat for the least Bell’s vireo (Vireo 9 bellii pusillus). Paper presented at the California Riparian Systems Conference, 10 University of California, Davis; September 1981. 11

Graymer, R.W., D.L. Jones, and E.E. Brabb. 2002. Geologic map and map database of 12 northeastern San Francisco Bay region, California. U. S. Geological Survey. 13

Green, R. H. 1979. Sampling design and statistical methods for environmental biologists. Wiley 14 Interscience, Chichester, England. 15

Grewell, B., M. DaPrato, P. Hyde, and E. Rejmánková. 2003. Reintroduction of Endangered Soft 16 Bird’s Beak (Cordylanthus mollis ssp. mollis) to Restored Habitat in Suisun Marsh 17 California. Final report for CALFED Ecosystem Restoration Program, Sacramento, CA. 18

Grewell, B.J. 2005. Population census and status of the endagnered soft bird’s-beak (Cordylanthus mollis 19 ssp. mollis) at Benicia State Recreation Area and Rush Ranch in Solano County, California. 20 Report for Solano County Water Agency, Solano County Endangered Species Conservation 21 Program. 22

Griggs, F.T. 2000. Vina Plains Preserve: eighteen years of adaptive management. Fremontia 23 27(4):48-51. 24

Grimaldo L, Z. Hymanson. 1999. What is the impact of introduced Brazilian waterweed Egeria 25 densa to the Delta ecosystem. Interagency Ecological Program. 12(1): 43-45. 26

Grimaldo L. 2006. South Delta fish studies: Do our fishes have behavioral problems? 27 Presentation at the Interagency Ecological Program Annual Meeting, Asilomar 28 Conference grounds, Pacific Grove, CA. March 1-3, 2006. 29

Grimaldo L.F., R.E. Miller, C.M. Peregrin, and Z.P. Hymanson. 2004. Spatial and temporal 30 distribution of native and alien ichthyoplankton in three habitat types of the Sacramento-31 San Joaquin Delta. American Fisheries Society Symposium 39:81-96. 32

Grinnell, J. and A. Miller. 1944. The Distribution of the Birds of California. Pacific Coast 33 Avifauna 27:615. 34



Hall, F.A. 1983. Status of the San Joaquin kit fox, Vulpes macrotis mutica, at the Bethany wind 1 turbine generating site, Alameda County, California. Unpubl. Rep., California Dept. Fish 2 and Game, Sacramento, CA, 34 pp. 3

Hallock R.J., R.F. Eldwell, and D.H. Fry. 1970. Migration of adult king salmon Oncorhynchus 4 tshawytscha in the San Joaquin Delta, as demonstrated by the use of sonic tags. Fish 5 Bulletin 151. California Department of Fish and Game, Sacramento, CA. 6

Halterman, M. D. 1991. Distribution and Habitat Use of the Yellow-Billed Cuckoo (Coccyzus 7 americanus occidentalis) on the Sacramento River, California, 1987-90, MS Thesis: 8 California State University: Chico, CA. 9

Hamilton, W.J. 2004. Tricolored Blackbird (Agelaius tricolor). In: The Riparian Bird 10 Conservation Plan: a strategy for reversing the decline of riparian-associated birds in 11 California. California Partners in Flight. Available at: 12 http://www.prbo.org/calpif/htmldocs/species/riparian/tricolored_blackbird.htm. 13

Hamilton, W.J., III, L. Cook, and R. Grey. 1995. Tricolored blackbird project, 1994. 14 Unpublished report. Prepared for the U.S. Fish and Wildlife Service, Portland, OR. 15

Hamilton, W.J., III. 1998. Tricolored Blackbird itinerant breeding in California. Condor 100: 16 218-226. 17

Hamilton, W.J., III. 2000. Tricolored Blackbird 2000 survey and population analysis. 18 Unpublished report prepared for U.S. Fish and Wildlife Service, Portland, OR. 19

Hammerschmidt, C.R., M.B. Sandheinrich, J.G. Wiener, R.G. Rada. 2002. Effects of dietary 20 methylmercury on reproduction of fathead minnows. Environmental Science and 21 Technology 36:877-883. 22

Hankin, D. G. 1982. Estimating escapement of Pacific salmon: marking practices to discriminate 23 wild and hatchery fish. Transactions of the American Fisheries Society 111:286-298. 24

Hankin, D. G. and J. Richards. The Northern Pikeminnow Management Program. An Independent 25 Review of Program Justification, Performance, and Cost-Effectiveness. Northwest Power 26 Planning Council. April 4, 2000. 27

Hansen, G.E. and J.M. Brode. 1980. Status of the giant garter snake Thamnophis couchii gigas 28 (Fitch). Inland Fisheries Endangered Species Special Publication 80(5):1-14. California 29 Department of Fish and Game, Sacramento, CA. 30

Hara, T.J., Y.M.C. Law, , S. MacDonald, . 1976. Effects of mercury and copper on the olfactory 31 response in rainbow trout (Salmo gairdneri ). Journal of the Fisheries Research Board of 32 Canada . 33: 1568-1573. 33

Harada, M. 1978. Congenital Minamata Disease: intrauterine methylmercury poisoning. Teratol. 34 18:285–288. 35

http://www.prbo.org/calpif/htmldocs/species/riparian/tricolored_blackbird.htm



Harrell W.C. and T.R. Sommer. 2003. Patterns of adult fish use on California’s Yolo Bypass 1 floodplain. In P.M. Faber, ed. California riparian systems: Processes and floodplain 2 management, ecology, and restoration. 2001 Riparian Habitat and Floodplains 3 Conference Proceedings, Riparian Habitat Joint Venture, Sacramento, California. Pages 4 88-93. 5

Harvey, T.E. 1990. California’s wildlife, birds, clapper rail. California Wildlife Habitat 6 Relationships System, California Interagency Wildlife Task Group, California 7 Department of Fish and Game, Sacramento, CA. 8

Haug, E.A., B.A. Millsap, and M.S. Martell. 1993. Burrowing owl (Speotyto cunicularia). In: 9 The Birds of North America, No. 61 (A. Poole and F. Gill [eds.]). Philadelphia: The 10 Academy of Natural Sciences; Washington D.C.: The American Ornithologist’s Union. 11

Hayhoe, K., D. Cayan, C.B.Field. 2004. Emissions pathways, climate change, and impacts on 12 California. PNAS, 101, 12422-12427 13

Heady, H. F, J. W Bartholome, M.D. Pitt, M.G. Stroud, and G. D. Savelle. 1991. California 14 Prairie. Pp 313-335 in R. T. Coupland, editor. Natural Grasslands. Ecosystems of the 15 World. Volume 8A. Elsevier Scientific, Amsterdam, The Netherlands. 16

Healey, M.C. 1991. Life history of Chinook salmon (Oncorhynchus tshawytscha). In: Groot C, 17 Margolis L, editors. Pacific salmon life histories. Vancouver (BC): University of British 18 Columbia Press. p 311-394. 19

Hecht, S.A., D.H. Baldwin, C.A. Mebane, T. Hawkes, S.J. Gross, and N.L. Scholz. 2007. An 20 overview of sensory effects on juvenile salmonids exposed to dissolved copper: 21 Applying a benchmark concentration approach to evaluate sublethal neurobehavioral 22 toxicity. Technical white paper. 23

Hedgecock D, Rashbrook VK, Hedrick PW (2000) Effective population size of winter-run 24 Chinook salmon based on microsatellite analysis of returning spawners. Can J Fish Aquat 25 Sci 57:2368-2373. 26

Hedrick PW, Hedgecock D, Hamelberg S (1995) Effective population size in winter-run 27 Chinook salmon. Conserv Biol 9(3):615-624 28

Heim, W.A., K.H. Coale, M. Stephenson, K. Choe, G. Gill, and C. Foe. 2007. Spatial and habitat 29 based variations in total and methyl mercury concentrations in surficial sediments in the 30 San Francisco Bay-Delta. Environmental Science and Technology. 41:3501-3507. 31

Heinz, GH. 1979. Methylmercury: reproductive and behavioral effects on three generations of 32 mallard ducks. Journal of Wildlife Management 43:394-401. 33

Helm, B. 1998. Biogeography of eight large branchiopods endemic to California. In: Witham, 34 C.W., E.T. Bauder, D. Belk, W.R. Ferrin Jr., R. Orduff (eds.). Ecology, conservation, and 35 management of vernal pool ecosystems − proceedings from a 1996 conference. California 36 Native Plant Society, Sacramento, CA. pp. 124-139. 37



Hemming J.M., H.J. Allen, K.A. Thuesen, P.K. Turner, W.T. Waller, J.M. Lazorchak, D. Lattier, 1 M. Chow, N. Denslow, and B. Venables. 2004. Temporal and spatial variability in the 2 estrogenicity of a municipal wastewater effluent. Ecotoxicology and Environmental 3 Safety. 57: 303-310. 4

Herren J.R. and S.S. Kawasaki. 2001. Inventory of water diversions in four geographic areas in 5 California’s Central Valley. Fish Bulletin. 179(2): 343-355. 6

Hetrick, F. M. , M. D. Knittel , and J. L. Fryer . 1979. Increased susceptibility of rainbow trout to 7 infectious hematopoietic necrosis virus after exposure to copper. Applied and 8 Environmental Microbiolgy 37:198–201. 9

Hey J, E.L. Brannon, D.E. Campton, R.W. Dowle, I.A. Fleming, M.T. Kinnison, R. Lande, J. 10 Olsen, D.P. Philipp, J. Travis, C.C. Wood, and H.H. Doremus. 2005. Considering life 11 history, behavioral, and ecological complexity in defining conservation units for Pacific 12 salmon. An independent panel report, requested by NOAA Fisheries. Available at: 13 http://www.nwfsc.noaa.gov/trt/regarding_salmon_esus.pdf 14

Hickman, J.C., ed. 1993. The Jepson Manual: Higher Plants of California. University of 15 California Press, Berkeley, CA. 16

Hickson, D. and T. Keeler-Wolf .2007. Vegetation classification of the Sacramento-San Joaquin River 17 Delta. Sacramento, CA, Unpublished report for California Department of Fish and Game, Bay 18 Delta Division. 19

Hobbs, J.A., W.A. Bennett, and J.E. Burton. 2006. Assessing nursery habitat quality for native 20 smelts (Osmeridae) in the low-salinity zone of the San Francisco estuary. Journal of Fish 21 Biology. 69: 907-922. 22

Hobbs, R.J. and H.A. Mooney. 1998. Broadening the extinction debate: population deletions and 23 additions in California and Western Australia. Conservation Biology 12:271-283. 24

Holbrook, C.M., R.W. Perry, and N.S. Adams. 2009. Distribution and joint fish-tag survival of juvenile 25 Chinook salmon migrating through the Sacramento-San Joaquin River Delta, 2008. US 26 Department of the Interior, US Geological Survey. Biological Resources Discipline Report to San 27 Joaquin River Group Authority. Cook, WA, US. 28

Holland, R.F. 1998. Great Valley vernal pool distribution, photorevised. Pages 71-75 In: C.W. 29 Witham, et al. (ed.). Ecology, Conservation, and Management of Vernal Pool 30 Ecosystems. California Native Plant Society, Sacramento, CA. 31

Howard, A.Q. and R.A. Arnold. 1980. The Antioch Dunes - safe at last? Fremontia. 8:3-12. 32

Huang C.H. and D.L. Sedlak. 2001. Analysis of estrogenic hormones in municipal wastewater 33 effluent and surface water using enzyme-linked immunosorbent assay and gas 34 chromatography/tandem mass spectrometry. Environmental Toxicology and Chemistry 35 20(1):133-139 36

http://www.nwfsc.noaa.gov/trt/regarding_salmon_esus.pdf



Humphrey, S.R. and T.H. Kunz. 1976. Ecology of a Pleistocene relict, the western big-eared bat 1 (Plecotus townsendii) in the southern Great Plains. Journal of Mammalogy 57:470-494. 2

ICF Jones & Stokes. 2008. Initial Testing of Aeration Facility Capacity and Efficiency. August. 3 (ICF J&S 00799.07.) Sacramento, CA. Prepared for: Department of Water Resources, 4 Bay-Delta Office. 5

IEP (Interagency Ecological Program 2001. Suisun Ecological Workgroup final report to the 6 State Water Resources Control Program The Interagency Ecological Program for the 7 Sacramento-San Joaquin Estuary. Available at 8 http://www.iep.ca.gov/suisun_eco_workgroup/final_report/SEWFinalReport.pdf 9

IEP. 2008a. Interagency ecological program 2008 work plan to evaluate the decline of pelagic 10 species in the upper San Francisco Estuary. Interagency Ecological Program for the San 11 Francisco Estuary, Sacramento, CA. 12

IEP (Interagency Ecological Program). 2008b. Pelagic organism decline progress report: 2007 13 synthesis of results. January 2008. 78 pp. Available at: http://www.fws.gov/sacramento 14 /es/documents/POD_report_2007.pdf 15

ISAB (Independent Scientific Advisory Board). 2003. Hatchery surpluses in the Pacific 16 Northwest. Fisheries. 27:16-27. 17

Jain, S. 1979. Some biogeographic aspects of plant communities in vernal pools. In: S. Jain, ed., 18 Vernal pools: their ecology and conservation. Institute of Ecology Publication No. 9. 19 University of California. Davis, CA. pp. 15-21. 20

Jassby A. 2008. Phytoplankton in the upper San Francisco Estuary: recent biomass trends, their 21 causes and their trophic significance. San Francisco Estuary and Watershed Science. Vol. 22 6, Issue 1 [February], Article 2. 23

