Longfin Smelt Research Articles

A baseline assessment of contamination in the Sacramento deep water ship channel

The Sacramento Deep Water Ship Channel (SDWSC) in the San Francisco Estuary, which is an active commercial port, is critical habitat for pelagic fish species including delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), and Sacramento perch (Archoplites interruptus). Pelagic organism decline has been attributed to covarying factors such as manipulation of habitat, introduction of invasive species, decrease in food production, and contaminant exposure. Quantification of bioavailable toxicant loads in the SDWSC is limited despite previous surveys that have detected elevated contaminant concentrations in the sediments. Therefore, the focus of the present study was to characterize the bioavailability of the contaminants in the SDWSC from six sites along the channel. At each site, organochlorine pesticides (OCPs), pyrethroid insecticides, polyaromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) were quantified in sediment, zooplankton, and suspended solids. In addition, Tenax extraction was used to measure the bioaccessible fraction of sediment-associated contaminants freely dissolved in the water. Bioaccessible contaminants in the sediment provided an uptake route for these stressors into invertebrates and fish with bioaccessible OCPs being found at all sites, particularly 4,4′-dichlorodiphenyldichloroethylene (DDE). Bifenthrin was the only pyrethroid detected in the chosen matrices and it was found at concentrations below levels of concern. Bioaccessible PAHs were found at all sites, with highest detections for phenanthrene and pyrene. No PCBs were detected in sediments, but were detected in both suspended solids and zooplankton. Contaminant concentrations overall were significantly higher in suspended solids, followed by zooplankton and sediments. The highest sediment concentrations of DDE, fluoranthene, pyrene, and dibenzo[a,h]anthracene exceeded sediment quality benchmarks indicating potential risk to sediment-dwelling species. Finally, elevated contaminant levels were found in both suspended solids and zooplankton, suggesting additional risk to pelagic species in the SDWSC.

The Influence of Time, Tide, and Place on Fine-Scale Nekton Distribution: Insights from the San Francisco Estuary

The location of estuarine organisms varies based on geophysical cycles and environmental conditions, which can strongly bias understanding of organism abundance and distribution. In the San Francisco Estuary, California, extensive monitoring surveys have provided insight into the life history and ecology of certain commercially important or legislatively protected fish species. However, there remains substantial uncertainty in factors influencing the vertical and lateral distributions of many other nekton species in the San Francisco Estuary, including longfin smelt Spirinchus thaleichthys, for whom such distributional information may highly influence interpretation of existing data. We carried out paired sampling using surface and demersal gears to address three questions: (1) Does diel phase influence the vertical position of nekton (e.g., surface versus demersal)? (2) Do environmental conditions, specifically turbidity, influence the vertical and lateral positions of nekton (e.g., center channel versus peripheral shoal)? (3) Does tidal variability influence vertical and lateral distributions of nekton? We documented variability in sampled nekton densities across diel phase (day/night), vertical position (surface/bottom), and lateral position (channel/shoal). Tidal phase and turbidity concentration influenced vertical and lateral distributions for some species at certain locations. Although infrequently encountered, we documented associations of longfin smelt with the lower water column and shoal habitats, with some evidence for upward vertical shifts in low light conditions brought about by nightfall or elevated turbidity. Observed habitat associations provide insight into how interacting geophysical and environmental factors may influence the distribution of nekton and thus the vulnerability of individual species to detection by sampling gears.

Variability in coastal habitat available for Longfin Smelt Spirinchus thaleichthys in the northeastern Pacific Ocean

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt (Spirinchus thaleichthys) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

Laboratory‐bred Longfin Smelt produced offspring in the first year in captivity

AbstractObjectiveThis study aims to develop the culture methods for Longfin Smelt Spirinchus thaleichthys in a laboratory setting, achieving the first production of a fully captive second generation (F2). The objective includes understanding the critical factors influencing the breeding and maturation of this species in captivity, contributing to conservation efforts and potential revival of this threatened species.MethodsLongfin Smelt broodstock were collected from the San Francisco Estuary and reared in controlled conditions at the University of California Davis Fish Conservation and Culture Laboratory (FCCL). The study involved spawning of wild broodstock, rearing of first generation (F1) progeny to adulthood, and subsequent spawning to produce F2 offspring. Key variables such as salinity, temperature, and diet were carefully managed throughout the process. Fertilization and hatching rates were calculated, and the larvae were reared using the same methods to closely monitor and understand their growth and development.ResultFirst generation Longfin Smelt successfully matured and spawned at age 1, earlier than commonly observed in the wild. From five crosses, four produced viable offspring. The study recorded a range of fertilization rates (10–40%) and high hatching rates (75–97%). Salinity was identified as a critical factor in both larval development and adult maturation. While initial larval survival was challenging, the larval rearing system used in this study proved effective.ConclusionThe study represents a major breakthrough in the cultivation of Longfin Smelt, showing that it is possible to complete their life cycle under controlled conditions. It has provided valuable understanding of the maturation and breeding processes in these fish, with an emphasis on the influence of salinity. These outcomes are crucial for conservation strategies, offering the potential to help establish a refuge population and laying the groundwork for further research aimed at refining captive breeding methods for this species.

