Publications

Publications

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.

Species introductions can alter food webs, disrupt life cycles, change life history expressions and the temporal scale of population dynamics in zooplankton communities. We examined physical, trophic, and zooplankton community dynamics were examined in the San Francisco Estuary across a 43-year dataset (1972-2014). Following the introduction of the Asian clam (Potamocorbula amurensis) in 1986, we observed a shift in peak phytoplankton bloom timing, with peak productivity now occurring in May compared to June prior to the invasion. Peak abundance of several zooplankton taxa — Eurytemora affinis, Pseudodiaptomus, other calanoids, and non-copepods — also shifted their appearances to earlier in the year. The most striking shift in phenology occurred for Eurytemora, with mean timing […]
Contaminants are suspected as culprits influencing the abundance of many aquatic species in the Sacramento-San Joaquin Delta. Organophosphates, effective insecticides that come with health risks, have been largely replaced by pyrethroids, which are safer humans. But large storm events can wash pyrethroids into waterways raising concerns about aquatic contamination; in fact they have been found at toxic levels in estuary waters close to urban areas after storm events. Our study focused on areas of Suisun Marsh area downstream from the city of Fairfield. Routine monitoring after a storm found pyrethroids in concentrations high enough to be of concern in few locations. The study found that pyrethroids caused paralysis in test […]
Management hypotheses assert that water export operations in the south Delta create directional flows that pull migrating salmonids off their main migration routes at channel junctions and toward export facilities into areas where net flows are often negative and toward the export pumps where survival can be poor. This hypothesized effect has severed as justification for regulations restricting export operations during salmonid migration periods. To test for that effect on out-migrating salmon, we paired 41 acoustic telemetry-based estimates of juvenile Chinook Salmon routing at six Delta channel junctions with hydrologic conditions at those junctions when salmon were passing through. A linear model of routing as a function of the proportion […]
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 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 […]
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 […]
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 […]
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 […]