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.

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 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.

scholarly journals Crime Scene San Francisco: Who Is Responsible for the Disappearance of Delta Smelt?

2021 ◽  
Vol 9 ◽  
Author(s):  
Mallory E. Bedwell ◽  
Craig Stuart ◽  
Melinda R. Baerwald
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
Native Species ◽  
Crime Scene ◽  
San Francisco Estuary ◽  
Invasive Fish ◽  
Delta Smelt

Delta smelt are becoming harder and harder to find in the San Francisco Estuary. Some of the suspects in their disappearance are invasive fish species that were introduced from other places into the Estuary. These invasive fish can impact their new habitat by eating the native species that were originally there. However, it is hard to understand what the invasive fish are eating. We found that we can use the DNA in the stomachs of invasive fish to figure out what they have eaten. We caught a common invasive fish in the Estuary, called the Mississippi silverside, and analyzed the DNA from their stomachs to see if it matched delta smelt DNA. We discovered that some Mississippi silversides had delta smelt DNA in their stomachs! We therefore believe that Mississippi silversides are one of the culprits causing the disappearance of delta smelt.

scholarly journals Delivering Food to Hungry Fish in the San Francisco Estuary

2021 ◽  
Vol 9 ◽  
Author(s):  
Laura Twardochleb ◽  
Leela Dixit ◽  
Mallory Bedwell ◽  
Brittany Davis ◽  
Jared Frantzich
Keyword(s):  
Invasive Species ◽  
San Francisco ◽  
Fish Species ◽  
San Francisco Estuary ◽  
Fish Food ◽  
Yolo Bypass ◽  
Delta Smelt ◽  
Endangered Fish ◽  
The Past

The San Francisco Estuary is home to an important endangered fish called delta smelt. Delta smelt eat small, nutritious animals called zooplankton to survive and grow. In turn, zooplankton grow by eating microscopic plant-like organisms called phytoplankton. In the past, the Estuary was full of plankton and delta smelt. Because people have removed water from the Estuary and invasive species now live there, the Estuary no longer has enough plankton to feed delta smelt, making it difficult for them to survive. Scientists have found a unique place in the Estuary, the Yolo Bypass, that has lots of fish food. The problem is that delta smelt do not live in the Yolo Bypass year-round. Scientists are working to solve this problem by sending river or farm water through the Yolo Bypass, to move fish food downstream to feed the hungry delta smelt and other fish species.

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

2004 ◽  
Keyword(s):  
San Francisco ◽  
Striped Bass ◽  
Open Water ◽  
Minimum Length ◽  
Ontogenetic Changes ◽  
Delta Smelt ◽  
Diel Cycles ◽  
Dorosoma Petenense ◽  
Threadfin Shad ◽  
Inland Silverside

<em>Abstract.</em>—In July 2000 and 2001, we sampled adjacent screened and unscreened agricultural irrigation diversions in the Sacramento River, California to (1) evaluate the effectiveness of a custom fish screen for excluding four open-water fishes: native delta smelt <em>Hypomesus transpacificus </em>and alien threadfin shad <em>Dorosoma petenense</em>, inland silverside <em>Menidia beryllina</em>, and striped bass <em>Morone saxatilis</em>; and (2) examine factors affecting entrainment of each species. We also compiled trawl and beach seine data from contemporaneous monitoring programs to make inferences about microhabitat use by these fishes and its implications for entrainment vulnerability. The fish screen reduced entrainment of each species by 99% or more and excluded many fish less than 25 mm, the approximate minimum length it was designed to exclude. Tidal and diel influences on entrainment through the unscreened diversion were observed, but diel cycles appeared to be more important, as most entrainment occurred at night or during crepuscular periods. Except for delta smelt, our results suggested that open-water fishes may undergo ontogenetic changes in vulnerability to unscreened irrigation diversions. Fishes entrained during daylight (threadfin shad and striped bass) averaged only 15–16 mm in length. At night, average lengths of entrained threadfin shad and inland silverside were 22–25 mm, even though larvae continued to be entrained. Similarly, a diel influence on striped bass entrainment was observed only in 2000, when individuals larger than 20 mm were consistently collected. No striped bass were collected at sizes greater than 35 mm, even though larger individuals occupied the study area. We found no evidence of size-related changes in delta smelt vulnerability to entrainment, but the monitoring data indicated that delta smelt were abundant offshore, whereas the other three species were most abundant nearshore. We think that low and inconsistent entrainment of delta smelt reflected (1) predominantly offshore habitat use by delta smelt, and (2) the relatively small hydrodynamic influence of the diversion.

