Fish Communities and Their Associations with Environmental Variables, Lower San Joaquin River Drainage, California

Twenty sites in the lower San Joaquin River drainage, California, were sampled from 1993 to 1995 to characterize fish communities and their associations with measures of water quality and habitat quality. The feasibility of developing an Index of Biotic Integrity was assessed by evaluating four fish community metrics, including percentages of native fish, omnivorous fish, fish intolerant of environmental degradation, and fish with external anomalies. Of the thirty-one taxa of fish captured during the study, only 10 taxa were native to the drainage. Multivariate analyses of percentage data identified four site groups characterized by different groups of species. The distributions of fish species were related to specific conductance, gradient, and mean depth; however, specific conductance acted as a surrogate variable for a large group of correlated variables. Two of the fish community metrics – percentage of introduced fish and percentage of intolerant fish – appeared to be responsive to environmental quality but the responses of the other two metrics – percentage of omnivorous fish and percentage of fish with anomalies – were less direct. The conclusion of the study is that fish communities are responsive to environmental conditions, including conditions associated with human-caused disturbances, particularly agriculture and water development. The results suggest that changes in water management and water quality could result in changes in species distributions. Balancing the costs and benefits of such changes poses a considerable challenge to resource managers.     

Identifying sources of dissolved organic carbon in agriculturally dominated rivers using radiocarbon age dating: Sacramento–San Joaquin River Basin, California

We used radiocarbon measurements of dissolved organic carbon (DOC) to resolve sources of riverine carbon within agriculturally dominated landscapes in California. During 2003 and 2004, average Δ¹⁴C for DOC was ?254‰ in agricultural drains in the Sacramento–San Joaquin Delta, ?218‰ in the San Joaquin River, ?175‰ in the California State Water Project and ?152‰ in the Sacramento River. The age of bulk DOC transiting the rivers of California’s Central Valley is the oldest reported for large rivers and suggests wide-spread loss of soil organic matter caused by agriculture and urbanization. Using DAX 8 adsorbent, we isolated and measured ¹⁴C concentrations in hydrophobic acid fractions (HPOA); river samples showed evidence of bomb-pulse carbon with average Δ¹⁴C of 91 and 76‰ for the San Joaquin and Sacramento Rivers, respectively, with older HPOA, ?204‰, observed in agricultural drains. An operationally defined non-HPOA fraction of DOC was observed in the San Joaquin River with seasonally computed Δ¹⁴C values of between ?275 and ?687‰; the source of this aged material was hypothesized to be physically protected organic-matter in high clay-content soils and agrochemicals (i.e., radiocarbon-dead material) applied to farmlands. Mixing models suggest that the Sacramento River contributes about 50% of the DOC load in the California State Water Project, and agricultural drains contribute approximately one-third of the load. In contrast to studies showing stabilization of soil carbon pools within one or two decades following land conversion, sustained loss of soil organic matter, occurring many decades after the initial agricultural-land conversion, was observed in California’s Central Valley.     

Genetic analysis reveals two distinct Sacramento splittail (<Emphasis Type="Italic">Pogonichthys macrolepidotus</Emphasis>) 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.     

Characterization of microsatellite loci in chinook salmon (Oncorhynchus tshawytscha) and cross‐species amplification in other salmonids

Previous studies of population genetic structure of fall‐run chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley have either not focused on or have been unable to resolve intertributary differences within the San Joaquin River basin. The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross‐species amplification of 17 microsatellite loci in six species of salmonids. Fourteen of these loci are polymorphic in fall‐run chinook from the San Joaquin River drainage. These results indicate the potential utility of microsatellite markers developed for one species, for both congenerics and species within a closely related genus.     

Invading species in the Eel River, California: successes, failures, and relationships with resident species

We examined invasions of non-native fishes into the Eel River, California. At least 16 species of fish have been introduced into the drainage which originally supported 12–14 fish species. Our study was prompted by the unauthorized introduction in 1979 of Sacramento squawfish, Ptychocheilus grandis, a large predatory cyprinid. From 1986 to 1990, we conducted growth and diet studies of squawfish, conducted intensive surveys of the distribution and habitat associations of both native and introduced species, and examined the nature of species-habitat and interspecies relationships. We found no evidence for increased growth or expanded feeding habits, compared to native populations, of Sacramento squawfish as they invaded the Eel River drainage. Ten of the introduced species were well established, with four species limited to a reservoir and six species established in streams. The success or failure of introductions of stream species appeared to be a function of the ability of a species to survive the fluctuating, highly seasonal, flow regime. The present mixture of native and exotic species has not formed stable fish assemblages but it seems likely that four habitat-associated assemblages will develop. The overall effect of the successful species introductions has been to assemble a group of species, with some exceptions, that are native to and occur together in many California streams. The assemblages now forming are similar to those found in other California streams. The assemblage characterized by squawfish and suckers is likely to be resistant to invasion, in the absence of human caused habitat modifications.     

Alien Fishes in Natural Streams: Fish Distribution, Assemblage Structure, and Conservation in the Cosumnes River, California, U.S.A.