Jassby A.D. and E.E. Van Nieuwenhuyse. 2005. Low dissolved oxygen in an estuarine channel 24 (San Joaquin River, California): mechanisms and models based on long-term time series. 25 San Francisco Estuary and Watershed Science. Vol. 3, Issue 2 [September], Article 2. 26

Jassby A.D. and J.E. Cloern. 2000. Organic matter sources and rehabilitation of the Sacramento-27 San Joaquin Delta (California, USA). Aquatic Conservation: Marine and Freshwater 28 Ecosystems. 10: 323-352. 29

Jennings, M.R. and M.P. Hayes. 1994. Amphibian and reptile species of special concern in 30 California. California Department of Fish and Game, Inland Fisheries Division, Rancho 31 Cordova, CA. iii+255 pp. 32

Jensen, C.C. 1972. San Joaquin kit fox distribution. U.S. Fish and Wildlife Service, Sacramento, 33 CA, Unpublished Report, 18 pp. 34

Jobling S., M. Nolan, C.R.Tyler, G. Brightly, and J.P. Sumpter. 1998. Widespread sexual 35 disruption in wild fish. Environmental Science and Technology. 32: 2498-2506. 36





Jobling, S., D.A. Sheahan, J.A. Osborne, P. Matthiessen, and P. Sumpter. 1996. Inhibition of 1 testicular growth in rainbow trout (Oncorhynchus mykiss) exposed to estrogenic 2 alkylphenolic compounds. Environmental Toxicology and Chemistry. 15(2): 194-202. 3

Johnson, J. J., T. Longcore, A. Clause, G. Pratt, J. Dunn, and K. Osbourne. 2007. Propagation 4 handbook for Lange's metalmark butterfly, Apodemia mormo langei. The Urban 5 Wildlands Group, Inc., Los Angeles, CA. 6

Jones and Stokes Associates, Inc. 1990. Sacramento County vernal pools: their distribution, 7 classification, ecology, and management. (JSA 89-303) Sacramento, CA. Prepared for 8 the Sacramento County Planning and Community Development Department, Sacramento, 9 CA. 10

Jones N.L., J.K. Thompson, and S.J. Monismith. 2008. A note on the effect of wind waves on 11 vertical mixing in Franks Tract, Sacramento-San Joaquin Delta, California. San Francisco 12 Estuary and Watershed Science, Vol. 6, Issue 2 [June], Article 4. 13

Katibah, E.F. 1983. A brief history of riparian forests in the Central Valley of California. Pages 14 23-29 in R.E. Warner, and K.M. Hendrix (eds.), California Riparian Systems: Ecology, 15 Conservation, and Productive Management. Berkeley, CA, University of California 16 Press. 17

Katibah, E.F. 1984. A brief history of riparian forests in the Central Valley of California. Pages 18 23-29 in: R.E. Warner and K.M. Hendrix (eds), California Riparian Systems: ecology, 19 conservation, and productive management. University of California Press. 20

Kavlock R.J., G.P. Daston, C. DeRosa, P. Fenner-Crisp, L.E. Gray, S. Kaattari, G. Lucier, M. 21 Luster, M.J. Mac, C. Maczka, R. Miller, J. Moore, R. Rolland, G. Scott, D.M. Sheehan, 22 T. Sinks, and H.A. Tilson. 1996. Research needs for the risk assessment of health and 23 environmental effects of endocrine disruptors: a report of the US EPA-sponsored 24 workshop. Environmental Health Perspectives. 104(Suppl. 4): 715-740. 25

Kerin E., C.C. Gilmour, E. Roden, M.T. Suzuki, J.D. Coates, R.P. Mason. 2006. Mercury 26 methylation among the dissimilatory iron-reducing bacteria. Applied and Environmental 27 Microbiology. 72: 7919-7921. 28

Kidd K.K., P.J. Blanchfield, K.H. Mills, V.P. Palace, R.E. Evans, J.M. Lazorchak, and R.W. 29 Flick. 2007. Collapse of a fish population after exposure to a synthetic estrogen. PNAS 30 104(21):8897-8901. 31

Kimmerer W. 2004. Open Water Processes of the San Francisco Estuary: From Physical Forcing 32 to Biological Responses. San Francisco Estuary and Watershed Science. Vol. 2, Issue 1 33 [February], Article 1. Available at: http://repositories.cdlib.org/jmie/sfews/vol2/iss1/art1 34

Kimmerer W.J. 2008. Losses of Sacramento River Chinook salmon and Delta smelt (Hypomesus 35 transpacificus) to entrainment in water diversions in the Sacramento-San Joaquin Delta. 36 San Francisco Estuary and Watershed Science. Vol. 6, Issue 2 [June], Article 2. 37

http://repositories.cdlib.org/jmie/sfews/vol2/iss1/art1



Kimmerer W.J. and J.J. Orsi. 1996. Changes in the zooplankton of the San Francisco Bay estuary 1 since the introduction of the clam Potamocorbula amurensis. In: J.T. Hollibaugh, ed., 2 San Francisco Bay: the ecosystem. San Francisco, CA: Pacific Division, American 3 Association for the Advancement of Science. pp. 403-424. 4

Kimmerer W.J., E.S. Gross, and M.L. MacWilliams. 2009. Is the response of estuarine nekton to 5 freshwater flow in the San Francisco Estuary explained by variation in habitat volume? 6 Estuaries and Coasts. Available at : http://www.springerlink.com/content/26pr3h 7 5574605083/ 8

Kjelson M.A., P.F. Raquel, and F.W. Fisher. 1982. Life history of fall-run juvenile Chinook 9 salmon, Oncorhychus tshawytscha, in the Sacramento-San Joaquin Estuary, California. 10 In: Kennedy VS, editor. Estuarine comparisons. Academic Press. New York, NY. p 393-11 411. 12

Kleinschmidt Associates. 2008. Cosumnes River Preserve Management Plan. Prepared for: The 13 Nature Conservancy, Galt, CA. 14

Klute, D.S., L.W. Ayers, M.T. Green, W.H. Howe, S.L. Jones, J.A. Shaffer, S.R. Sheffield, and 15 T.S. Zimmerman. 2003. Status assessment and conservation plan for the western 16 burrowing owl in the United States. U.S. Fish and Wildlife Service, Technical 17 Publication FWS/BTP-R6001-2003, Washington, D.C. 18

Knapp, D.K. 1978. Effects of agricultural development in Kern County, California, on the San 19 Joaquin kit fox in 1977. California Dept. Fish and Game, Sacramento, CA, Nongame 20 Wildl. Invest., Unpubl. Rep., 57 pp. 21

Knowles N. and D. Cayan. 2002. Potential effects of global warming on the Sacramento/San 22 Joaquin watershed and the San Francisco estuary. Geophysical Research Letters. 29: 38-23 1-38-4. 24

Knowles, N., and D. Cayan, 2004, Elevational Dependence of Projected Hydrologic Changes in 25 the San Francisco Estuary and Watershed. Climatic Change, 62, 319-336. 26

Knudsen F.R., P.S. Enger, O. Sand. 1992. Awareness reactions and avoidance responses to 27 sound in juvenile Atlantic salmon Salmo salar L. Journal of Fish Biology. 13: 655-673. 28

Knudsen F.R., P.S. Enger, O. Sand. 1994. Avoidance responses to low frequency sound in 29 downstream migrating juvenile Atlantic salmon, Salmo salar. Journal of Fish Biology. 30 45: 227-233. 31

Kowalski RK, Hliwa P, Andronowska A, Krόl J, Dietrich GJ, Wojtczak M, Stabiński R, Ciereszko A 32 (2006) Semen biology and stimulation of milt production in the European smelt (Osmerus 33 eperlanus L.). Aquaculture 261(2006):760-770. 34

http://www.springerlink.com/content/26pr3h%205574605083/

http://www.springerlink.com/content/26pr3h%205574605083/



Laetz, C.A., D.H. Baldwin, T.K. Collier, V. Hebert, J.D. Stark, and N. L. Scholz. 2009. The 1 synergistic toxicity of pesticide mixtures: implications for risk assessment and the 2 conservation of endangered Pacific salmon. Environmental Health Perspectives. 3 117(3):348-353. 4

Lande, R. 1988. Genetics and demography in biological conservation. Science 241:1455-1460. 5

Larsen, C.J. 1989. A Status Review of the Suisun Song Sparrow (Melospiza melodia maxillaris) 6 in California, Report to the Fish and Game Commission. Wildlife Management Division, 7 Nongame Bird and Mammal Section, Department Candidate Species Status Report 89-6. 8 California Department of Fish and Game, Sacramento, CA. 9

Laughrin, L. 1970. San Joaquin kit fox: its distribution and abundance. California Dept. Fish and 10 Game, Sacramento, Wildlife Management Branch, Administrative Report No. 70-2, 20 11 pp. 12

Lavado R., J. Loyo-Rosales, D. Sedlak, I. Werner, and D. Schlenk. 2009. In vitro and in vivo 13 evaluation of estrogenic activity and chemical contamination in surface waters of the 14 Sacramento River Delta, CA USA. Presentation at California Estuarine Research Society 15 2009 Annual Meeting, Bodega Bay, CA, March 17-18, 2009. 16

Laymon, S.A. and M. D. Halterman. 1985. Yellow-billed Cuckoo in the Kern River Valley: 17 1985 population, habitat use and management recommendations. Administrative Report 18 prepared for The Nature Conservancy, Kern River Preserve, P. O. Box 1662, Weldon, 19 CA. 20

Laymon, S.A. and M.D. Halterman. 1989. A proposed habitat management plan for Yellow-21 billed Cuckoos in California. U.S. Department of Agriculture, Forest Service General 22 Technical Report PSW-110:272–277. 23

Lee H., X. Swamikannu, D. Radulescu, S. Kim, and M.K. Stenstrom. 2007. Design of 24 stormwater monitoring programs. Water Research. 41(18): 4186-4196. 25

Lehman P.W. 2000. The influence of climate on phytoplankton community biomass in San 26 Francisco Bay Estuary. Limnology and Oceanography. 45(3): 580-590 27

Lehman P.W., G. Boyer, M. Stachwell, and S. Waller. 2008. The influence of environmental 28 conditions on the seasonal variation of Microcystis cell density and microcystins 29 concentration in San Francisco Estuary. Hydrobiologia. 600: 187-204. 30

Leigh Fisher Associates. 2005. Byron Airport Master Plan: Final Report. Contra Costa Public 31 Works Department. Concord, CA. 32

Leipsic-Baron, T. 1992. Anthropogenic influences on the biogeography of clapper rails in 33 California. M.S. Thesis, University of California., Los Angeles, CA. 34



Lincoln-Smith, M. P., K. A. Pitt, J. D. Bell and B. D. Mapstone (2006). "Using impact assessment 1 methods to determine the effects of a marine reserve on abundances and sizes of valuable tropical 2 invertebrates." Canadian Journal of Fisheries and Aquatic Sciences 63(6): 1251-1266. 3

Lindley, S. T, R. Schick, E. Mora, P. Adams, J. Anderson, S. Greene, Sheila, C. Hansen, B. 4 May, D. McEwan, B.MacFarlane, C. Swanson, and J. Williams. 2007. Framework for 5 Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the 6 Sacramento-San Joaquin Basin. San Francisco Estuary and Watershed Science, 5(1). 7

Lindley, S. T. and M. S. Mohr. 2003. Modeling the effect of striped bass (Morone saxatilis) on 8 the population viability of Sacramento River winter-run chinook salmon (Oncorhynchus 9 tshawytscha). Fish Bulletin 101:321-331. 10

Linsley, E.G. and J.A. Chemsak. 1972. Cerambycidae of North America, Part VI, No.1. 11 Taxonomy and Classification of the Subfamily Lepturinae. University of California 12 Publications in Entomology 69:1-138. 13

Linville, R.G., S.N. Luoma, L. Cutter, and G.A. Cutter. 2002. Increased selenium threat as a 14 result of invasion of the exotic bivalve Potamocorbula amurensis into the San Francisco 15 Bay-Delta. Aquatic Toxicology 57:51-64. 16

Littlefield, C.D. and G.L. Ivey. 2000. Conservation assessment for Greater Sandhill Cranes 17 wintering on the Cosumnes River Floodplain and Delta Regions of California. The 18 Nature Conservancy, Galt, CA. 19

Lonzarich, D.G., T.E. Harvey, and J.E. Takekawa. 1990. Trace element and organochlorine 20 concentrations in California clapper rail (Rallus longirostris obsoletus) eggs. Archives of 21 Environment Contamination Toxicology 23:47-153. 22

Lowe R.L. and R.W. Pillsbury. 1995. Shifts in benthic algal community structure and function 23 following the appearance of zebra mussels (Dreissena polymorpha) in Saginaw Bay, 24 Lake Huron. Journal of Great Lakes Research. 24(4): 558-566. 25

LSA (LSA Associates, Inc.). 2007. California clapper rail. Working Draft 2.2, Natural 26 Community and Species Accounts, Solano Habitat Conservation Plan. Solano County 27 Water Agency. 28

Lund J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle. 2007. Envisioning Futures 29 for the Sacramento-San Joaquin Delta. Public Policy Institute of California (PPIC). 30 February 2007, 324 pp. ISBN 978-1-58213-126-9. 31

Lund J., E. Hanak, W. Fleenor, W. Bennett, R. Howitt, J. Mount, and P. Moyle. 2008. 32 Comparing futures for the Sacramento-San Joaquin Delta. Public Policy Institute of 33 California. Available at: http://www.ppic.org/main/publication.asp?i=810 34

