135 results on '"Longfin smelt"'
Search Results
2. Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) North of the San Francisco Estuary
- Author
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Brennan, Colin A., Hassrick, Jason L., Kalmbach, Andrew, Cox, Daniel M., Sabal, Megan C., Zeno, Ramona L., Grimaldo, Lenny F., and Acuña, Shawn
- Subjects
Longfin Smelt ,osmerid ,northern California ,recruitment ,habitat ,estuary - Abstract
Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the SFE at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a metapopulation. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River and detected no Longfin Smelt in the Klamath and Mad Rivers, while in the dry winter of 2020, we detected larvae in two additional estuaries. Possibly elevated freshwater outflow in 2019 increased transport rates to sea, resulting in the observed low larval recruitment. Our results suggest that, while populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under sampled or are not permanently inhabited by Longfin Smelt. This suggests that the threatened SFE Longfin Smelt population may lack resiliency afforded by metapopulations and advocates for increased monitoring over a range of hydrologic conditions and improving detection probabilities for future assessments of gene flow between populations.
- Published
- 2022
3. Trends in fish and invertebrate populations of Suisun Marsh January 2020 - December 2020.
- Author
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O'Rear, Teejay Alexander, Montgomery, Jacob, Moyle, Peter B, and Durand, John R
- Subjects
Suisun Marsh ,Sacramento splittail ,striped bass ,longfin smelt - Published
- 2021
4. Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary
- Author
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Grimaldo, Lenny, Burns, Jillian, Miller, Robert E., Kalmbach, Andrew, Smith, April, Hassrick, Jason, and Brennan, Colin
- Subjects
estuarine ecosystem ,forage fish ,mysid shrimp ,Longfin Smelt ,Pacific Herring ,San Francisco Estuary ,larval fish - Abstract
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.
- Published
- 2020
5. Population Abundance and Diversion Losses in a Threatened Estuarine Pelagic Fish.
- Author
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Kimmerer, Wim and Gross, Edward
- Subjects
WATER diversion ,ESTUARINE fishes ,PELAGIC fishes ,FRESHWATER flow into estuaries ,NEGATIVE binomial distribution ,POPULATION dynamics - Abstract
Variation in freshwater flow into estuaries can profoundly alter abundance of estuarine organisms through a variety of mechanisms. In the San Francisco Estuary, California, an annual abundance index of juvenile longfin smelt Spirinchus thaleichthys has varied by ~ 100-fold over the range of flow, and over the last five decades the index has declined by over 100-fold. The unknown mechanisms for variation with flow may include removal of larvae by freshwater diversions during low-flow periods. Using data from larval trawl surveys during January–March 2009–2020, we estimated larval population size, its response to freshwater flow, and losses of larvae to freshwater diversions. Population size was estimated by a Bayesian hierarchical model linking a process model, with salinity and water clarity as covariates, to an observation model representing catch by a negative binomial distribution. Population size averaged across surveys within years—an index of the number of larvae produced—decreased over the study period from ~ 10
9 to 108 larvae. Population size was unrelated to freshwater flow in the year of hatching but positively related to the subsequent juvenile abundance index. Thus, the mechanisms underlying the strong variability in the annual abundance index of longfin smelt with freshwater flow are constrained to occur after March. Estimated proportional losses to water diversions accumulated over the period of vulnerability averaged 1.5% of the population, too low to measurably influence population dynamics. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
6. An Evaluation of Three Fish Surveys in the San Francisco Estuary, 1995–2015
- Author
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Peterson, James T. and Barajas, Miguel F.
- Subjects
incomplete capture ,multistate occupancy ,systematic bias ,trends ,Delta Smelt ,Longfin Smelt ,Striped Bass ,Sacramento Splittail - Abstract
https://doi.org/10.15447/sfews.2018v16iss4art2Resource 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.
- Published
- 2018
7. Space‐for‐time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay‐Delta
- Author
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Adam Duarte and James T. Peterson
- Subjects
Delta Smelt ,incomplete capture ,Longfin Smelt ,occupancy model ,space‐for‐time substitution ,species distribution model ,Ecology ,QH540-549.5 - Abstract
Abstract Occupancy models are often used to analyze long‐term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non‐detection data at a sample unit and many long‐term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e., space‐for‐time substitution). Still, the efficacy of fitting occupancy models using a space‐for‐time substitution has not been fully explored and is likely context dependent. Herein, we fit occupancy models to Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) catch data collected by two different monitoring programs that use the same sampling gear in the San Francisco Bay‐Delta, USA. We demonstrate how our inferences concerning the distribution of these species changes when using a space‐for‐time substitution. Specifically, we found the probability that a sample unit was occupied was much greater when using a space‐for‐time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent. Overall, our findings highlight the importance of considering how the unique characteristics of monitoring programs influences inferences, which has broad implications for how to appropriately leverage existing long‐term monitoring data to understand the distribution of species.
- Published
- 2021
- Full Text
- View/download PDF
8. Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary
- Author
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Michelle J. Jungbluth, Jillian Burns, Lenny Grimaldo, Anne Slaughter, Aspen Katla, and Wim Kimmerer
- Subjects
diet ,larval fish ,longfin smelt ,metabarcoding ,mtCOI ,Pacific herring ,Environmental sciences ,GE1-350 ,Microbial ecology ,QR100-130 - Abstract
Abstract Food limitation can dampen the survival and growth of fish species during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples, in comparison with results from abundance analyses of zooplankton samples. Overall, both fish consumed the prey that were commonly available and relatively abundant: Diets were dominated by arthropods but also included soft‐bodied and difficult to identify organisms. Prey taxa substantially overlapped between the two species (Schoener's index = 0.66), and alpha diversity analysis suggested high variability in the content of guts from different individuals. Abundant prey taxa in both fish species included the copepods Eurytemora carolleeae, Acanthocyclops americanus, and A. robustus; Acanthocyclops spp. are difficult to distinguish morphologically. Differential abundance analysis suggested that both species consumed the most abundant zooplankton in lower proportions than their availability in the environment. A few uncommon prey observed in the diets may hint at feeding strategies employed by the larvae, such as herring DNA in the longfin smelt diets, suggesting feeding on eggs near substrates or schooling behavior. Herring consumed the small (
- Published
- 2021
- Full Text
- View/download PDF
9. Incorporating expanded sampling into an alternative abundance index for the Fall Midwater Trawl survey
- Author
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James R. White and Randall D. Baxter
- Subjects
abundance index ,american shad ,california ,delta smelt ,fall midwater trawl ,longfin smelt ,striped bass ,threadfin shad ,Science - Abstract
The Fall Midwater Trawl (FMWT) Survey has been conducted near continuously since 1967 to assess the abundance and distribution of pelagic fish species throughout the San Francisco Bay/Sacramento-San Joaquin estuary (Bay Delta). For most of this period, sampling 100 core stations provided data for abundance and distribution analyses. Another 22 (non-core) stations were added to the FMWT 8 to 28 years ago to supplement the original 100 (core) stations. However, relative abundance indices are published annually from only the data collected at the core stations. Here we incorporate data from non-core stations along with core station data to calculate an alternative index that also integrates modern estimates of water volume within the Bay Delta into an index calculation. The use of data from non-core stations in calculating the alternative index was particularly useful for American Shad (Alosa sapidissima) and Threadfin Shad (Dorosoma petenense). Consistently high catches at non-core stations for a couple species and modest catches for a couple additional species highlight the value of these additional catch data for our understanding of how fishes are distributed in the estuary.
- Published
- 2022
- Full Text
- View/download PDF
10. Spatial Heterogeneity in Prey Availability, Feeding Success, and Dietary Selectivity for the Threatened Longfin Smelt.
- Author
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Barros, Arthur, Hobbs, James A., Willmes, Malte, Parker, Christina M., Bisson, Micah, Fangue, Nann A., Rypel, Andrew L., and Lewis, Levi S.