Effects of incubation temperature on the upper thermal tolerance of the imperiled longfin smelt (Spirinchus thaleichthys).

Upper thermal limits in many fish species are limited, in part, by the heart's ability to meet increased oxygen demand during high temperatures. Cardiac plasticity induced by developmental temperatures can therefore influence thermal tolerance. Here, we determined how incubation temperatures during the embryonic stage influence cardiac performance across temperatures during the sensitive larval stage of the imperiled longfin smelt. We transposed a cardiac assay for larger fish to newly hatched larvae that were incubated at 9°C, 12°C or 15°C. We measured heart rate over increases in temperature to identify the Arrhenius breakpoint temperature (TAB), a proxy for thermal optimum and two upper thermal limit metrics: temperature when heart rate is maximized (Tpeak) and when cardiac arrhythmia occurs (TArr). Higher incubation temperatures increased TAB, Tpeak and TArr, but high individual variation in all three metrics resulted in great overlap of individuals at TAB, Tpeak and TArr across temperatures. We found that the temperatures at which 10% of individuals reached Tpeak or TArr and temperatures at which number of individuals at TAB relative to Tpeak (ΔN(TAB,Tpeak)) was maximal, correlated more closely with upper thermal limits and thermal optima inferred from previous studies, compared to the mean values of the three cardiac metrics of the present study. Higher incubation temperatures increased the 10% Tpeak and TArr thresholds but maximum ΔN(TAB,Tpeak) largely remained the same, suggesting that incubation temperatures modulate upper thermal limits but not Topt for a group of larvae. Overall, by measuring cardiac performance across temperatures, we defined upper thermal limits (10% thresholds; Tpeak, 14.4-17.5°C; TArr, 16.9-20.2°C) and optima (ΔN(TAB,Tpeak), 12.4-14.4°C) that can guide conservation strategies for longfin smelt and demonstrated the potential of this cardiac assay for informing conservation plans for the early life stages of fish.

Phylogenetic relationships and introduction history inferred from complete mitochondrial genomes of four smelts (Osmeridae) of the modern San Francisco Estuary

We announce complete mitogenomes of four smelts (Osmeridae) of the San Francisco Estuary (SFE): endemic Hypomesus transpacificus, native H. pretiosus and Spirinchus thaleichthys, and non-native H. nipponensis. The genomes each contained 13 protein coding, 2 ribosomal RNA and 22 transfer RNA genes, a control region (D-loop), and a putative origin of replication of the light strand (OL); gene order followed other osmerids. Total genomes were 16,767 base-pairs (bp) for H. transpacificus; 16,672bp for H. pretiosus; 16,811bp for S. thaleichthys; and 16,779bp for H. nipponensis. GC content was from 47.8% (S. thaleichthys) to 49.4% (H. pretiosus). Phylogenetic analyses of mitogenomes placed H. transpacificus sequences within the H. pretiosus [Oregon + SFE] clade and most closely related to H. pretiosus [SFE], whereas affinities of derivative cytochrome b sequences supported a Lake Suwa origin for SFE H. nipponensis.

Informing extinction risk: Summarizing population viability through a meta-analysis of multiple long-term monitoring programs for a declining estuarine fish species

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.

Effects of Salinity on Fertilization, Hatching, and Larval Performance of Longfin Smelt Spirinchus thaleichthys

Understanding the spawning and rearing habitats of fishes is critical to effective fisheries management and conservation. Longfin smelt Spirinchus thaleichthys is an imperiled migratory fish that is believed to spawn and rear in habitats of varying salinities; however, optimal conditions for each stage remain unknown. Here, we examined the effects of variation in salinity on egg fertilization, hatch success, and larval growth and survival. Eggs that were fertilized in freshwater (0.4 ppt) exhibited a significantly higher fertilization rate (81%) than those fertilized in brackish water (62% at 5 ppt), with no detectible effects of fish origin or female size. In contrast to fertilization rates, once the eggs were fertilized, their hatching rates were not affected by the fertilization salinity, incubation salinity, nor their interaction; however, hatching success and larval survival both increased with increasing maternal body mass. Larval growth rate appeared to be independent of salinity and maternal size. Taken together, the results indicate that fertilization is possible at a range of salinities, but optimal at lower salinities for longfin smelt; however, embryos and larvae can perform well across a range of salinities. Furthermore, results indicated that larger mothers produced high-quality offspring, a finding that supports the “bigger is better” paradigm in fisheries science and management. These results likely explain, in part, the spawning and rearing behaviors of wild longfin smelt and suggest that the conservation culture program would likely be optimized by utilizing freshwater fertilization and larger females as broodstock.

