Over Under Sideways Down*: Characterizing Dynamic Regime Shifts in the San Francisco Estuary (*the Yardbirds, 1966)

We evaluated the possibility that dynamic regime shifts underlie declines in native fishes over the last decade in the San Francisco Estuary and Delta. Estuaries are transitional systems between freshwater and ocean environments, and among the world's most valuable yet most damaged ecosystems. In both oceanic and freshwater systems widespread evidence for regime shifts raises the likelihood that they are also associated with declining estuarine resources. However, oceanic regime shifts appear easier to reverse, whereas in lakes they are often catastrophic (i.e. hysteresis) and largely irreversible, suggesting distinct endpoints along a continuum of dynamic responses. Thus, regime shifts in estuaries may exhibit dynamics that are similar or intermediate between ocean and lake systems, such that it may be relatively easy or extremely difficult to reverse, or restore, damaged estuaries to a more desirable state. 

We compared the relative dynamics among various ecosystem components for sub-regions along the longitudinal axis of the estuary using long-term data sets extending back to the 1970s. First, we examined the degree to which fishes in the various sub-regions could be grouped into assemblages with similar responses to changing habitat using ten metrics to define species’ life history strategies and environmental tolerances. Then a multivariate analysis distinguished several distinct fish assemblages, with groups composed of primarily exotic invasive species exhibiting distinct, or opposite, responses from native (and endangered) species. Patterns in dynamic behavior consistent with a regime shift were explored in phase space among various fish assemblages and ecosystem measures, and then we applied two techniques for detecting "leading indicators" of a pending regime shift; e.g. critical slowing down of system dynamics. Our results provide robust support for a dynamic and catastrophic regime shift occurring in the Delta region following 2000-2001. Although evidence for similar shifts was equivocal in other regions and across the entire estuary, leading indicators of a pending regime shift suggest future dramatic change may occur in sub-regions such as Suisun Marsh. Interestingly, the undesirable conditions characterizing the Delta regime shift, high water clarity, exotic submerged aquatic vegetation, and exotic centrarchid fishes, suggest the desirable regime for the Delta is the reverse of that widely reported for temperate lakes. Overall, our results suggest that estuaries, as transitional ecosystems, are likely to exhibit a variety of system dynamics along the apparent continuum between those reported for temperate lakes and the open ocean, with important implications for the potential for estuarine restoration.