Randall D. Baxter

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

Abstract Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-hyphen;agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, ...

Population Dynamics and Distribution Patterns of Longfin Smelt in the San Francisco Estuary

The San Francisco Estuary supports several endemic species of fish and the southernmost populations of other species. Many of these native species and populations are imperiled or have experienced recent population declines that indicate a general decline in the estuarys capacity to support pelagic fish species. We studied the distribution and abundance of one of the estuarys native species, longfin smelt Spirinchus thaleichthys, using data from three long-term aquatic sampling programs. Each of the sampling programs we studied revealed a substantial reduction in the abundance of longfin smelt. These trends support the idea that the estuarys capacity to support pelagic fish species has been significantly reduced over the past three decades. Longfin smelt in the estuary displayed consistent patterns in relative abundance and distribution during their life cycle. We also found significant, but weak, spatial autocorrelation among sampling stations. These patterns in distribution reveal differential habitat use and migratory behavior. Managers can use these insights into longfin smelt distribution patterns to improve interpretation of sampling program results.

Spatial-Temporal Distribution and Habitat Associations of Age-0 Splittail in the Lower San Francisco Estuary Watershed

Abstract The Splittail (Pogonichthys macrolepidotus) is a cyprinid endemic to the San Francisco Estuary and its lower watershed. Although it was recently removed from the Federal Endangered Species Act list of threatened species, it is still a species of concern because of uncertainties regarding its abundance and distribution. Because little information is available on early life stages for which to base management decisions, we examined historical long-term monitoring data and conducted a field study in 2002 and 2003 to examine the distribution and habitat associations of age-0 Splittail. During winter and spring, adults migrate from the upper San Francisco Estuary and the Sacramento-San Joaquin Delta upstream into freshwater tributaries and floodplains to spawn. Although previous work suggested a decreasing upstream range for this species, we found that catch data for age-0 Splittail (≤ 50 mm fork length) during a monitoring program spanning 28 years (1976–2003) indicated the upstream-most distribution in the Sacramento River has remained persistent at 232– 296 km upstream from the estuary. Additionally, centers of distribution in the Sacramento and San Joaquin Rivers varied according to hydrology; distance upstream was similar in years of high and intermediate river flows, but increased during low flow years. In all years, age-0 Splittail became abundant in April or May and by June and July had a center of distribution downstream at the margin of the Sacramento-San Joaquin Delta. Our field study showed that in addition to these two primary tributaries, substantial spawning also occurred in other smaller tributaries with previously uncertain importance to Splittail production, namely the Petaluma River, Napa River, and Butte Slough. We also found that age-0 Splittail favor low velocity shallow-water habitats. Compared to main channel habitats, age-0 Splittail were 6.5 times more common in backwaters in upstream riverine locations, and 3.5 times more common in offchannel intertidal habitats in downstream tidal locations. Our study demonstrates the distribution of Splittail is more widespread than previously believed and underscores the importance of offchannel habitats as nursery areas for age-0 fish.

Long-Term Shifts in the Lateral Distribution of Age-0 Striped Bass in the San Francisco Estuary

Abstract Like several other fishes in the pelagic community of the upper San Francisco Estuary, age-0 striped bass Morone saxatilis have shown a major decline based on a midwater trawl sampling program that has been conducted for over 40 years. We hypothesized that the apparent decline in age-0 striped bass might be partially attributable to a behavioral shift away from the channels sampled by the trawls. We found no evidence of an upstream–downstream shift in age-0 distribution. Instead, age-0 striped bass distribution remains closely associated with the low-salinity zone of the estuary. However, the survey data suggest a substantial long-term distribution shift away from channels and toward shoal areas. The hypothesis that young striped bass are undersampled by midwater trawls is supported by modeling of demographic patterns, which showed that the decline in numbers of age-0 fish was not consistent with increasing trends in age-1 fish. We hypothesize that reduced food availability in pelagic habitat is ...