Lye, C.M., C.L.J. Frid, and M.E. Gill. 1998. Seasonal reproductive health of flounder Platichthys 35 flesus exposed to sewage effluent, Marin Ecology Progress Series. 170: 249-260. 36

http://www.ppic.org/main/bio.asp?i=354

http://www.ppic.org/main/bio.asp?i=72

http://www.ppic.org/main/publication.asp?i=810



MacFarlane, R.B., S. Hayes, B. Wells. 2008. Coho and Chinook salmon decline in California 1 during the spawning seasons of 2007/08. Paper distributed at 2/8/2008 BDCP Steering 2 Committee. Available at: http://www.resources.ca.gov/bdcp/docs/2.8.08_HO_Dec 3 line_of_salmon_in_California_in_2007.pdf 4

Manly B.F.J. 2002. Analysis of cross channel effects. Western EcoSystems Technology Inc. 5 Report Dated April 21, 2002. 6

Manly B.F.J. 2008. Review of the report an evaluation of four Sacramento-San Joaquin River 7 Delta juvenile salmon survival studies by K.B. Newman. Western EcoSystems 8 Technology Inc. Report Dated July 16, 2008. 9

Mann R. and J.M. Harding. 2003. Salinity tolerance of larval Rapana venosa: Implications for 10 dispersal and establishment of an invading predatory gastropod on the North American 11 Atlantic Coast. Biological Bulletin. 204: 96-103. 12

Manolis, T. 1978. Status of the black rail in central California. Western Birds 9:151-158. 13

Marschalek, Daniel A. 2009. California Least Tern Breeding Survey - 2008 Season. Final Report 14 submitted to California Department of Fish and Game, Sacramento CA. 15

Marsh, D.O. 1987. Dose-response relationships in humans: Methyl mercury epidemics in Japan 16 and Iraq. In: The toxicity of methyl mercury. Eccles, CU, Annau, Z, editors. Baltimore 17 (MD): John Hopkins University Press. p 45-53. 18

Marsh, D.O., G.J. Myers, T.W. Clarkson, L. Amin-Zaki, S. Tikriti, and M.A. Majeed. 1980. 19 Fetal methylmercury poisoning: Clinical and toxicological data on 29 cases. Annals of 20 Neurology 7:348-353. 21

Marsh, D.O., T.W. Clarkson, C. Cox, G.J. Myers, L. Amin-Zaki, and S. Al-Tikriti. 1987. Fetal 22 methylmercury poisoning: Relationship between concentration in single strands of 23 maternal hair and child effects. Archives of Neurology 44:1017-1022. 24

Marty, J.T. 2005. Effects of cattle grazing on diversity in ephemeral wetlands. Conservation 25 Biology 19:1626-1632. 26

Marvin-DiPasquale, M, Cox, MH. 2007. Legacy mercury in Alviso Slough, South San Francisco 27

Marvin-DiPasquale, M.D., J.L. Agee, R.M. Bouse, and B.E. Jaffe. 2003. Microbial cycling of 28 mercury in contaminated pelagic and wetland sediments of San Pablo Bay, California. 29 Environmental Geology 43:260–267. 30

Massey, B. W. 1974. Breeding biology of the California Least Tern. Proceedings of the 31 Linnaean Society. New York 72:1-24. 32

Matica, Z, and M. L. Nobriga. 2005. Modifications to an agricultural water diversion to permit 33 fish entrainment sampling. California Department of Fish and Game 91(1):53-56. 34

http://www.resources.ca.gov/bdcp/docs/2.8.08_HO_Dec%20line_of_salmon_in_California_in_2007.pdf

http://www.resources.ca.gov/bdcp/docs/2.8.08_HO_Dec%20line_of_salmon_in_California_in_2007.pdf



Matsumoto, H., G. Koya, and T. Takeuchi. 1964. Fetal Minamata Disease: a neuropathological 1 study of two cases of intrauterine intoxication by a methyl mercury compound. Journal of 2 Neuropathology and Experimental Neurology. 24:563-574. 3

Medeiros, J.L. 1976. Vernal pools and vernal lakes in the eastern Central Valley of California.in 4 S. Jain, editor. Vernal pools: their ecology and conservation. Institute of Ecology 5 Publication Number 9, Davis, California. 6

Meisler, J. A. 2002. Site Conservation Plan for the JepsonPrairie-Prospect Island Corridor. 7 Prepared for the Solano County Land Trust. 27 pp. plus appendices. 8

Meisler, J. A. 2002. Site Conservation Plan for the JepsonPrairie-Prospect Island Corridor. 9 Prepared for the Solano County Land Trust. 27 pp. plus appendices. 10

Messer C. and T. Veldhuizen. 2005. Zebra mussel early detection and public outreach program 11 final report. CDWR, Sacramento, CA. 12

Michener, W.K. 1997. Quantitatively evaluating restoration experiments: research design, 13 statistical analysis, and data management considerations. Restoration Ecology 5(4):324-14 337. 15

Miller, W. J. 2007. Testimony before the subcommittee on water and power. Presented at: 16 Extinction is not a sustainable water policy: The Bay-Delta crisis and the implications for 17 California water management. 7/2/2007. 18

Miranda, J, R. Padilla, J. Morinaka, J. DuBois, M. Horn. 2010. Release site predation study. CA 19 Department of Water Resources. Available at: 20 http://baydeltaoffice.water.ca.gov/announcement/Element2FinalReport5-2010.pdf 21

Mitsch, W. J. and J.G. Gosselink. 2000. Wetlands 3rd ed. Wiley & Sons Inc., New York. 22

Morrell, S.H. 1972. Life history of the San Joaquin kit fox. California Fish and Game 58:162-23 174. 24

Morrell, S.H. 1975. San Joaquin kit fox distribution and abundance in 1975. California Dept. 25 Fish and Game, Sacramento, Wildlife Management Branch, Administrative Report No. 26 75-3, 28 pp. 27

Moss, B. 2007. Ecology of Fresh Waters 3rd ed. Blackwell Publishing, Oxford. 28

Mount, J. and R. Twiss. 2005. Subsidence, sea level rise, seismicity in the Sacramento-San 29 Joaquin Delta. San Francisco Estuary and Watershed Science [online serial]. Volume 3, 30 Issue 1 (March 2005), Article 5. 31

Moyle P.B. 2002. Inland Fishes of California, Revised and Expanded. University of California 32 Press, Berkeley, California. 502 pp. 33

Moyle P.B. 2002. Inland Fishes of California, Revised and Expanded. University of California 34 Press, Berkeley, California. 502 pp. 35



Moyle P.B. and D. White. 2002. Effects of screening diversions on fish populations in the 1 Central Valley: what do we know? Report for the Science Board, CALFED Ecosystem 2 Restoration Program. January 2002. 3

Moyle P.B., J. A. Israel, and S. E. Purdy. 2008. Salmon, steelhead, and trout in California: status 4 of an emblematic fauna. Report for the Center for Watershed Sciences, University of 5 California, Davis, CA. 6

Moyle P.B., R.D. Baxter, T. Sommer, T.C. Foin, and S.A. Matern. 2004. Biology and population 7 dynamics of the Sacramento splittail (Pogonichthys macrolepidotus) in the San Francisco 8 Estuary: a review. San Francisco Estuary and Watershed Science [online serial]. Volume 9 2, Issue 2 (May 2004), Article 4. 10

Mueller-Solger A.B. 2007. Delta smelt count-down: famine or other foe? Poster presented at the 11 State of the Estuary Conference, Oakland, CA. October 16-18, 2007. 12

Muir, W. D., G. T. McCabe, Jr., M. J. Parsley, and S. A. Hinton. 2000. Diet of first feeding 13 larval and young-of-the-year white sturgeon in the lower Columbia River. Northwest 14 Science 74:25-33. 15

Museum of Vertebrate Zoology. 2008. Collections Database Query. Available at: 16 Hhttp://mvz.berkeley.edu/Herp_Collection.html H. 17

Nakano, S., and M. Murakami. 2001. Reciprocal subsidies: Dynamic interdependence between 18 terrestrial and aquatic food webs. Proceedings of the National Academy of Sciences of 19 the United States of America 98:166-170. 20

NatureServe. 2008. NatureServe Explorer: An online encyclopedia of life [web application]. 21 Version 7.0. NatureServe, Arlington, Virginia. Accessed on September 9, 2008. 22 Available at: http://www.natureserve.org/explorer. 23

Neff, J.A. 1937. Nesting distribution of the Tricolored Red-wing. Condor 39: 61-81. 24

Nesom, G.L. 1991. Taxonomy of Isocoma (Asteraceae: Astereae). Phytologia 70: 69-114. 25

Newman K.B. 2008. An evaluation of four Sacramento-San Joaquin River Delta juvenile salmon 26 survival studies. Technical Report submitted to the U.S. Fish and Wildlife Service, 27 Stockton, CA. Available at: 28 www.science.calwater.ca.gov/pdf/psp/PSP_2004_final/PSP_CalFed_FWS_salmon_studi29 es_final_033108.pdf. 30

Newman K.B., Hicks A.C., Hankin D.G. 2004. A marking, tagging, and recovery program for 31 Central Valley hatchery chinook salmon. Unpublished report for California Department 32 of Fish and Game and the CALFED Ecosystem Restoration Program. 33

Nicholls, R. J., F. M. J. Hoozemans & M. Marchand, 1999. Increasing flood risk and wetland losses due 34 to global sea-level rise: regional and global analyses. Global Environmental Change 9: S69–35 S87. 36

http://mvz.berkeley.edu/Herp_Collection.html

http://www.natureserve.org/explorer

http://www.science.calwater.ca.gov/pdf/psp/PSP_2004_final/PSP_CalFed_FWS_salmon_studies_final_033108.pdf

http://www.science.calwater.ca.gov/pdf/psp/PSP_2004_final/PSP_CalFed_FWS_salmon_studies_final_033108.pdf



Nilo P, S. Tremblay, A. Bolon, J. Dodson, P. Dumont, R. Fortin (2006) Feeding ecology of 1 juvenile lake sturgeon in the St. Lawrence River System. Transactions American 2 Fisheries Society 135:1044–1055. 3

NMFS (National Marine Fisheries Service). 2004. Biological Opinion on the Long-Term Central 4 Valley Project and State Water Project Operations Criteria and Plan. National Marine 5 Fisheries Service, Southwest Region, Long Beach, California. October 2004. 6

NMFS (National Marine Fisheries Service). 2008. Biological Opinion: Environmental Protection 7 Agency registration of pesticides containing chlorpyrifos, diazinon, and malathion. 8 National Marine Fisheries Service Endangered Species Act Section 7 Consultation. 9 Available at: http://www.nmfs.noaa.gov/pr/pdfs/pesticide_biop.pdf 10

NMFS (National Marine Fisheries Service). 2009. Public draft recovery plan for the evolutionary 11 significant units of Sacramento River winter-run chinook salmon and Central Valley 12 spring-run chinook salmon and the distinct population segment of Central Valley 13 steelhead. Sacramento, CA. 14

Nobriga M., F. Feyrer, R. Baxter, and M. Chotkowski. 2005. Fish community ecology in an 15 altered river delta: spatial patterns in species composition, life history strategies, and 16 biomass. Estuaries and Coasts 28: 776-785. 17

Nobriga M.L, T.R. Sommer, F. Feyrer, and K. Fleming. 2008. Long-term trends in summertime 18 habitat suitability for delta smelt (Hypomesus transpacificus). San Francisco Estuary and 19 Watershed Science. Vol. 6, Issue 1 (February), Article 1. 20

Nobriga M.L., Z. Matica, and Z.P. Hymanson. 2004. Evaluating entrainment vulnerability to 21 agricultural irrigation diversions: a comparison among open-water fishes. American 22 Fisheries Society Symposium. 39: 281-295. 23

Nobriga ML, Feyrer F (2008) Diet composition in San Francisco Estuary striped bass: does trophic 24 adaptability have its limits? Environ Biol Fish (DOI 10.1007/s10641-008-9376-0) 9pp. might 25 need to add a to differentiate 26

Nobriga, M., and F. Feyrer. 2007. Shallow-water piscivore-prey dynamics in the Sacramento-San Joaquin 27 Delta. San Francisco Estuary and Watershed Science Vol5 (Article4), Iss2 May 2007 28

Nordstrom K.F. 1992. Estuarine beaches: An introduction to the physical and human factors 29 affecting use and management of beaches in estuaries, lagoons, bays and fjords. Elsevier 30 Science Publishing Company, Inc. New York, NY. 252 pp. 31

Noss R.F., E.T. LaRoe, J.M. Scott. 1995. Endangered Ecosystems of the United States: A Preliminary 32 Assessment of Loss and Degradation.Washington (DC): US Department of the Interior. 33 Biological Report 28. 34

Nowak, G.M., Tabor, RA, Warner E.J., Fresh, K.L. and Quinn T.P. 2004. Ontogenetic shifts in habitat 35 and diet of cutthroat trout in Lake Washington, Washington. North American Journal of Fisheries 36 Management 24:624-635. 37

http://www.nmfs.noaa.gov/pr/pdfs/pesticide_biop.pdf

http://www.water.ca.gov/aes/docs/Nobriga&Feyrer2007.pdf

http://www.water.ca.gov/aes/docs/Nobriga&Feyrer2007.pdf



NRCS (Natural Resources Conservation Service, United States Department of Agriculture). 1 2009. Soil Survey Geographic (SSURGO) Database. Available online at 2 http://soildatamart.nrcs.usda.gov accessed May, 2009. 3

O'Connor, D.J., and S.W. Nielsen. 1981. Environmental survey of methylmercury levels in wild 4 mink (Mustela vision) and otter (Lutra canadensis) from the northeastern United States 5 and experimental pathology of methylmercurialism in the otter. In Chapman, JA, Pursley, 6 D. (eds) The Worldwide Furbearer Conference Proceedings. Maryland: Worldwide 7 Furbearer Conference. 8

