scholarly journals Fish Misidentification and Potential Implications to Monitoring Within the San Francisco Estuary, California

2018 ◽  
Vol 9 (2) ◽  
pp. 467-485
Author(s):  
Joseph E. Kirsch ◽  
Julie L. Day ◽  
James T. Peterson ◽  
David K. Fullerton
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
False Positive ◽  
Juvenile Fish ◽  
Monitoring Program ◽  
San Francisco Estuary ◽  
Full Time ◽  
Monitoring Programs ◽  
Observer Experience ◽  
Fish Monitoring

Abstract Fish monitoring programs often rely on the collection, species identification, and counting of individual fish over time to inform natural resource management decisions. Thus, the utility of the data used to inform these decisions can be negatively affected by species misidentification. Fish species misidentification bias can be minimized by confirming identification using genetic techniques, training observers, or adjusting monitoring data using estimates of incomplete detection and false-positive misidentification. Despite the existence of well-established fish identification training and quality control programs, there is considerable uncertainty about fish species false-positive misidentification rates and the effectiveness of fish identification training programs within the San Francisco Estuary. We evaluated the misidentification of fish species among Delta Juvenile Fish Monitoring Program observers by conducting five fish identification exams under controlled conditions at the Lodi Fish and Wildlife Office in Lodi, California, between 2012 and 2014. To assess the variability in false-positive misidentification, we fitted data to species and observer characteristics using hierarchical logistic regression. We found that fish species misidentification was fairly common, averaging 17% among 155 test specimens and 32 observers. False-positive misidentification varied considerably among species and was negatively related to fish size, the abundance of the species within monitoring samples, and observer experience. In addition, observers who were not formally trained or used as full-time observers were, on average, 6.0 times more likely to falsely identify a species. However, false-positive misidentification rates among observers and specimens still varied considerably after controlling for observer experience and training, and species and size, respectively. Our results could be used to improve fish identification training and testing, increase the accuracy of fish occupancy or abundance estimation, and justify the allocation of resources to continually use and formally train full-time observers within long-term monitoring programs operating in the system.

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 Introduction of Bluefin Killifish (Lucania goodei) into the Sacramento–San Joaquin Delta

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Brian Mahardja ◽  
Andrew Goodman ◽  
Alisha Goodbla ◽  
Andrea Schreier ◽  
Catherine Johnston ◽  
...  
Keyword(s):  
San Francisco ◽  
Juvenile Fish ◽  
Ecological Impact ◽  
Monitoring Program ◽  
San Francisco Estuary ◽  
Native Fish ◽  
Close Relative ◽  
Proactive Management ◽  
Lucania Goodei ◽  
Bluefin Killifish

Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

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.

scholarly journals Evaluating the Role of Boat Electrofishing in Fish Monitoring of the Sacramento–San Joaquin Delta

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ryan McKenzie ◽  
Brian Mahardja
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
Life Stages ◽  
Detection Rates ◽  
Resource Managers ◽  
Fish Catch ◽  
Current Sampling ◽  
Fish Monitoring

The San Francisco Estuary is an incredibly diverse ecosystem with a mosaic of aquatic habitats inhabited by a number of economically, culturally, and ecologically important fish species. To monitor the temporal and spatial trends of this rich fish community, long-term fish monitoring programs within the estuary use a variety of gear types to capture fish species across life stages and habitats. However, concerns have been raised that current sampling gears may fail to detect certain species—or life stages—that inhabit areas that are not accessible by current gear types (e.g., riprap banks, shallow vegetated areas). Boat electrofishing is one sampling method that has been proposed to supplement current long-term fish monitoring in the upper estuary. In this study, we used fish catch data from past boat electrofishing studies, a long-term beach seine survey, and a couple of long-running trawl surveys to compare the relative probability of detecting various fishes across these sampling gears. Overall, we found that boat electrofishing led to notable improvements in the detection rates for many native and non-native fishes we examined. Boat electrofishing gear was better at detecting the majority of species in the spring (20 out of 38 species, 53%) and fall-winter (24 out of 34 species, 70%) sampling periods. Based on these findings, we recommend that resource managers consider the implementation of a long-term boat electrofishing survey to help them in their long-term conservation planning for fishes within the upper estuary.

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 Estuaries, A Happy Place For Fish

2021 ◽  
Vol 9 ◽  
Author(s):  
Pedro Morais ◽  
Ester Dias
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
San Francisco Estuary ◽  
Estuarine Species ◽  
Special Places

Anchovies, salmon, sardines, gobies, mullets, flounder, bass, barbels, eels, shad, and even sharks—what do they have in common? Well, at certain points in their lives you may find them in estuaries, the final sections of rivers before they meet the ocean. Some fish live in estuaries their entire lives. However, some fish species prefer living in the freshwater parts of estuaries, others only live close to the ocean, and a few others spread throughout the estuary. Some species prefer living close to the bottom, some in marshes, and some constantly swim around in the estuary. Some prefer eating other fish, while other species like worms, or insects, or microscopic animals. Unfortunately, many estuarine species are in danger, and all because of humans. In this article, we will tell you why estuaries are such special places for fish and describe some of the species that call the San Francisco Estuary their home.

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