Author: Center For California Water

Factors controlling calanoid copepod biomass and distribution in the upper San Francisco estuary and implications for managing the imperiled delta smelt

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 […]
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The low-salinity zone in the San Francisco Estuary as a proxy for delta smelt habitat: a case study in the misuse of surrogates in conservation planning

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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Independent scientific review under the Endangered Species Act

Peer review, more accurately described as independent scientific review, is an essential contributor to the federal wildlife agencies’ ability to meet the “best available science” standard required for determinations under the federal Endangered Species Act. Despite the high risk of extinction experienced by a number of native fishes in the upper San Francisco Estuary and the attending social and economic costs of implementing the Act’s prohibitions, neither federal nor state resource agencies employ independent outside expert review as frequently as would be prudent. Moreover, such reviews when engaged often fail to meet acceptable standards. We describe nine essential attributes of a rigorous independent scientific review that necessarily should be met […]
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Prey availability, environmental constraints, and aggregation dictate population distribution of an imperiled fish

The study took a spatiotemporal modeling approach in an effort to account for sampling and observation variation by employing both stochastic and deterministic elements. Smelt density was spatially and temporally autocorrelated, strongly tracking prey availability, while constrained by hydrological factors, salinity, turbidity, and velocity. Specifically, juvenile smelt preferred slightly saline, turbid, and slow‐moving water with ample copepod prey. Poor swimming capabilities reduced the capacity of juvenile delts smelt to mix throughout the estuary and disperse from areas with habitat of lesser quality to locate areas that offer better habitat conditions. Through-Delta outflow appeared to influence the spatial distribution of covariates and juvenile smelt, with delta smelt densities tending to peak […]
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Analysis of limiting factors across the life cycle of delta smelt

Identifying the environmental factors that are responsible for the decline in numbers of delta smelt is prerequisite to identifying management actions that can contribute to reversing the trend and recovering the species. A number of empirical models that consider multiple environmental factors and employ innovative multivariate-statistical approaches have attempted to identify the causes of the decline, but they have produced inconsistent and even contradictory results. That explanatory ambiguity has been unhelpful to resource managers responsible for protecting the delta smelt and its habitat in the degraded upper San Francisco Estuary, and has resulted in the implementation of ineffective and often costly management actions. In this paper we approach the problem […]
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Analysis of data on endangered species consultations reveals nothing regarding their economic impacts

Defenders of Wildlife personnel analyzed data gathered from the U.S. Fish and Wildlife Service and National Marines Fisheries Service from 2008 to 2015 regarding their consultations under section 7 of the Endangered Species Act (ESA). The authors reported that approximately 80 percent of formal consultations are completed within the time limit mandated by the ESA. They also reported that the number of instances where consultation led to a determination that a proposed action is likely to jeopardize one or more listed species or result in the destruction or adverse modification of designated critical habitat is extremely small. Based on those observations, the authors conclude that consultation does not hinder economic […]
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Best available science under the U.S. Endangered Species Act

Congress displayed great prescience when it directed the US Fish and Wildlife Service and National Marine Fisheries Service to use “the best available scientific and commercial data” to inform its determinations under the federal Endangered Species Act. But those agencies’ stubbornly default to surmise and assertion in many regulatory and decisions that rightfully should be informed by scientific information. We describe the role of the best science directive in the implementation of the Act and best practices that should be employed to realize Congress’s intent. We identify the types of data, analyses, and modeling efforts that can serve as best science in support of agency findings and policy documents. Finally, […]
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Long-term seasonal trends in the prey community of delta smelt within the Sacramento-San Joaquin Delta, California

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 […]
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Stormwater-related transport of the insecticides bifenthrin, fipronil, imidacloprid, and chlorpyrifos into a tidal wetland, San Francisco Bay, California

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 […]
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Predicting juvenile Chinook salmon routing in riverine and tidal channels of a freshwater estuary

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 […]
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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 […]
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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 […]
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