Aspects of Sacramento pikeminnow biology in nearshore habitats of the Sacramento-San Joaquin Delta, California

Abstract We documented distribution, relative abundance, diet composition, and body condition of Sacramento pikeminnow Ptychocheilus grandis during 2001 and 2003 at 5 sites in the Sacramento–San Joaquin Delta, California. Sacramento pikeminnow densities in nearshore habitats were higher in 2003 than 2001. In both years, spatial distribution of beach seine densities was similar. There were no significant differences in density among sampling sites except for the southernmost site where the catch was near zero. Based on rotary screw-trap data from a 6th site, we found relative abundance of Sacramento pikeminnow entering the Delta via an artificial floodplain was positively correlated with flow. Most individuals collected using all 3 gear types were age 1 or older, and appeared to grow quickly based on data from previous studies. Sacramento pikeminnow had diverse diets composed of freshwater and estuarine invertebrate and fish taxa. Incidence of piscivory was only 2% of the diet of individuals <150 mm, but increased to 50% for fish over 150 mm. No salmonids were observed in foregut contents during the study. In both years body condition declined abruptly in July. Our results suggest Sacramento pikeminnow are more common in the turbid, tidal freshwater habitats of the Delta than was previously recognized. Stream flows may play an important role in moving juvenile Sacramento pikeminnow into the Delta from upstream areas. Similar to northern pikeminnow P. oregonensis, but in seeming contrast to endangered Colorado pikeminnow P. lucius, the present study showed that Sacramento pikeminnow can be successful in altered habitats.

SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Studying rare and sensitive species is a challenge in conservation biology. The problem is exemplified by the case of the imperiled delta smelt Hypomesus transpacificus, a small delicate fish species endemic to the San Francisco Estuary, California. Persistent record-low levels of abundance and relatively high sensitivity to handling stress pose considerable challenges to studying delta smelt in the wild. To attempt to overcome these and other challenges we have developed the SmeltCam, an underwater video camera codend for trawled nets. The SmeltCam functions as an open-ended codend that automatically collects information on the number and species of fishes that pass freely through a trawled net without handling. We applied the SmeltCam to study the fine-scale distribution of juvenile delta smelt in the water column in the upper San Francisco Estuary. We learned that during flood tides delta smelt were relatively abundant throughout the water column and that during ebb tides delta smelt were significantly less abundant and occurred only in the lower half and sides of the water column. The results suggest that delta smelt manipulate their position in the water column to facilitate retention in favorable habitats. With the application of the SmeltCam we increased the survival of individual delta smelt by 72% compared to using a traditional codend, where all of the fish would have likely died due to handling stress. The SmeltCam improves upon similar previously developed silhouette photography or video recording devices and demonstrates how new technology can be developed to address important questions in conservation biology as well as lessen the negative effects associated with traditional sampling methods on imperiled species.

Foraging and metabolic consequences of semi-anadromy for an endangered estuarine fish

Diadromy affords fish access to productive ecosystems, increasing growth and ultimately fitness, but it is unclear whether these advantages persist for species migrating within highly altered habitat. Here, we compared the foraging success of wild Delta Smelt—an endangered, zooplanktivorous, annual, semi-anadromous fish that is endemic to the highly altered San Francisco Estuary (SFE)—collected from freshwater (<0.55 psu) and brackish habitat (≥0.55 psu). Stomach fullness, averaged across three generations of wild Delta Smelt sampled from juvenile through adult life stages (n = 1,318), was 1.5-fold higher in brackish than in freshwater habitat. However, salinity and season interacted, with higher fullness (1.7-fold) in freshwater than in brackish habitat in summer, but far higher fullness in brackish than freshwater habitat during fall/winter and winter/spring (1.8 and 2.0-fold, respectively). To examine potential causes of this interaction we compared mesozooplankton abundance, collected concurrently with the Delta Smelt, in freshwater and brackish habitat during summer and fall/winter, and the metabolic rate of sub-adult Delta Smelt acclimated to salinities of 0.4, 2.0, and 12.0 psu in a laboratory experiment. A seasonal peak in mesozooplankton density coincided with the summer peak in Delta Smelt foraging success in freshwater, and a pronounced decline in freshwater mesozooplankton abundance in the fall coincided with declining stomach fullness, which persisted for the remainder of the year (fall, winter and spring). In brackish habitat, greater foraging ‘efficiency’ (prey items in stomachs/mesozooplankton abundance) led to more prey items per fish and generally higher stomach fullness (i.e., a higher proportion of mesozooplankton detected in concurrent trawls were eaten by fish in brackish habitat). Delta Smelt exhibited no difference in metabolic rate across the three salinities, indicating that metabolic responses to salinity are unlikely to have caused the stomach fullness results. Adult migration and freshwater spawning therefore places young fish in a position to exploit higher densities of prey in freshwater in the late spring/summer, and subsequent movement downstream provides older fish more accessible prey in brackish habitat. Thus, despite endemism to a highly-altered estuary, semi-anadromy provided substantial foraging benefits to Delta Smelt, consistent with other temperate migratory fish.