The Cosumnes River is the largest stream without a major dam on its mainstem in the Sacramento–San Joaquin drainage, central California, U.S.A. We studied its fishes over a 3-year period to answer the following questions: (1) Was the native fish fauna still present? (2) Why were alien fishes so abundant in a river system with a 'natural' flow regime, which elsewhere has been shown to favor native fishes? (3) Were there assemblages of fishes that reflected environmental differences created by the underlying geology? (4) Were there features of the watershed that consistently favored native fishes or that could be managed to favor native fishes? Of the 25 species collected, 17 were alien species; 14 species (five native) were abundant or widely distributed enough to use in detailed analyses. Of the native species, only rainbow trout, Oncorhynchus mykiss, still occupied much of its native range in headwater streams. Other native species have been extirpated or persisted mainly above barriers to alien invasions. The most widely distributed alien species was redeye bass, Micropterus coosae, previously unknown from the river, whose abundance was associated with low-numbers of native species. Other aliens were found primarily in low-land habitats on the valley floor or foothills. Canonical Correspondence Analysis indicated that both native and alien species located on environmental gradients determined largely by elevation, temperature, flow, and emergent vegetation, but the associations with these variables were not strong. While most alien fishes were found in lowland sections of river flowing through agricultural regions, the general relationships between species abundance and landscape-level variables were weak. Assemblages of fishes were poorly defined mixtures of native and alien species. The strikingly distinct geological regions of the basin no longer supported distinct fish assemblages. Species distributions were highly individualistic, reflecting dynamic patterns of introductions, invasions, and local extinctions, as well as physiological tolerances and life history patterns. Most native fishes are likely to persist in the Cosumnes River only if summer flows are increased and if populations above natural barriers are protected from further invasions by alien species, especially redeye bass. General conclusions from this study include: (1) altered habitats can support native species under some circumstances; (2) new fish assemblages with characteristics of 'natural' communities are likely to develop in invaded systems; (3) restoring flow regimes to favor native fishes may require restoring minimum summer flows as well as high channel-forming flows. However, reversing or even reducing, the impact of the predatory redeye bass, pre-adapted for California streams, is probably not possible.     

Invasion by Non-Native Annual Grasses: The Importance of Species Biomass, Composition, and Time Among California Native Grasses of the Central Valley

The Central Valley of California is noted for its dearth of remnant native grass populations and for low native grass seedling establishment within grasslands now dominated by non‐native annual species. In contrast, remnant populations are common along the coast, and studies have shown an ability for seedlings and adults to compete with non‐native annual grasses. The invasibility of well‐established populations of native grasses in the Central Valley remains unclear. The objectives of this study were to compare the invasibility of native grasses differing in density and species composition and, given the species in this study, to assess the ability of mixes with greater species richness to resist invasion relative to their abilities in monoculture. In the Sacramento Valley of California, six species of native grasses were planted at three densities in monospecific and mixed‐species plots. Percent cover of native perennial and non‐native annual grasses was measured in years 2 and 3, and biomass was sampled in year 5. Native grass biomass and, to a lesser extent, species composition were important in explaining variation in non‐native grass invasibility in the fifth year. Species‐rich treatments did not experience less invasion than would be expected by the proportional invasibility of each species in monoculture. However, invasibility of plots consisting of slower growing, shorter statured species decreased over time, suggesting a successional benefit to diverse communities. This study demonstrates that established stands of native grasses in the Sacramento Valley can resist invasion by non‐native annual grasses and that stand biomass is a particularly important factor in determining invasibility.     

Characterization of microsatellite loci in Sacramento perch (Archoplites interruptus)

We characterized 23 polymorphic tetranucleotide microsatellite loci for Sacramento perch (Archoplites interruptus). This species is extirpated in its native range, the Sacramento–San Joaquin Delta (California, USA), and is therefore targeted for recovery. A concerted effort is currently underway to re‐establish self‐sustaining populations of Sacramento perch in its native range. These microsatellites will be used to analyse the population structure of the species and, in conjunction with life history and physiological data, develop a comprehensive recovery plan.     

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.     

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.     

Seasonal abundance of Draeculacephala minerva and other Xylella fastidiosa vectors in California almond orchards and vineyards

