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Objective: To support the declining wild population of Delta Smelt, a conservation hatchery has expanded its mission from maintaining a backup population as insurance against extinction to also producing fish for release into the wild. The substantially higher production demands require a balance between producing large numbers of fish while adhering to conservation genetic principles that maximize retention of effective population size (Ne) and thus overall diversity. Methods: We performed spawning experiments at the hatchery to evaluate the genetic consequences of two spawning strategies: (1) a pooled strategy where we fertilized premixed eggs from three dams with premixed milt from three sires and (2) a partial-factorial strategy where eggs from three dams were mixed and then apportioned among three containers, each container then receiving milt from one sire. We used genetic parentage analysis of larval offspring to determine the reproductive success of spawners in 10 replicate crosses of each strategy. Result: The contributions of parents to offspring were more even in partial-factorial crosses and consequently resulted in higher Ne (average Ne = 5.50 ± 0.38; expected Ne = 6.0), suggesting its potential for maintaining genetic diversity over time. In contrast, our pooled spawning experiment produced lower and more variable Ne values (average Ne = 3.86 ± 1.30), demonstrating that this more efficient method of production entails high costs in terms of long-term genetic management. Treating our experiments as hypothetical pools of fish for release, we combined the Ne values for pooled or partial-factorial crosses to calculate the effective size of a release population (NeR). Unequal family sizes reduced NeR for our pooled experiment to half of the expected value, whereas the partial-factorial experiment NeR was 88% of the expected value. Conclusion: We discuss the benefits and risks of each method and how these can be considered when designing a spawning strategy for Delta Smelt supplementation.

Accurate species identification is critical to monitoring programs because mis-identifications can lead to incorrect assessments of population status and trends. In the San Francisco Estuary, efforts to monitor the imperiled osmerid Delta Smelt (Hypomesus transpacificus) using morphology can be challenging because of the presence of the similar-looking non-native osmerid Wakasagi (Hypomesus nipponensis). In 2017, the US Fish and Wildlife Service’s field office in Lodi implemented a two-stage verification process for Wakasagi to help prevent Delta Smelt from being mis-identified as Wakasagi. Under this process, Wakasagi are initially identified in the field, independently identified a second time by an experienced staff member in the laboratory, then stored on-site where they can be made available for future studies. Using the recently developed Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) assay for Wakasagi, we evaluated how well verification protocols performed by genetically identifying a subset of Wakasagi collected during routine sampling between 2017 and 2021. Through this study, we found that the protocols have served as an effective quality control measure for over 4 years and across multiple surveys. With the development of field-deployable genetics tools such as SHERLOCK, genetic identification will likely play an increasingly important role in ecological monitoring. We expect that hybrid approaches that combine morphological identifications by trained field crew with application of field-based genetic tools may offer an effective and efficient approach to ensuring data accuracy in the future.

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

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.

While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento–San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter “first flush” flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km/d, a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently “hold” in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.