Complex life histories discovered in a critically endangered fish

Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery

A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.

Monitoring post-spawning movement, habitat use, and survival of adult anadromous rainbow smelt using acoustic telemetry in a New Hampshire estuary

Anadromous rainbow smelt (Osmerus mordax, [Mitchill 1814]) are found along the northeast Atlantic coastline of North America, with their range now limited to north of Cape Cod, Massachusetts, USA. Although their anadromous life cycles are described broadly, gaps remain regarding how adult rainbow smelt use estuaries post-spawning, including movement behaviors, habitats used, and specific timing of emigration to coastal waters. In spring 2021, we used acoustic telemetry to characterize movements during and after the spawning season of rainbow smelt captured in tributaries to Great Bay, New Hampshire, USA, a large estuarine system near the southern edge of their range. Forty-four adult rainbow smelt (n = 35 male, n = 9 female) were tagged with Innovasea V5 180-kHz transmitters and an array of 22,180 kHz VR2W receivers were deployed throughout Great Bay to detect movements of tagged fish from March to October 2021. Rainbow smelt were detected 14,186 times on acoustic telemetry receivers, with 41 (93%) of the tagged individuals being detected at least once post-tagging. Individuals were detected moving between tributaries, revealing that rainbow smelt can use multiple rivers during the spawning season (March-April). Mark-recapture Cormack-Jolly-Seber models estimated 83% (95% confidence interval 66%-92%) of rainbow smelt survived to the mainstem Piscataqua River, and a minimum of 50% (22 of 44) reached the seaward-most receivers and were presumed to have survived emigration. Most individuals that survived remained in the estuary for multiple weeks (average = 19.47 ± 1.99 standard error days), displaying extended use of estuarine environments. Downstream movements occurred more frequently during ebb tides and upstream movements with flood tides, possibly a mechanism to reduce energy expenditures. Fish emigrated from the estuary by mid-May to the coastal Gulf of Maine. Our results underscore that rainbow smelt need access to a variety of habitats, including multiple tributaries and high-quality estuarine habitat, to complete their life cycle.

Interactive Effects of Salinity and Mosquito Larvicides Toxicity to Larvae of Aedes Taeniorhynchus

Understanding the influence of salinity on the efficacy of mosquito larvicides in brackish water habitats is crucial for effective salt-marsh Aedes taeniorhynchus control. This study investigated the interactive effects of salinity on the toxicity of 3 commonly used mosquito larvicides: Bacillus thuringiensis israelensis (VectoBac® 12AS), spinosad (Natular® SC), and S-methoprene (Altosid® 12AS) against Ae. taeniorhynchus larvae. Four salinity levels (0 ppt [parts per thousand], 8 ppt, 16 ppt, and 32 ppt) were tested in laboratory bioassays. The results revealed distinct responses of these larvicides to varying salinity levels. VectoBac 12AS displayed consistent efficacy across all salinity levels, indicating its suitability for brackish water habitats. In contrast, Natular 2EC exhibited increased effectiveness with higher salinity, making it a preferable choice for saline environments. Altosid 12AS showed its highest efficacy in freshwater, with reduced effectiveness as salinity increased. These findings underscore the need to consider salinity levels when selecting and applying mosquito larvicides in diverse aquatic habitats. Understanding the complex interplay between salinity and larvicide performance is essential for optimizing mosquito control strategies and mitigating mosquito-borne diseases in various environments.

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Effects of turbidity, temperature and predation cue on the stress response of juvenile delta smelt

