Frederick Feyrer

Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the San Francisco Estuary

We compared dietary patterns within a temperate estuarine fish assemblage (Suisun Marsh, CA, U.S.A.) during a period of high mysid shrimp abundance and after a major decline in mysid abundance caused by the invasion of the overbite clam Potamocorbula amurensis. Prior to the invasion, high dietary overlap, high stomach fullness, and low niche breadth occurred among the fishes in spring when mysid populations were high. Dietary overlaps decreased and niche breadth increased for all species but the endemic splittail Pogonichthys macrolepidotus in fall when mysid populations were low. Eight native species exhibited lower overall collective overlaps and fuller stomachs than five alien species, suggesting more efficient resource partitioning. After mysid abundance declined, only alien striped bass Morone saxatilis preyed upon mysids in greater than trace amounts. An alien mysid became an important prey for small striped bass, but striped bass also switched to piscivory at a smaller size than when mysids were abundant. Eight of 13 species exhibited significant declines in abundance during the study period, which were concordant with the original importance of mysids in their diets. Our results suggest that altered lower food web dynamics in the San Francisco Estuary caused by the invasion of the overbite clam changed fish diets and have contributed to declines in fish abundance.

Fish Community Ecology in an Altered River Delta: Spatial Patterns in Species Composition, Life History Strategies, and Biomass

We sampled nearshore fishes in the Sacramento-San Joaquin Delta, California, United States, during 2001 and 2003 with beach seines and gill nets. We addressed three questions. How and why did fish assemblages vary, and what local habitat features best explained the variation? Did spatial variation in assemblages reflect greater success of particular life history strategies? Did fish biomass vary among years or, across habitats? Nonmetric multidimensional scaling showed that habitat variables had more influence on fish assemblages than temporal variables. Results from both gear types indicated fish assemblages varied between Sacramento and San Joaquin River sampling sites. Results from gill net sampling were less pronounced than those from beach seine sampling. The Sacramento and San Joaquin river sites differed most notably in terms of water clarity and abundance of submerged aquatic vegetation (SAV), suggesting a link between these habitat characteristics and fish relative abundance. Among-site differences in the relative abundance of periodic and equilibrium strategist species suggested a gradient in the importance of abiotic versus biotic community structuring mechanisms. Fish biomass varied among years, but was generally higher in SAV-dominated habitats than the turbid, open habitats in which we found highest abundances of striped bassMorone saxatilis and special-status native fishes such as delta smeltHypomesus transpacificus, Chinook salmonOncorhyncus tschawytscha, and splittailPogonichthys macrolepidotus. The low abundance of special-status fishes in the comparatively productive SAV-dominated habitats suggests these species would benefit more from large-scale restoration actions that result in abiotic variability that mirrors natural river-estuary habitat than from actions that emphasize local (site-specific) productivity.

Fish community structure and environmental correlates in the highly altered southern Sacramento-San Joaquin Delta

We sampled 11 sites in the southern Sacramento-San Joaquin Delta from 1992–1999, to characterize fish communities and their associations with environmental variables. Riparian habitats were dominated by rock-reinforced levees, and large water diversion facilities greatly influenced local hydrodynamics and water quality. We captured 33 different taxa, only eight of which were native. None of the native species represented more than 0.5% of the total number of individuals collected. The abundance of native species was consistently low but typically peaked during high outflow periods. Fish communities were predominantly structured along environmental gradients of water temperature and river flow. Native species (tule perch, Hysterocarpus traski, & Sacramento sucker, Catostomus occidentalis) were associated with conditions of high river flow and turbidity, while the majority of the non-native species were associated with either warm water temperature or low river flow conditions. The exceptions were the non-native striped bass, Morone saxatilis, and white catfish, Ameiurus catus, which were positively associated with relatively high river flow. Variation in fish community structure was greater among river locations within years than within river locations among years, thus fish communities at each river location were consistently different each year. Differences in fish communities among river locations were correlated with river flow and turbidity. We predict that the fish communities of this region will remain numerically dominated by non-native species if the environmental conditions we observed persist in the future.

Otolith Microchemistry Provides Information Complementary to Microsatellite DNA for a Migratory Fish

Abstract We investigated the ability of otolith microchemistry to discriminate natal habitats of the splittail Pogonichthys macrolepidotus, a migratory cyprinid endemic to the San Francisco Estuary, California. Splittails are broadly distributed in the brackish and freshwater portions of the lower estuary and make long-distance upstream migrations during winter to rivers and floodplains for spawning. We found that the ratios of Sr: Ca and 87Sr: 86Sr in the otoliths (ascertained by laser ablation inductively coupled mass spectrometry) of age-0 fish collected from natal habitats significantly varied among four primary spawning rivers. Based on these two constituents, quadratic discriminant function analysis correctly classified 71% of the fish to their natal rivers. Recent work with microsatellite DNA indicates that splittails from these same rivers represent two genetically distinct populations. Thus, integrating data obtained from otolith microchemistry and microsatellite DNA can provide complementary inf...

Diet composition in San Francisco Estuary striped bass: does trophic adaptability have its limits?

