This paper reviews what has been learned about Delta Smelt and its status since the publication of The State of Bay-Delta Science, 2008 (Healey et al. 2008). The Delta Smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain the population. As a listed species living in the central node of California's water supply system, Delta Smelt has been the focus of a large research effort to understand causes of decline and identify ways to recover the species. Since 2008, a remarkable record of innovative research on Delta Smelt has been achieved, which is summarized here. Unfortunately, research has not prevented the smelt's continued decline, which is the result of multiple, interacting factors. A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta. Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed Delta Smelt to record low levels in 2014-2015. The rapid decline of the species and failure of recovery efforts demonstrate an inability to manage the Delta for the "co-equal goals" of maintaining a healthy ecosystem and providing a reliable water supply for Californians. Diverse and substantial management actions are needed to preserve Delta Smelt.

To investigate the timing of the initial entry of green sturgeon Acipenser medirostris into seawater, we examined the ratios of strontium and barium to calcium in pectoral fin rays via laser ablationinductively coupled plasma-mass spectrometry. In a reference group of six hatchery fish that was reared 1-2 years in freshwater and 1-3 years in seawater, we found a significant increase in the Sr:Ca ratio, a decrease in the Ba:Ca ratio, and an increase in the Sr:Ba ratio in calcified growth zones during the transition from freshwater to seawater. In 10 wild adults captured in the Klamath River, California, combined evaluation of the Sr:Ca and Ba:Ca ratios provided a clearer understanding of fish movements than the Sr:Ba ratio, probably because wild fish have a more complex life history. The Ba:Ca ratio dropped significantly between growth zones 1 and 2 (ages 0.5-1.5), indicating a transition into saline waters, such as the Klamath River estuary. The Sr:Ca ratio increased slightly in the same location but attained the values found in reference fish held in seawater between growth zones 3 and 4 (ages 2.5-3.5). The Sr:Ca, Ba:Ca, and Sr:Ba ratios in growth zones 4-6 (ages 4.5-6.5) of wild fish were similar to those found in reference fish held in seawater and corroborated the results of previous physiological studies as well as the limited field data. These results demonstrate the usefulness of trace element analyses of green sturgeon pectoral fin rays and confirm an early age of entry into seawater for this species.

The abundance of Delta Smelt (Hypomesus transpacificus), a fish species endemic to the upper San Francisco Estuary (SFE), is declining. Several causes for the population decline have been proposed, including food limitation and contaminant effects. Here, using juvenile Delta Smelt collected from throughout their range, we measured a suite of indices across three levels of biological organization (cellular, organ, individual) that reflect fish condition at temporal scales ranging from hours to weeks. Using these indices, the relative conditions of fish collected from five regions in the SFE were compared: Cache Slough, Sacramento River Deep Water Ship Channel, Confluence, Suisun Bay and Suisun Marsh. Fish sampled from Suisun Bay and, to a lesser extent the Confluence, exhibited relatively poor short-term nutritional and growth indices and morphometric condition, while fish from the freshwater regions of the estuary, and Cache Slough in particular, exhibited the most apparent histopathological signs of contaminant exposure. In contrast, fish from the Suisun Marsh region exhibited higher short-term nutrition and growth indices, and better morphometric and histopathological condition. For instance, fish collected from Suisun Marsh had a mean stomach fullness, expressed as a percentage of fish weight, that was 3.4-fold higher than fish collected from Suisun Bay, while also exhibiting an incidence of histopathological lesions that was 11-fold lower than fish collected from Cache Slough. Thus, our findings support the hypothesis that multiple stressors, including food limitation and contaminants, are contributing to the decline of Delta Smelt, and that these stressors influence Delta Smelt heterogeneously across space.

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.

Rainbow trout (Oncorhynchus mykiss) have diverse life histories, including both freshwater-resident and anadromous “steelhead” life-history forms. Here, we demonstrate that female resident rainbow trout produce anadromous offspring that survive and return to spawn as adult steelhead. This study represents the first successful attempt to quantify steelhead production rates from female resident rainbow trout across a large watershed. Otolith microchemistry (87Sr/86Sr) techniques were used to determine the maternal life history (resident or anadromous) of 498 emigrating steelhead kelts in the Yakima Basin, Washington. Five geochemically distinct freshwater rearing regions were identified within the basin. All five regions were predicted to produce steelhead with resident maternal life histories. Basin-wide, 20% and 7% of steelhead collected in 2010 and 2011, respectively, had resident maternal life histories. Cross-life-history form production may be critical to persistence of anadromous life histories within partially anadromous salmonid populations, particularly in areas where anadromous fish abundance is low due to natural or anthropogenic influences.