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Delta Watch

Science Watch

On science and the Delta conservation challenge

The Sacramento-San Joaquin Delta has long been the subject of intensive study. Yet, not all of these studies have made for good science and resource managers have only sporadically incorporated findings from the best science into the design and implementation of management actions intended to protect and restore the ailing estuary.

We recognize that the more difficult challenges in the Delta share essential information needs, many of which remain largely unaddressed after a decade and a half of targeted efforts by multiple federal and state agencies. A recent treatment of the issue of best available science in implementation of the federal Endangered Species Act, supported by the Coalition, includes the following recommendations for the scientific information required to make defensible regulatory decisions, develop responsive species recovery plans, and design effective restoration efforts --

  • Be spatially explicit, presenting information in the form of maps that reflect geographic variation and site-specific environmental conditions
  • Test discrete hypotheses, that is, attempt some form of falsification exercise, that confront(s) proposed management actions with available data
  • Be clear on assumptions and uncertainties that affect the management decisions under consideration, clearly stating limitations of findings that can be drawn from the science that is available
  • Be set in an appropriate spatial context in order to address the ecological challenge subject to decision and management
  • Build on available ecological theory
  • Take advantage of all available pertinent information, including previous work, that both supports and does not support the best judgment of resource managers, and attempts to explain discrepancies
  • Consider all available information, and ranks or grades of that information, based on the reliability of its sources – published, unpublished, agency publications, etc.
  • Emerge from an explicit conceptual model of targeted species, their relationships with the environmental attributes of their habitats and targeted ecosystems, and the full range of stressors that affect them
  • Use analytical tools appropriate to the conservation challenge being confronted
  • Use a structured approach to an effects analysis (or risk assessment), particularly population viability analysis where appropriate, to exercise available data
  • Employ a rigorous specification of response and environmental variables in any analyses used to guide management or policy decisions

With an eye to these characteristics of “best available science,” we have identified a number of publications, studies, and presentations that exhibit at least several of the attributes of good and useful science, making their results and findings worthy information sources that can be applied in guiding the Delta’s ambitious conservation programs. 


On Delta ecosystems, including the low-salinity zone

On the Delta’s native fishes and other “pelagic” organisms

On salmon and steelhead and other species that migrate through the Delta

On science as a guide and helpmate to Delta resource managers and policy makers


On Delta ecosystems, including the low-salinity zone

Alpine AE, and Cloern JE. 1992. Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary. Limnology and Oceanography 37:946-955.

Brown LR. 2003. Will tidal wetland restoration enhance populations of native fishes? San Francisco Estuary and Watershed Science 1(1).

Carlton JT, Thompson JK, Schemel LE, and Nichols FH. 1990. Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis.  Marine Ecology Progress Series 66:81-94.

Jassby AD, Kimmerer WJ, Monismith SG, Armor C, Cloern CE, Powell M, and Vendlinski JR. 1995. Isohaline position as a habitat indicator for estuarine populations. Ecological Applications 5: 272-289.

Merz JE, Hamilton S, Bergman PS, and Cavallo B. 2011. Spatial perspective for delta smelt: a summary of contemporary survey data. California Department of Fish and Game Bulletin 97:164-189.

Monismith SG, Burau JR, and Stacey MT. 1996. Stratification dynamics and gravitational circulation in northern San Francisco Bay. In Hollibaugh JT, editor -- San Francisco Bay: The Ecosystem. American Association for the Advancement of Science.

Orsi JJ and Mecum WL. 1996. Food limitation as the probable cause of a long-term decline in the abundance of Neomysis mercedis the opossum shrimp in the Sacramento-San Joaquin estuary. In Hollibaugh JT, editor -- San Francisco Bay: The Ecosystem. 542 pp.

Parker AE, Dugdale RC, Wilkerson FP. 2012. Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary. Marine Pollution Bulletin 64:574-586

Parker AE, Hogue VE, Wilkerson FP, Dugdale RC. 2012. The effect of inorganic nitrogen speciation on primary production in the San Francisco estuary. Estuarine, Coastal, and Shelf Science.

Peterson HA and Vayssières M. 2010. Benthic assemblage variability in the upper San Francisco estuary: A 27-year retrospective. San Francisco Estuary and Watershed Science 8(1).

Schoellhamer DH. 2011. Sudden clearing of estuarine waters upon crossing the threshold from transport to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999. Estuaries and Coasts 34:885-899.

Wright-Walters M and Volz C. 2009. Municipal wastewater concentrations of pharmaceutical and xeno-estrogens: Wildlife and human health implications. In Proceedings of the National Conference on Environmental Science and Technology 3:103–113.


