Population Dynamics of an Estuarine Forage Fish: Disaggregating Forces Driving Long-Term Decline of Longfin Smelt in California's San Francisco Estuary

2015 ◽  
Vol 145 (1) ◽  
pp. 44-58 ◽  
Author(s):  
Matthew L. Nobriga ◽  
Jonathan A. Rosenfield
Keyword(s):  
Population Dynamics ◽  
San Francisco ◽  
San Francisco Estuary ◽  
Forage Fish ◽  
Longfin Smelt

scholarly journals Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary

2020 ◽  
Vol 18 (3) ◽  
Author(s):  
Lenny Grimaldo ◽  
Jillian Burns ◽  
Robert E. Miller ◽  
Andrew Kalmbach ◽  
April Smith ◽  
...  
Keyword(s):  
Habitat Use ◽  
San Francisco ◽  
Fish Larvae ◽  
San Francisco Estuary ◽  
High Flow ◽  
Low Flow ◽  
Forage Fish ◽  
Pacific Herring ◽  
Freshwater Flow ◽  
Longfin Smelt

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the low-flow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions.

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 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.

Sampling Uncharted Waters: Examining Rearing Habitat of Larval Longfin Smelt (Spirinchus thaleichthys) in the Upper San Francisco Estuary

2017 ◽  
Vol 40 (6) ◽  
pp. 1771-1784 ◽  
Author(s):  
Lenny Grimaldo ◽  
Fred Feyrer ◽  
Jillian Burns ◽  
Donna Maniscalco
Keyword(s):  
San Francisco ◽  
San Francisco Estuary ◽  
Longfin Smelt

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.

Long-term Bioaccumulation Monitoring with Transplanted Bivalves in the San Francisco Estuary

1999 ◽  
Vol 38 (3) ◽  
pp. 170-181 ◽  
Author(s):  
Andrew J. Gunther ◽  
Jay A. Davis ◽  
Dane D. Hardin ◽  
Jordan Gold ◽  
David Bell ◽  
...  
Keyword(s):  
San Francisco ◽  
San Francisco Estuary
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