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

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

Delta Smelt (Hypomesus transpacificus) Exhibit Wide Variation in Spawning Behavior: An Investigation of Substrate Type, Diel Timing, and Participants

Studies of cultured populations can be invaluable to the conservation of imperiled species for which little is known and whose very low abundance in the wild can preclude studies with robust sample sizes. For example, in endangered delta smelt (Hypomesus transpacificus), conservation measures developed to mitigate population decline are hindered by a lack of knowledge regarding spawning behavior. However, the availability of a cultured population allows important questions about spawning to be addressed experimentally. We examined the effect of substrate type on spawning behavior and egg fertilization success in cultured H. transpacificus under laboratory conditions. We also examined the diel frequency of spawning and the sex and number of spawning participants. We found that the frequency of spawns and resulting egg fertilization success did not differ between sand, gravel, and control (acrylic) substrates. We also demonstrated that spawning was predominantly nocturnal, though rare diurnal spawns were observed. Of the five mature males and five ripe females available within a given trial, spawns included up to seven participants, but most frequently occurred between a single female and one or two males. Our results highlight the wide behavioral variation exhibited by H. transpacificus during spawning, particularly in terms of substrate use, diel timing, and participants. These findings provide the most detailed and experimentally robust data regarding H. transpacificus spawning behavior to date and thereby provide ongoing conservation efforts with much-needed information.

Escape From the Heat: Thermal Stratification in a Well-Mixed Estuary and Implications for Fish Species Facing a Changing Climate

Climate change may cause organisms to seek thermal refuge from rising temperatures, either by shifting their ranges or seeking microrefugia within their existing ranges. We evaluate the potential for thermal stratification to provide refuge for two fish species in the San Francisco Estuary (SFE): Chinook Salmon (Oncorhynchus tshawytscha) and Delta Smelt (Hypomesus transpacificus). We compiled water temperature data from multiple monitoring programs to evaluate spatial, daily, hourly, intra-annual, and inter-annual trends in stratification using generalized additive models. We used our data and models to predict the locations and periods of time that the bottom of the water column could function as thermal refuge for salmon and smelt. Periods in which the bottom was cooler than surface primarily occurred during the peak of summer and during the afternoons, with more prominent stratification during warmer years. Although the SFE is often exceedingly warm for fish species and well-mixed overall, we identified potential for thermal refugia in a long and deep terminal channel for Delta Smelt, and in the periods bordering summer for Chinook Salmon. Thermal stratification may increase as the climate warms, and pockets of cooler water at depth, though limited, may become more important for at-risk fishes in the future.

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.

Simulated Fishing to Untangle Catchability and Availability in Fish Abundance Monitoring

In fisheries monitoring, catch is assumed to be a product of fishing intensity, catchability, and availability, where availability is defined as the number or biomass of fish present and catchability refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Programs often deal with this problem by assuming that catchability is constant, but if catchability is not constant, it is not possible to separate the effects of catchability and population size using monitoring data alone. This study uses individual-based simulation to separate the effects of changing environmental conditions on catchability and availability in environmental monitoring data. The simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies. Results of this study indicate that given constraints on Delta Smelt swimming ability, it is unlikely that the apparent declines in Delta Smelt abundance are the result of changing water clarity affecting catchability.

A Fish Story: Hot Water and Dangerous Behavior!

Climate change is warming up water all over the world, including in the San Francisco Estuary. This has caused fish who live there to change their behavior in unexpected ways. All animals, including fish, have regular and specialized behaviors that help them to survive. Fish swim, by themselves or in groups, to move to safer habitats, to find food or mates, or just to avoid danger. Scientists worry that changes to these behaviors brought on by warming water will make estuaries less safe for rare and endangered fish like the delta smelt. In the San Francisco Estuary, we found that warmer waters caused delta smelt to swim faster and further away from their neighbors, and to be eaten more often by predators. All these changes could hurt the ability of delta smelt to survive in the future.

Delivering Food to Hungry Fish in the San Francisco Estuary

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

What Does Not Kill Can Weaken: How Herbicides Impact Fish In The San Francisco Estuary

Farmers in the San Francisco Estuary have been using increasing amounts of weed killers, also called herbicides, on their farms. Herbicides kill unwanted weeds without hurting food crops. However, did you know that herbicides can hurt fish as well, especially those that live in the Estuary, like delta smelt? Delta smelt are small, translucent fish that only occur in the San Francisco Estuary. In the past, delta smelt could be found everywhere in the Estuary. However, they are currently threatened with extinction, largely due to human activities. In this study, we tested the toxicity of fluridone, a commonly used herbicide found in the San Francisco Estuary, on delta smelt. None of the fish died from fluridone, but we found that it weakened them, even after as little as 6 h of exposure!