On the Delta’s native fishes and other “pelagic” organisms

Bennett WA. 2005. Critical assessment of the delta smelt population in the San Francisco estuary, California. San Francisco Estuary and Watershed Science 3(2).

Glibert PM, 2010. Long-term changes in nutrient loading and stoichiometry and their relationships with changes in the food web and dominant pelagic fish species in the San Francisco estuary, California. Reviews in Fishery Science 18:211-232.

Glibert PM, Fullerton D, Burkholder JM, Cornwell JC and Kana TM. 2011. Ecological stoichiometry, biogeochemical cycling, invasive species and aquatic food webs: San Francisco estuary and comparative systems. Reviews in Fishery Science19:358-417.

Hobbs JA, Lewis LS, Ikemiyagi N, Sommer T and Baxter R. 2010. Identifying critical nursery habitat for an estuarine fish with otolith strontium isotopes. Environmental Biology of Fishes 89:557-569.

Kimmerer WJ. 2004. Open water processes of the San Francisco estuary: From physical forcing to biological responses. San Francisco Estuary and Watershed Science 2(1).

Kimmerer W, Gross E and MacWilliams M. 2009. Is the response of estuarine nekton to freshwater flow in the San Francisco Estuary explained by variation in habitat volume? Estuaries and Coasts 32:375-389.

MacNally R, Thomson JR, Kimmerer WJ, Feyrer F, Kewman KB, Sih A, Bennett WA, Brown L, Fleischman E, Culberson SD, Castillo G.  2010.  Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR).  Ecological Applications 20:1417-1430.

Maunder MN, Deriso RB. 2011. A state-space multi-stage lifecycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt. Canadian Journal of Fisheries 68:1285-1306.

Miller WJ, Manly BFJ, Murphy DD, Fullerton D, and RR Ramey. 2012. An investigation of factors affecting the decline of delta smelt (Hypomesus transpacificus) in the Sacramento-San Joaquin Estuary. Reviews in Fisheries Science 20:1-19.

Spies RB, Rice Jr DW, and J Felton. 1988. Effects of organic contaminants on reproduction of the starry flounder Platichthys stellatus in San Francisco Bay. Marine Biology 98:181-189.

Thomson JR, Kimmerer WJ, Brown LR, Newman KB, MacNally R, Bennett WA, Feyrer F, and Fleishman E. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications 20:1431-1448.

Wang JCS. 1986. Fishes of the Sacramento-San Joaquin estuary and adjacent waters, California: A guide to the early life histories. Interagency Ecological Program, technical Report no. 9.

Young PS, Cech JJ. 1996. Environmental tolerances and requirements of splittail. Transactions of the American Fisheries Society 125:664-678.


On salmon and steelhead and other species that migrate through the Delta

Cummins, K.  2008. Listen to the River: An Independent Review of the CVPIA Fisheries Program.

Kimmerer WJ, Murphy DD and Angermeier PL. 2005. A landscape-level model for ecosystem restoration in the San Francisco Estuary and its watershed. San Francisco Estuary and Watershed Science 3:14-33.

Lindley, ST et al.  2007. Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin. San Francisco Estuary and Watershed Science 5(1).

Murphy DD, Weiland PS and Cummins KW. 2011. A critical assessment of the use of surrogate species in conservation planning in the Sacramento-San Joaquin California (U.S.A.). Conservation Biology 25:873-878.


On science as a guide and helpmate to Delta resource managers and policy makers

Bradshaw CJA, and BW Brook. 2010. The conservation biologist’s toolbox – prinvciples for the design and analysis of conservation studies. Pp. 313-339 in Sohdi and PR Ehrlich: Conservation biology for all. Oxford University Press.

Caro TJ, Eadie J, and Sih A. 2005. Use of substitute species in conservation biology. Conservation Biology 19:1821-1826.

DiGennaro, B. et al. 2012. Using conceptual models and decision-support tools to guide ecosystem restoration planning and adaptive management: an example from the Sacramento-San Joaquin Delta, California. San Francisco Estuary and Watershed Science 10(3).

Healy MC. 2008. The state of Bay-Delta science. CALFED Bay-Delta Program.

Kondolf, G.M., et al.  2008.  Prioritizing river restoration: projecting cumulative benefits of multiple projects.  Environmental Management 6:933-945.

Murphy, D.D. and P.A. Weiland. 2011.The route to best science in implementation of the Endangered Species Act’s consultation mandate: the benefits of structured effects analysis. Environmental Management 47:167-172.