Oetken M., J. Bachman, U. Schulte-Oehlmann, and J. Oehlmann. 2004. Evidence of endocrine 9 disruption in invertebrates. International Review of Cytology. 236: 1-44. 10

Ohlendorf, H.M. and W.J. Fleming. 1988. Birds and environmental contaminants in San 11 Francisco and Chesapeake Bays. Marine Pollution Bulletin 19:487-495. 12

Ohlendorf, H.M., K.C. Marois, R.W. Lowe, T.E. Harvey, and P.R. Kelly. 1989. Environmental 13 contaminants and diving ducks in San Francisco Bay. In Selenium and agricultural 14 drainage: proceedings of the fourth selenium symposium, Berkeley, CA. March 21, 15 1987. The Bay Institute of San Francisco, Sausalito, CA. pp. 60-69. 16

Orr, R.T. 1935. Description of three new races of brush rabbit from California. Proc. Biol. Soc. 17 Washington 48:27-30. 18

Orsi, J. J., and W. L. Mecum. 1996. Food limitation as the probable cause of a long term decline 19 in the abundance of Neomysis mercedis the opossum shrimp in the Sacramento– San 20 Joaquin estuary. Pages 375–401 in J. T. Hollibaugh, editor. San Francisco Bay: the 21 ecosystem. American Association for the Advancement of Science, San Francisco.CA. 22

Pait A.S. and J.O. Nelson. 2002. Endocrine disruption in fish: An assessment of recent research 23 and results. NOAA Tech. Memo. NOS NCCOS CCMA 149. Silver Spring, MD: NOAA, 24 NOS, Center for Coastal Monitoring and Assessment. 55pp. Available at: 25 http://coastalscience.noaa.gov/documents/techmemo149.pdf. 26

Panov V.E. 1996. Establishment of the Baikalian endemic amphipod Gmelinoides fasciatus 27 Stebb. in Lake Ladoga. Hydrobiologia. 322: 187-192. 28

Panter, G.H., R.S. Thompson, and J.P. Sumpter. 1998. Adverse reproductive effects in male 29 fathead minnows (Pimephales promelas) exposed to environmentally relevant 30 concentrations of the natural oestrogens, oestradiol and oestrone. Aquatic Toxicology. 31 42(4): 243-253. 32

Paovey, A. G. and K. D. Getsinger. 2002. Impacts of inorganic turbidity on Diquat efficacy 33 against Egeria densa. Journal of Aquatic Plant Management. 40: 6-10. 34

http://coastalscience.noaa.gov/documents/techmemo149.pdf



Paovey, A. G., M. D. Netherland, W. Crowell. 2008. Effects of turbidity on Fluridone treatments 1 for curlyleaf pondweed control. APRC Technical Notes Collection. ERDC/TN APCRP-2 CC-06. U.S. Army Engineer Research and Development Center, Vicksberg, MS. March 3 2008. 4

Parker A. and R. Dugdale. 2008. Progress report – Sacramento algae/NH4 studies. Unpublished 5 report to the State Water Resources Control Board. Nov. 12, 2008. 6

Parker A. and R. Dugdale. 2008. Progress report – Sacramento algae/NH4 studies. Unpublished 7 report to the State Water Resources Control Board. Nov. 12, 2008. 8

Patten, M.A. 2001. The roles of habitat and signaling in speciation: Evidence from a contact 9 zone of two song sparrow (Melospiza melodia) subspecies. Ph.D. dissertation. Univ. 10 Calif., Riverside, CA. 11

Patton, R.T. 2002. California least tern breeding survey, 2000 Season. California Department of 12 Fish and Game, Species Conservation and Recovery Program Report, 24 pp. 13

Paveglio, F.L. and S.D. Clifton. 1988. Selenium accumulation by San Joaquin kit foxes and 14 coyotes in the Kesterson National Wildlife Refuge area--draft. U.S. Fish and Wildlife 15 Service, Los Banos, CA, Unpubl. Rep., 59 pp. 16

Perry R.W. and J.R. Skalski. 2008. Migration and survival of juvenile Chinook salmon through 17 the Sacramento-San Joaquin River Delta during the winter of 2006-2007. Technical 18 report submitted to the U.S. Fish and Wildlife Service, Stockton, CA. September 2008. 19

Perry R.W. and J.R. Skalski. 2009. Survival and route migration probabilities of juvenile 20 Chinook salmon in the Sacramento-San Joaquin River Delta during the winter of 2007-21 2008. Final report submitted to the U.S. Fish and Wildlife Service, Stockton, CA. July 22 15, 2009. 23

Perry, R.W., J.R. Skalski, P.L. Brandes, P.T. Sandstrom, A.P. Klimley, A. Ammann, and B. MacFarlane. 24 2009. Estimating Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the 25 Sacramento–San Joaquin River Delta. North American Journal of Fisheries Management. 30: 26 142-156. 27

Pierson, E.D. and W.E. Rainey. 1998b. Townsend’s big-eared bat, Corynorhinus townsendii 28 pallescens and C. t. townsendii. Terrestrial Mammal Species of Special Concern in 29 California, Bolster, B. C., editor. Draft Bird and Mammal Conservation Program Report 30 No. 98-14, California Department of Fish and Game. 31

Pierson, E.D., M.C. Wackenhut, J.S. Altenbach, P. Bradley, P. Call, D.L. Genter, C.E. Harris, 32 B.L. Keller, B. Lengus, L. Lewis, B. Luce, K.W. Navo, J.M. Perkins, S. Smith, and L. 33 Welch. 1999. Species Conservation Assessment and Conservation Strategy for the 34 Townsend’s big-eared bat. (Corynorhinus townsendii townsendii and Corynorhinus 35 townsendii pallescens). Idaho Conservation Effort, Idaho Department of Fish and Game, 36 Boise, ID. 37



PSCSFEC (Pacific Salmon Commission Selective Fisheries Evaluation Committee). 2005. 1 Review of 2005 mass marking and mark selective fishery proposals. Report SFEC (05)-1. 2 October 2005. 3

PSCSFEC (Pacific Salmon Commission Selective Fisheries Evaluation Committee). 2008a. 4 Review of 2007 mass marking and mark selective fishery proposals. Report SFEC (08)-1. 5 September 2008. 6

Purchase C. F., D. J. Hasselman, L. K. Weir. 2007 Relationship between fertilization success and the 7 number of milt donors in rainbow smelt Osmerus mordax (Mitchell): implications for population 8 growth rates. Journal of Fish Biology. 70(3): 934–946, 9

Rains, M.C., R.A. Dahlgren, R.J. Williamson, G.E. Fogg, and T. Harter. 2008. Geological 10 control of physical and chemical hydrology in vernal pools, Central Valley, California. 11 Wetlands. 28:347-362. 12

Randall D.J. and T.K.N. Tsui. 2002. Ammonia toxicity in fish. Marine Pollution Bulletin. 45: 17-13 23. 14

RECON (Regional Environmental Consultants). 1989. Comprehensive species management plan 15 for the least Bell’s vireo (Vireo bellii pusillus). Prepared for San Diego Assoication of 16 Governemnts, San Diego. 17

Reiner, R.J. and R. Swenson. 2000. Saving vernal pools in the Cosumnes River watershed. 18 Fremontia 28:33-37. 19

Remsen, J.V. Jr. 1978. Bird species of special concern in California. Wildlife Management 20 Branch Administrative Report No. 78.1. California Department of Fish and Game, 21 Sacramento, CA. 22

Resources Agency, California Department of Water Resources, and California Department of 23 Fish and Game. 2007. Pelagic Fish Action Plan March 2007. Sacramento, CA. 24

RHJV (Riparian Habitat Joint Venture). 2004. Version 2.0. The riparian bird conservation plan: a 25 strategy for reversing the decline of riparian associated birds in California. California 26 Partners in Flight. http://www.prbo.org/calpif/pdfs/riparian.v-2.pdf. 27

Ricciardi A., F.G. Whoriskey, and J.B. Rasmussen. 1996. Impact of the Dreissena invasion on 28 native unionid bivalves in the upper St. Lawrence River. Canadian Journal of Fisheries 29 and Aquatic Sciences. 53: 1434-1444. 30

Ricciardi A., F.G. Whoriskey, and J.B. Rasmussen. 1997. The role of the zebra mussel 31 (Dreissena polymorpha) in structuring macroinvertebrate communities on hard substrata. 32 Canadian Journal of Fisheries and Aquatic Science. 54: 2596-2608. 33

Richards, J.M., M.J. Hansen, C.R. Bronte, S.P. Sitar. (2004) Recruitment dynamics of the 1971–1991 34 year classes of lake trout in Michigan waters of Lake Superior. North American Journal of Fish 35 Management 24:475–489. 36

http://www.prbo.org/calpif/pdfs/riparian.v-2.pdf



Rosenberg, K. V., R. C. Ohmart, W. C. Hunter, and B. W. Anderson. 1991. Birds of the lower 1 Colorado River Valley. University of Arizona Press, Tucson, AZ 2

Saiki, M.K., M.R. Jennings, and R.H. Wiedmeyer. 1992. Toxicity of agricultural subsurface 3 drainwater from the San Joaquin Valley, California, to juvenile chinook salmon and 4 striped bass. Transactions of the American Fisheries Society 121:78-93. 5

Salata, L. 1981. Least Bell’s vireo research, Camp Pendleton Marine Corps Base, San Diego 6 County, California, 1981. Unpubl. Rept., Natural Res. Off., Camp Pendleton. 7

Salata, L. 1983. Status of the least Bell’s vireo on Camp Pendleton, California: report on 8 research done in 1983. Unpubl. Rept., U.S. Fish and Wildlife Service, Laguna Niguel, 9 CA. 10

San Francisco Estuary Institute (SFEI), Blankinship and Associates, Marin Municipal Water 11 District, Reclamation District 999, and Contra Costa County Public Works Department. 12 2003. Field Evaluations of Alternative Pest Control Methods in California Waters. B. K. 13 Greenfield, Ed. APMP Technical Report. SFEI Contribution #95. San Francisco Estuary 14 Institute, Oakland, CA. 15

San Joaquin River Group Authority (SJRGA), 2006. 2005 Annual Technical Report on the 16 Implementation and Monitoring of the San Joaquin River Agreement and the Vernalis Adaptive 17 Management Plan. January 2006. 131 pgs. 18

Sandheinrich, M.B., and K.M.Miller. 2006. Effects of dietary methylmercury on reproductive 19 behavior of fathead minnows (Pimephales Promelas). Environmental Toxicology and 20 Chemistry. 25(11): 3053–3057. 21

Sawyer, J. O., and T. Keeler-Wolf. 1995. A manual of California vegetation. California Native Plant 22 Society. Sacramento, California. 23

Schaffter, R.G. and D.W. Kohlhorst. .1999. Status of white sturgeon in the Sacramento-San Joaquin 24 Estuary. California Fish and Game 85 (1):37-41. Referenced in white sturgeon conceptual model. 25

Scheffer M. 2004. Ecology of shallow lakes. Kluwer Academic Publishers, Boston. 26

Schemel L.E., S.W. Hagar, and D. Childers. 1996. The supply and carbon content of suspended 27 sediment from the Sacramento River to San Francisco Bay. In: J.T. Hollibaugh, ed. San 28 Francisco Bay: The Ecosystem. Pacific Division of the American Association for the 29 Advancement of Science, San Francisco, CA. Pages 237-260 30

Schlorff, R. and P.H. Bloom. 1984. Importance of Riparian Systems to Nesting Swainson’s 31 Hawks in the Central Valley of California. In: R.E. Warner and K.M. Hendrix, eds., 32 California riparian systems: ecology, conservation, and productive management. 33 University of California Press, Berkeley, CA. pp. 612-618 34

Schoellhammer D., S. Wright, J. Drexler, and M. Stacy. 2007. Sedimentation conceptual model. 35 Sacramento, (CA): Delta Regional Ecosystem Restoration Implementation Plan. 36



Servos M.R. and M.C. Servos. 2006. Emerging chemicals derived from municipal wastewater. 1 Background document prepared for the CRD Scientific and Technical Review Panel, 2 Capital Regional District Core Area Liquid Waste Management Plan. 3

SFEI (San Francisco Estuary Institute). 2010. Draft East Contra Costa Historical Ecology Study. 4 Contra Costa County and the Contra Costa County Watershed Forum, Oakland, CA. 5

Shaffer, H.B., R.N. Fisher, and S.E. Stanley. 1993. Status report: the California tiger salamander 6 (Ambystoma californiense). Final report for the California Department of Fish and 7 Game. 36 pp. 8

Shellhammer, H.S. 1989. Salt marsh harvest mice, urban development, and rising sea levels. 9 Conservation Biology 3(1):59-65. 10

Showers, M.T. 1996. Cordylanthus palmatus habitat survey, mitigation potential, and 11 management recommendations. PAR Environmental Services, Inc, Sacramento, CA. 12

Shuford, W.D. and T. Gardali, eds. 2008. California Bird Species of Special Concern: A ranked 13 assessment of species, subspecies, and distinct populations of birds of immediate 14 conservation concern in California. Studies of Western Birds No 1. Western Field 15 Ornithologists, Camarillo, California, and California Department of Fish and Game, 16 Sacramento, CA. 17

Siegel S.W. 2007. Starting the Discussion: Foundation concepts and some initial activities to 18 restore ecosystem functions to the California Delta. Technical report prepared for the 19 Delta Vision Blue Ribbon Task Force. First Draft, December 14, 2007. Available at: 20 http://deltavision.ca.gov/BlueRibbonTaskForce/Feb2008/Item_11_Attachment_2_Ecosys21 tem_Functions.pdf 22