- Subjects
PREY availability ,FISH larvae ,SALT marshes ,SMELL ,HETEROGENEITY ,SPATIAL variation - Abstract
Food availability is a key determinant of the nursery value of a given habitat for larval and juvenile fishes. Growth, survival, and recruitment success are often inter-correlated and influenced by prey availability and associated feeding success. This is likely true for the threatened population of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary (SFE) which has collapsed in recent decades along with its preferred prey. In years with high precipitation and freshwater outflow, larval Longfin Smelt are found in shallow wetland habitats throughout the SFE, but variation in the availability of food and feeding success in these habitats remains unexplored. To examine spatial variation in the trophic value of different rearing habitats, we quantified variation in prey availability, feeding success, and prey selection for larval and juvenile Longfin Smelt captured in restored tidal marshes, sloughs, and open-water habitats in the northern and southern SFE. Prey abundance varied spatially, with densities approximately tenfold greater in southern sloughs and restored tidal ponds relative to northern and open-water habitats. Feeding success of larval Longfin Smelt was positively correlated with both fish length and prey density. Larval Longfin Smelt fed selectively on the copepod Eurytemora affinis, with larger individuals (> 25 mm total length) exhibiting an ontogenetic diet shift to larger mysid shrimps. Our results suggest that wetland habitats across the SFE vary greatly in their trophic value, with previously unexplored habitats exhibiting the highest densities of prey and the highest foraging success for larval Longfin Smelt. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
11. Assessing the distribution and abundance of larval Longfin Smelt: What can a larval monitoring program tell us about the distribution of a rare species?
- Author
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Michael Eakin
- Subjects
california endangered species act ,larval fish ,longfin smelt ,san francisco estuary ,smelt larva survey ,Science - Abstract
Following its listing as threatened under the California Endangered Species Act in 2009, Longfin Smelt (Spirinchus thaleichthys) became a focus of resource managers in the San Francisco Estuary. Water exports were identified as one of the factors affecting Longfin Smelt abundance, and managers were challenged with balancing freshwater flows through the Sacramento-San Joaquin River Delta between human and ecosystem needs. This balance becomes especially challenging during the winter and spring when Longfin Smelt are spawning. Resource managers identified that the impact associated with entrainment of larval Longfin Smelt in the winter was uncertain, and to understand and manage this risk, new data was needed. In 2009 the Smelt Larva Survey was implemented and has since sampled newly hatched larvae from January–March. Here, I analyze this data and ask specific questions regarding distribution and densities of the larvae throughout five regions of the Upper Estuary – Napa River, Suisun, Confluence, Northern Delta, and Southern Delta – with the goal of understanding the spatial and temporal patterns of larval distribution since 2009. I found that larvae were most prevalent in the Suisun, Confluence, and Northern Delta regions, and less common in the Southern Delta and Napa River regions. Larval Longfin Smelt densities changed following a recent drought and record low population abundances. Median per-station averaged densities ranged from 154 to 274 fish per 1,000 m3 between 2009 and 2013 but declined to 1 to 65 fish per 1,000 m3 from 2014 to 2019. This survey data demonstrates that Longfin Smelt reproductive output has declined since their listing in 2009 and that their distribution into the Southern Delta is low relative to the rest of the Upper Estuary. These results reaffirm the species’ continued decline since its listing, and that improving the abundance of spawning adults is one of the many important steps needed for long-term recovery and resilience.
- Published
- 2021
- Full Text
- View/download PDF
12. The value of long-term monitoring of the San Francisco Estuary for Delta Smelt and Longfin Smelt
- Author
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Trishelle L. Tempel, Timothy D. Malinich, Jillian Burns, Arthur Barros, Christina E. Burdi, and James A. Hobbs
- Subjects
california endangered species act ,delta smelt ,endangered species act ,hypomesus transpacificus ,longfin smelt ,long term monitoring ,sacramento-san joaquin delta ,san francisco estuary ,spirinchus thaleichthys ,Science - Published
- 2021
- Full Text
- View/download PDF
13. Turbidity and temperature effects on growth and gene transcription of threatened juvenile Longfin Smelt (Spirinchus thaleichthys).
- Author
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Biefel, Felix, Pasparakis, Christina, Cocherell, Dennis E., Hung, Tien-Chieh, Carson, Evan W., Fangue, Nann A., Geist, Juergen P., Todgham, Anne E., and Connon, Richard E.
- Subjects
- *
CITRATE synthase , *THERMAL stresses , *GENE expression , *GENETIC transcription , *TEMPERATURE effect - Abstract
The Longfin Smelt (LFS, Spirinchus thaleichthys) population within the San Francisco Estuary, California, has experienced a substantial reduction, diminishing to <1% of their historical abundance. This decline has culminated in their classification as a threatened species under the purview of the California Endangered Species Act. Understanding their physiology and stress response in relation to varying environmental conditions, such as temperature and turbidity, is crucial for LFS culturing, management, and conservation. In this study, we assessed juvenile LFS (age range during exposure: 181 to 228 days post hatch, dph) performance as measured by growth and gene expression following four weeks at two temperatures (11 °C and 14 °C) and three turbidity levels (1, 4, and 11 nephelometric turbidity units (NTU)). At the end of the 4-week exposure period, we conducted assessments encompassing fork length, wet weight, condition factor, and examined alterations in the transcription of 12 genes. The selection of these genes aimed at determining responses associated with osmoregulation, growth, metabolism, and general stress, as all of which are potentially influenced by temperature and/or turbidity. Weight and condition factor was significantly higher at lower temperature, whereas turbidity had no effect on growth, condition factor, and transcriptomic stress-response. Instead, the lower expression levels of Catalase , Citrate Synthase and Growth Factor Receptor Bound Protein 10 at 14 °C were indicative of metabolic and growth-related changes governed by temperature. This suggests that rearing of LFS at 11 °C and low turbidity (<11 NTU) is suitable for the juvenile stage, whereas growth as well as metabolic capacity is limited at slightly warmer temperatures. • Juvenile Longfin Smelt exhibited increased growth at 11 °C compared to 14 °C. • Turbidity levels of up to 11 NTU demonstrated no discernible impact juvenile Longfin Smelt. • Rearing of juvenile Longfin Smelt at 11 °C and at low turbidity (<11NTU) is adequate for captive culture. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
14. Determining thermal tolerances of longfin smelt and inland silverside and develop biomarkers of thermal stress using new genomics technology
- Author
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Jeffries, Ken
- Subjects
thermal tolerance ,longfin smelt ,inland silverside ,delta smelt ,thermal stress ,habitat - Published
- 2017
15. Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary
- Author
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Zair P. Lojkovic Burris, Randall D. Baxter, and Christina E. Burdi
- Subjects
diet ,fullness ,longfin smelt ,san francisco estuary ,selectivity ,zooplankton ,Science - Abstract
The density and quality of zooplankton prey affect the feeding success of larval and juvenile fishes and thus can drive growth, survival, and recruitment. As part of a larger effort investigating potential causes of a pelagic fish decline, we examined regional feeding success (food presence/absence, stomach fullness), diet composition and prey selection of young Longfin Smelt (Spirinchus thaleichthys) in spring and summer as a function of fish size and prey availability in the San Francisco Estuary. We conducted our sampling during two wet and two dry years, because weather and river flow influence prey community composition and location. Larval and juvenile fish showed evidence of food limitation: high proportions of empty stomachs (≤ 70%) and stomach contents totaling
