Abstract
Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multi-survey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are under-sampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies.
Highlights
The San Francisco Estuary is an anthropogenically altered, geographically complex estuary that drains a watershed of more than 194,000 square kilometers in northern California (Conomos et al 1985)
We combined the data from these surveys into one, open-access data set with associated water quality and catch data, which we call the “SFE Integrated Data Set” (SFE IDS)
Mississippi Silverside (Menidia audens) is the most frequently caught species in the three beach seine surveys, and nearly the most caught species in the Mossdale Kodiak Trawl (MKT); but it is mostly absent from the two Bay Study surveys, and only marginally represented in the Fall Midwater Trawl (FMWT), the Sacramento Midwater Trawl (SMWT), and the Chipps Island Midwater Trawl (CIMWT) (Table 2)
Summary
The San Francisco Estuary (estuary) is an anthropogenically altered, geographically complex estuary that drains a watershed of more than 194,000 square kilometers in northern California (Conomos et al 1985). Rapid human population growth and increasing demands for water resulted in overharvest of many fish species, invasions of nonnative species, and widespread habitat alteration (Nichols et al 1986; Cloern and Jassby 2012). These factors led in turn to the decline of some native and long-established non-native species, as well as some extinctions (Kohlhorst 1999; Moyle 2002, Sommer et al 2007). Methodologies remained largely consistent, and survey crews generally recorded all species captured, resulting in a long-term record of trends in fish abundance and diversity
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