The San Francisco Estuary (SFE) is one of the most degraded ecosystems in the United States, and organisms that inhabit it are exposed to a suite of environmental stressors. The delta smelt (Hypomesus transpacificus), a small semi-anadromous fish endemic to the SFE and considered an indicator species, is close to extinction in the wild. The goal of this study was to investigate how environmental alterations to the SFE, such as reductions in turbidities, higher temperatures and increased prevalence of invasive predators affect the physiology and stress response of juvenile delta smelt. Juvenile delta smelt were exposed to two temperatures (17 and 21°C) and two turbidities (1-2 and 10-11 NTU) for 2 weeks. After the first week of exposure, delta smelt were exposed to a largemouth bass (Micropterus salmoides) predator cue at the same time every day for 7 days. Fish were measured and sampled on the first (acute) and final (chronic) day of exposures to predator cues and later analyzed for whole-body cortisol, glucose, lactate, and protein. Length and mass measurements were used to calculate condition factor of fish in each treatment. Turbidity had the greatest effect on juvenile delta smelt and resulted in reduced cortisol, increased glucose and lactate, and greater condition factor. Elevated temperatures reduced available energy in delta smelt, indicated by lower glucose and total protein, whereas predator cue exposure had negligible effects on their stress response. This is the first study to show reduced cortisol in juvenile delta smelt held in turbid conditions and adds to the growing data that suggest this species performs best in moderate temperatures and turbidities. Multistressor experiments are necessary to understand the capacity of delta smelt to respond to the multivariate and dynamic changes in their natural environment, and results from this study should be considered for management-based conservation efforts.

Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.

Graphical abstract

Diversity of life history and population connectivity of threadfin fish Eleutheronema tetradactylum along the coastal waters of Southern China

Understanding the diversity of life history, life stage connectivity and population is essential to determine the spatial scale over which fish populations operate. Otolith microchemistry analysis is a powerful tool to elucidate the life history and population connectivity of fish, providing important insights to the natal origin and population structure. In this study, we used laser ablation inductively coupled plasma mass spectrometry to analyze the chemical composition of otoliths throughout the entire lifetime of endangered fourfinger threadfin species, Eleutheronema tetradactylum. We reconstructed the life history of E. tetradactylum from Southern China collected from different locations over a spatial scale of 1200 km. Sr:Ca and Ba:Ca ratios profiles from otolith core-to-edge analysis suggested two contrasting life history patterns. Based on the differences in early life stages, we identified some fish spending their first year in an estuarine environment with subsequent movement to marine coastal systems, while some fish remaining in the coastal systems throughout their entire early life history stages. The non-metric multi-dimensional scaling showed a strong overlap in otolith core elemental composition, indicating a large-scale connectivity in the life history of E. tetradactylum. The immature fish from different natal origins mixed to a large extent when they fed and overwintered in the extensive offshore waters. Clustering of near core chemistry pointed to three possible sources of nursery for the threadfin fish. This study demonstrated the diversity of life history patterns of E. tetradactylum in Southern Chinese waters. Restoration in egg and larvae densities in coastal waters and estuaries may enhance their population abundances.

Comparative behavioral ecotoxicology of Inland Silverside larvae exposed to pyrethroids across a salinity gradient

Pyrethroids, a class of commonly used insecticides, are frequently detected in aquatic environments, including estuaries. The influence that salinity has on organism physiology and the partitioning of hydrophobic chemicals, such as pyrethroids, has driven interest in how toxicity changes in saltwater compared to freshwater. Early life exposures in fish to pyrethroids cause toxicity at environmentally relevant concentrations, which can alter behavior. Behavior is a highly sensitive endpoint that influences overall organism fitness and can be used to detect toxicity of environmentally relevant concentrations of aquatic pollutants. Inland Silversides (Menidia beryllina), a commonly used euryhaline model fish species, were exposed from 5 days post fertilization (~1-day pre-hatch) for 96 h to six pyrethroids: bifenthrin, cyfluthrin, cyhalothrin, cypermethrin, esfenvalerate and permethrin. Exposures were conducted at three salinities relevant to brackish, estuarine habitat (0.5, 2, and 6 PSU) and across 3 concentrations, either 0.1, 1, 10, and/or 100 ng/L, plus a control. After exposure, Inland Silversides underwent a behavioral assay in which larval fish were subjected to a dark and light cycle stimuli to determine behavioral toxicity. Assessment of total distanced moved and thigmotaxis (wall hugging), used to measure hyper/hypoactivity and anxiety like behavior, respectively, demonstrate that even at the lowest concentration of 0.1 ng/L pyrethroids can induce behavioral changes at all salinities. We found that toxicity decreased as salinity increased for all pyrethroids except permethrin. Additionally, we found evidence to suggest that the relationship between log K_OW and thigmotaxis is altered between the lower and highest salinities.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Temperature and salinity preferences of endangered Delta Smelt (Hypomesus transpacificus, Actinopterygii, Osmeridae)