- Published
- 2022
- Full Text
- View/download PDF
16. Suisun Marsh Fish Study trends in fish and invertebrate populations of Suisun Marsh January 2013 - December 2013.
- Author
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O'Rear, Teejay Alexander and Moyle, Peter B
- Subjects
Suisun Marsh ,longfin smelt ,Mississippi silverside ,Menidia audens - Published
- 2015
17. Effects of high temperatures on threatened estuarine fishes during periods of extreme drought
- Author
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Jeffries, Ken M, Connon, Richard E, Davis, Brittany E, Komoroske, Lisa M, Britton, Monica T, Sommer, Ted, Todgham, Anne E, and Fangue, Nann A
- Subjects
Life on Land ,Animals ,California ,Droughts ,Endangered Species ,Environment ,Estuaries ,Gene Expression Profiling ,Gene Ontology ,Osmeriformes ,Oxygen Consumption ,RNA ,Messenger ,Temperature ,Longfin smelt ,Spirinchus thaleichthys ,Delta smelt ,Hypomesus transpacificus ,Transcriptomics ,Endangered fishes ,Biological Sciences ,Medical and Health Sciences ,Physiology - Abstract
Climate change and associated increases in water temperatures may impact physiological performance in ectotherms and exacerbate endangered species declines. We used an integrative approach to assess the impact of elevated water temperature on two fishes of immediate conservation concern in a large estuary system, the threatened longfin smelt (Spirinchus thaleichthys) and endangered delta smelt (Hypomesus transpacificus). Abundances have reached record lows in California, USA, and these populations are at imminent risk of extirpation. California is currently impacted by a severe drought, resulting in high water temperatures, conditions that will become more common as a result of climate change. We exposed fish to environmentally relevant temperatures (14°C and 20°C) and used RNA sequencing to examine the transcriptome-wide responses to elevated water temperature in both species. Consistent with having a lower temperature tolerance, longfin smelt exhibited a pronounced cellular stress response, with an upregulation of heat shock proteins, after exposure to 20°C that was not observed in delta smelt. We detected an increase in metabolic rate in delta smelt at 20°C and increased expression of genes involved in metabolic processes and protein synthesis, patterns not observed in longfin smelt. Through examination of responses across multiple levels of biological organization, and by linking these responses to habitat distributions in the wild, we demonstrate that longfin smelt may be more susceptible than delta smelt to increases in temperatures, and they have little room to tolerate future warming in California. Understanding the species-specific physiological responses of sensitive species to environmental stressors is crucial for conservation efforts and managing aquatic systems globally.
- Published
- 2016
18. Predation on Fishes in the Sacramento–San Joaquin Delta: Current Knowledge and Future Directions
- Author
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Grossman, Gary D.
- Subjects
Delta Smelt ,Longfin Smelt ,Chinook Salmon ,Rainbow Trout ,Striped Bass ,Largemouth Bass ,Pikeminnow ,predator–prey interactions - Abstract
The Sacramento–San Joaquin Delta (Delta) is a heterogeneous, highly modified aquatic system. I reviewed relevant predator–prey theory, and described extant data on predator–prey relationships of Delta fishes. I ranked predator consumption rates as occasional, moderate, and common, based on frequency-of-occurrence data, and evaluated the frequency, and hypothesized the effects of predation on native and invasive species. I identified 32 different predator categories and 41 different prey categories. Most predators were occasional consumers of individual prey species, although I also observed moderate and common consumption of some prey types. My analysis yielded few generalizations regarding predator–prey interactions for Delta fishes; most predators consumed a variety of both native and invasive fishes. The only evidence for predator specialization on either native or invasive fishes occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. Both Striped and Largemouth Bass exhibited wide dietary breadth, preying upon 32 and 28 categories of fish prey respectively. Sacramento Pikeminnow, a native predator, also displayed wide dietary breadth of piscine prey, with 14 different prey categories consumed. Data for reptilian, avian, and mammalian predators were sparse; however, these predators may be significant fish predators in altered habitats or when hatchery salmonids are released. The database for predators and their fish prey was not strong, and I recommend long-term dietary studies combined with prey availability and behavioral and experimental studies to establish predator preferences and anti-predator behaviors, rather than just consumption. The behavioral effects of contaminants on prey species also warrant further examination. Although it has been suggested that a reduction in the Striped Bass population be implemented to reduce predation mortality of Chinook Salmon, the large number of salmon predators in the Delta make it unlikely that this effort will significantly affect salmon mortality.
- Published
- 2016
19. Space‐for‐time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay‐Delta.
- Author
-
Duarte, Adam and Peterson, James T.
- Subjects
- *
GEOGRAPHICAL distribution of fishes , *SPECIES distribution , *DATA distribution , *PELAGIC fishes , *SYSTEM dynamics - Abstract
Occupancy models are often used to analyze long‐term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non‐detection data at a sample unit and many long‐term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e., space‐for‐time substitution). Still, the efficacy of fitting occupancy models using a space‐for‐time substitution has not been fully explored and is likely context dependent. Herein, we fit occupancy models to Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) catch data collected by two different monitoring programs that use the same sampling gear in the San Francisco Bay‐Delta, USA. We demonstrate how our inferences concerning the distribution of these species changes when using a space‐for‐time substitution. Specifically, we found the probability that a sample unit was occupied was much greater when using a space‐for‐time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent. Overall, our findings highlight the importance of considering how the unique characteristics of monitoring programs influences inferences, which has broad implications for how to appropriately leverage existing long‐term monitoring data to understand the distribution of species. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
20. San Francisco Estuary mysid abundance in the fall, and the potential for competitive advantage of Hyperacanthomysis longirostris over Neomysis mercedis
- Author
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Michelle Avila and Rosemary Hartman
- Subjects
crustaceans ,delta smelt ,fish diets ,invasive species ,longfin smelt ,mysidacea ,sacramento ,san joaquin delta ,striped bass ,temperature tolerance ,zooplankton ,Science - Abstract
Historically, the native mysid Neomysis mercedis was a key source of food for fish in the San Francisco Estuary (SFE). Following the introductions of the over-bite clam and many invasive zooplankton species in the mid-1980s, populations of native zooplankton species plummeted, including N. mercedis. In July 1993, Hyperacanthomysis longirostris, an invasive mysid, was first documented in the SFE, and it quickly became the most abundant mysid in the upper estuary. Since 2011, the California Department of Fish and Wildlife has sampled mysid abundance throughout the upper SFE concurrently with their Fall Midwater Trawl, which targets juvenile Striped Bass. We analyzed data from these mysid trawls to investigate environmental correlates of N. mercedis and H. longirostris abundance. We found that H. longirostris was found at higher temperatures significantly more often than N. mercedis, and there was a trend towards greater frequency of H. longirostris at higher salinities. Increases in water temperature over time, coupled with H. longirostris’s smaller size at maturity and lower food needs may partially explain its success in the SFE.
- Published
- 2020
- Full Text
- View/download PDF
21. Understanding the Extent of Hyperactivity and Related Behavioral Alterations in Delta Smelt and Longfin Smelt
- Author
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Patullo, Caitlyn Elaine
- Subjects
Toxicology ,Aquatic sciences ,Conservation biology ,behavioral toxicology ,Delta smelt ,endangered species ,hyperactivity ,Longfin smelt ,pentylenetetrazole - Abstract
Agricultural and urban contaminants enter aquatic environments at concentrations that can affect a variety of sublethal endpoints, including organismal behavior, which can in turn lead to impacts at the population level. The San Francisco Bay Delta (SFBD) is home to multiple threatened aquatic species, such as Delta smelt (Hypomesus transpacificus) and Longfin smelt (Spirinchus thaleichthys), with contaminant exposure likely playing a role in widespread population declines. Pesticides induce hyperactive or hypoactive states in these species, though little is known of the extent of hyperactivity that could be elicited by exposure to neurotoxic compounds. My study used pentylenetetrazole (PTZ), a γ-aminobutyrate (GABA) receptor antagonist, to explore hyperactive behavior in Delta smelt and Longfin smelt. I evaluated induced and spontaneous movement in light and dark conditions following exposure to increasing concentrations of PTZ. Delta smelt and Longfin smelt exposed to PTZ experienced changes in behaviors reflective of induced hyperactivity, including distance moved and swimming velocity, as well as spontaneous hyperactivity, such as time and frequency spent freezing, bursting, or entering the center of the arena (anti-thigmotaxis). The maximum hyperactivity for Delta smelt larvae was recorded following exposure to 8mM PTZ and for Longfin smelt larvae to 4mM PTZ. Together, this information not only confirms that PTZ could be used as a positive control in future behavioral toxicology studies for hyperactivity, but also provides for a better understanding of hyperactive behavior in these species of ecological concern.
