C. Armor | USGS Science

USGS2007

The collapse of pelagic fishes in the upper San Francisco estuary

Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-hyphen;agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, and reduced food availability due to invasive species.

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USGS1995

Isohaline position as a habitat indicator for estuarine populations

Populations of native and introduced aquatic organisms in the San Francisco Bay/Sacramento-San Joaquin Delta Estuary ("Bay/Delta") have undergone significant declines over the past two decades. Decreased river inflow due to drought and increased freshwater diversion have contributed to the decline of at least some populations. Effective management of the estuary's biological resources requires a sensitive indicator of the response to freshwater inflow that has ecological significance, can be measured accurately and easily, and could be used as a "policy" variable to set standards for managing freshwater inflow. Positioning of the 2% (grams of salt per kilogram of seawater) bottom salinity value along the axis of the estuary was examined for this purpose. The 2% bottom salinity position (denoted by X 2 ) has simple and significant statistical relationships with annual measures of many estuarine resources, including the supply of phytoplankton and phytoplankton-derived detritus from local production and river loading; benthic macroinvertebrates (molluscs); mysids and shrimp; larval fish survival; and the abundance of planktivorous, piscivorous, and bottom-foraging fish. The actual mechanisms are understood for only a few of these populations. X 2 also satisfies other recognized requirements for a habitat indicator and probably can be measured with greater accuracy and precision than alternative habitat indicators such as net freshwater inflow into the estuary. The 2% value may not have special ecological significance for other estuaries (in the Bay/Delta, it marks the locations of an estuarine turbidity maximum and peaks in the abundance of several estuarine organisms), but the concept of using near-bottom isohaline position as a habitat indicator should be widely applicable. Although X 2 is a sensitive index of the estuarine community's response to net freshwater inflow, other hydraulic features of the estuary also determine population abundances and resource levels. In particular, diversion of water for export from or consumption within the estuary can have a direct effect on population abundance independent of its effect on X 2 . The need to consider diversion, in addition to X 2 , for managing certain estuarine resources is illustrated using striped bass survival as an example. The striped bass survival data were also used to illustrate a related important point: incorporating additional explanatory variables may decrease the prediction error for a population or process, but it can increase the uncertainty in parameter estimates and management strategies based on these estimates. Even in cases where the uncertainty is currently too large to guide management decisions, an uncertainty analysis can identify the most practical direction for future data acquisition.

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