Dennis D. Murphy’s research while affiliated with CA State Water Resources Control Board and other places

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 population size increases, despite their ongoing long-term downward trajectory in numbers. The differences in environmental conditions that occur in years that prompt different population responses can provide insight into the environmental factors that limit species recovery. Nine temporally and spatially explicit covariates emerged from analyses that explain changes in inter-annual delta smelt abundance indices. We contrast those environmental factors with the factors that influence occupancy because distinguishing and focusing conservation actions on factors affecting delta smelt performance, rather than occupancy, should lead to the implementation of management and habitat-restoration actions that are more likely to benefit the fish. We think that the approach taken in this study can be a model for other species where salient data are limited and information needs are pressing.

The use of surrogates in conservation planning for at-risk species is both a necessary and a fraught practice. Here we assess the use of the position of the low-salinity zone in California's Sacramento-San Joaquin Delta as a surrogate for the extent and quality of habitat available to the imperiled delta smelt. The U.S. Fish and Wildlife Service issued a biological opinion and incidental take statement under the Endangered Species Act analyzing the impacts of ongoing operation of two large water infrastructure projects on the delta smelt. The Service's analysis and the conservation actions it imposed are based on the assumption that the low-salinity zone can serve as a "surrogate indicator" for delta smelt habitat. We demonstrate that available scientific information on the species countermands use of the low-salinity zone to represent delta smelt habitat in conservation planning for the species, and that the U.S. Fish and Wildlife Service erred by assuming the existence of a surrogate relationship absent validation using the best available scientific information. Notably, large expanses within the low-salinity zone are unoccupied by delta smelt and the species consistently occurs outside of it. This case serves to remind scientists of the dysfunction between a consensus in the scientific literature that calls for analytical validation prior to the use of species surrogates and habitat proxies, and the commonplace practice of using surrogates and proxies based on surmise and assertion.

The directive from Congress in the Endangered Species Act obliging the US Fish and Wildlife Service and National Marine Fisheries Service along with other federal agencies to use the best available scientific information in their determinations-and calls from stakeholder communities to show that they have done so-have led the federal wildlife agencies to seek external, expert review of their determinations with increasing frequency over time. In the present article, we survey the agency determinations that may be subject to independent science review and the technical tasks embedded in those determinations that can benefit from such review. We go on to identify common failures in scientific review that compromise the quality and reliability of agency determinations and then describe the attributes of independent scientific reviews that enable the agencies to discharge their statutory duties while seeking to conserve threatened and endangered species and the ecosystems on which they depend.

We developed a mechanistic life-cycle model derived from the elicitation of multiple factors influencing the success of individual life-stages of the imperiled delta smelt (Hypomesus transpacificus). We discuss the relevance of limiting factors in population ecology and problems with additive models in detecting them. We identify limiting factors and assess their significance using a non-linear optimization routine, combined with traditional metrics to assess the value of covariates and model performance. After reviewing previous conceptual models and multivariate analyses, we identified a set of factors that were consistent with conceptual models and useful in explaining the erratic fluctuations in a common abundance index: food at certain times in certain locations, predation by introduced species primarily in the spring, and entrainment. The analytical approach provides a transparent and intuitive framework in which to consider the contribution of covariates and consequences for population trends, and has the potential to assist with the evaluation of proposed recovery measures.

The Endangered Species Act's best available science mandate has been widely emulated and reflects a Congressional directive to ensure that decisions made under the Act are informed by reliable knowledge applied using a structured approach. We build on a standing literature by describing the role of the best science directive in the Act's implementation and best practices that can be employed to realize the directive. Next we describe recurring impediments to realizing determinations by the federal wildlife agencies that are based on the best available science. We then identify the types of data, analyses, and modeling efforts that can serve as best science. Finally, we consider the role and application of best available science in effects analysis and adaptive management. We contend that more rigorous adherence by the wildlife agencies to the best available science directive and more assiduous judicial oversight of agency determinations and actions is essential for effective implementation of the Act, particularly where it has substantial ramifications for listed species, stakeholder segments of society, or both.

AimTo evaluate three phylogeographical models associated with the presence of mountains (montane vicariance, sky island and parapatry) as drivers of intraspecific diversification in the sandhill skipper, Polites sabuleti (Lepidoptera: Hesperiidae), a morphologically variable species found in a variety of habitats from sea level to the alpine zone.LocationWestern North America.Methods The mitochondrial cytochrome c oxidase subunit II region was sequenced in 189 P. sabuleti individuals. Mitochondrial sequences were used in a spatial analysis of molecular variance (SAMOVA) to evaluate geographical population structure. AFLP markers were also generated for 347 individuals in order to estimate admixture proportions and examine population differentiation based on the nuclear genome.ResultsTwenty-five mitochondrial haplotypes and 42 anonymous AFLP loci were found across 36 collection localities. Mitochondrial variation suggests a degree of regional population structure, although at least one of the inferred population groups extends over nearly the entire geographical range of the species. Analyses of nuclear data (AFLPs) identified five genetic clusters, including one restricted to high elevations in the Sierra Nevada.Main conclusionsThe distribution of genetic variation within Polites sabuleti, a species with a broad elevational range, does not strictly support either mountain-associated vicariance or ‘sky island’ isolation as the dominant process. Instead, we find complex population structure, including evidence for divergence between high- and low-elevation populations in the Sierra Nevada mountains.

The US Fish and Wildlife Service and National Marine Fisheries Service recently 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 filling in for a species that is challenging to observe or measure, or a land-cover type or another habitat attribute, as proxies for the amount or extent of anticipated take. We contend that the proposed rule leaves the process of surrogate selection and application without essential implementation details and describe five essential steps in surrogate selection and validation. In sum, an obligatory validation procedure should clearly articulate the reasoning behind the selection of the surrogate, including describing the similarities in responses by the surrogate and target species to the same environmental phenomena, linking demographic responses to habitat extent and condition, and describing the uncertainties that accompany the relationship between the status and trends of the surrogate and those of the target species or its habitat under common circumstances.

Scientists and policy makers have shown great in-dustry in popularizing the concept of adaptive management for imperiled species, principally by promulgating slightly varying, multi-step adaptive-management cycles. 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. Successful adaptive management must be implemented as a step-wise, structured approach to incor-porating scientific information into decision making. This may necessitate reconsideration of the overly simplified, cartoonish version of adaptive management being presented to policy makers, resource managers, and the public. We contend that adaptive management that targets listed species represents a complex process that can be resource intensive, including in its demand for guidance from research, monitoring, and modeling, therefore requiring substantial technical and institutional capac-ity. That considered, adaptive management has a great potential to improve the effectiveness and efficacy of resource manage-ment actions provided it is properly implemented.