- Published
- 2022
22. Salinity Tolerances and Biomarkers of Salt Stress in Longfin and Delta Smelt
- Author
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Kammerer, Brittany
- Subjects
salinity tolerance ,longfin smelt ,delta smelt ,Delta Science Fellow ,San Francisco Bay ,estuary ,salinity - Published
- 2014
23. Characterization and evaluation of polymorphic microsatellite markers in the anadromous fish Spirinchus thaleichthys
- Author
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Israel, Joshua A. and May, Bernie
- Subjects
Life Sciences ,Evolutionary Biology ,Animal Anatomy / Morphology / Histology ,Plant Sciences ,Conservation Biology/Ecology ,Longfin smelt ,Conservation ,Propagation ,Pelagic Organism decline - Abstract
We describe seventeen microsatellite loci isolated from longfin smelt, Spirinchus thaleichthys, which is an anadromous fish inhabiting estuarine and nearshore marine waters along the western Pacific coast. Five to 16 alleles per locus were detected, the expected heterozygosity ranged from 0.33–0.93, and moderate levels of differentiation were found between collections. These polymorphic microsatellites will provide useful tools for studying population genetic structure at ecological scales within wild and propagated populations.
- Published
- 2010
24. The use of otolith strontium isotopes (87Sr/86Sr) to identify nursery habitat for a threatened estuarine fish
- Author
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Hobbs, James A., Lewis, Levi S., Ikemiyagi, Naoaki, Sommer, Ted, and Baxter, Randall D.
- Subjects
Life Sciences ,Nature Conservation ,Environment, general ,Animal Systematics/Taxonomy/Biogeography ,Zoology ,Freshwater & Marine Ecology ,Otolith ,Strontium isotopes ,Nursery habitat ,Longfin Smelt ,POD - Abstract
Nursery habitats are larval or juvenile habitats that disproportionately contribute individuals to adult populations of a species. Identifying and protecting such habitats is important to species conservation, yet evaluating the relative contributions of different larval habitats to adult fish populations has proven difficult at best. Otolith geochemistry is one available tool for reconstructing previous habitat use of adult fishes during the early life history, thus facilitating the identification of nursery habitats. In this study, we compared traditional catch surveys of larval-stage longfin smelt (Spirinchus thaleichthys) occurring in habitats of different salinities to corresponding larval-stage salinity distributions of sub-adult/adult longfin smelt estimated using otolith geochemical techniques. This allowed us to evaluate the relative contribution of larvae from waters of various salinities to sub-adult/adult populations of longfin smelt. We used laser ablation MC-ICP-MS on otoliths and an empirically-derived relationship between strontium isotope ratios (87Sr/86Sr) of waters across the estuarine salinity gradient to reconstruct the larval salinity history of longfin smelt. Salinity values from the larval region of sub-adult/adult otoliths (corresponding to standard lengths of ca.10-mm) were compared to corresponding catch distribution of larval longfin smelt (≤ 10-mm) from 4 year-classes (1999, 2000, 2003 and 2006) in the San Francisco Estuary spanning a period when the population underwent a dramatic decline. Though the catch distribution of larval-stage longfin smelt was centered around 4-ppt and did not vary significantly among years, salinity distributions of sub-adult/adult were lower and narrower (ca. 2-ppt), suggesting that low-salinity habitats disproportionally contributed more recruits relative to both freshwater and brackish water habitats and, therefore, may function as important nursery areas. Furthermore, the relative importance of the low salinity zone (ca. 2-ppt) to successful recruitment appeared greatest in years following the longfin smelt population decline. Our results indicate that otolith strontium isotopes (87Sr/86Sr) are a powerful tool for identifying nursery habitats for estuarine fishes.
- Published
- 2010
25. San Francisco Estuary mysid abundance in the fall, and the potential for competitive advantage of Hyperacanthomysis longirostris over Neomysis mercedis.
- Author
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AVILA, MICHELLE and HARTMAN, ROSEMARY
- Subjects
COMPETITIVE advantage in business ,STRIPED bass ,FISH as food ,INTRODUCED species ,WATER temperature - Abstract
Historically, the native mysid Neomysis mercedis was a key source of food for fish in the San Francisco Estuary (SFE). Following the introductions of the over-bite clam and many invasive zooplankton species in the mid-1980s, populations of native zooplankton species plummeted, including N. mercedis. In July 1993, Hyperacanthomysis longirostris, an invasive mysid, was first documented in the SFE, and it quickly became the most abundant mysid in the upper estuary. Since 2011, the California Department of Fish and Wildlife has sampled mysid abundance throughout the upper SFE concurrently with their Fall Midwater Trawl, which targets juvenile Striped Bass. We analyzed data from these mysid trawls to investigate environmental correlates of N. mercedis and H. longirostris abundance. We found that H. longirostris was found at higher temperatures significantly more often than N. mercedis, and there was a trend towards greater frequency of H. longirostris at higher salinities. Increases in water temperature over time, coupled with H. longirostris's smaller size at maturity and lower food needs may partially explain its success in the SFE. [ABSTRACT FROM AUTHOR]
- Published
- 2020
26. Informing extinction risk: Summarizing population viability through a meta-analysis of multiple long-term monitoring programs for a declining estuarine fish species.
- Author
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Tobias, Vanessa D., Chen, Ernest, Hobbs, James, Eakin, Michael, and Detwiler, Steven
- Subjects
- *
ENDANGERED species , *POPULATION viability analysis , *FISH declines , *ESTUARINE fishes , *WILDLIFE conservation , *TIME series analysis , *META-analysis - Abstract
Decisions about whether to designate a species for conservation and protection depend on the ability to summarize their population trajectories and their risk of extinction. Such decisions may rely on quantitative population viability analyses based on a time series of abundance index values that are derived from a monitoring program. In the case of the Longfin Smelt (Spirinchus thaleichthys), a decision to protect a distinct population segment of the species under the U.S. Endangered Species Act was informed by several indices of population abundance. In this paper, we combined individual population viability analyses into a single metric for extinction risk using a meta-analysis framework. Individual monitoring surveys for this species generally agreed that the trajectory of abundance was downward, but variation introduced uncertainty. Combining data from several surveys produced a better summary of the population growth rate. We also used the population growth rates in a simulation to estimate the probability that the abundance of Longfin Smelt dropped too low to recover. We found that this probability of quasi-extinction was substantial, exceeding 20 % over two decades. This study demonstrates a practical way that having multiple sources of information creates better information about the trajectory of a population. Individually, the surveys contribute information about specific life stages or ages to our understanding of the population. Combined into one metric and an associated graphical summary, this analysis succinctly communicates risk and creates a benchmark for evaluating future management decisions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
27. An Evaluation of Three Fish Surveys in the San Francisco Estuary, California, 1995-2015.
- Author
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Peterson, James T. and Barajas, Miguel F.
