Ecosystem analysis of pelagic organism declines in the Upper San Francisco Estuary

• Erica Fleishman

Abstract
In late 2004, scientists noted that abundance indices of several pelagic fishes in the upper San Francisco Estuary (delta smelt, age-0 striped bass, longfin smelt, and threadfin shad) had remained unusually low since 2001. Delta smelt is an endemic species listed as threatened under both the California and U.S. Endangered Species Acts. Protection of delta smelt often determines water management actions in the estuary, which supplies drinking water to more than 22 million people and supports a multi-billion dollar agricultural industry. The abundance of longfin smelt, another native species, has a strong positive relationship to freshwater outflow. Striped bass and threadfin shad are both introduced species that contribute substantially to the total biomass of pelagic fishes in the ecosystem and support valuable recreational fisheries. NCEAS and the Interagency Ecological Program are collaborating to convene several working groups on issues related to decline of pelagic organisms. We hope not only to gain a better understanding of the specific causes and mechanisms behind the organism declines in the San Francisco Estuary, but to place these declines in the broader context of estuarine degradation, organism declines, and approaches to solving these problems in other geographic regions. Among other goals, we seek to examine simultaneously the effects of multiple potential drivers on one or more fishes. Further, we aim to investigate whether fishes differ in their response to given drivers. We also wish to explore the ability of Bayesian analysis, path analysis, or other modeling approaches to draw inference regarding ecological relationships among pelagic fishes, human actions, and inherent variability in the estuarine system.