Temperature and salinity often define the distributions of aquatic organisms. This is at least partially true for Delta Smelt, an imperiled species endemic to the upper San Francisco Estuary. While much is known about the tolerances and distribution of Delta Smelt in relation to these parameters, little is known regarding the temperature and salinity preferences of the species. Therefore, the temperature and salinity preferences of sub-adult Delta Smelt were investigated across a wide range of thermal (8–28 °C) and salinity (0–23 ppt) conditions. Replicates of ten fish were allowed to swim between two circular chambers with different temperature or salinity, and the distribution of fish between the chambers was recorded. We found that Delta Smelt showed no temperature preference below 15 °C, a modest aversion to the warmer tank from 15 to 28 °C, and a strong aversion to the warmer tank with elevated mortality at temperatures above 28 °C. Delta Smelt also preferred lower salinities, and this preference became more pronounced as salinity increased toward 23 ppt. These results indicate that Delta Smelt can tolerate high temperatures and salinities for a short time, and that their preferences for lower temperature and salinity strengthens as these variables increase.

Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient

Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state-space models using age-0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4- to 3.5-fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6-fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity-life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function.

Broad Whitefish (Coregonus nasus) isotopic niches: Stable isotopes reveal diverse foraging strategies and habitat use in Arctic Alaska

Understanding the ecological niche of some fishes is complicated by their frequent use of a broad range of food resources and habitats across space and time. Little is known about Broad Whitefish (Coregonus nasus) ecological niches in Arctic landscapes even though they are an important subsistence species for Alaska’s Indigenous communities. We investigated the foraging ecology and habitat use of Broad Whitefish via stable isotope analyses of muscle and liver tissue and otoliths from mature fish migrating in the Colville River within Arctic Alaska. The range of δ¹³C (-31.8– -21.9‰) and δ¹⁵N (6.6–13.1‰) across tissue types and among individuals overlapped with isotope values previously observed in Arctic lakes and rivers, estuaries, and nearshore marine habitat. The large range of δ¹⁸O (4.5–10.9‰) and δD (-237.6– -158.9‰) suggests fish utilized a broad spectrum of habitats across elevational and latitudinal gradients. Cluster analysis of muscle δ¹³Cˈ, δ¹⁵N, δ¹⁸O, and δD indicated that Broad Whitefish occupied four different foraging niches that relied on marine and land-based (i.e., freshwater and terrestrial) food sources to varying degrees. Most individuals had isotopic signatures representative of coastal freshwater habitat (Group 3; 25%) or coastal lagoon and delta habitat (Group 1; 57%), while individuals that mainly utilized inland freshwater (Group 4; 4%) and nearshore marine habitats (Group 2; 14%) represented smaller proportions. Otolith microchemistry confirmed that individuals with more enriched muscle tissue δ¹³Cˈ, δD, and δ¹⁸O tended to use marine habitats, while individuals that mainly used freshwater habitats had values that were less enriched. The isotopic niches identified here represent important foraging habitats utilized by Broad Whitefish. To preserve access to these diverse habitats it will be important to limit barriers along nearshore areas and reduce impacts like roads and climate change on natural flow regimes. Maintaining these diverse connected habitats will facilitate long-term population stability, buffering populations from future environmental and anthropogenic perturbations.