scholarly journals An Evaluation of Three Fish Surveys in the San Francisco Estuary, 1995–2015

2018 ◽  
Vol 16 (4) ◽  
Keyword(s):  
San Francisco ◽  
Secchi Depth ◽  
Specific Conductance ◽  
San Francisco Estuary ◽  
Fish Populations ◽  
Midwater Trawl ◽  
Important Region ◽  
Spatio Temporal ◽  
Species Specific

Resource managers rely on long-term monitoring surveys conducted in the San Francisco Estuary to evaluate the status and trends of resident fish populations in this important region. These surveys are potentially confounded because of the incomplete detection of individuals and species, the magnitude of which is often related to the same factors that affect fish populations. We used multistate occupancy estimators to evaluate the distribution, abundance, and detection probability of four fish species collected during 1995–2015 with three long-term surveys. Detection probabilities varied positively with fish abundance and negatively with Secchi depth. Detection varied among species and was greatest for the 20-mm Survey and least for the midwater trawl used for the midwater trawl used in the San Francisco Bay Study. Incomplete detection resulted in underestimates of occupancy and abundance across species and surveys and were greatest for the Bay Study. However, trends in occupancy and abundance of the study period appeared to be unbiased. Fish occupancy and abundance were generally related to salinity or specific conductance, day-of-the year, and water temperature, but the nature of the relations varied among surveys and species. There also was strong spatial and temporal dependence in species-specific occupancy and abundance that changed through time and were unrelated to the covariates considered. Our results suggest that managers consider incorporating methods for estimating detection and adjusting data to ensure data quality. Additionally, the strong spatio-temporal patterns in the monitoring data suggest that existing protocols may need to be modified to ensure that data and inferences reflect system-wide changes rather than changes at a specific set of non-randomly selected locations.

scholarly journals Examining Retention-at-Length of Pelagic Fishes Caught in the Fall Midwater Trawl Survey

2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Lara Mitchell ◽  
◽  
Randall Baxter ◽  
Keyword(s):  
Striped Bass ◽  
Fish Species ◽  
Body Shape ◽  
American Shad ◽  
Trawl Survey ◽  
Retention Data ◽  
Delta Smelt ◽  
Midwater Trawl ◽  
Selectivity Curve ◽  
Threadfin Shad

The Fall Midwater Trawl Survey has provided data on aquatic organisms in the San Francisco Estuary for over five decades. In 2014–2015, a study was conducted to investigate and quantify the efficiency of this trawl for catching the endangered fish species Delta Smelt (Hypomesus transpacificus). In an analysis based on that study, we calculated retention probability—the probability that a Delta Smelt is retained in the cod end of the trawl—as a function of fish length and fit a selectivity curve reflecting the relationship between size and retention. Here we return to the same gear efficiency study and further utilize the data set by (1) fitting selectivity curves for three additional pelagic fish species: Threadfin Shad (Dorosoma petenense), American Shad (Alosa sapidissima), and Mississippi Silverside (Menidia beryllina), (2) refitting the selectivity curve for Delta Smelt to incorporate between-haul variability, and (3) calculating the lengths of 50% and 95% retention in order to characterize and compare the resulting selectivity curves. We also present retention data on age-0 Striped Bass (Morone saxatilis), all of which were retained in the cod end. We found that Threadfin Shad, American Shad, and Delta Smelt are 95% retained at 45, 49, and 61 mm fork length, respectively. Because data were limited for Mississippi Silverside, American Shad, and age-0 Striped Bass, we used body shape, in conjunction with retention data, to develop hypotheses about selectivity based on whether each species’ body shape resembles that of Threadfin Shad, which are more deep-bodied and laterally compressed, or Delta Smelt, which are more fusiform. We also found that retention-at-length was more variable for Delta Smelt than for Threadfin Shad, potentially because length is a good predictor of retention in deep-bodied, laterally compressed fish whereas maximum girth is a better predictor of retention in fusiform fish.

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.

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