Bifenthrin, a Ubiquitous Contaminant, Impairs the Development and Behavior of the Threatened Longfin Smelt during Early Life Stages.

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.

A Spatiotemporal History of Key Pelagic Fish Species in the San Francisco Estuary, CA

Estuaries across the globe have been subject to extensive abiotic and biotic changes and are often monitored to track trends in species abundance. The San Francisco Estuary has been deeply altered by anthropogenic factors, which is reflected in substantial declines in some native and introduced fishes. To track trends in fish abundance, a multitude of monitoring programs have conducted regular fish surveys, some dating back to the late 1950s. While these surveys are all designed to track population-scale changes in fish abundance, they are methodologically distinct, with different target species, varying spatial coverage and sampling frequency, and different gear types. To compensate for individual survey limitations, we modeled pelagic fish distributions with integrated data from many sampling programs. We fit binomial generalized linear mixed models with spatial and spatiotemporal random effects to map annual trends in the spatially explicit detection probabilities of striped bass, Delta smelt, longfin smelt, threadfin shad, and American shad for the years 1980 to 2017. Overall, detection probability has declined by approximately 50% for striped bass and is now near zero for the two smelt species, while threadfin shad and American shad have both experienced fluctuations with only slightly reduced detection probabilities by 2017. Detection probabilities decreased dramatically for these fishes in the Central and South Delta, especially after the year 2000. In contrast, Suisun Marsh and the North Delta acted as refuge habitats with reduced levels of decline or even increased detection probabilities for some species. Our modeling approach, using disparate datasets, demonstrates the simultaneous spatially driven decline of pelagic fish species in a highly altered estuary.

Vital dye immersion evaluations with juvenile delta smelt

AbstractImmersion‐based vital dyes were tested as a marking method for use in larval smelt mark–recapture studies. We assessed five fluorescent dyes as a mark for juvenile osmerids: 4‐Di‐1‐ASP, BODIPY FL C12, BODIPY 505/515, Nile red, and calcein. We marked juvenile Delta Smelt, Hypomesus transpacificus, as a proxy for Longfin Smelt, Spirinchus thaleichthys, to determine the efficacy of each as a batch marking technique for osmerids based on dye performance and survival. All groups of Delta Smelt including control groups exhibited high mortality (71%–100%, 5 days after trial), and lowest survival was observed in 4‐Di‐1‐ASP‐treated fish. Highest survival was observed in Nile red‐ and BODIPY FL C12‐treated fish. Fluorescence observations indicated that the brightest, visible fluorescence was seen in calcein and to a lesser extent, 4‐Di‐1‐ASP, followed by BODIPY FL C12 and Nile red. In addition to dye performance, it is recommended that immersion techniques that improve survival be considered.

Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) north of the San Francisco Estuary

Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (the SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the estuary 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 meta-population. 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 the 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; in the dry winter of 2020, we detected larvae in two additional estuaries. Possibly elevated freshwater outflow in 2019 increased transport rates to the 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 estuary Longfin Smelt population may lack the resiliency afforded by meta-populations and advocates for increased monitoring over a range of hydrologic conditions and improving detection probabilities for future assessments of gene flow between populations.

Population Abundance and Diversion Losses in a Threatened Estuarine Pelagic Fish

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 ~ 109 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.

Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary

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.

Captive Rearing of Longfin Smelt Spirinchus thaleichthys: First Attempt of Weaning Cultured Juveniles to Dry Feed.

