Publication

Integrating monitoring and optimization modeling to inform flow decisions for Chinook salmon smolts

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 […]
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An evaluation of the effectiveness of Fall Outflow Actions for delta smelt

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 […]
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Identifying environmental factors limiting recovery of an imperiled estuarine fish

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 […]
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An overview of the listing process under the California Endangered Species Act

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 […]
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Revisiting “small populations in jeopardy:” a rejoinder to Bork et al.

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 […]
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Use of affinity analysis to guide habitat restoration and enhancement for the imperiled delta smelt

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 […]
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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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