Publications & Reports

Publications & Reports

The Center supports research on issues of immediate importance to resource managers and policymakers who are challenged to manage the San Francisco Estuary’s natural resources. Obligated to provide a reliable supply of water to agriculture and urban users while protecting and recovering threatened and endangered species and restoring their degraded habitats, responsible state and federal resources agencies face misinformation and critical uncertainties about how at-risk fishes and their habitats are affected by environmental stressors. The Center recognizes Congress’ directive that determinations and decision under the federal Endangered Species Act should be informed by the best available scientific information. The Center’s investigative agenda is intended to provide that scientific information and offer procedural guidance to engage it in structured decision-making and adaptive resource management.

Monitoring is usually among the first actions taken to help inform recovery planning for declining species, but these data are rarely used formally to inform conservation decision making. For example, Central Valley Chinook salmon were once abundant, but anthropogenic activities have led to widespread habitat loss and degradation resulting in significant population declines. Monitoring data suggest survival through the southern Sacramento-San Joaquin River Delta, in particular, may be a limiting factor for juvenile Chinook salmon outmigrating from the San Joaquin River and its tributaries. However, survival and routing monitoring data have not been formally used to inform water management in a decision analytic framework. Here, we illustrate how estimates derived […]
A Fall X2 Action, intended to benefit delta smelt by increasing outflow through the Sacramento-San Joaquin Delta in years with greater precipitation in the watershed that feeds the Delta, wetter years, was included in the USFWS 2008 Biological Opinion as a “reasonable and prudent alternative.” The management action requires increases in outflow through the Delta during September and October of wet and above-normal years. A similar flow-enhancing management action, but with differing outflow targets, was included in the operations analyzed in the 2019 Biological Opinion. Those Fall X2 Actions have been controversial since first being implemented because of their uncertain conceptual foundations, their large water costs, and the difficulty in […]
Correctly identifying the environmental factors that limit population growth and recovery of imperiled species is an essential element of any targeted conservation program. Abundance index values for delta smelt (Hypomesus transpacificus), an imperiled fish in the upper San Francisco Estuary, have exhibited substantial inter-annual variation and the population is now at historically low numbers. Drawing from conceptual ecological models, we developed and applied a new multivariate analytical technique that incorporates a fundamental characteristic of limiting environmental factors– recognition that certain factors influence abundance in certain seasons or years, but they may have no influence on the species’ performance at other times. We observe that delta smelt occasionally experience years with […]
The California Endangered Species Act (CESA) is one of the most impor- tant legal tools available to the Fish and Game Commission and Department of Fish and Wildlife to protect the State’s wildlife resources. The listing process, together with the prohibitions in section 2080 of the Fish and Game Code, are the law’s regulatory teeth. At the same time, because any interested person can petition to list a species, the listing process invites citizen participation in the regulatory scheme. Listing decisions can be the difference between persistence and extinction of a species. They can also cause severe economic disruption and, for this reason, should in our view be made with […]
In a recent Comment in these pages, five researchers affiliated with the University of California, Davis critiqued a biological opinion issued by the U.S. Fish and Wildlife Service (FWS) under §7(a)(2) of the Endangered Species Act (ESA) that analyzes the effects of ongoing operations of the Central Valley Project (CVP) and State Water Project (SWP) on the Delta smelt. The subject is consequential because the Delta smelt’s historical habitat has been transformed and severely degraded since the California Gold Rush, leading to a significant decline in the size of its population; and because the CVP and SWP are far and away the two largest water supply projects in California, delivering […]
The habitat for any species results from a complex interplay of the environmental conditions that meet the resource needs of each of its life stages. In this paper, available data on water clarity, temperature, salinity, prey, and water body type are used to specify ranges of suitable conditions for delta smelt through its life cycle. The authors develop “affinity curves” that portray the adequacy of environmental conditions for each life stage. The curves are fundamentally important in guiding conservation management decisions for delta smelt. They depict, for example, when salinity is too low or too high for delta smelt to develop and how much food is sufficient to keep them feeding […]
The tiny crustaceans referred to as copepods comprise the prey, the main food source, for delta smelt. The lack of copepods in certain areas of the Delta and at certain times in much of the Delta is a primary factor limiting the abundance of delta smelt. It has been assumed that increased flows though the Delta should bring food into areas occupied by delta smelt; however the supply of food to the fish is determined by multiple factors, such as the number of copepods already in an area, availability of certain nutrients, water temperature and clarity, and copepod residence time, that is, how long copepods may stay in suitable ambient […]
The extent of the low-salinity zone has long been used as a measure of the health of the aquatic ecosystem in the upper San Francisco Estuary. Consistent with that concept, the US Fish and Wildlife Service in analyzing and responding to the impacts of ongoing water export operations on delta smelt has imposed conservation actions that assume that the low-salinity zone can serve as a “surrogate indicator” for the fish’s habitat. When freshwater is exported in autumns in years with greater freshwater input into the estuary, habitat for delta smelt is assumed to be reduced in extent and quality. But available scientific information countermands that finding. Notably large expanses of […]


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