- Subjects
FISH surveys ,ESTUARIES ,FISH populations ,WATER temperature ,DATA quality - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2018
28. Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific
- Author
-
İsmail K. Sağlam, James A. Hobbs, Levi S. Lewis, Alyssa Benjamin, Randall D. Baxter, Amanda J. Finger, Sağlam, İsmail Kudret (ORCID 0000-0003-3136-7334 & YÖK ID 168783), Hobbs, James, Baxter, Randall, Lewis, Levi S., Benjamin, Alyssa, Finger, Amanda J., College of Sciences, and Department of Molecular Biology and Genetics
- Subjects
geography ,geography.geographical_feature_category ,Ecology ,Genome wide analysis ,Estuary ,Longfin smelt ,Aquatic Science ,Biology ,biology.organism_classification ,Gene flow ,Genetic structure ,Thaleichthys ,Fishering ,Spirinchus ,Fisheries ,Marine and freshwater ,Ecology, Evolution, Behavior and Systematics - Abstract
The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations., The authors thank Colin Grant (US Fish and Wildlife Service), who made many of the initial inquiries soliciting longfin smelt samples, and Josh Israel (US Bureau of Reclamation), who performed initial genetic analyses. The authors also thank the following individuals and agencies for help collecting samples: Hobbslab and staff -UC Davis; Matt Dekar and staff -US Fish and Wildlife Service; Kathy Hieb, Jennifer Giannetta, Jeremiah Bautista, Aaron Ng, Rebecca Garwood, James Ray, Justin Garwood, and Mike Wallace -California Department of Fish and Wildlife; Laurie Lloyd, Olaf Langness -Washington Department of Fish and Wildlife, Thomas Quinn, University of Washington; Eric Taylor -The University of British Columbia, John Kelson -Fish BiologistConsultant, Smithers, British Columbia; Mayumi Arimitsu -US Geological Survey, Alaska Science Center. Finally, the authors also thank a number of internal reviewers, Genomic Variation Lab Personnel, and other agency biologists who helped this project, including Matthew Campbell, Daphne Gille, Levi Lewis, Andrea Schreier, Josh Israel, and Alisha Goodbla. Funding for this project was generously provided by the California Department of Water Resources, Agreement Number 4600011196.
- Published
- 2021
29. Space‐for‐time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay‐Delta
- Author
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James T. Peterson and Adam Duarte
- Subjects
Delta ,Ecology ,biology ,species distribution model ,Substitution (logic) ,incomplete capture ,space‐for‐time substitution ,Longfin smelt ,Pelagic zone ,biology.organism_classification ,Space (mathematics) ,Delta Smelt ,Longfin Smelt ,Distribution (mathematics) ,Oceanography ,Bay ,Research Articles ,occupancy model ,QH540-549.5 ,Ecology, Evolution, Behavior and Systematics ,Geology ,Research Article ,Nature and Landscape Conservation - Abstract
Occupancy models are often used to analyze long‐term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non‐detection data at a sample unit and many long‐term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e., space‐for‐time substitution). Still, the efficacy of fitting occupancy models using a space‐for‐time substitution has not been fully explored and is likely context dependent. Herein, we fit occupancy models to Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) catch data collected by two different monitoring programs that use the same sampling gear in the San Francisco Bay‐Delta, USA. We demonstrate how our inferences concerning the distribution of these species changes when using a space‐for‐time substitution. Specifically, we found the probability that a sample unit was occupied was much greater when using a space‐for‐time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent. Overall, our findings highlight the importance of considering how the unique characteristics of monitoring programs influences inferences, which has broad implications for how to appropriately leverage existing long‐term monitoring data to understand the distribution of species., We demonstrate how inferences concerning the distribution of pelagic fishes change when using a space‐for‐time substitution and occupancy models. Specifically, we found the probability that a sample unit was occupied was much greater when using a space‐for‐time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent.
- Published
- 2021
30. Sampling Uncharted Waters: Examining Rearing Habitat of Larval Longfin Smelt ( Spirinchus thaleichthys) in the Upper San Francisco Estuary.
- Author
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Grimaldo, Lenny, Feyrer, Fred, Burns, Jillian, and Maniscalco, Donna
- Subjects
SPAWNING ,SALT marsh ecology ,SMELT fisheries ,FISH habitat improvement ,ESTUARIES - Abstract
The southern-most reproducing Longfin Smelt population occurs in the San Francisco Estuary, California, USA. Long-term monitoring of estuarine habitat for this species has generally only considered deep channels, with little known of the role shallow waters play in supporting their early life stage. To address the need for focused research on shallow-water habitat, a targeted study of Longfin Smelt larvae in littoral habitat was conducted to identify potential rearing habitats during 2013 and 2014. Our study objectives were to (1) determine if larval densities vary between littoral habitats (tidal slough vs. open-water shoal), (2) determine how larval densities in littoral habitats vary with physicochemical and biological attributes, (3) determine if larval densities vary between littoral habitats and long-term monitoring channel collections, and (4) determine what factors predict larval rearing distributions from the long-term monitoring channel collections. Larval densities did not vary between littoral habitats but they did vary between years. Water temperature, salinity, and chlorophyll a were found important in predicting larval densities in littoral habitats. Larval densities do not vary between littoral and channel surveys; however, the analysis based on channel data suggests that Longfin Smelt are hatching and rearing in a much broader region and under higher salinities (∼2-12 psu) than previously recognized. Results of this study indicate that conservation efforts should consider how freshwater flow, habitat, climate, and food webs interact as mechanisms that influence Longfin Smelt recruitment in estuarine environments. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
31. The value of long-term monitoring of the San Francisco Estuary for Delta Smelt and Longfin Smelt
- Author
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Timothy D. Malinich, James A. Hobbs, Arthur Barros, Jillian Burns, Christina Burdi, and Trishelle L. Tempel
- Subjects
Delta ,geography ,geography.geographical_feature_category ,hypomesus transpacificus ,biology ,Science ,endangered species act ,Longfin smelt ,Estuary ,sacramento-san joaquin delta ,long term monitoring ,biology.organism_classification ,san francisco estuary ,delta smelt ,Fishery ,longfin smelt ,Long term monitoring ,spirinchus thaleichthys ,Value (economics) ,Environmental science ,california endangered species act ,Smelt - Published
- 2021
32. Bifenthrin, a Ubiquitous Contaminant, Impairs the Development and Behavior of the Threatened Longfin Smelt during Early Life Stages.
- Author
-
Mauduit F, Segarra A, Sherman JR, Hladik ML, Wong L, Young TM, Lewis LS, Hung TC, Fangue NA, and Connon RE
- Subjects
- Animals, Endangered Species, Osmeriformes, Pyrethrins toxicity, Water Pollutants, Chemical
- Abstract
The Longfin Smelt ( Spirinchus thaleichthys ) population in the San Franscisco Bay/Sacramento-San Joaquin Delta (Bay-Delta) has declined to ∼1% of its pre-1980s abundance and, as a result, is listed as threatened under the California Endangered Species Act. The reasons for this decline are multiple and complex, including the impacts of contaminants. Because the spawning and rearing seasons of Longfin Smelt coincide with the rainy season, during which concentrations of contaminants increase due to runoff, we hypothesized that early life stages may be particularly affected by those contaminants. Bifenthrin, a pyrethroid insecticide commonly used in agricultural and urban sectors, is of concern. Concentrations measured in the Bay-Delta have been shown to disrupt the behavior, development, and endocrine system of other fish species. The objective of the present work was to assess the impact of bifenthrin on the early developmental stages of Longfin Smelt. For this, embryos were exposed to 2, 10, 100, and 500 ng/L bifenthrin from fertilization to hatch, and larvae were exposed to 2, 10, and 100 ng/L bifenthrin from one day before to 3 days post-hatch. We assessed effects on size at hatch, yolk sac volume, locomotory behavior, and upper thermal susceptibility (via cardiac endpoints). Exposure to these environmentally relevant concentrations of bifenthrin did not significantly affect the cardiac function of larval Longfin Smelt; however, exposures altered their behavior and resulted in smaller hatchlings with reduced yolk sac volumes. This study shows that bifenthrin affects the fitness-determinant traits of Longfin Smelt early life stages and could contribute to the observed population decline.