Identifying Environmental Factors Limiting Recovery of an Imperiled Estuarine Fish

Correctly identifying the environmental factors that limit population growth and recovery of imperiled species is an essential element of any targeted conservation program. Abundance index values for delta smelt (Hypomesus transpacificus), an imperiled fish in the upper San Francisco Estuary, have exhibited substantial inter-annual variation and the population is now at historically low numbers. Drawing from conceptual ecological models, we developed and applied a new multivariate analytical technique that incorporates a fundamental characteristic of limiting environmental factors– recognition that certain factors influence abundance in certain seasons or years, but they may have no influence on the species’ performance at other times. We observe that delta smelt occasionally experience years with population size increases, despite their ongoing long-term downward trajectory in numbers. The differences in environmental conditions that occur in years that prompt different population responses can provide insight into the environmental factors that limit species recovery. Nine temporally and spatially explicit covariates emerged from analyses that explain changes in inter-annual delta smelt abundance indices. We contrast those environmental factors with the factors that influence occupancy because distinguishing and focusing conservation actions on factors affecting delta smelt performance, rather than occupancy, should lead to the implementation of management and habitat-restoration actions that are more likely to benefit the fish. We think that the approach taken in this study can be a model for other species where salient data are limited and information needs are pressing.

Strontium isotopes reveal diverse life history variations, migration patterns, and habitat use for Broad Whitefish (Coregonus nasus) in Arctic, Alaska

Conservation of Arctic fish species is challenging partly due to our limited ability to track fish through time and space, which constrains our understanding of life history diversity and lifelong habitat use. Broad Whitefish (Coregonus nasus) is an important subsistence species for Alaska's Arctic Indigenous communities, yet little is known about life history diversity, migration patterns, and freshwater habitat use. Using laser ablation Sr isotope otolith microchemistry, we analyzed Colville River Broad Whitefish 87Sr/86Sr chronologies (n = 61) to reconstruct movements and habitat use across the lives of individual fish. We found evidence of at least six life history types, including three anadromous types, one semi-anadromous type, and two nonanadromous types. Anadromous life history types comprised a large proportion of individuals sampled (collectively, 59%) and most of these (59%) migrated to sea between ages 0-2 and spent varying durations at sea. The semi-anadromous life history type comprised 28% of samples and entered marine habitat as larvae. Nonanadromous life history types comprised the remainder (collectively, 13%). Otolith 87Sr/86Sr data from juvenile and adult freshwater stages suggest that habitat use changed in association with age, seasons, and life history strategies. This information on Broad Whitefish life histories and habitat use across time and space will help managers and conservation planners better understand the risks of anthropogenic impacts and help conserve this vital subsistence resource.

Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance

Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought.

Decline in Thermal Habitat Conditions for the Endangered Delta Smelt as Seen from Landsat Satellites (1985-2019)

This study uses Landsat 5, 7, and 8 level 2 collection 2 surface temperature to examine habitat suitability conditions spanning 1985-2019, relative to the thermal tolerance of the endemic and endangered delta smelt (Hypomesus transpacificus) and two non-native fish, the largemouth bass (Micropterus salmoides) and Mississippi silverside (Menidia beryllina) in the upper San Francisco Estuary. This product was validated using thermal radiometer data collected from 2008 to 2019 from a validation site on a platform in the Salton Sea (RMSE = 0.78 °C, r = 0.99, R² = 0.99, p < 0.01, and n = 237). Thermally unsuitable habitat, indicated by annual maximum water surface temperatures exceeding critical thermal maximum temperatures for each species, increased by 1.5 km² yr^-1 for the delta smelt with an inverse relationship to the delta smelt abundance index from the California Department of Fish and Wildlife (r = -0.44, R² = 0.2, p < 0.01). Quantile and Theil-Sen regression showed that the delta smelt are unable to thrive when the thermally unsuitable habitat exceeds 107 km². A habitat unsuitable for the delta smelt but survivable for the non-natives is expanding by 0.82 km² yr^-1. Warming waters in the San Francisco Estuary are reducing the available habitat for the delta smelt.

Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish

Background

The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE.

Methods

Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt.

Results

Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.