Trophic adaptability is a term used to describe feeding flexibility in fishes. Though a useful conceptual starting point, fishes often face constraints on their ability to switch prey that could limit feeding success even when prey switching is observed. We compared striped bass diet compositions summarized from previously published studies in California’s Sacramento-San Joaquin Delta during two time periods (1963–1964 and 2001–2003), which allowed us to evaluate trophic adaptability in San Francisco Estuary striped bass at multiple time scales, ranging from intra-annual to multidecadal. The Delta is the landward region of the San Francisco Estuary; over time between the study periods, the Delta underwent substantial changes in potential prey availability for striped bass. We found evidence for trophic adaptability in San Francisco Estuary (SFE) striped bass at all temporal scales examined. Despite this ability to adapt to changes in prey availability, the relative abundance and carrying capacity of young striped bass have declined. This decline has previously been associated with substantial declines in their dominant historical prey—mysid shrimp. Our results, coupled with these previous findings, indicate that trophic adaptability may have limited usefulness as a conceptual model to predict foraging success when other food web constraints are not considered. We speculate that this is particularly true in highly invaded ecosystems like the San Francisco Estuary because invading species often introduce substantial and permanent changes into food webs, decreasing the likelihood that a predator will find prey assemblages that fully replace historical prey assemblages.

Importance of Flood Dynamics versus Intrinsic Physical Habitat in Structuring Fish Communities: Evidence from Two Adjacent Engineered Floodplains on the Sacramento River, California

Abstract We examined the factors structuring fish communities at two adjacent engineered floodplain systems on the Sacramento River, California: Yolo and Sutter bypasses. We intensively sampled fishes at each location during January–June 2002 and 2004 by rotary screw trap, collecting a total of 126,635 fish comprised of 29 species. Nonmetric multidimensional scaling indicated that distinct fish communities persisted between the locations during our study, despite nearly identical hydrographs and water temperature regimes. Regression models evaluated with an information-theoretic approach also indicated that location was an important factor explaining the abundances of selected species. Overall, Yolo Bypass had more species and a greater proportion of native species than did Sutter Bypass. Sutter Bypass had a greater proportion of species classified as freshwater, while Yolo Bypass had a greater proportion of species classified as either estuarine or anadromous. We believe these results are related to subs...

Spawning and Rearing of Splittail in a Model Floodplain Wetland

Abstract The splittail Pogonichthys macrolepidotus, which has been listed as threatened by the U.S. government, does not produce strong year-classes unless it has access to the floodplain habitat of the San Francisco estuary and its tributaries. In this small-scale, single-year study, we tested the hypothesis that managed inundation of a floodplain can be used to support splittail reproduction in dry years, when this habitat type is not readily available. Adult splittails were captured on their 2001 upstream spawning migration and transferred to a 0.1-ha model floodplain wetland. Our results suggest that adults will successfully spawn if they are provided access to floodplain habitat in dry years. In snorkel surveys, progeny showed a significant association with the lower portion of the water column. Young splittails (15-20 mm fork length (FL)) concentrated in edge habitat near an inflow during the day but at night moved into deeper-water habitats, including open water and habitats with submerged vegetati...

Genetic analysis reveals two distinct Sacramento splittail (Pogonichthys macrolepidotus) populations

The Sacramento splittail is an endemic cyprinid fish of the San Francisco estuary and its tributaries, which is a highly manipulated, constantly changing ecosystem. Splittail is the only extant member of its genus and is listed as a federal and California Species of Special Concern due to uncertainties regarding long-term abundance trends. Determining population structure for splittail is important because unique populations may contain different adaptive genetic variation, which can allow one population to persist through future environmental or demographic stochasticity while others become extirpated. To assess splittail population structure, 13 microsatellite markers were used to genotype 489 young-of-year splittail from five major rivers draining into the estuary: Cosumnes, Napa, Petaluma, Sacramento, and San Joaquin Rivers. Two genetically distinct populations were found to exist within our study region; one largely comprised of splittail collected from the Petaluma and Napa Rivers and the second comprised of splittail collected from tributaries in Californiaȁ9s Central Valley: Cosumnes, Sacramento, and San Joaquin Rivers. These results were replicated in two consecutive years with both distance and model-based algorithms. The genetic distinction between these two populations appears correlated with salinity differences between migratory regions and spawning grounds. Splittail from the Petaluma River exhibited a significantly higher degree of differentiation from the Central Valley population than did Napa River splittail. Our results suggest on-going monitoring programs are probably highly biased towards sampling splittail from the Central Valley population. Understanding population dynamics of splittail could be improved if monitoring programs were expanded to include all splittail populations.

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.

Living in a Dynamic Environment: Variability in Life History Traits of Age-0 Splittail in Tributaries of San Francisco Bay

Splittail Pogonichthys macrolepidotus is a relatively large cyprinid endemic to the San Francisco Estuary watershed. During late winter and early spring, splittails migrate from the estuary to upstream rivers and floodplains for spawning. During 2002 and 2003, we examined the diet composition, muscle stable isotope signatures (d 13 C and d 15 N), and growth rates of age-0 splittails in the four primary rivers used for spawning. Overall, we found substantial variability in all three traits in spatial and temporal comparisons. Age-0 splittails consumed a variety of prey taxa, consisting almost exclusively of aquatic invertebrates, larval stages of chironomids or copepods generally being the most common. We found that the d 15 N and d 13 C signatures of age-0 splittails significantly varied spatially and temporally (d 15 N range ¼ 6.1- 19.6%; d 13 C range ¼� 36.3 to � 17.5%). Environmental conditions, namely flow and how it manipulates habitat connectivity, appeared to affect d 13 C. Age-0 splittails exhibited substantial variability in growth rate both spatially and temporally. However, this variability was not associated with diet composition or stable isotope signatures, suggesting that food availability and physical habitat conditions were important factors affecting growth rates during our study.