Siemering G. and J. Hayworth. 2005. Aquatic herbicides: overview of usage, fate and transport, 23 potential environmental risk, and future recommendations for the Sacramento-San 24 Joaquin Delta and Central Valley. San Francisco Estuary Institute, Oakland, CA. 25

Siemering G., J. Hayworth, and B.K. Greenfield. 2008. Assessment of potential aquatic herbicide 26 impacts to California aquatic ecosystems. Archives Environmental Contamination and 27 Toxicology. 55: 415-433. 28

Silveira, J.G. 1998. Avian uses of vernal pools and implications for conservation practice. Pp. 29 92-106 In: C.W. Witham et al. (eds.). Ecology, conservation, and management of vernal 30 pool ecosystems—proceedings from a 1996 conference. California Native Plant Society, 31 Sacramento, CA. 32

Skinner, M.W. and B.M. Pavlik. 1994. Inventory of rare and endangered vascular plants in 33 California. 5th edition. (Special Publication No. 1.) California Native Plant Society. 34 Sacramento, CA. 35

Small, A. 1994. California birds: their status and distribution. Ibis Publishing Co., Vista, CA. 36

http://deltavision.ca.gov/BlueRibbonTaskForce/Feb2008/Item_11_Attachment_2_Ecosystem_Functions.pdf/

http://deltavision.ca.gov/BlueRibbonTaskForce/Feb2008/Item_11_Attachment_2_Ecosystem_Functions.pdf/



Snyder, R.D. 1971. Congenital mercury poisoning. New England Journal of Medicine. 1 218:1014-1016. 2

Solomeshch, A.I., M.J. Barbour, and R.F. Holland. 2007. Vernal pools. In: M.J. Barbour, T. 3 Keeler-Wolf, A. A. Schoenherr eds., Terrestrial vegetation of California. Berkeley, CA: 4 pp. 394-424. 5

Sommer T, B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001a. 6 California’s Yolo Bypass: evidence that flood control can be compatible with fisheries, 7 wetlands, wildlife, and agriculture. Fisheries 26(8):6-16. 8

Sommer T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, 9 M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, M. Nobriga, and K. Souza. 10 2007a. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 11 32:270-277 12

Sommer T., R. Baxter, and B. Herbold. 1997. Resilience of splittail in the Sacramento-San 13 Joaquin Estuary. Transactions of the American Fisheries Society. 126:961-976. 14

Sommer T.R., W.C. Harrell, M.L. Nobriga, and R. Kurth. 2003. Floodplain as habitat for native 15 fish: Lessons from California’s Yolo Bypass. In PM Faber, ed. California riparian 16 systems: Processes and floodplain management, ecology, and restoration. 2001 Riparian 17 Habitat and Floodplains Conference Proceedings, Riparian Habitat Joint Venture, 18 Sacramento, California. Pages 81-87. 19

Sommer T.R., W.C. Harrell, R. Kurth, F. Feyrer, S.C. Zeug, and G. O’Leary. 2004a. Ecological 20 patterns of early life stages of fishes in a river-floodplain of the San Francisco Estuary. 21 In: F Feyrer, LR Brown, RL Brown, JJ Orsi, eds. Early Life History of Fishes in the San 22 Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, 23 Maryland. Pages 111-123. 24

Sommer T.R., W.C. Harrell, Z. Manteca, and F. Feyrer. 2008. Habitat associations and behavior 25 of adult and juvenile splittail (Cyprinidae: Pogonichthys macrolepidotus) in a managed 26 seasonal floodplain wetland. San Francisco Estuary and Watershed Science 6(2): 1-16. 27

Sommer, T., L. Conrad, G. O’Leary, F. Feyrer, and W. Harrell. 2002. Spawning and rearing of 28 splittail in a model floodplain wetland. Transactions of the American Fisheries Society 29 131:966-974. 30

Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. Batham, and W.J. Kimmerer. 2001b. Floodplain 31 rearing of juvenile Chinook salmon: Evidence of enhanced growth and survival. 32 Canadian Journal of Fisheries and Aquatic Sciences 58(2):325-333. 33

Sommer, T.R., R.D. Baxter, and F. Feyrer. 2007b. Splittail “delisting”: A review of recent 34 population trends and restoration activities. American Fisheries Society Symposium 35 53:25-38. 36



Sophie S. Parker, Joshua P. Schimel. 2010. Invasive Grasses Increase Nitrogen Availability in 1 California Grassland Soils. Invasive Plant Science and Management: March-May, Vol. 3, 2 No. 1, pp. 40-47. 3

Sorensen PW (1998) Hormonally derived sex pheromones in goldfish: A model for understanding the 4 evolution of sex pheromone systems in fish. Biological Bulletin 183:173-177. 5

Spautz, H. and N. Nur. 2008. Suisun Song Sparrow (Melospiza melodia maxillaris). In: Shuford, W.D. 6 and T. Gardali, editors. California Bird Species of Special Concern: A ranked assessment of 7 species, subspecies, and distinct population of birds of immediate conservation concern in 8 California. Studies of Western Birds 1, Western Field Ornithologists, Camarillo, California, and 9 California Department of Fish and Game, Sacramento, CA. Spencer, W.D., P. Beier, K. Penrod, 10 K. Winters, C. Paulman, H. Rustigian- Romsos, J. Strittholt, M. Parisi, and A. Pettler. 2010. 11 California Essential Habitat Connectivity Project: A Strategy for Conserving a Connected 12 California. Prepared for California Department of Transportation, California Department of Fish 13 and Game, and Federal Highways Administration. 14

Spautz, H., N. Nur, and D. Stralberg. 2005. California black rail (Laterallus jamaicensis 15 coturniculus) distribution and abundance in relation to habitat and landscape features in 16 the San Francisco Bay estuary. USDA Forest Service General Technical Report PWS-17 GTR-191. 18

Spiegel, L.K. and M. Bradbury. 1992. Home range characteristics of the San Joaquin kit fox in 19 western Kern County, California. Transactions of the Western Section of The Wildlife 20 Society 28:83-92. 21

SRCSD (Sacramento Regional County Sanitation District). 2003. Draft Environmental Impact 22 Report for the Sacramento Regional County Sanitation District, Sacramento Regional 23 Wastewater Treatment Plant 2020 Master Plan. Volume 1 – EIR Text. 24

Stacey M.T. 2003. Hydrodynamics of shallow water habitats in the Sacramento-San Joaquin 25 Delta. University of California Water Resources Center, Berkeley, CA. 26

Stebbins, R. C. 1985. A field guide to western reptiles and amphibians. Houghton Mifflin Co., Boston, 27 MA. Mild. Nat. 77:323-355. 28

Stebbins, R.C. 2003. A Field Guide to Western Reptiles and Amphibians. Third edition 29 Houghton Mifflin Company, Boston, MA. 533 pp. 30

Stevens, D.E. 1966. Food habits of striped bass (Roccus saxatilis) in the Sacramento-San Joaquin 31 Delta. California Department of Fish and Game Fish Bulletin 136, Part 2:68-96. 32

Stewart T.W., J,G. Miner, and R.L. Lowe. 1998. Macroinvertebrate communities on hard 33 substrates in Western Lake Erie: structuring effects of Dreissena. Journal of Great Lakes. 34 254(4): 868-879. 35

Stromberg, M.R., J.D. Corbin, and C.M. D'Antonio. 2007. California grasslands: ecology and 36 management. 390 pages 37



Suisun Ecological Workgroup. 2001. Suisun Ecological Workgroup final report to the State 1 Water Resources Control Board. State Water Resources Control Board, Sacramento. 2

Sumpter J.P. and S. Jobling. 1995. Vitellogenesis as a biomarker for estrogenic contamination of 3 the aquatic environment. Environmental Health Perspectives. 103(SUPPL. 7): 173-178. 4

Sutherland, A.B. and J.L. Meyer. (2007). Effects of increased suspended sediment on growth rate 5 and gill condition of two southern Appalachian minnows. Environmental Biology of 6 Fishes. 80:389-403. 7

Sveinsson, T., T.J. Hara. (1995) Mature males of Arctic charr, Salvvelinus alpinus, release F-type 8 prostaglandins to attract conspecific mature female and stimulate their spawning behavior. 9

Swick, C.D. 1973. Determination of San Joaquin kit fox range in Contra Costa, Alameda, San 10 Joaquin, and Tulare Counties, 1973. California Dept. Fish and Game, Sacramento, 11 Special Wildlife Investigations, Unpubl. Rep., 15 pp. 12

Swiecki, T.J. and E. Bernhardt. 2008. Effects of grazing in upland vegetation at Jepson Prarie Preserve, 13 Solano County, CA: third year (2007) results and final report. Solano Land Trust, Fairfield, CA. 14

Takata L., M. Falkner, and S. Gilmore. 2006. Commercial vessel fouling in California: analysis, 15 evaluation, and recommendations to reduce nonindigenous species release from the non-16 ballast water vector. California State Lands Commission, Sacramento, CA. 17

Takata, H. K., M. J. Reesman, G. E. Reed, L. D. Layng, and T. A. Jones. 2007. Development of a system-18 wide predator control program: indexing and fisheries evaluation. Oregon Department of Fish and 19 Wildlife, Contract Number DEB1719- 94BI24514. 2006 Annual Report to the Bonneville Power 20 Administration, Portland, Oregon. 21

Takekawa, J., Woo, I., Spautz, H., Nur, N., Grenier, J. L., Malamud-Roam, K., Nordby, J. C., 22 Cohen, A. N., Malamud-Roam, F., and Wainwright-De La Cruz, S. E. 2006. 23 Environmental threats to tidal-marsh vertebrates of the San Francisco Bay estuary. 24 Studies Avian Biol. 32:176–197. 25

Teh S.J., M. Lu, F.C. Teh, S. Lesmeister, I. Werner, J. Krause, and L. Deanovic. 2008. Final 26 Report: Toxic effects of surface water in the upper San Francisco Estuary on Eurytemora 27 affinis. Submitted to the San Luis and Delta-Mendota Water Authority. 28

Teh, S.J., D.F. Deng, I. Werner, F.C. Teh, and S.S.O. Hung. 2005. Sublethal toxicity of orchard 29 stormwater runoff in Sacramento splittail (Pogonichthys macrolepidotus) larvae. Marine 30 Environmental Research. 59:203-216. 31

Temple, R., K. Daily, T. Shrader, and B. Hooton.1998. Predation issues: introduced fishes. Draft 32 review. Oregon Department of Fish and Wildlife. Salem, OR. June 17, 1998. 33

The Bay Institute (TBI) 1998. From the Sierra to the Sea: The Ecological History of the San 34 Francisco Bay Watershed. 35



The Bay Institute (TBI) 1998. From the Sierra to the Sea: The Ecological History of the San 1 Francisco Bay Watershed. 2

Thomas, J.L. 1967. The diet of juvenile and adult striped bass, Roccus saxatilis, in the Sacramento-San 3 Joaquin river system. California Fish and Game 53:49–62. 4

Toft J.D., C.A. Simenstad, J.R. Cordell, and L.F. Grimaldo. 2003. The effects of introduced 5 water hyacinth on habiat structure, invertebrate assemblages, and fish diets. Estuaries. 6 26(3): 746-758. 7

Turner, T., M. Osborne. (2008) Management of genetic resources in the federally endangered Rio Grande 8 silvery minnow, Hybognathus amarus. CALFED Science Program Workshop – The Use of 9 Artificial Propagation as a Tool for Central Valley Salmonid and Delta smelt Conservation. July 10 24, 2008. 11

Turner, T.F., T.E Dowling., P.C.Marsh, B.R. Kesner, and A.T.Kelsen. (2007) Effective size, census size, 12 and genetic monitoring of the endangered razorback sucker, Xyrauchen texanus. Conservation 13 Genetics 8:417-425. 14

Underwood, A.J. (1992). Beyond BACI: the detection of environmental impacts on populations 15 in the real, but variable, world. Journal of Experimental Marine Biology and Ecology 16 161, 145–178. 17

USBR (U.S. Bureau of Reclamation). 2008. Central Valley Project and State Water Project 18 Operations Criteria and Plan Biological Assessment. May 2008. 19

USBR, USFWS, DFG, and ICF International. 2010. Suisun Marsh Habitat Management, 20 Preservation, and Restoration Plan Draft Environmental Impact Statement/ 21 Environmental Impact Report. Sacramento, CA. 22

USCG (United States Coast Guard). 2004. Mandatory Ballast Water Management Program for 23 U.S. Waters. Federal Register Final Rule. 69 FR 44952. July 28, 2004.USEPA (U.S. 24 Environmental Protection Agency). 1993. Guidance specifying management measures for 25 sources of nonpoint pollution in coastal waters. EPA 840-B-92-002. January 1993. 26 Available at: http://www.epa.gov/owow/nps/MMGI/index.html. 27

USEPA (United States Environmental Protection Agency). (1993). Handbook - Urban Runoff 28 Pollution Prevention and Control Planning. EPA-625-R-93-004. Washington, DC. 29

USEPA (U.S. Environmental Protection Agency). 1999. 1999 update of ambient water quality 30 criteria for ammonia. EPA 822-R-99-014. December 1999. Available at: 31 http://www.epa.gov/waterscience/criteria/ammonia/99update.pd. 32

USFWS (United States Fish & Wildlife Service). 1984a. Revised recovery plan for three 33 endangered species endemic to Antioch Dunes, California. Portland, OR. 34