Romain SJ, Pedersen EI, Siddiqui S, Chappell PE, White JW, Armbrust KL, Brander SM. Salinity Alters Toxicity of Commonly Used Pesticides in a Model Euryhaline Fish Species (Menidia beryllina)

Changing salinity in estuaries due to sea level rise and altered rainfall patterns, as a result of climate change, has the potential to influence the interactions of aquatic pollutants as well as to alter their toxicity. From a chemical property point of view, ionic concentration can increase the octanol–water partition coefficient and thus decrease the water solubility of a compound. Biologically, organism physiology and enzyme metabolism are also altered at different salinities with implications for drug metabolism and toxic effects. This highlights the need to understand the influence of salinity on pesticide toxicity when assessing risk to estuarine and marine fishes, particularly considering that climate change is predicted to alter salinity regimes globally and many risk assessments and regulatory decisions are made using freshwater studies. Therefore, we exposed the Inland Silverside (Menidia beryllina) at an early life stage to seven commonly used pesticides at two salinities relevant to estuarine waters (5 PSU and 15 PSU). Triadimefon was the only compound to show a statistically significant increase in toxicity at the 15 PSU LC₅₀. However, all compounds showed a decrease in LC₅₀ values at the higher salinity, and all but one showed a decrease in the LC₁₀ value. Many organisms rely on estuaries as nurseries and increased toxicity at higher salinities may mean that organisms in critical life stages of development are at risk of experiencing adverse, toxic effects. The differences in toxicity demonstrated here have important implications for organisms living within estuarine and marine ecosystems in the Anthropocene as climate change alters estuarine salinity regimes globally.

Salinity Changes the Dynamics of Pyrethroid Toxicity in Terms of Behavioral Effects on Newly Hatched Delta Smelt Larvae

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.

Strontium and Oxygen Isotope Analyses Reveal Late Cretaceous Shark Teeth in Iron Age Strata in the Southern Levant

Skeletal remains in archaeological strata are often assumed to be of similar ages. Here we show that combined Sr and O isotope analyses can serve as a powerful tool for assessing fish provenance and even for identifying fossil fish teeth in archaeological contexts. For this purpose, we established a reference Sr and O isotope dataset of extant fish teeth from major water bodies in the Southern Levant. Fossil shark teeth were identified within Iron Age cultural layers dating to 8–9th century BCE in the City of David, Jerusalem, although the reason for their presence remains unclear. Their enameloid 87Sr/86Sr and δ18OPO4 values [0.7075 ± 0.0001 (1 SD, n = 7) and 19.6 ± 0.9‰ (1 SD, n = 6), respectively], are both much lower than values typical for modern marine sharks from the Mediterranean Sea [0.7092 and 22.5–24.6‰ (n = 2), respectively]. The sharks’ 87Sr/86Sr are also lower than those of rain- and groundwater as well as the main soil types in central Israel (≥0.7079). This indicates that these fossil sharks incorporated Sr (87Sr/86Sr ≈ 0.7075) from a marine habitat with values typical for Late Cretaceous seawater. This scenario is in line with the low shark enameloid δ18OPO4 values reflecting tooth formation in the warm tropical seawater of the Tethys Ocean. Age estimates using 87Sr/86Sr stratigraphy place these fossil shark teeth at around 80-million-years-old. This was further supported by their taxonomy and the high dentine apatite crystallinity, low organic carbon, high U and Nd contents, characteristics that are typical for fossil specimens, and different from those of archaeological Gilthead seabream (Sparus aurata) teeth from the same cultural layers and another Chalcolithic site (Gilat). Chalcolithic and Iron Age seabream enameloid has seawater-like 87Sr/86Sr of 0.7091 ± 0.0001 (1 SD, n = 6), as expected for modern marine fish. Fossil shark and archaeological Gilthead seabream teeth both preserve original, distinct enameloid 87Sr/86Sr and δ18OPO4 signatures reflecting their different aquatic habitats. Fifty percent of the analysed Gilthead seabream teeth derive from hypersaline seawater, indicating that these seabreams were exported from the hypersaline Bardawil Lagoon in Sinai (Egypt) to the Southern Levant since the Iron Age period and possibly even earlier.

