scholarly journals The value of long-term monitoring of the San Francisco Estuary for Delta Smelt and Longfin Smelt

2021 ◽  
pp. 148-171
Author(s):  
Trishelle L. Tempel ◽  
Timothy D. Malinich ◽  
Jillian Burns ◽  
Arthur Barros ◽  
Christina E. Burdi ◽  
...  
Keyword(s):  
San Francisco ◽  
San Francisco Estuary ◽  
Delta Smelt ◽  
Long Term Monitoring ◽  
Term Monitoring ◽  
Longfin Smelt

scholarly journals Comparing and Integrating Fish Surveys in the San Francisco Estuary: Why Diverse Long-Term Monitoring Programs are Important

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Dylan Stompe ◽  
Peter Moyle ◽  
Avery Kruger ◽  
John Durand
Keyword(s):  
Survey Data ◽  
San Francisco ◽  
Monitoring Program ◽  
San Francisco Estuary ◽  
Data Sets ◽  
Data Set ◽  
Monitoring Programs ◽  
Long Term Monitoring ◽  
Term Monitoring

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.

scholarly journals Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary

2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Brock Huntsman ◽  
◽  
Federick Feyrer ◽  
Matthew Young ◽  
◽  
...  
Keyword(s):  
San Francisco ◽  
Biological Data ◽  
San Francisco Estuary ◽  
Sampling Efficiency ◽  
Modeling Framework ◽  
Retention Efficiency ◽  
Handling Stress ◽  
Delta Smelt ◽  
Northern Anchovy

Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can be responsible for detecting or not detecting biological trends. The SmeltCam is an imaging apparatus developed as a potential sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, California, to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus). Although believed to be a reliable alternative to closed cod-end trawling surveys, no formal test of sampling efficiency has been implemented using the SmeltCam. We used a paired deployment of the SmeltCam and a conventional closed cod-end trawl within the Napa River and San Pablo Bay, a Bayesian binomial N-mixture model, and data simulations to determine the sampling efficiency of both deployed gear types to capture a Delta Smelt surrogate (Northern Anchovy, Engraulis mordax) and to test potential bias in our modeling framework. We found that retention efficiency—a component of detection efficiency that estimates the probability a fish is retained by the gear, conditional on gear contact—was slightly higher using the SmeltCam (mean = 0.58) than the conventional trawl (mean = 0.47, Probability SmeltCam retention efficiency > trawl retention efficiency = 94%). We also found turbidity did not affect the SmeltCam’s retention efficiency, although total fish density during an individual tow improved the trawl’s retention efficiency. Simulations also showed the binomial model was accurate when model assumptions were met. Collectively, our results suggest the SmeltCam to be a reliable alternative to sampling with conventional trawling gear, but future tests are needed to confirm whether the SmeltCam is as reliable when applied to taxa other than Northern Anchovy over a greater range of conditions.

Multidecadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, USA

2007 ◽  
Vol 64 (4) ◽  
pp. 723-734 ◽  
Author(s):  
Frederick Feyrer ◽  
Matthew L Nobriga ◽  
Ted R Sommer
Keyword(s):  
Water Quality ◽  
San Francisco ◽  
Striped Bass ◽  
Fish Species ◽  
Habitat Suitability ◽  
Specific Conductance ◽  
San Francisco Estuary ◽  
Delta Smelt ◽  
Threadfin Shad

We examined a 36-year record of concurrent midwater trawl and water quality sampling conducted during fall to evaluate habitat trends for three declining fish species in the San Francisco Estuary, California, USA: delta smelt (Hypomesus transpacificus), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). Generalized additive modeling revealed that Secchi depth and specific conductance were important predictors of occurrence for delta smelt and striped bass, while specific conductance and water temperature were important for threadfin shad. Habitat suitability derived from model predictions exhibited significant long-term declines for each species; the southeastern and western regions of the estuary exhibited the most dramatic changes. Declines in habitat suitability were associated with anthropogenic modifications to the ecosystem. For delta smelt, an imperiled annual species endemic to the estuary, the combined effects of fall stock abundance and water quality predicted recruit abundance during recent years of chronically low food supply. Our results are consistent with existing evidence of a long-term decline in carrying capacity for delta smelt and striped bass and demonstrate the utility of long-term data sets for evaluating relationships between fish and their habitat.