USFWS (U.S. Fish and Wildlife Service). 1984b. Salt Marsh harvest mouse and California 35 clapper rail Recovery Plan. U.S. Fish and Wildlife Service, Pacific Region, Portland, 36 Oregon. 141 pp. http://ecos.fws.gov/docs/recovery_plan/841116.pdf 37

http://www.epa.gov/owow/nps/MMGI/index.html

http://www.epa.gov/waterscience/criteria/ammonia/99update.pd



USFWS (U.S. Fish and Wildlife Service). 1984c. Valley Elderberry Longhorn Beetle Recovery 1 Plan. Portland, OR. 2

USFWS (U.S. Fish and Wildlife Service). 1996. Recovery Plan for the Sacramento/San Joaquin 3 Delta Native Fishes. 4

USFWS (U.S. Fish and Wildlife Service). 1998a. Recovery Plan for Upland Species of the San 5 Joaquin Valley, California. 340 pp. Available at 6 http://ecos.fws.gov/docs/recovery_plan/980930a.pdf 7

USFWS (U.S. Fish and Wildlife Service). 1998b. Draft recovery plan for the least Bell’s vireo. 8 Portland, OR. 9

USFWS (USFWS (U.S. Fish and Wildlife Service). 1998c. California Clapper Rail Rallus 10 longirostris obsoletus. Available at: 11 http://www.fws.gov/sacramento/es/animal_spp_acct/ca_clapper_rail.pdf 12

USFWS (U.S. Fish and Wildlife Service). 1999a. Draft Recovery Plan for the Giant Garter Snake 13 (Thamnophis gigas). U.S. Fish and Wildlife Service, Portland, Oregon. pp ix+ 192. 14

USFWS (U.S. Fish and Wildlife Service). 1999b. Conservation Guidelines for the Valley 15 Elderberry Longhorn Beetle, July 9, 1999. 16

USFWS (United States Fish & Wildlife Service). 2001a. Antioch Dunes National Wildlife Refuge 17 Draft comprehensive conservation plan: plan and environmental assessment. USFWS, 18 Sacramento, CA. 19

USFWS (U.S. Fish and Wildlife Service). 2001b. Salt marsh harvest mouse. Endangered Species 20 Division, Sacramento Fish and Wildlife Office, Sacramento, CA. Available at: 21 http://sacramento.fws.gov/es/animal_spp_acct/salt_marsh_harvest_mouse.htm. 22

USFWS (U.S. Fish and Wildlife Service. 2002. Recovery Plan for the California Red-legged 23 Frog (Rana aurora draytonii). Portland, OR. 24

USFWS (U.S. Fish and Wildlife Service). 2004. Impacts of riprapping to aquatic organisms and 25 river functioning, Lower Sacramento River, California. 2nd Edition. Available at: 26 www.fws.gov/sacramento/es/animal_spp_account/acctfish.htm. 27

USFWS (U.S. Fish and Wildlife Service). 2005. Recovery plan for Vernal Pool Ecosystems of 28 California and Southern Oregon. Available at: 29 http://www.fws.gov/sacramento/es/recovery_plans/vp_recovery_plan_links.htm. 30

USFWS (U.S. Fish and Wildlife Service). 2006. California Least Tern (Sterna antillarum 31 browni). Five-Year Review, Summary and Evaluation. Carlsbad, CA. 32

USFWS (U.S. Fish and Wildlife Service). 2007a. Stone Lakes National Wildlife Refuge 33 Comprehensive Conservation Plan. January, Sacramento, CA. 34

http://ecos.fws.gov/docs/recovery_plan/980930a.pdf

http://www.fws.gov/sacramento/es/animal_spp_acct/ca_clapper_rail.pdf

http://sacramento.fws.gov/es/animal_spp_acct/salt_marsh_harvest_mouse.htm

http://www.fws.gov/sacramento/es/animal_spp_account/acctfish.htm

http://www.fws.gov/sacramento/es/recovery_plans/vp_recovery_plan_links.htm



USFWS (U.S. Fish and Wildlife Service. 2007b. Species Account: California red-legged frog 1 (Rana aurora draytonii), Sacramento Fish and Wildlife Office, Sacramento, CA. 2

USFWS (United States Fish & Wildlife Service). 2008. Lange's metalmark butterfly (Apodemia 3 mormo langei), Antioch Dunes evening-primrose, (Oenothera deltoides subsp. howellii), 4 Contra Costa wallflower (Erysimum capitatum var. angustatum) - Five-year review: 5 summary and evaluation. USFWS, Sacramento, CA. 6

USFWS (United States Fish & Wildlife Service). 2009a. Cirsium hydrophilum var. hydrophilum 7 (Suisun thistle) 5-year review: summary and evaluation. Sacramento, CA. 8

USFWS (United States Fish & Wildlife Service). 2009b. Cordylanthus mollis ssp. mollis (soft 9 bird’s-beak) 5-year review: summary and evaluation. USFWS, Sacramento, CA. 10

USFWS (United States Fish & Wildlife Service). 2009c. Formal Endangered Species Act 11 Consultation on the Proposed Coordinated Operations of the Central Valley Project (CVP) and 12 State Water Project (SWP). December 15, 2008. Available at: 13 http://www.fws.gov/sacramento/es/documents/SWP-CVP_OPs_BO_12-15_final_OCR.pdf 14

USFWS (United States Fish & Wildlife Service). 2010. Draft Recovery Plan for Tidal Marsh 15 Ecosystems of Northern and Central California.Ustin S.L., J.A. Greenberg, M. Santos, S. 16 Khanna, E. Hestir, P. Haverkamp, and S. Kefauver. 2008. Mapping invasive plant species 17 in the Sacramento-San Joaquin River Delta using hyperspectral imagery. California 18 Department of Boating and Waterways, Davis, CA. 19

Van Wijngaarden R.P.A., T.C.M. Brock, and P.J. Van den Brink. 2005. Threshold levels for 20 effects of insecticides in freshwater ecosystems: A review. Ecotoxicology, 14:355-380. 21

Vanderploeg, H. A., J. R. Liebig, W. W. Carmichael, M. A. Agy, T. H. Johengen, G. L. 22 Fahnenstiel, and T. F. Nalepa. 2001. Zebra mussel (Dreissena polymorpha) selective 23 filtration promoted toxic Microcystis blooms in Saginaw Bay (Lake Huron) and Lake 24 Erie. Canadian Journal of Fisheries and Aquatic Sciences. 58: 1208-1221. 25

Vanderwalker JG. 1967. Response of salmonids to low frequency sound. In: W. Tavolga (ed.) 26 Marine Acoustics, Vol. 2. New York, Pergamon Press, 295 pp. 27

Viant, M.R., C.A. Pincetich, and R.S. Tjeerdema. 2006. Metabolic effects of dinoseb, diazinon 28 and esfenvalerate in eyed eggs and alevins of Chinook salmon (Oncorhynchus 29 tshawytscha) determined by 1H NMR metabolomics. Aquatic Toxicology. 77:359-371. 30

Wallace S., J. Higgins, A. Crolla, C. Kinsley, A. Bachand, and S. Verkuijl. 2006. High-rate 31 ammonia removal in aerated engineered wetlands. Paper presented at the 10th 32 International Conference on Wetland Systems for Water Pollution Control. September 33 23-29, 2006: Lisbon, Portugal. 34

Wallace, W.G., and S.N. Luoma. 2003. Subcellular compartmentalization of Cd and Zn in two 35 bivalves. II. Significance of trophically available metal (TAM). Marine Ecology Progress 36 Series 257:125-137. 37



Wang J.C.S. 1986. Fishes of the Sacramento-San Joaquin estuary and adjacent waters, 1 California: a guide to the early life histories. Interagency Ecological Study Program for 2 the Sacramento-San Joaquin Estuary, Tech. Rep. 9. Stockton, CA. 3

Wanner, G. A., D. A. Shuman, and D. W. Willis. 2007. Food habits of juvenile pallid sturgeon 4 and adult shovel nose sturgeon in the Missouri River downstream of Fort Randall Dam, 5 South Dakota. Journal of Freshwater Ecology 22:81-92. 6

Ward, A. K., R. G. Wetzel. 1980. Interactions of light and nitrogen source among planktonic 7 blue-green algae. Archiv fur Hydrobiologie 90: 1-25. 8

Warren KS. 1962. Ammonia toxicity and pH. Nature. 195: 47-49. 9

Watson, E B. and R. Byrne. 2009. Abundance and diversity of tidal marsh plants along the salinity 10 gradient of the San Francisco Estuary: implications for global change ecology. Plant Ecology: An 11 International Journal, 205(1), pp 113-128. 12

Watson, E.B. 2006. Environmental change in San Francisco Estuary Tidal Marshes. Ph.D. 13 dissertation, University of California, Berkeley, CA. 14

Webb H., R. Wilder, and K. Vargas. 2006b. Diel activity patterns of fishes of special interest in 15 the Sacramento-San Joaquin River Delta. 4th Biennial CALFED Science Conference. 16 10/23-10/25/2006. Sacramento, CA. 17

Webb MA, GW Feist, MS Fitzpatrick, EP Foster, CB Schreck, M Plumlee, C Wong, and DT 18 Gundersen. 2006a. Mercury concentrations in gonad, liver, and muscle of white sturgeon 19 Acipenser transmontanus in the lower Columbia River. Archives of Environmental 20 Contamination and Toxicology. 50(3):443-51. 21

Webber, H. M. and, T. A. Haines. 2003. Mercury effects on predator avoidance behavior of a 22 forage fish, golden shiner (Notemigonus crysoleucas). Environmental Toxicology and 23 Chemistry 22(7): 1556-1561. 24

Weber, E. D. and K. D. Fausch. 2005. Competition between hatchery-reared and wild juvenile 25 chinook salmon in enclosures in the Sacramento River, California. Transactions of the 26 American Fisheries Society 134:44–58. 27

Welton, JS, WRC Beaumont, RT Clarke. 2002. The efficacy of air, sound and acoustic bubble 28 screens in deflecting Atlantic salmon, Salmo salar L., smolts in the River Frome, UK. 29 Fisheries Management and Ecology. 9:11-18. 30

Werner I. 2007. Pyrethroids in the water column- Is there reason for concern? Presentation at UC 31 Davis, Nov 8, 2007. 32

Werner I. and K. Moran. 2008. Effects of pyrethroid insecticides on aquatic organisms. In: J. 33 Gan, F. Spurlock, P. Hendley, D.P. Weston, eds., Synthetic Pyrethroids: Occurrence and 34 Behavior in Aquatic Environments. American Chemical Society, ACS Symposium Series 35 991, American Chemical Society, Washington, DC, USA. pp. 310-335. 36



Werner I. and Oram J. 2008. Pyrethroid insecticides conceptual model. Sacramento (CA): Delta 1 Regional Ecosystem Restoration Implementation Plan. 2

Werner I. and Oram J. 2008. Pyrethroid insecticides conceptual model. Sacramento (CA): Delta 3 Regional Ecosystem Restoration Implementation Plan. 4

Werner I., L. Deanovic, D. Markiewicz, M. Stillway, N. Offer, R. Connon, S. Brander, 2008b. 5 Final Report. Pelagic Organism Decline (POD): Acute and Chronic Invertebrate and Fish 6 Toxicity Testing in the Sacramento-San Joaquin Delta 2006-2007. UC Davis – Aquatic 7 Toxicology Laboratory, Davis, CA. 8

Werner I., L. Deanovic, M. Stillway, D. Markiewicz, 2009.The Effects of Wastewater Treatment 9 Effluent-Associated Contaminants on Delta Smelt. Draft Final Report, Central Valley 10 Regional Water Quality Control Board, January 28, 2009. 11

Werner I., S. Anderson, K. Larsen, and J. Oram. 2008a. Chemical stressors conceptual model. 12 Sacramento (CA): Delta Regional Ecosystem Restoration Implementation Plan. 13

Western Ecological Services. 1986. A review of the population status of the Suisun shrew (Sorex 14 ornatus sinuosus). Final Report for the U.S. Fish and Wildlife Service, Sacramento, CA. 15 pp 59. 16

Weston D.P., J. You, and M.J. Lydy. 2004. Distribution and toxicity of sediment-associated 17 pesticides in agriculture-dominated water bodies of California’s Central Valley. 18 Environmental Science and Technology, 38(10):2752-2759. 19

Weston D.P., R. Holmes, and M. Lydy. 2008. Residential runoff as a source of pyrethroid 20 insecticides to surface waters. 5th Biennial CALFED Science Conference. 10/22-21 10/24/2008. Sacramento, CA. 22

Weston D.P., R. W. Holmes, and M. J. Lydy. 2009. Residential runoff as a source of pyrethroid 23 insecticides to urban creeks. Environmental Pollution. 157:287-294. 24

Weston D.P., R.W. Holmes, J. You, and M.J. Lydy. 2005. Aquatic toxicity due to residential use 25 of pyrethroid insecticides. Environmental Science and Technology, 39(24):9778-9784. 26

White, P. J., and K. Ralls. 1993. Reproduction and spacing patterns of kit foxes relative to 27 changing prey availability. Journal of Wildlife Management 57:861–867. 28

White, P.J. and R.A. Garrott. 1999. Population dynamics of kit foxes. Canadian Journal of 29 Zoology 77(3):486-493. 30

White, P.J. and R.A. Garrott. 1999. Population dynamics of kit foxes. Canadian Journal of 31 Zoology 77(3):486-493. 32

Wilder R.M. and J.F. Ingram. 2006. Temporal patterns in catch rates of juvenile Chinook salmon 33 and trawl net efficiencies in the lower Sacramento River. IEP Newsletter.19(1): 18-28. 34



Wilkerson, F.P., R.C. Dugdale, V.E. Hogue and A. Marchi. 2006. Phytoplankton blooms and 1 nitrogen productivity in San Francisco estuary. Estuaries and Coasts 29: 401-416. 2

