Joseph E. Merz, Paul S. Bergman, Joseph L. Simonis, David Delaney, James Pierson, Paul Anders: Long-Term Seasonal Trends in the Prey Community of Delta Smelt (Hypomesus transpacificus) Within the Sacramento-San Joaquin Delta, California (2016)

We present the first evidence of a shift in the timing of peak abundance for zooplankton species that are key prey items of delta smelt, a federally threatened pelagic fish species. These timing shifts may have exacerbated well-documented food limitations of delta smelt due to declines in primary productivity since the invasion of the overbite clam. 

William Miller, Bryan Manly, Dennis Murphy, David Fullerton, Rob Roy Ramey: An Investigation of Factors Affecting the Decline of Delta Smelt in the Sacramento-San Joaquin Estuary (2012)

Three questions are addressed here: What is the relative importance of environmental factors with direct effects on abundance? Do factors that may have indirect effects provide an explanation of abundance changes? Are effects of environmental factors better accounted for individually or as criteria defining the volume of water with suitable abiotic attributes?

Patricia Glibert,University of Maryland: Ecological stoichiometry and its implications for aquatic ecosystem sustainability (2011)

Multiple feedbacks serve to alter food web structure when nutrient loads are altered. Such feedbacks may also lead to conditions conducive to invasive species and altered stable states as illustrated for the San Francisco Bay Delta and the Rhine River.

Mark Maunder, Richard Deriso: A state–space multistage life cycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt (2011)

Our results indicate that density dependence and a few key factors impact the delta smelt population. Temperature, prey, and predators dominated the factors supported by the data and operated on different life stages. The included factors explain the recent declines in delta smelt abundance and may provide insight into the cause of the pelagic species decline in the San Francisco Estuary.

James thomson, Wim Kimmerer, Lary Brown, et al.: Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary (2010)

We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, over 40 years using Bayesian change point models.  There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2% isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species’ abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.

James Hobbs, Levi Lewis, Naoaki Ikemiyagi, Ted Sommer, Randall Baxter: The use of otolith strontium isotopes to identify nursery habitat for a threatened estuarine fish (2010)

Our results indicate that otolith strontium isotopes are a powerful tool for identifying nursery habitats for estuarine fishes.  Low salinity habitats disproportionally contributed more recruits relative to both freshwater and brackish water habitats and, therefore, may function as important nursery areas. Furthermore, the relative importance of the low salinity zone to successful recruitment appeared greatest in years following the longfin smelt population decline.

Patricia Glibert, University of Maryland: Long-term Changes in Nutrient Loading and Stoichiometry and their Relationships with Changes in the Food Web and Dominant Pelagic Fish Species in the San Francisco Estuary, California (2010)

This analysis tests the hypothesis that changes in nutrient loads, imbalances in nitrogen: phosphorus, and changes in nitrogen form, especially shifts to increasing loads of chemically reduced, rather than oxidized nitrogen, can have major impacts on food webs, from primary producers through secondary producers to fish.

Ralph McNally, James Thomson, Wim Kimmerer, et al.: Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (2010)

Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt, longfin smelt, striped bass, and threadfin shad. Our application of the MAR model provides evidence from a multivariate analysis of how abiotic habitat factors directly relate to declining fish abundance in the upper San Francisco Estuary and indirectly to these fish populations through the food web.

Wim Kimmerer, Edward Gross, Michael L. MacWilliams: Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume? (2009)

In this paper, we determine how the quantity of habitat for estuarine nekton, defined by salinity and water depth, responds to changes in freshwater flow in the San Francisco Estuary and the extent to which species-specific habitat responses translate to flow responses. 

William Bennett, UC Davis: Critical Assessment of the Delta Smelt Population in the San Francisco Estuary, California (2005)

Overall, a better understanding of the life history, habitat requirements, and limiting factors will be essential for developing tools for management and restoration.  therefore, given the implications for managing California water supply and the current state of population abundance, a good investment would be to fill the critical data gaps outlined here through a comprehensive program of research.

Wim Kimmerer, San Francisco State University: Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses (2004)

This paper reviews the current state of knowledge of the open waters of the San Francisco Estuary. Opportunities for restoration in the open waters of the estuary are somewhat limited by the lack of scientific basis for restoration, and the difficulty in detecting ecosystem responses in the context of high natural variability.

Paciencia Young, Joseph Cech Jr: Environmental Tolerances and Requirements of Splittail  (1996)

The range of splittail PogolliciJlhys macro/epidollls has decreased to less than a third of its original range due to loss or alteration of habitats. A lack of sufficient flooded vegetation for spawning and rearing. narrower environmental tolerances of other life stages (i.e .. eggs. larvae. and adult spawners). or biotic factors (e.g., predation. competition) may be limiting splittail abundance and distribution. 

For species descriptions visit the follow pages: