San Francisco Estuary and Watershed Science

Abstracts are not presented with Editorials. -SFEWS Editors

The delta smelt is a small, endemic fish that resides in the upper San Francisco Estuary. They are listed under state and federal Endangered Species Acts. Since 2002, their abundance has been at record low levels. Delta smelt are entrained at state (Banks) and federal (Jones) pumping plants that export water to much of California. Export cutbacks to limit entrainment have been controversial, making delta smelt arguably the most important fish in California. Kimmerer (2008) published the first estimates of proportional entrainment (mortality relative to population size) of delta smelt at the water export pumping plants, improving on previous estimates of absolute numbers entrained. This paper comments on Kimmerer’s estimates, which ranged from 0% to 40% annually with considerable uncertainty reflecting the challenge in estimating the distribution and numbers of this scarce fish. Kimmerer’s high estimates in some recent years and his conclusion that entrainment effects could be episodically important are counter to a lack of statistically significant correlation between entrainment and subsequent abundance. Analysis herein justifies estimates of lower proportional entrainment than suggested by Kimmerer. Based on alternative assumptions, his highest annual estimates of adult proportional entrainment would have been no more than 13% and could even be in the range of 5% to 10%. Most adjustments resulting from alternative assumptions underlying high estimates of larval-juvenile proportional entrainment cannot be quantified. However, it is argued here that eight of ten key assumptions underlying those estimates resulted in upward bias. Lower estimates of proportional entrainment would be consistent with the lack of statistically significant relationships between entrainment and subsequent abundance in previous studies and suggest that assessment of the importance of entrainment awaits additional analyses that narrow uncertainty. Findings of detection problems with adult and larval-juvenile surveys suggest adding more stations and other adjustments to resolve these problems.

I previously estimated proportional losses of delta smelt to the water export facilities in the south Delta (Kimmerer 2008). This note is in response to Miller (2010), who disputes these estimated losses on several grounds. A re-analysis using a better analytical approach suggests a slight downward revision of the previous estimates for adult smelt. The distribution of smelt seems to have shifted northward in the last few years; if so, the delta smelt may now be less vulnerable to export losses than they previously were, although the reasons for such a shift are a concern. I argue, however, that it is legitimate to attempt such estimates in the absence of perfect information, and that mechanistic analyses are a valid way of estimating population-level impacts even in the absence of statistically significant correlations of estimated impact with subsequent population size.

Blue oak tree-ring chronologies correlate highly with winter–spring precipitation totals over California, with Sacramento and San Joaquin river stream flow, and with seasonal variations in the salinity gradient in San Francisco Bay. The convergence of fresh and saline currents can influence turbidity, sediment accumulation, and biological productivity in the estuary. Three selected blue oak chronologies were used to develop a 625-year-long reconstruction of the seasonal salinity gradient, or low salinity zone (LSZ), which provides a unique perspective on the interannual-to-decadal variability of this important estuarine habitat indicator. The reconstruction was calibrated with instrumental LSZ data for the winter–spring season, and explains 73% of the variance in the February–June position of the LSZ from 1956 to 2003. Because this calibration period post-dates the sweeping changes that have occurred to land cover, channel morphology, and natural streamflow regimes in California, the reconstruction provides an idealized estimate for how the LSZ might have fluctuated under the seasonal precipitation variations of the past 625 years, given the modern geometry and bathymetry of the estuary and land cover across the drainage basin. The February–June season integrates precipitation and runoff variability during the cool season, and does not extend into the late-summer dry season when LSZ extremes can negatively affect Sacramento–San Joaquin Delta (Delta) agriculture and some aquatic organisms. However, there is such strong inter-seasonal persistence in the instrumental LSZ data that precipitation totals during the cool season can strongly pre-condition LSZ position in late summer. The 625-year-long reconstruction indicates strong interannual and decadal variability, the frequent recurrence of consecutive 2-year LSZ maxima and minima, large-scale ocean atmospheric forcing, and an interesting asymmetrical influence of warm El Niño–Southern Oscillation (ENSO) events.

This paper is a review of the biology of Sacramento perch (Archoplites interruptus) based mainly on recent studies of their distribution, ecology, physiology, and genetics. The Sacramento perch is the only member of the family Centrarchidae that is endemic to California. It is most closely related to the rock basses (Ambloplites spp.) and is thought to have split from its eastern cousins during the Middle Miocene Period (15.5 to 5.2 million years ago, MYA). Their native range includes the Central Valley, Pajaro and Salinas rivers, tributaries to the San Francisco Estuary (e.g., Alameda Creek), and Clear Lake (Lake County). Today, they are most likely extirpated from all of their native range. They are known to persist in 28 waters outside their native range: 17 in California, nine in Nevada, and one each in Utah and Colorado. Disappearance from their native range coincided with massive changes to aquatic habitats in the Central Valley and with the introduction of alien species, including other centrarchids. Unfortunately, many populations established outside their native range have also disappeared and are continuing to do so.

Many native fishes in the San Francisco Estuary and its watersheds have reached all-time low abundances. Some of these declining species (e.g., Chinook salmon Oncorhynchus tschawytscha) have been under artificial propagation for decades. For others (e.g., delta smelt, Hypomesus transpacificus, and green sturgeon, Acipenser medirostris), this management option is just beginning to be discussed and implemented. Propagation strategies, in which organisms spend some portion of their lives in captivity, pose well-documented genetic and ecological threats to natural populations. Negative impacts of propagation have been documented for all Central Valley Chinook salmon runs, but limited efforts have been made to adapt hatchery operations to minimize the genetic and ecological threats caused by propagated fishes. A delta smelt propagation program is undergoing intensive design and review for operations and monitoring. However, if limiting factors facing this species in its estuarine habitat are not effectively addressed, captive propagation may not be a useful conservation approach, regardless of how carefully the propagation activity is designed or monitored. Scientifically defensible, ecologically based restoration programs that include monitoring and research aimed at quantifying natural population vital rates should be fully implemented before there is any attempt to supplement natural populations of delta smelt. Green sturgeon are also likely to face risks from artificial propagation if a large–scale program is implemented before this species’ limiting factors are better understood. In each of these cases, restoring habitats, and reducing loss from human actions, are likely to be the best strategy for rebuilding and supporting self–sustaining populations.