Williams J.G. 2006. Central Valley Salmon: A perspective on Chinook and steelhead in the 3 Central Valley of California. San Francisco Estuary and Watershed Science [online 4 serial]. Volume 4, Issue 3 (December 2006), Article 2.Williamson K.S. and B. May. 5 2002. Incidence of phenotypic female Chinook salmon positive for the male Y-6 chromosome-specific marker OtY1 in the Central Valley, California. Journal of Aquatic 7 Animal Health. 14:176-183. 8

Williams, D.F. 1986. Mammalian Species of Special Concern in California. California 9 Department of Fish and Game, Wildlife Management Division, Admin. Rep. 86-1:1-112. 10

Williams, D.F. 1986. Mammalian Species of Special Concern in California. California 11 Department of Fish and Game, Wildlife Management Division, Admin. Rep. 86-1:1-112. 12

Williams, D.F. 1993. Population censuses of riparian brush rabbits and riparian woodrats at 13 Caswell Memorial State Park during January 1993. California Dept. Parks and 14 Recreation, Lodi, CA, 15 pp. 15

Williams, D.F., L.P. Hamilton, M.R. Lloyd, E. Vincent, C. Lee, A. Edmondson, J.J. Youngblom, 16 K. Gilardi, and P.A. Kelly. 2002a. Controlled propagation and translocation of riparian 17 brush rabbits: annual report for 2002. Report to the U.S. Bureau of Reclamation, U.S. 18 Fish and Wildlife Service, and California Department of Fish and Game, Sacramento, 19 CA. 20

Williams, D.F., P.A. Kelly, L.P. Hamilton, M.R. Lloyd, E.A. Williams, and J.J. Youngblom. 21 2008. Recovering the endangered riparian brush rabbit (Sylvilagus bachmani riparius): 22 reproduction and growth in confinement and survival after translocation. In Lagomorph 23 Biology: Evolution, Ecology, and Conservation; P.C. Alves, N. Ferrand, and K. 24 Hacklander (Eds.); pages 349361; Springer-Verlag Berlin Heidelberg 2008; proceedings 25 of the 2nd World Lagomorph Conference, Vairao, Portugal, July 2004. 26

Williams, P.B. 1985. An overview of the impact of accelerated sea level rise on San Francisco 27 Bay. Report to the Bay Conservation and Development Commission, San Francisco, CA. 28

Williamson K.S. and B. May. 2005. Inheritance studies implicate a genetic mechanism for 29 apparent sex reversal in Chinook salmon. Transactions of the American Fisheries Society 30 134: 1253-1261. 31

Williamson, R., G. Fogg, M. Rains, and T. Harter. 2005. Hydrology of vernal pools at three sites, 32 southern Sacramento Valley. Final technical report to the California Department of 33 Transportation, Sacramento, CA. 34

Witham, C.W. 2003. Tule Ranch vernal pools botanical resources survey report. Yolo Basin 35 Foundation, Davis, CA. 36



Witham, C.W. 2006. Greater Jepson Prairie ecosystem regional management plan. Fairfield: 1 Solano Land Trust. 2

Wolfe, M.F., S. Schwarzbach, and R.A. Sulaiman. 1998. Effects of mercury on wildlife: a 3 comprehensive review. Environmental Toxicology and Chemistry. 17:146-160. 4

Wood, M., P. Morris, J. Cooke, S. Louie and D. Bosworth. 2008. Amendments to The Water 5 Quality Control Plan for the Sacramento River and San Joaquin River Basins for the 6 Control of Methylmercury and Total Mercury in the Sacramento-San Joaquin Delta 7 Estuary. Central Valley Regional Water Quality Control Board, Draft Staff Report for 8 Public Review. Sacramento. February. 9

Wren, C.D., D.B. Hunter, J.E. Leatherland, and P.M. Stokes. 1987. The effects of 10 polychlorinated biphenyls and methylmercury, singly and in combination, on mink. I: 11 Uptake and toxic responses. Archives of Environmental Contamination and Toxicology. 12 16:441-447. 13

Wright S.A., D.H. Schoellhamer. 2004. Trends in the sediment yield of the Sacramento River, 14 California, 1957-2001. San Francisco Estuary and Watershed Science [online serial]. Vol. 15 2, Issue 2 (May 2004), Article 2. 16

Wylie, G.D., M.L. Casazza, and J.K. Daugherty. 1997. 1996 Progress Report for the Giant 17 Garter Snake Study. May 1, 1997. Dixon Research Station, California Science Center, 18 USGS Biological Resources Division, Dixon, CA. 19

Yolo Natural Heritage Program. 2008. Species Account. Technology Associates International 20 Corporation, Woodland, CA. 21

Yolo Natural Heritage Program. 2009. Species account. Yolo County, CA. 22

Young FR. 1997. Development of a systemwide predator control program: stepwise 23 implementation of a predator index, predator control fisheries, and evaluation plan in the 24 Columbia River basin. Section I: Implementation. 1996 Annual Report. November 1997. 25 Available at: http://www.fishlib.org/library/Documents/BPA_Fish_and_Wildlife/24514-26 3.pdf 27

Zarn, M. 1974. Burrowing Owl (Speotyto cunicularia hypugaea). Habitat management series for 28 unique or endangered species, U.S. Bureau of Land Management Technical Note 242. 29 Denver, CO. 25 pp. 30

Zedler, P.H. 1987. The ecology of southern California vernal pools: a community profile. U. S. 31 Fish & Wildlife Service. 32

Zedler, P.H. 1990. Life histories of vernal pool vascular plants.in D.H. Ikeda and R.A. Schlising, 33 editors. Vernal pools: their habitat and biology. Herbarium, California State University 34 Chico, Number 8, Chico, California. 35

http://www.fishlib.org/library/Documents/BPA_Fish_and_Wildlife/24514-3.pdf

http://www.fishlib.org/library/Documents/BPA_Fish_and_Wildlife/24514-3.pdf



Zeiner, D.C., W.F. Laudenslayer, Jr., K.E. Mayer, and M. White, eds. 1990. California’s 1 Wildlife. Volume 2. Birds. State of California, Department of Fish and Game. 2 Sacramento, California. 731 pp. 3

Zelikoff, J. T. 1998. Biomarkers of immunotoxicity in fish and other non-mammalian sentinel 4 species: Predictive value for mammals? Toxicology, 129:63-71. 5

Zhang, M., L. Wilhoit, and C. Geiger. 2004. Dormant season organophosphate use in California 6 almonds. Report prepared for California Department of Pesticide Regulation. January 7 2004. 8

Zoellick, B.W., T.P. O'Farrell, and T.T. Kato. 1987b. Movements and home range of San 9 Joaquin kit foxes on the Naval Petroleum Reserves, Kern County, California. Rep. No. 10 EGG 10282-2184, EG&G Energy Measurements, Goleta, CA, 38 pp. 11


Burau, J. USGS, Discussion with BDCP Hood Bypass Sub-Group about Delta hydrology, 13 8/20/2008. 14

Burkhard, B., Incident Commander, California Department of Water Resources (916-376-9761). 15 Telephone conversation with J-L Cartron, July 22, 2010 regarding functioning of Suisun 16 Marsh salinity control gates and patterns of land use in Suisun Marsh. 17

Chappell, S. Executive Director, Suisun Resource Conservation District. Telephone conversation 18 with J-L Cartron on 7/22/2010 regarding functioning of salinity gates and patterns of land 19 use at Suisun Marsh, and development and release of the Suisun Marsh Habitat 20 Management, Preservation, and Restoration Plan. 21

Clarke, R. USFWS. Conversation with Alison Willy (USFWS) regarding delta smelt refugial 22 hatchery population. 2/3/2009. 23

Cline, R. CDFA. Phone conversation with H. Gellerman, DFG, about additional border 24 protection inspection stations. 6/12/09. 25

DeGeorge, J. RMA. Presentation to the BDCP Conveyance Working Group on Hydrodynamic 26 effects of restoration of tidal habitat in Suisun Marsh: initial evaluation. 5/28/08. 27

Ellis, S. Environmental Program Manager, CDFG, Telephone conversations/e-mail 28 communications with M. Hood 5/28/09, 6/2/09 and 6/5/09. 29

Fullerton, D. 2007. Principal Resource Specialist, MWD, CALFED Brown Bag Seminar: The 30 interaction among turbidity, salinity, and smelt during fall and winter: a work in progress. 31 11/27/07. 32

Gellerman, H. Biologist, Invasive Species Program, DFG. Phone conversation with R. Wilder 33 about potential actions to reduce the risk of invasive species introductions in the Delta. 34 5/18/09. 35



Holderman, M. Chief, Temporary Barriers Project and Lower San Joaquin, DWR. Telephone 1 conversation with R. Wilder regarding the 2009 DWR Head of Old River Non-Physical 2 Barrier Test Project, 6/10/2009. 3

Larsen, K. Senior Environmental Scientist, CVRWQCB, e-mail communication with M. Hood 4 6/19/09. 5

Lindberg, J. Director, Fish Conservation and Culture Lab, UC Davis. Written comments sent via 6 email to R. Wilder, 5/26/09. 7

Majors, D. 2009. Engineer, Metropolitan Water District of Southern California. Presentation to 8 the BDCP Integration Team on the 2-gate project. 2/3/09. 9

Meier, D. 2008. Anadromous Fish Screen Program Manager, USFWS, Telephone conversation 10 with R. Wilder, 4/29/08. 11

Nobriga, M. Biologist, DFG, Phone conversation with R. Wilder about non-native species, 12 4/14/08. 13

Norton, D.. 2009. DFG, Conversation with H. Gellerman, DFG, about costs of boat wash 14 stations. 6/12/09. 15

Trenham, P. Biologist, California Tiger Salamander Workshop 2010, Elkhorn Slough National 16 Estuarine Research Reserve. 3/23/10. 17

Vogel, D. 2008 Senior Scientist, Natural Resource Scientists, Inc. Conversation with C. Hanson. 18 2008. 19

Volkoff, M. Invasive Mussel Program, DFG. Telephone conversation with J. Gerlach about 20 strategies for dealing with invasive mussels, 8/29/08. 21

CHAPTER 4. DESCRIPTION OF COVERED ACTIVITIES AND ASSOCIATED FEDERAL 22 ACTIONS 23

Alexander, B.S., G.H. Mendell, and G. Davidson. Report of the Board of Commissioners on the 24 Irrigation of the San Joaquin, Tulare, and Sacramento Valleys of the State of California. 25 Government Printing Office, Washington D.C., 1874. 26

Department of Public Works. The State Water Plan. Public works Bulletin No. 25. A Report to 27 the Legislature of 1931. Sacramento, CA, 1930. 28

Lund, J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, P. Moyle. 2007. Envisioning futures for the 29 Sacramento-San Joaquin Delta. San Francisco, CA, Public Policy Institute of California. 30

USBR (US Bureau of Reclamation). 2008. Central Valley Project and State Water Project 31 operations criteria and plan biological assessment. 32



2008 National Marine Fisheries Service Biological Opinion for the Temporary Barriers Project 1

CHAPTER 5. OVERVIEW OF THE EFFECTS ANALYSIS 2

Baerwald, M. R., F. Feyrer, and B. May. 2008. Distribution of genetically differentiated splittail 3 populations during the nonspawning season. Transactions of the American Fisheries 4 Society 137:1335-1345. 5

Baxter, R.D. 1999. Status of splittail in California. California Fish and Game 85:28–30. 6

Benigno, G. M. and T. R. Sommer. 2008. Just add water: sources of chironomid drift in a large 7 river floodplain. Hydrobiologia 600: 297-305. 8

CDWR and USBR (California Department of Water Resources, U.S. Bureau of Reclamation). 9 1994. Effects of the Central Valley Project and State Water Project on delta smelt and 10 Sacramento splittail. Biological Assessment. Prepared for U.S. Fish and Wildlife Service, 11 Ecological Services, Sacramento Field Office, Sacramento, California. 12

Clark, K. W., M. D. Bowen, R. B. Mayfield, K. P. Zehfuss, J. D. Taplin, and C. H. Hanson. 13 2009. Quantification of Pre-Screen Loss of Juvenile Steelhead in Clifton Court Forebay. 14 California Department of Water Resources. Sacramento, CA. 15

Crain, P. K., K. Whitener, and P. B. Moyle. 2004. Use of a restored central California floodplain 16 by larvae of native and alien fishes. American Fisheries Society Symposium 39: 125-140. 17

Danley M. L., Mayr S. D., Young P. S., Cech J. J. Jr. 2002. Swimming performance and 18 physiological stress responses of splittail exposed to a fish screen. North American 19 Journal of Fisheries Management 22:1241-1249. 20

Enos, C., S. Sutherland, M. L. Nobriga. 2007. Results of a Two Year Fish Entrainment Study at 21 Morrow Island Distribution System in Suisun Marsh. Interagency Ecological Program 22 Newsletter 20(1):10-19. 23

Feyrer, F. 2004. Length-weight relationships and conversions for fresh and ethanol-preserved 24 Age-0 splittail. Interagency for Ecological Program 10-11. 25

Feyrer, F., J. Hobbs and T. Sommer. 2004. Salinity inhabited by age-0 splittail (Pogonichthys 26 macrolepidotus) as determined by direct field observation and retrospective analyses with 27 otolith chemistry. San Francisco Estuary and Watershed Science, 8(2). 28

