Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)

Abstract

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 (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2 per thousand isohaline (a measure of the physical response of the estuary to freshwater flow) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey): Our results were relatively robust with respect to the form of stock-recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state-space models that describe more fully the life-history dynamics of the declining species.

A Conceptual Model of the Aquatic Food Web of the Upper San Francisco Estuary

“…In the 2000s, another steep decline in pelagic production and fishes became known as the "pelagic organism decline," (POD) and remains not fully explained. It includes special-status native fishes such as delta smelt (Hypomesus transpacificus) and longfin smelt (Spirinchus thaleichthys), and naturalized species such as striped bass (Morone saxatilis) and threadfin shad (Dorosoma petenense) Mac Nally et al 2009). Other native and endemic fishes are in decline, including winter-run Chinook salmon (Oncorhynchus tshawytscha) and southern green sturgeon (Acipenser medirostris).…”

“…Linkages emphasize trophic relationships that increase or reduce food supply for fish. Fish are integrators of ecosystem function (Vadeboncoeur et al 2002;Vander Zanden and Vadeboncoeur 2002), and of particular importance in the estuary because of declines Mac Nally et al 2009). Choices about inclusion in the food web were based upon direct or indirect importance to fish populations.…”

“…Fish declines after 2002, during the POD, appear to mirror declines in zooplankton, although it is uncertain whether the relationship is causal or merely correlative (Mac Nally et al 2009). Presumably, low zooplankton density limits fish foraging effectiveness.…”

Zooplankton of tidal marsh channels in relation to environmental variables in the upper San Francisco Estuary

“…Subsequently, levees on a number of these islands have either failed, or were intentionally breached to restore tidal ecosystems, resulting in reconnection of the interior marshland to the surrounding channels. These, and the remaining predevelopment tidal marshes of the SFE have come under increasing scrutiny in recent years, coincident with declines in the abundance of native and common non-native nekton species, now commonly referred to as the 'Pelagic Organism Decline' (Sommer et al 2007, Mac Nally et al 2010). This has led to intensified interest in conservation and restoration of the SFE in general (Moyle 2008), and shallow water habitats specifically (Brown 2003, Lopez et al 2006, although the exact relationship between shallow water habitat and pelagic organisms remains obscure.…”

“…Given that zooplankton are important prey items for many larval and adult fish in the SFE (Meng & Orsi 1991, Moyle et al 1992, Nobriga 2002, Bollens & Sanders 2004, Visintainer et al 2006, Cohen & Bollens 2008, Howe et al 2014, Whitley & Bollens 2014), a need exists to investigate the basic ecology of tidal marsh zooplankton. More specifically, if the composition and abundance of zooplankton in tidal marshes are found to be suitable prey resources for fish and other higher-level consumers, this could provide a critical link between shallow water habitats (Brown 2003, Lopez et al 2006) and conservation and restoration of pelagic species in the SFE (Sommer et al 2007, Moyle 2008, Mac Nally et al 2010.…”