- Published
- 2023
- Full Text
- View/download PDF
33. Predation on Fishes in the Sacramento–San Joaquin Delta: Current Knowledge and Future Directions
- Author
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Gary D. Grossman
- Subjects
Delta Smelt ,Longfin Smelt ,Chinook Salmon ,Rainbow Trout ,Striped Bass ,Largemouth Bass ,Pikeminnow ,predator–prey interactions ,Environmental sciences ,GE1-350 - Abstract
doi: http://dx.doi.org/10.15447/sfews.2016v14iss2art8The Sacramento–San Joaquin Delta (Delta) is a heterogeneous, highly modified aquatic system.I reviewed relevant predator–prey theory, and described extant data on predator–prey relationships of Delta fishes. I ranked predator consumption rates as occasional, moderate, and common, based on frequency-of-occurrence data, and evaluated the frequency, and hypothesized the effects of predation on native and invasive species. I identified 32different predator categories and 41 different prey categories. Most predators were occasional consumers of individual prey species, although I also observed moderate and common consumption of some prey types. My analysis yielded few generalizations regarding predator–prey interactions for Delta fishes; most predators consumed a variety of both native and invasive fishes. The only evidence for predator specialization on either native or invasive fishes occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. BothStriped and Largemouth Bass exhibited wide dietary breadth, preying upon 32 and 28 categories of fish prey respectively. Sacramento Pikeminnow, a native predator, also displayed wide dietary breadth of piscine prey, with 14 different prey categories consumed. Data for reptilian, avian, and mammalian predators were sparse; however, these predators may be significant fish predators in altered habitats or when hatchery salmonids are released. The database for predators and their fish prey was not strong, and I recommend long-term dietary studies combined with prey availability and behavioral and experimental studies to establish predator preferences and antipredator behaviors, rather than just consumption.The behavioral effects of contaminants on prey species also warrant further examination. Although it has been suggested that a reduction in the StripedBass population be implemented to reduce predation mortality of Chinook Salmon, the large number of salmon predators in the Delta make it unlikely that this effort will significantly affect salmon mortality.
- Published
- 2016
34. Incorporating expanded sampling into an alternative abundance index for the Fall Midwater Trawl survey.
- Author
-
White, James R. and Baxter, Randall D.
- Subjects
TRAWLING ,PELAGIC fishes ,DRILL core analysis ,GEOGRAPHICAL distribution of fishes ,DATA distribution - Abstract
The Fall Midwater Trawl (FMWT) Survey has been conducted near continuously since 1967 to assess the abundance and distribution of pelagic fish species throughout the San Francisco Bay/Sacramento-San Joaquin estuary (Bay Delta). For most of this period, sampling 100 core stations provided data for abundance and distribution analyses. Another 22 (non-core) stations were added to the FMWT 8 to 28 years ago to supplement the original 100 (core) stations. However, relative abundance indices are published annually from only the data collected at the core stations. Here we incorporate data from non-core stations along with core station data to calculate an alternative index that also integrates modern estimates of water volume within the Bay Delta into an index calculation. The use of data from non-core stations in calculating the alternative index was particularly useful for American Shad (Alosa sapidissima) and Threadfin Shad (Dorosoma petenense). Consistently high catches at non-core stations for a couple species and modest catches for a couple additional species highlight the value of these additional catch data for our understanding of how fishes are distributed in the estuary. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
35. Use of state-space population dynamics models in hypothesis testing: advantages over simple log-linear regressions for modeling survival, illustrated with application to longfin smelt (Spirinchus thaleichthys).
- Author
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Maunder, Mark N., Deriso, Richard B., and Hanson, Charles H.
- Subjects
- *
FISH populations , *REGRESSION analysis , *SMELT fisheries , *DATA analysis , *FISHERY management - Abstract
Factors impacting the survival of individuals between two life stages have traditionally been evaluated using log-linear regression of the ratio of abundance estimates for the two stages. These analyses require simplifying assumptions that may impact the results of hypothesis tests and subsequent conclusions about the factors impacting survival. Modern statistical methods can reduce the dependence of analyses on these simplifying assumptions. State-space models and the related concept of random effects allow the modeling of both process and observation error. Nonlinear models and associated estimation techniques allow for flexibility in the system model, including density dependence, and in error structure. Population dynamics models link information from one stage to the next and over multiple time periods and automatically accommodate missing observations. We investigate the impact of observation error, density dependence, population dynamics, and data for multiple stages on hypothesis testing using data for longfin smelt in the San Francisco Bay-Delta. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
36. Fewer and Farther between: Changes in the Timing of Longfin Smelt (Spirinchus thaleichthys) Movements in the San Francisco Estuary
- Author
-
Tobias and Baxter R
- Subjects
Fishery ,geography ,geography.geographical_feature_category ,Occupancy ,Habitat ,Long term monitoring ,%22">Fish ,Thaleichthys ,Estuary ,Longfin smelt ,Biology ,biology.organism_classification ,Spirinchus - Abstract
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.
- Published
- 2021
37. Hybridization between delta smelt and two other species within the family Osmeridae in the San Francisco Bay-Delta.
- Author
-
Fisch, Kathleen, Mahardja, Brian, Burton, Ronald, and May, Bernie
- Subjects
POND smelt ,MICROSATELLITE repeats ,SPECIES hybridization ,SINGLE nucleotide polymorphisms ,SMELTS ,MITOCHONDRIAL DNA - Abstract
Hybridization among closely related species may pose a threat to species persistence, especially between native and introduced species. We analyzed nine microsatellite loci, mitochondrial sequences and 16 species-specific single nucleotide polymorphisms (SNPs) in two native species (delta smelt and longfin smelt) and one introduced species (wakasagi smelt) in the family Osmeridae to describe the extent of hybridization among these species in the San Francisco Bay-Delta, CA, USA. We identified 29 putative hybrids with a microsatellite-based Bayesian assignment method, and we further screened these putative hybrids with the SNP loci and mitochondrial DNA (mtDNA) sequencing. From the Yolo Bypass, 11 % of morphologically ambiguous individuals were F hybrids and 0.1 % of positively identified delta smelt from throughout the San Francisco Bay-Delta were F hybrids according to their SNP genotypes. mtDNA sequencing revealed wakasagi smelt as the maternal parent for all five delta smelt × wakasagi smelt hybrids and longfin smelt as the maternal parent for the single longfin smelt × delta smelt hybrid. Hybridization among these three species appears to occur at relatively low frequencies and may not be an immediate threat to the persistence of the imperiled native species; however, the presence of hybrid individuals warrants continued monitoring. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
38. Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary
- Author
-
Anne M. Slaughter, Michelle J. Jungbluth, Aspen Katla, Jillian Burns, Wim J. Kimmerer, and Lenny Grimaldo
- Subjects
Acanthocyclops ,Herring ,biology ,Zoology ,Longfin smelt ,Pacific herring ,Clupea ,biology.organism_classification ,Smelt ,Zooplankton ,Predation - Abstract
Food limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoener’s index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepodsEurytemora carolleeae, Acanthocyclops americanus, andA. robustus; theAcanthocyclopsspp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (Limnoithona tetraspinamore frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarianHydra oligactis, the polychaeteDasybranchussp., and a newly identified speciesMesocyclops pehpeiensis. “Unknown” DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.
- Published
- 2020
39. Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary
- Author
-
Andrew Kalmbach, Lenny Grimaldo, April Smith, Colin Brennan, Jillian Burns, Jason L. Hassrick, and Robert E. Miller
- Subjects
geography ,geography.geographical_feature_category ,biology ,Estuary ,Pacific herring ,Longfin smelt ,Clupea ,Aquatic Science ,biology.organism_classification ,Fishery ,Habitat ,Forage fish ,Ecosystem ,Bay ,Water Science and Technology - Abstract
Author(s): Grimaldo, Lenny; Burns, Jillian; Miller, Robert E.; Kalmbach, Andrew; Smith, April; Hassrick, Jason; Brennan, Colin | Abstract: 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.