Feyrer, F., T. R. Sommer, R. D. Baxter. 2005. Spatial-Temporal Distribution and Habitat 29 Associations of Age-0 Splittail in the Lower San Francisco Estuary Watershed. Copeia 30 2005: 159–168.Feyrer, F., T. Sommer, and W. Harrell. 2006. Managing floodplain 31



inundation for native fish: production dynamics of age-0 splittail (Pogonichthys 1 macrolepidotus) in California’s Yolo Bypass. Hydrobiologia 573:213-226. 2

Gingras M. 1997. Mark/recapture experiments at Clifton Court forebay to estimate pre-screening 3 loss to entrained juvenile fishes: 1976-1993. IEP Technical Report No. 55 . November 4 1997. 5

Grosholz, E. and E. Gallo. 2006. The influence of flood cycle and fish predation on invertebrate 6 production on a restored California floodplain. Hydrobiologia 568: 91-109 7

Harrell, W. C., T. R. Sommer and F. Feyrer. In review. Fish migration and residency in a large 8 river floodplain of the Sacramento River, California. Western North American Naturalist. 9

Larry Walker Assoicates. 2010. A Review of Delta Fish Population Losses from Pumping 10 Operations in the Sacramento-San Joaquin River Delta 11

Kimmerer, W., S. R. Avent, S. M. Bolent, F. Feyrer, L. Grimaldo, P. B. Moyle, M. Nobriga and 12 T. Visintainer. 2005. Variability in length-weight relationships used to estimate biomass 13 of estuarine fish from survey data. Transactions of the American Fisheries Society 14 134:481-495. 15

Kolodziej, E.P. and D.L. Sedlack. 2007. Rangeland grazing as a source of steroid hormones to 16 surface waters. Environ. Sci. Technol. 41(10): 3514-3520. 17

Kuivila, K.M. and G.E. Moon. 2004. Potential exposure of larval and juvenile delta smelt to 18 dissolved pesticides in the Sacramento-San Joaquin Delta, California. American Fisheries 19 Society Symposium 39: 229- 242 20

Kurth, R., and M. Nobriga. 2001. Food habits of larval splittail. Interagency Ecological Program 21 Newsletter 14(3): 40-42. 22

Moyle, P. B., R. D. Baxter, T. Sommer, T. C. Foin, and S. A. Matern. 2004. Biology and 23 population dynamics of the Sacramento splittail (Pogonichthys macrolepidotus) in the 24 San Francisco Estuary: a review. San Francisco Estuary and Watershed Science 2(2). 25

Moyle, P. B, P. K. Crain and K. Whitener. 2007. Patterns in the use of a restored California 26 Floodplain by Native and Alien Fishes. San Francisco Estuary and Watershed Science, 27 5(3).Oros ,D. R. and I. Werner. 2005. Pyrethroids White Paper. Interagency Ecological 28 Program, Sacramento, CA. 29

NMFS (National Marine Fisheries Service). 2009. Biological Opinion on the Long-Term Central 30 Valley Project and State Water Project Operations Criteria and Plan. 31

Oros ,D. R. and I. Werner. 2005. Pyrethroids White Paper. Interagency Ecological Program, 32 Sacramento, CA. 33



Purdom, C. E., P. A. Hardiman, V. J. Bye, N. C. Eno, C. R. Tyler, and J. P. Sumpter. 1984. 1 Estrogenic effects of effluents from sewage treatment works. Chem. Ecol. 8:275-285. 2

Rigby, M. C., X. Deng, T. M. Grieb, S. J. Teh, S. S. O. Hung. 2010. Effect Threshold for 3 Selenium Toxicity in Juvenile Splittail, Pogonichthys macrolepidotus A. Bulletin of 4 Environmental Contaminants Toxicology 84:76-79. 5

Routledge, E. J., J. Parker, J. Odum, J. Ashby, and J. P. Sumpter, 1998. Some alkyl hydroxy 6 benzoate preservatives (parabens) are estrogenic. Toxicology and Applied Pharmacology 7 153:12-19. 8

Sommer, T. R., R. D. Baxter, and F. Feyrer. 2007. Splittail “Delisting”: A Review of Recent 9 Population Trends and Restoration Activities. American Fisheries Society Symposium 10 53:25-38. 11

Sommer, T., R. Baxter, and B. Herbold. 1997. Resilience of splittail in the Sacramento-San 12 Joaquin Estuary. Transactions of the American Fisheries Society 126:961-976. 13

Sommer, T. R.; W. C. Harrell; Z. Matica; and F. Feyrer. 2008. Habitat associations and behavior 14 of adult and juvenile splittail (Cyprinidae: Pogonichthys macrolepidotus) in a managed 15 seasonal floodplain wetland. San Francisco Estuary and Watershed Science. Vol. 6, Issue 16 2 (June), Article 3. 17

Sommer, T. R., W. C. Harrell, A. Mueller-Solger, B. Tom and W. J. Kimmerer. 2004. Effects of 18 flow variation on channel and floodplain biota and habitats of the Sacramento River, 19 California, USA. Aquatic Conservation: Marine and Freshwater Ecosystems 14: 247-261. 20

Stewart, A.R., S.N. Luoma, C.E. Schlekat, M.A. Doblin, and K.A. Hieb. 2004. Food web 21 pathway determines how selenium affects aquatic ecosystems: A San Francisco Bay case 22 study. Environmental Science & Technology 38: 4519-4526. 23

Teh S. J., G. H. Zhang, T. Kimball, F. C. Teh. 2004. Lethal and sublethal effects of esfenvalerate 24 and diazinon on splittail larvae. American Fisheries Society Symposium 39: 243-253. 25

Teh, S. J., D. F. Deng, I. Werner, F.C. Teh, S. S. O. Hung. 2005. Sublethal toxicity of orchard 26 stormwater runoff contaminated with esfenvalerate and diazinon in Sacramento splittail 27 (Pogonichthys macrolepidotus) larvae. Marine Environmental Research 59:203-216. 28

USFWS (United States Fish & Wildlife Service). 1984. Revised recovery plan for three 29 endangered species endemic to Antioch Dunes, California. USFWS, Portland, OR. 30

USFWS (United States Fish & Wildlife Service). 2001. Antioch Dunes National Wildlife Refuge 31 Draft comprehensive conservation plan: plan and environmental assessment. USFWS, 32 Sacramento, CA. 33



USFWS (United States Fish & Wildlife Service). 2008. Lange's metalmark butterfly (Apodemia 1 mormo langei), Antioch Dunes evening-primrose, (Oenothera deltoides subsp. howellii), 2 Contra Costa wallflower (Erysimum capitatum var. angustatum) - Five-year review: 3 summary and evaluation. USFWS, Sacramento, CA. 4

Weston, D. P. and M. J. Lydy. 2010. Urban and agricultural sources of pyrethroid insecticides to 5 the Sacramento-San Joaquin Delta of California. Environmental Science and Technology. 6 DOI: 10.1021/es9035573. 7

Wood, M. L., C. G. Foe, J. Cooke and S. J. Louie. 2010. Sacramento-San Joaquin Delta Estuary 8 TMDL for Methymercury, Central Valley Regional Water Quality Control Board Staff 9 Report. April. 10

Young P. S., Cech J. J. Jr. 1996. Environmental tolerances and requirements of splittail. 11 Transactions of the American Fisheries Society 125:664-678. 12

Young P. S., Swanson C., Reid T, Cech J. J. Jr. 1999. Comparative swimming performance of 13 native (delta smelt and splittail) and introduced (inland silverside and wakasagi) Delta 14 fish. Interagency Ecological Program Newsletter 12(1):45-49. 15

CHAPTER 6. PLAN IMPLEMENTATION 16


CHAPTER 7. IMPLEMENTATION STRUCTURE 18


CHAPTER 8. IMPLEMENTATION COSTS AND FUNDING SOURCES 20

Betchart, William. 2008. Delta Levees – Types, Uses, and Policy Options, August 2008. 21

California Department of Water Resources. 2008. Delta Risk Management Strategy (DRMS) 22 Phase 1 Risk Analysis Report. December, 2008 23

CSFMRA 2009 Trends in Agricultural Land and Lease Values. California Chapter of the 24 American Society of Farm Managers and Rural Appraisers, 2009 25

CVRWQCB 2008 Amendments to the Water Quality Control Plan for the Sacramento River and 26 San Joaquin River Basins for the Control of Methylmercury and Total Mercury in the 27 Sacramento-San Joaquin Delta Estuary. Central Valley Regional Water Quality Control 28 Board, Draft Staff Report for Public Review. Sacramento 2008. 29



DBW 2006 Egeria Densa Control Program (EDCP): Second Addendum to 2001 Environmental 1 Impact Report with Five-Year Program Review and Future Operations Plan. Department 2 of Boating and Waterways, 2006 3

Delta Habitat Conservation and Conveyance Program. 2008. Technical Study #2: Evaluation of 4 North Delta Migration Corridors: Yolo Bypass. December 2008 5

Jones & Stokes. 2006. East Contra Costa County Habitat Conservation Plan and Natural 6 Community Conservation Plan. October (J&S 01478.01) San Jose, CA. 7

SAIC, Inc. 2010. Terrestrial Habitat Restoration Land Base Requirements. June 2010 8

Suddeth, Robyn, J. Mount, and J. Lund. 2010. “Levee Decisions and Sustainability for the 9 Sacramento-San Joaquin Delta.” San Francisco Estuary & Watershed Science, August 10 2010. 11

U.S. Army Corps of Engineers. 2009. Alternatives Report – 80,000 LF (107 Sites) Sacramento 12 River Bank Protection Project. U.S. Army Corps of Engineers, Sacramento District, April 13 2009 14

U.S. Army Corps of Engineers, Civil Works Construction Cost Index System. EM 1110-2-1304, 15 March 31, 2000. Tables Revised as of September 30, 2010 16

U.S. Department of Agriculture, National Agricultural Statistics Service, Land Values and Cash 17 Rents 2010 Summary, August 2010 18

U.S. Department of Labor, Bureau of Labor Statistics, Consumer Price Index Series 19 CUURA422SAO 20

U.S. Fish and Wildlife Service. 2007. Banking on Nature 2006: The Economic Benefits to Local 21 Communities of National Wildlife Refuge Visitation. September, Washington, DC 22

U.S. Office of Management and Budget, Circular No. A-94, Appendix C (Revised January 2008) 23

The Association for the Advancement of Cost Estimating (AACE International). Recommended 24 Practice No. 17R-97. 25

California Chapter of the American Society of Farm Managers and Rural Appraisers 26 (CSFMRA). 2009 California Trends in Agricultural Land and Lease Values. 27

California Department of Finance. 2009. FY 2008-09 salary scales for reference positions within 28 the California Department of Fish and Game (DFG). 29 www.dof.ca.gov/budget/historical/2008-09/salaries_and_wages/index.htm 30

http://www.dof.ca.gov/budget/historical/2008-09/salaries_and_wages/index.htm



Department of Boating and Waterways (DBW). 2006. Ergeria densa Control Program (EDCP): 1 Second Addendum to 2001 Environmental Impact Report with 5-year Program Review 2 and Future Operations Plan, December 8, 2006. 3

Department of Boating and Waterways (DBW). 2010. Vessel removal costs ( 2002-03 and 4 2003-04). www.dbw.ca.gov/PDF/Reports/AVAC_Report.pdf, page 10, accessed on 5 3/25/2010. 6

DHCCP-Engineering. 2010. Yolo Bypass Construction Cost Estimate, dated September 14, 7 2010. 8

Suddeth, Robyn, J. Mount, and J. Lund. 2010. Levee Decisions and Sustainability for the 9 Sacramento-San Joaquin Delta. San Francisco Estuary & Watershed Science. 10


Clarke, R.. Regional Program Coordinator, National Fish Passage Program, U.S. Fish and 12 Wildlife Service. 13

Davis, A. Letter correspondence with Allan Davis, Supervising Land Agent, Department of 14 Water Resources (DWR), January 29, 2010. 15

Gause, M. Resource Ecologist, Westervelt Ecological Services. Pers. Comm., June 28, 2010. 16

Holderman, M. Supervising Engineer, Bay –Delta Office, California DWR. Personal 17 Communication. 18

Kindopp, J. Feather River Program, California DWR. Personal Communication. 19

Lee, D. Consulting Fisheries Scientist. Personal Communication. 20

Lindberg, J. Co-Director, Fish Culture Laboratory, University of California, Davis. Personal 21 Communication. 22

McLaughlin, W. Senior Engineer, SDWSC Demonstration Dissolved Oxygen Project Bay-Delta 23 Office California DWR. Personal Communication. 24

McLaughlin, W. Senior Engineer, Stockton Deep Water Ship Channel Demonstration Dissolved 25 Oxygen Project Bay-Delta Office California Department of Water Resources. Personal 26 Communication 27

Naslund, B. Captain, Delta-Bay Enhanced Enforcement Program, California Department of Fish 28 and Game. Personal Communication 29



Naslund, B. Captain, Delta-Bay Enhanced Enforcement Program, DFG. Personal 1 Communication. 2

Powell, D. Contra Cost County Sheriff Department. Personal Communication. 3

Shaffer, K. Environmental Scientist, Native Anadromous Fish and Watershed Branch, 4 California Department Fish and Game. Personal Communication. 5

CHAPTER 9. ALTERNATIVES TO TAKE 6


CHAPTER 10. INTEGRATION OF INDEPENDENT SCIENCE IN BDCP DEVELOPMENT 8

Public Policy Institute of California 2007. Envisioning Futures for the Sacramento-San Joaquin 9 Delta 10

Public Policy Institute of California 2008. Comparing Futures for the Sacramento-San Joaquin 11 Delta 12

State Water Resources Control Board and California Environmental Protection Agency. 2010. 13 Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem. 14 Prepared Pursuant to the Sacramento-San Joaquin Delta Reform Act of 2009. 15

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