Early Life History of Fishes in the San Francisco Estuary and Watershed

2004 ◽  
Keyword(s):  
Life History ◽  
San Francisco ◽  
Striped Bass ◽  
Early Life ◽  
Early Life History ◽  
San Francisco Estuary ◽  
Delta Smelt ◽  
History Of ◽  
Acanthogobius Flavimanus ◽  
Longfin Smelt

<em>Abstract.</em>—We analyzed data on spring and summertime larval and juvenile fish distribution and abundance in the upper San Francisco Estuary (SFE), California between 1995 and 2001. The upper SFE includes the tidal freshwater areas of the Sacramento–San Joaquin Delta downstream to the euryhaline environment of San Pablo Bay. The sampling period included years with a variety of outflow conditions. Fifty taxa were collected using a larval tow net. Two common native species, delta smelt <em>Hypomesus transpacificus </em>and longfin smelt <em>Spirinchus thaleichthys</em>, and four common alien taxa, striped bass <em>Morone saxatilis</em>, threadfin shad <em>Dorosoma petenense</em>, gobies of the genus <em>Tridentiger</em>, and yellowfin goby <em>Acanthogobius flavimanus</em>, were selected for detailed analysis. Outflow conditions had a strong influence on the geographic distribution of most of the species, but distribution with respect to the 2 psu isohaline (X2) was not affected. The distribution patterns of delta smelt, longfin smelt, and striped bass were consistent with larvae moving from upstream freshwater spawning areas to downstream estuarine rearing areas. There were no obvious relationships of outflow with annual abundance indices. Our results support the idea of using X2 as an organizing principle in understanding the ecology of larval fishes in the upper SFE. Additional years of sampling will likely lead to additional insights into the early life history of upper SFE fishes.

scholarly journals Fewer and Farther between: Changes in the Timing of Longfin Smelt (Spirinchus thaleichthys) Movements in the San Francisco Estuary

2021 ◽  
Author(s):  
Vanessa Tobias ◽  
Randall Baxter
Keyword(s):  
San Francisco ◽  
Additive Model ◽  
San Francisco Estuary ◽  
Estuarine Fish ◽  
Data Set ◽  
Midwater Trawl ◽  
Recovery Planning ◽  
Monitoring Study ◽  
Longfin Smelt

Abundance of estuarine fish species has declined globally. In the San Francisco Estuary (SFE), long-term monitoring documented declines of many species including the anadromous species Longfin Smelt (Spirinchus thaleichthys). To improve management and recovery planning, we identified patterns in the timing, seasonal occupancy, and distribution of Longfin Smelt in a monitoring study (San Francisco Bay Study) for five regions of the SFE using a generalized additive model. We then investigated the year-to-year variability in the shape of the seasonal relationships using functional data analysis (FDA). FDA separated the variability due to population size from variability due to differences in occupancy timing. We found that Longfin Smelt have a consistent seasonal distribution pattern, that two trawl types were needed to accurately describe the pattern, and that the pattern is largely consistent with the hypothesized conceptual model. After accounting for variability in occupancy due to year-class strength, the timing of occupancy has shifted in three regions. The most variable period for the upstream regions Suisun Bay and Confluence was age-0 summer and for the downstream region Central Bay, was age-0 late fall. This manifested as a recent delay in the typical fall re-occupation of upstream regions, reducing Longfin Smelt abundance as calculated by another monitoring study (Fall Midwater Trawl); thus, a portion of recent reductions in Fall Midwater Trawl abundance of Longfin Smelt result from changes in behavior rather than a decline in abundance. The presence of multiple monitoring surveys allowed analysis of distribution from one data set to interpret patterns in abundance of another. Future investigations will examine environmental conditions as covariates during these periods and could improve our understanding of what conditions contribute to the shifting occupancy timing of Longfin Smelt, and possibly provide insight into the long-term quality of the San Francisco Estuary as habitat.

Future Needs for Long-Term Monitoring Design

2003 ◽  
Author(s):  
Barbara S. Minsker ◽  
Charles Davis ◽  
David Dougherty ◽  
Gus Williams
Keyword(s):  
Monitoring Design ◽  
Future Needs ◽  
Long Term Monitoring ◽  
Term Monitoring
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