Predators can influence the structure and function of ecosystems by altering the composition or behavior of herbivore communities. Overexploitation of predators, therefore, may lead to habitat loss by altering important top‐down interactions that facilitate habitat‐forming species. In seagrass beds, top‐down control of algal growth by mesograzers appears to facilitate seagrass production. The indirect consequences of higher‐order trophic interactions, however, remain unclear. Although predators may limit the beneficial effects of algal mesograzers, it is also possible that they limit the abundance of invertebrates that consume and foul seagrasses. We used experimental enclosure and exclosure cages to explore the direct and indirect effects of microcarnivorous fishes on epifaunal invertebrates, epiphytic loads, and seagrass growth in a natural eelgrass (Zostera marina) bed in San Diego Bay, California, USA. Contrary to expectations, when fishes were excluded, invertebrate abundance increased by 300–1000%, fouling on eelgrass leaves increased by 600%, and eelgrass production declined by 50%. Despite high densities of predators in enclosures, subsequent effects did not differ from ambient conditions. When predators were excluded, however, abundances of epifauna (including tube‐building crustaceans and an eelgrass‐grazing limpet) increased dramatically, resulting in reduced seagrass production. Our results are supported by several studies of eelgrass communities in the northeastern Pacific, characterized by coastal upwelling, inverse estuaries, and a voracious seagrass‐consuming limpet. These strong, positive, indirect effects of microcarnivores on seagrass production contrast with the beneficial mesograzer paradigm, highlighting the need for hypotheses to be tested across a variety of ecosystems with varying biophysical characteristics.

Effective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California’s endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized “hot-spots” of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.

A comprehensive understanding of the life history strategies and habitat use of species is essential for developing accurate ecological models and effective management and conservation strategies. For example, omitting critical habitats of endangered species when estimating their abundance and when designing conservation plans for them can severely limit our understanding of population dynamics and lead to poor management outcomes.

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.

Chinook Salmon (Oncorhynchus tshawytscha) populations in California are in decline due to the combined effects of habitat degradation, water diversions, and climate change. Reduced life‐history diversity within these populations inhibits their ability to respond to these stressors. Putah Creek, a small creek in California’s Central Valley that once supported Chinook Salmon, is undergoing restoration to provide spawning habitats for this imperiled species. Beginning in 2014, increasing numbers of Chinook Salmon spawned throughout the creek and emigrating juveniles were observed in the following months. Here we used otolith annual growth bands and microchemistry to investigate the age structure and natal origins of the adult spawners. Most individuals were 2 or 3 years old and originated from at least seven different natal sources, overwhelmingly from Central Valley hatcheries (~88%). These findings highlight that straying fall‐run Central Valley Chinook Salmon can rapidly utilize restored habitats, potentially establishing new populations. However, to facilitate local adaptations, straying rates and gene flow will have to be managed over time. Reconnecting migratory pathways and restoring many small and diverse streams like Putah Creek thus provides an opportunity to increase life‐history diversity, strengthening the recovery and resilience of Chinook Salmon.