- Published
- 2020
40. Silicon Valley's Threatened Longfin Smelt: Evidence of Spawning And Recruitment in A Restored Tidal Wetland
- Author
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Levi S. Lewis, James A. Hobbs, Patrick K. Crain, Malte Willmes, and Arthur Barros
- Subjects
Fishery ,geography ,geography.geographical_feature_category ,Silicon valley ,biology ,Threatened species ,Environmental science ,Wetland ,Longfin smelt ,General Medicine ,biology.organism_classification - Published
- 2020
41. Use of single nucleotide polymorphisms identifies backcrossing and species misidentifications among three San Francisco estuary osmerids
- Author
-
James A. Hobbs, Brian Mahardja, Alyssa Benjamin, Tien-Chieh Hung, Amanda J. Finger, and İsmail K. Sağlam
- Subjects
0106 biological sciences ,0301 basic medicine ,Delta ,Life on Land ,SNP ,Zoology ,Introgression ,Longfin smelt ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Hypomesus transpacificus ,Genetics ,Hybridization ,Ecology, Evolution, Behavior and Systematics ,Hybrid ,Evolutionary Biology ,biology ,Hypomesus nipponensis ,RADseq ,San Francisco Estuary ,Biological Sciences ,biology.organism_classification ,Delta Smelt ,030104 developmental biology ,Backcrossing ,Smelt ,Environmental Sciences - Abstract
Two threatened osmerid species native to the San Francisco Estuary (SFE)—Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys)—are subject to broad human influence, including significant habitat alteration and the presence of the introduced osmerid, Wakasagi (Hypomesus nipponensis). The identification of these closely related species and their hybrids is difficult in field collected specimens which are subject to damage through handling and may be difficult to identify morphologically, especially when young. In addition, it is known that these three species hybridize, but the extent and effect of hybridization is difficult to quantify and monitor. We developed assays for 24 species-specific single nucleotide polymorphisms (SNPs) that identify whether a sample is a pure species (Delta Smelt, Longfin Smelt, or Wakasagi), a first generation (F₁) hybrid, or a backcross. We used this SNP panel to genetically identify wild osmerids collected in Yolo Bypass from 2010 to 2016 and detected nine Delta Smelt×Wakasagi F₁ hybrids and two Wakasagi×(Delta Smelt×Wakasagi) backcross hybrids; all assayed hybrids had Wakasagi as the maternal parent. The backcrossing into Wakasagi suggests that hybridization may only occur in one direction and thus preclude introgression to Delta Smelt. We also found substantial morphological field misidentifications (32.7%) in the Yolo Bypass samples resulting in more Wakasagi and fewer Delta Smelt than previously recorded when based on morphology. The SNP panel described in this study constitutes a valuable resource for monitoring hybridization in the SFE and assigning species identifications with accuracy and efficiency.
- Published
- 2018
42. Understanding imperfect detection in a San Francisco Estuary long-term larval and juvenile fish monitoring programme
- Author
-
M. J. Young, Brian Mahardja, Brian M. Schreier, and Ted Sommer
- Subjects
0106 biological sciences ,Delta ,geography ,geography.geographical_feature_category ,Ecology ,biology ,010604 marine biology & hydrobiology ,Estuary ,Pelagic zone ,Longfin smelt ,Juvenile fish ,Aquatic Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Fishery ,Abundance (ecology) ,Hypomesus transpacificus ,Smelt - Abstract
Imperfect detection can present a significant challenge when monitoring for a rare and imperilled species. Here, a long-term larval and early-juvenile fish monitoring programme in the upper San Francisco Estuary was examined to evaluate its overall reliability in detecting various fish species, including the imperilled delta smelt, Hypomesus transpacificus McAllister, for which the programme was designed. Using occupancy modelling, detection probability of species with pelagic larval or juvenile life stages was found to be generally high (≥.95) based on the current sampling effort of three larval net tows per site. However, detection probability can vary considerably from year to year depending on the species’ level of larval production. Water temperature and turbidity were identified as important predictors of occurrence for young-of-year delta smelt, longfin smelt Spirinchus thaleichthys (Ayres) and striped bass Morone saxatilis (Walbaum), and there was evidence for fish size selectivity by the sampling gear in all three species. These results highlight the need to consider adaptively managing detection probability by increasing sampling effort in years when young-of-year delta smelt abundance is expected to be low, especially when information on the species’ occurrence at a particular region is critical.
- Published
- 2017
43. Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary.
- Author
-
Burris, Zair P. Lojkovic, Baxter, Randall D., and Burdi, Christina E.
- Subjects
SIZE of fishes ,FORAGE fishes ,FISH larvae ,ESTUARIES ,FISH declines ,SUCCESS ,FISH evolution - Abstract
The density and quality of zooplankton prey affect the feeding success of larval and juvenile fishes and thus can drive growth, survival, and recruitment. As part of a larger effort investigating potential causes of a pelagic fish decline, we examined regional feeding success (food presence/absence, stomach fullness), diet composition and prey selection of young Longfin Smelt (Spirinchus thaleichthys) in spring and summer as a function of fish size and prey availability in the San Francisco Estuary. We conducted our sampling during two wet and two dry years, because weather and river flow influence prey community composition and location. Larval and juvenile fish showed evidence of food limitation: high proportions of empty stomachs (≤ 70%) and stomach contents totaling <10% of maximum stomach content volume. The total weight of prey consumed increased with fish length, and in most regions and years this resulted from fish consuming larger prey as they grew; however, in many regions during dry years, fish consumed greater numbers of prey instead of larger prey as they grew. Larval fish preferentially consumed Eurytemora spp. except when rotifers or barnacle nauplii occurred in extremely high densities. Juvenile fish consumed a greater diversity of prey yet relied on mysids in most regions and years. Adult calanoid copepods (Pseudodiaptomus spp., Eurytemora spp., and Acartia spp.) were regionally important in juvenile diets and were positively selected when mysids were in low densities, mostly in eastern regions during dry years. This switch from much larger mysids to smaller calanoid copepods explains the increase in prey number (instead of prey size) consumed in these regions. These results, coupled with food limitation in most regions, suggest that the current densities and quality of zooplankton in the San Francisco Estuary are limiting feeding success and potentially growth and survival of young Longfin Smelt. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
44. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary.
- Author
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Thomson, James R., Kimmerer, Wim J., Brown, Larry R., Newman, Ken B., Ralph Mac Nally, William A. Bennett, Frederick Feyrer, and Erica Fleishman
- Subjects
PELAGIC fishes ,STRIPED bass ,THREADFIN shad ,MARINE ecology ,BAYESIAN analysis - Abstract
The article presents a study which analyzes the trends in abundance of several pelagic fish species, including striped bass, threadfin shad and delta smelt in the upper estuary in San Francisco, California. It highlights the utilization of the change point with Bayesian model to identify biotic or abiotic covariates. It mentions several abiotic variables which affect the abundances including water clarity, volume of exported freshwater and position of the two percent isohaline.
- Published
- 2010
- Full Text
- View/download PDF
45. Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR).
- Author
-
MacNally, Ralph, Thomson, James R., Kimmerer, Wim J., Feyrer, Frederick, Newman, Ken B., Sih, Andy, Bennett, William A., Brown, Larry, Fleishman, Erica, Culberson, Steven D., and Castillo, Gonzalo
- Subjects
PELAGIC fishes ,STRIPED bass ,THREADFIN shad ,MULTIVARIATE analysis - Abstract
The article presents a study regarding the decline in the species of pelagic fish in an estuary in San Francisco, California. It highlights the utilization of multivariate autoregressive modeling (MAR) which is essential in the analysis of several pelagic species including delta smelt, striped bass and threadfin shad. It recommends that further study should be conducted using state-space models to enhance the results.