Use of affinity analysis to guide habitat restoration and enhancement for the imperiled delta smelt

Habitat restoration efforts in the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, California, move forward, despite a paucity of information on the environmental requirements of many targeted species. The endemic delta smelt Hypomesus transpacificus, protected under the federal Endangered Species Act, is a primary focus of those efforts despite uncertainties regarding many aspects of its relationship with the estuary’s physical and biotic resources. Here we use time-series data from 4 trawl surveys and data on environmental attributes collected from throughout the delta smelt’s distribution to identify ranges of conditions acceptable to delta smelt for each of 5 environmental attributes: water-body type, temperature, turbidity, salinity, and prey availability. Low turbidity and elevated water temperatures render a large portion of the estuary seasonally unsuitable for delta smelt. Within areas in which water quality is suitable, patterns of delta smelt occurrences indicate that habitat is found in subregions where channels of intermediate depth adjoin shallow water. In certain subregions, conditions are inadequate for at least one of the environmental attributes for periods up to several months. We suggest a habitat-restoration strategy that can achieve adequate habitat conditions for delta smelt regardless of through-Delta flow levels, and which can be carried out at a number of locations, but not necessarily the same locations, during each life stage.

Histopathological assessment of seven year-classes of Delta Smelt

The Delta Smelt (Hypomesus transpacificus) is an imperiled, annual fish endemic to the Sacramento-San Joaquin Delta and San Francisco Estuary. This study examined the severity and prevalence of liver and gill lesions of juvenile through adult Delta Smelt from 2011 through 2017 collected from five regions throughout its habitat (n = 1,053). The first and last years of the study were wet, but bracketed an extreme drought in CA (2012-2016), during which the Delta Smelt population reached historical lows. Overall, the three most common lesions were gill ionocyte hyperplasia, liver lipidosis, and gill aneurysm. Individuals with higher fork lengths exhibited increased gill and liver lesion score (summations of the severity scores), suggesting that Delta Smelt accumulate lesions through their lives, and that larger individuals were more tolerant of liver and gill lesions. Liver lesion score showed significant regional differences, while salinity was a better predictor of gill lesions than region, with lower gill lesion scores associated with higher salinities. Largely consistent with previously reported histopathology patterns, Delta Smelt collected from the Confluence and Suisun Marsh had the lowest liver lesion score, while Delta Smelt collected from Cache Slough and Suisun Bay had the highest lesion scores, and Suisun Marsh had the lowest glycogen depletion, suggesting heterogeneous levels of exposure to environmental stressors across regions. Gill and liver lesion score also varied significantly with year-class. The highest gill lesion score occurred in the 2015/16 year-class, and the lowest occurred in the 2017/18 year-class, a 2.8-fold difference. Controlling for size and regional effects, individuals with comparatively high liver lesion scores were prevalent in the population until the 2014/15 year-class. In the two subsequent year-classes, Delta Smelt livers were in the best condition, coinciding with peak drought conditions and record low abundances.

Factors Controlling Calanoid Copepod Biomass and Distribution in the Upper San Francisco Estuary and Implications for Managing the Imperiled Delta Smelt (Hypomesus transpacificus)

Delta smelt struggle to persist in a dramatically altered estuarine environment. Complex and incompletely understood relationships between food availability, environmental stressors, other components of the species' habitat, and the abundance of delta smelt impede the effective management and recovery of the species. The empirical modeling presented in this study quantitatively describes spatial-temporal biomass values of calanoid copepods, a key prey item for delta smelt, in relation to multiple potential controlling factors. The results underscore the role that river flows through the estuary have in determining prey availability, and demonstrate contributions of water temperature, salinity, and macronutrients in determining copepod biomass. The analysis also shows the importance of non-native, invasive bivalves in determining copepod biomass. Importantly, the analysis describes spatial-temporal shifts in the relative importance of modeled covariates across sampling locations in the Delta. Model results indicate that increasing flows in the fall of wetter years adversely affected copepod biomass, while increases in flows in the spring of drier years provided regional increases in biomass. The results of this analysis can inform resource management decisions and contribute to a comprehensive model that can meaningfully guide efforts to recover the imperiled delta smelt.