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.

Controls on the entrainment of juvenile Chinook salmon into large water diversions and estimates of population-level loss

The potential impact on Chinook salmon populations from entrainment of juveniles at the Central Valley Project and State Water Project export pumps has been estimated by examining the number of individuals salvaged at the export facilities in the south Delta. That use of available data has been codified into regulations controlling water-export operations in the 2019 Biological Opinion that addresses impacts from the operations. However, without knowing the number of salmon available to be salvaged, the population-level impact – the percent of the total salmon populations — cannot be determined. Furthermore, there is considerable uncertainty about the individual runs of salmon that appear at the facilities, only certain ones enjoy […]

The use of surrogates in implementation of the federal Endangered Species Act—proposed fixes to a proposed rule

In 2013 the US Fish and Wildlife Service and National Marine Fisheries Service proposed to amend existing regulations that implement the Endangered Species Act’s interagency consultation process by codifying their pre-existing practice of using surrogates to express the amount or extent of incidental take of listed species. The agencies contend that amendments both are necessary as a practical matter and are defensible on ecological grounds. They propose the use of surrogates, either in the form of a substitute species to fill in for a species that is challenging to observe, count, or otherwise measure, or a land-cover type or another habitat attribute, as a proxy for the amount or extent […]

A critical assessment of the use of surrogate species in conservation planning in the Sacramento-San Joaquin Delta, California (U.S.A.)

The use of surrogates in conservation planning is commonplace in California and elsewhere.  A substantial body of empirical literature has demonstrated the limited effectiveness of surrogates as management tools unless it is first established that the target species and surrogate will respond similarly to a given set of environmental conditions.  We explain that, while the National Marine Fisheries Service historically used hatchery Chinook salmon survival data as a surrogate for wild Chinook salmon, steelhead, and green sturgeon survival, it erred by doing so without first validating that the surrogate responds in the same manner to environmental conditions as the target species.  The consequence of use of surrogates absent validation is […]

Science and structured decision making: fulfilling the promise of adaptive management for imperiled species

Scientists and policy makers have popularized the concept of adaptive management for imperiled species, industriously building variations on multi-step adaptive-management cycles. Too many to count. Thirty years after the appearance of adaptive management in the scientific literature, the concept has gained acceptance as a readily recognized, conceptually simple conservation-planning vehicle, despite its lackluster track record. Herein we describe how adaptive management to be successful must be implemented as a stepwise, structured approach to incorporating scientific information into decision making. We contend that approach necessitates reconsideration of the overly simplified, cartoonish version of adaptive management being presented to policy makers, resource managers, and the public. Adaptive management that targets listed species […]

Longfin smelt: spatial dynamics and ontogeny in the San Francisco Estuary, California

The first step to understanding the ecological needs of a threatened or endangered species is to identify its geographic range and its temporal distribution within that range. Longfin smelt, listed under the California Endangered Species Act as threatened, is distributed throughout coastal and estuarine areas of the northern Pacific Ocean. The San Francisco Estuary is close to the southern end of its range. The distribution of the fish’s life stages is poorly known, in part because targeted searches for longfin smelt have been few and the species is not sampled well by trawl surveys that have been carried out in the Bay-Delta for decades; also because a large percentage of […]

Eastward migration or marshward dispersal: understanding seasonal movements by delta smelt

Sometimes, the result of the same people talking to the same people in the same institutions leads to commonly held conclusions that are not supported by available data and analyses. Such was the case with disinformation on dispersion of delta smelt prior to their spawning each year.  Numerous presentations at numerous conferences, as well as conceptual diagram repeated in agency documents, depicted delta smelt adults migrating eastward migration taking them from the center of their range into the central and south delta where the population would be vulnerable to entrainment at state and federal water-export facilities. That description of inter-seasonal movements of delta smelt stands in contrast to findings drawn from previous […]

Application of a life cycle simulation model to evaluate impacts of water management and conservation actions on an endangered population of Chinook salmon

Winter-run Chinook salmon complete their life cycle across a diversity of habitat types (or habitat strata), which complicates attempts to understand how specific environmental stressors impact the population as a whole. In this study we constructed a life-cycle model for Sacramento River winter-run Chinook to evaluate potential management actions and project operations on their population dynamics. The model incorporates multiple life-history stages, including spawning, egg incubation, fry rearing, smolt migration/Delta passage, and ocean rearing.  The investigation describes model functions and presents a sensitivity analysis to estimate fish-environmental factor relationships with strong effects on the winter-run Chinook population. Evaluation of potential management actions was demonstrated by perturbing flow, export volumes, and […]

Effects of predator and flow manipulation on Chinook salmon survival in an imperiled estuary

Previous studies indicate that both river flows and predation by non-native predatory fishes, such as largemouth bass, striped bass, and sunfish, can influence survival of out-migrating juvenile salmon in the Delta. This study was the first of its kind in the Delta to manipulate experimentally both predators and flows to assess responses in juvenile salmon survival and migration rate.  Chinook salmon with acoustic tags were released in study reaches before and after predator removal using electrofishing. Salmon survival improved significantly after the first predator removal, but survival rates returned to pre-removal levels one week later. Opening of the Delta Cross Channel (DCC) gates caused hydrodynamic conditions in the study area to […]

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