- Published
- 2010
- Full Text
- View/download PDF
46. Effects of temperature on hatching and growth performance of embryos and yolk-sac larvae of a threatened estuarine fish: Longfin smelt (Spirinchus thaleichthys)
- Author
-
Yuzo R. Yanagitsuru, James A. Hobbs, Richard E. Connon, Levi S. Lewis, Nann A. Fangue, Madison A. Main, and Tien-Chieh Hung
- Subjects
0303 health sciences ,Larva ,animal structures ,food.ingredient ,biology ,Hatching ,Foraging ,Longfin smelt ,04 agricultural and veterinary sciences ,Aquatic Science ,biology.organism_classification ,03 medical and health sciences ,food ,medicine.anatomical_structure ,Animal science ,Dry weight ,Yolk ,embryonic structures ,040102 fisheries ,medicine ,0401 agriculture, forestry, and fisheries ,Yolk sac ,Spirinchus ,030304 developmental biology - Abstract
The abundance of longfin smelt (Spirinchus thaleichthys) in the San Francisco Estuary (SFE) has declined to less than 1% of historic numbers, contributing to their listing as “threatened” under the California Endangered Species Act. To prevent local extirpation, a captive culture program is being developed for the longfin smelt at the Fish Conservation Culture Laboratory at UC Davis. To begin systematically addressing current issues with larviculture methods, we tested the effects of temperature on longfin smelt embryos from 7 clutches with different parentages. We reared embryos and newly hatched non-feeding yolk-sac larvae in freshwater at 9, 12, or 15 °C until the age when these fish underwent mass mortality (>90% mortality) during the experiment (3, 4, or 5 days post-hatch (dph), depending on rearing temperature). We measured hatch success, hatch morphometrics (notochord length, dry mass, yolk volume, and oil volume), length and dry mass growth rates, yolk and oil resorption rates, routine oxygen consumption rate, and locomotor activity (percent of time spent moving, total distance travelled, and average swimming velocity). Embryos and larvae reared at 15 °C performed poorly, experiencing reduced hatch success, hatch notochord lengths, growth rates, and earlier mass mortality. Embryos reared at 9 and 12 °C had similar hatch success but at hatch, larvae were longer at 9 compared to 12 °C. However, larvae grew faster in 12 compared to 9 °C resulting in both temperature groups having similar lengths prior to mass mortality (4 dph for 12 °C and 5 dph for 9 °C). Temperature had no effect on routine oxygen consumption rate among temperature groups but locomotor activity was elevated at 9 and 15 °C groups compared to 12 °C, suggesting that locomotor activity consumed a higher proportion of the energy budget, leaving a smaller fraction for growth. Finally, larval swimming speeds, one day prior to each temperature's respective day of mass mortality, were higher at 12 °C (3 dph) compared to 9 (4 dph) and 15 °C (2 dph), which could lead to higher foraging success. Interclutch variation was high, however, suggesting that parentage effects may result in brood-specific variation in the responses of larvae to water temperature. Taken together, these data suggest that rearing longfin smelt at 15 °C would have detrimental effects and we suggest that cooler temperatures such as 9 or 12 °C may improve the culturing of the earliest life stages of longfin smelt.
- Published
- 2021
47. Assessing nursery habitat quality for native smelts ( Osmeridae) in the low-salinity zone of the San Francisco estuary.
- Author
-
Hobbs, J. A., Bennett, W. A., and Burton, J. E.
- Subjects
- *
SMELTS , *FISH habitats , *SALINITY , *ESTUARIES - Abstract
Habitat quality was assessed for two native osmerids, delta smelt Hypomesus transpacificus and longfin smelt Spirinchus thaleichthys, between two distinct nursery areas located in the low-salinity zone of the San Francisco estuary. The relationship between several variables was investigated including fish density, fish size, feeding success and the general condition of larvae as well as juveniles for both species. The nursery habitats that were evaluated included the North and South Channels of Suisun Bay. The results showed higher densities of zooplankton and decreased water velocities for the North Channel when compared to the South Channel. The dominant prey item was calanoid copepod Pseudodiaptomus forbesi for both species although longfin smelt residing in the North Channel also included another copepod in their diets, Acanthocyclops spp. In both locations, delta smelt fed predominantly during daytime flood tides, while longfin smelt feeding appeared to continue into the night hours. When both locations were compared, delta smelt in the North Channel exhibited higher densities, larger sizes, increased somatic condition and larvae <15 mm standard length demonstrated greater feeding success. Longfin smelt, exhibited similar densities, feeding success and size distributions between both channels, but generally showed poorer somatic condition for the South Channel, potentially due to energetic costs associated with documented vertical migration behaviour. Overall, the physical conditions of the North Channel provided superior habitat for both species, while the South Channel afforded only marginal habitat for longfin smelt and very poor habitat for delta smelt. Therefore, the North Channel of Suisun Bay acts as critical nursery habitat by providing better feeding and growing conditions leading to increased health and survival for both species. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
48. Sampling Uncharted Waters: Examining Rearing Habitat of Larval Longfin Smelt (Spirinchus thaleichthys) in the Upper San Francisco Estuary
- Author
-
Frederick Feyrer, Donna M. Maniscalco, Lenny Grimaldo, and Jillian Burns
- Subjects
0106 biological sciences ,Larva ,geography ,education.field_of_study ,geography.geographical_feature_category ,Ecology ,biology ,010604 marine biology & hydrobiology ,Population ,Shoal ,Longfin smelt ,Estuary ,Aquatic Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Salinity ,Fishery ,Habitat ,Littoral zone ,Environmental science ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
The southern-most reproducing Longfin Smelt population occurs in the San Francisco Estuary, California, USA. Long-term monitoring of estuarine habitat for this species has generally only considered deep channels, with little known of the role shallow waters play in supporting their early life stage. To address the need for focused research on shallow-water habitat, a targeted study of Longfin Smelt larvae in littoral habitat was conducted to identify potential rearing habitats during 2013 and 2014. Our study objectives were to (1) determine if larval densities vary between littoral habitats (tidal slough vs. open-water shoal), (2) determine how larval densities in littoral habitats vary with physicochemical and biological attributes, (3) determine if larval densities vary between littoral habitats and long-term monitoring channel collections, and (4) determine what factors predict larval rearing distributions from the long-term monitoring channel collections. Larval densities did not vary between littoral habitats but they did vary between years. Water temperature, salinity, and chlorophyll a were found important in predicting larval densities in littoral habitats. Larval densities do not vary between littoral and channel surveys; however, the analysis based on channel data suggests that Longfin Smelt are hatching and rearing in a much broader region and under higher salinities (∼2–12 psu) than previously recognized. Results of this study indicate that conservation efforts should consider how freshwater flow, habitat, climate, and food webs interact as mechanisms that influence Longfin Smelt recruitment in estuarine environments.
- Published
- 2017
49. Newly discovered spawning and recruitment of threatened Longfin Smelt in restored and underexplored tidal wetlands
- Author
-
Patrick K. Crain, Levi S. Lewis, Arthur Barros, Malte Willmes, and James A. Hobbs
- Subjects
geography ,Conservation of Natural Resources ,geography.geographical_feature_category ,Watershed ,Marsh ,biology ,Ecology ,Estuary ,Wetland ,Longfin smelt ,biology.organism_classification ,Novel ecosystem ,Osmeriformes ,Wetlands ,Threatened species ,Animals ,Spirinchus ,Estuaries ,Ecology, Evolution, Behavior and Systematics ,Ecosystem - Published
- 2019
50. Population Dynamics of an Estuarine Forage Fish: Disaggregating Forces Driving Long-Term Decline of Longfin Smelt in California's San Francisco Estuary
- Author
-
Jonathan A. Rosenfield and Matthew L. Nobriga
- Subjects
0106 biological sciences ,education.field_of_study ,geography.geographical_feature_category ,biology ,Primary producers ,Ecology ,010604 marine biology & hydrobiology ,Fish farming ,Population ,Longfin smelt ,Estuary ,Aquatic Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Fishery ,Geography ,Productivity (ecology) ,Forage fish ,Ecosystem ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Forage fish production has become a central concern of fisheries and ecosystem managers because populations of small fish are a critical energetic pathway between primary producers and predator populations. Management of forage fish often focuses on controlling exploitation rates, but it is also possible to manage productivity of these species in coastal ecosystems, particularly estuaries. Like several forage fish species that are native to the San Francisco Estuary (SFE) in California, the Longfin Smelt Spirinchus thaleichthys has experienced dramatic population declines over the past few decades. This population is not fished commercially or recreationally; trends in its relative abundance have been described statistically, but the mechanisms that drive population dynamics are still poorly understood. Our objective was to evaluate alternative conceptual models of Longfin Smelt population dynamics to better understand the forces that may constrain the species' productivity during different phases...
- Published
- 2015
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