Simple SummaryLongfin smelt Spirinchus thaleichthys is an imperiled estuarine species in California, USA. A captive culture program is currently being developed; however, prior to this study, longfin smelt have only fed on live prey in the hatchery. Here, we report on our first successful attempt to wean cultured juveniles onto a dry commercial pellet feed. A subset of F1 fish was switched to a mixed diet of reduced Artemia and dry feed for 62 days, with growth, survival, and body condition compared between feeding treatments. Our results highlight that juvenile longfin smelt can utilize dry feeds while maintaining a healthy body condition.The rapid decline of longfin smelt Spirinchus thaleichthys, a threatened euryhaline forage fish in California, is a serious concern for scientists and resource managers. To recover and conserve this species, a captive culture program was initiated, focusing on the collection, captive rearing and breeding of wild broodstock, and the rearing of their offspring. Although progress has been made in the collection of broodstock and the production and culturing of larvae, no studies have evaluated the rearing of juvenile life stages in captivity. The present study examines methodological considerations for culturing F1 juvenile longfin smelt, specifically, the first efforts toward weaning juveniles to a dry commercial pellet feed. Cultured juvenile longfin smelt were fed live Artemia only or co-fed Artemia and dry feed for 62 days, and the effects of feed type on juvenile survival, growth, body condition, and fatty acid profiles were examined. No significant differences were observed between feeding treatments, despite an 80% reduction in Artemia in the co-feeding treatment. Furthermore, examination of fish stomach contents at the end of the trial confirmed the transition to dry feed. This is the first study to indicate successful feeding by longfin smelt on dry commercial pellets, and suggests that juvenile longfin smelt can be fully weaned onto dry feeds. Results of this study are critical for closing the lifecycle of longfin smelt in captivity and developing a successful conservation culture program for this imperiled species.

Spatial Heterogeneity in Prey Availability, Feeding Success, and Dietary Selectivity for the Threatened Longfin Smelt

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.

Hatching distribution, abundance, and losses to freshwater diversions of longfin smelt inferred using hydrodynamic and particle-tracking models

The distribution of larval fishes is influenced by where they hatch and their movements after hatching. In the San Francisco Estuary, the threatened longfin smeltSpirinchus thaleichthysspawns adhesive eggs in fresh to brackish water. Attached eggs hatch and the larvae disperse seaward toward higher-salinity water. Actual locations of spawning and hatching are unknown, and cannot reliably be inferred from distributions of larvae because intense tidal mixing obscures the history of movement. Human interventions such as manipulations and diversions of freshwater flow may contribute to the ongoing decline of this species, and these effects depend on where the fish hatch. We combined movement estimated using hydrodynamic and particle-tracking modeling with trawl data using a Bayesian model to estimate the location and timing of hatching, as well as natural mortality of larvae and losses to freshwater diversions. Results indicate that longfin smelt may hatch further seaward than previously believed, and that estimated direct losses due to diversions were small relative to other sources of mortality. Abundance of this species varies ~100-fold with freshwater flow, but our results suggest that proportional entrainment was practically zero during an extreme wet year and relatively low (2%) in a moderately dry year. This method could be applied to other estuarine and coastal systems where strong mixing reduces the ability of simpler models to predict hatching locations and larval movements.

Growth, osmoregulation and ionoregulation of longfin smelt (Spirinchus thaleichthys) yolk-sac larvae at different salinities.

Longfin smelt (Spirinchus thaleichthys) is a threatened anadromous fish species that spawns in freshwater to moderately brackish (i.e. 5-10ppt) reaches of the upper San Francisco Estuary and has declined to ~1% of its pre-1980s abundances. Despite 50+ years of population monitoring, the efficacy of 10+ years of conservation efforts for longfin smelt remain uncertain due to a limited understanding of how the species responds to environmental variation, such as salinity. For example, high mortality during larval stages has prevented culture efforts from closing the life cycle in captivity. Here, we investigated the effects of salinity on longfin smelt yolk-sac larvae. Newly hatched larvae from four single-pair crosses were acutely transferred to and reared at salinities of 0.4, 5, 10, 20 or 32ppt. We compared whole-body water and sodium ion (Na+) content, notochord length and yolk-sac volume at 12, 24, 48, 72, and 96hours post-transfer for each salinity treatment. We found that larvae maintained osmotic and ionic balance at 0.4-10ppt, whereas salinities ˃10ppt resulted in decreased water and increased whole-body Na+ content. We also found that larvae grew largest and survived the longest when reared at 5 and 10ppt, respectively, and that yolk resorption stalled at 0.4ppt. Finally, there were significant but small interclutch variations in responses to different salinities, with clutch accounting for <8% of the variance in our statistical models. Overall, our results indicate that longfin smelt yolk-sac larvae likely perform best at moderately brackish conditions, thus yielding a mechanism that explains their distribution in field surveys and providing key information for future conservation efforts.

Space-for-time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay-Delta.

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.

Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

AbstractFood 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 (&lt;0.5 mm) copepod Limnoithona tetraspina much more 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 cnidarian Hydra oligactis, the polychaete Dasybranchus sp., and the copepod Mesocyclops pehpeiensis, a species not previously described in the San Francisco Estuary. Our findings illustrate the power of molecular methods in revealing feeding patterns and novel plankton diversity that can be undetectable with complementary morphological analysis methods.