Almond leaf scorch (ALS) disease is caused by the bacterium Xylella fastidiosa and transmitted by xylem-feeding insects. Reports of increased incidence of ALS-diseased trees in California prompted surveys in three almond [Prunus dulcis (Mill.) D. A. Webb]-growing regions, from June 2003 to September 2005, to determine insect vector species composition and abundance. For comparison, sampling in and near vineyards in the San Joaquin Valley, California, also was completed. Sampling in or near almond orchards collected >42,000 Cicadomorpha of which 4.8% were xylem feeders, including 1912 grass sharpshooter, Draeculacephala minerva Ball; five Xyphon fulgida Nottingham; and a single spittlebug, Philaenus spumarius L. The most abundant vector was D. minerva. Season-long sampling indicated that D. minerva was a year-round resident in and/or near almonds in the Sacramento Valley, but not in the San Joaquin Valley. Similarly, D. minerca was rare in vineyards in the San Joaquin Valley, but was abundant in irrigated pastures near vineyards. D. minerva was most frequently collected along orchard margins, and peak densities were observed in summer, the period of time when bacterial titers are reported to increase in infected trees. Screening of D. minerva for presence of X.fastidiosa found that 1.1% of insects collected near almond orchards and 4.5% of insects collected from pastures tested positive. The X. fastidiosa subspecies and genotype detected in insects collected from orchards matched those collected from ALS-diseased almond trees in the same orchard. Of the few X. fulgida and P. spumarius collected, none tested positive for X. fastidiosa. Results are discussed with respect to X. fastidiosa vector control and detection methods.     

Characterization of microsatellite loci for five members of the minnow family Cyprinidae found in the Sacramento–San Joaquin Delta and its tributaries

Two microsatellite‐enriched libraries [(CAGA)_n, (TAGA)_n] were constructed using pooled DNA from three cyprinid species native to the Sacramento–San Joaquin Delta of California: Sacramento splittail (Pogonichthys macrolepidotus); Sacramento pikeminnow (Ptychocheilus grandis); and tui chub (Siphateles bicolor). Primers were designed for 105 loci and tested for levels of polymorphism in five cyprinid species found in the Delta: Sacramento splittail, Sacramento pikeminnow, tui chub, hitch (Lavinia exilicauda), and Sacramento blackfish (Orthodon microlepidotus). Fifty‐one loci were polymorphic for at least one species and 31 loci were polymorphic for multiple species. The number of polymorphic loci per species ranged from 16 to 26.     

An unfortunate alliance: Native shrubs increase the abundance,performance, and apparent impacts of Bromus tectorum across a regional aridity gradient

Interspecific facilitation contributes to the assembly of desert plant communities. However, we know little of how desert communities invaded by exotic species respond to facilitation along regional-scale aridity gradients. These measures are essential for predicting how desert plant communities might respond to concomitant plant invasion and environmental change. Here, we evaluated the potential for Bromus tectorum (a dominant invasive plant species) and the broader herbaceous plant community to form positive associations with native shrubs along a substantial aridity gradient across the Great Basin, Mojave, and San Joaquin Deserts in North America. Along this gradient, we sampled metrics of abundance and performance for B. tectorum, all native herbaceous species combined, all exotic herbaceous species combined, and the total herbaceous community using 180 pairs of shrub and open microsites. Across the gradient, B. tectorum formed strong positive associations with native shrubs, achieving 1.6–2.2 times greater abundance, biomass, and reproductive output under native shrubs than away from shrubs, regardless of relative aridity. In contrast, the broader herbaceous community was not positively associated with native shrubs. Interestingly, increasing B. tectorum abundance corresponded to decreasing native abundance, native species richness, exotic species richness, and total species richness under but not away from shrubs. Taken together, these findings suggest that native shrubs have considerable potential to directly (by increasing abundance and performance) and indirectly (by increasing competitive effects on neighbors) facilitate B. tectorum invasion across a large portion of the non-native range.     

Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus)

Species ranges that span different geographic landscapes frequently contain cryptic species‐ or population‐level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However, comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However, two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (Cottus pitensis), display ranges based on morphological identifications that do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial and microsatellite markers, we hypothesized that proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C. gulosus represent a unique lineage, and ‘true’ C. gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C. pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C. gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification.     

Migratory patterns of lower Feather River natural and hatchery-origin Oncorhynchus mykiss

Oncorhynchus mykiss are known to exhibit variable life histories expressed under genetic control or through the influence of the environment. Altered environmental conditions and the presence of large numbers of non-indigenous hatchery fish can affect the rate of anadromy observed in California’s Central Valley O. mykiss. The lower Feather River, a large regulated river in Northern California, supports one of the largest populations of O. mykiss in the Central Valley, heavily subsidized by hatchery production. I examined downstream migratory behavior, movement rate, and success of natural-origin juveniles, natural-origin adults, and hatchery-origin fish using acoustic telemetry. I found that all three groups displayed a mix of migratory and non-migratory life histories. Hatchery-origin adults exhibited more migratory behavior (anadromy) than natural-origin juveniles and natural-origin adults, 41 %, 24 %, and 13 % respectively. Downstream migrants were also significantly larger than non-migratory fish. Migration timing was similar among the three groups, but natural-origin juveniles displayed the most rapid rate of movement. The relative success of each group was highest for fish migrating through the Sacramento-San Joaquin Delta to the Pacific Ocean. Hatchery-origin adults migrating through the lower Feather River showed the lowest relative success (33 %). The dominance of non-migratory life histories pattern among lower Feather River O. mykiss may be in response to the suitable habitat provided by hypolimnetic releases below dams and the current hydrological regime within the highly altered Sacramento-San Joaquin watershed.     

Movement of Sacramento Sucker, Catostomus occidentalis, and Hitch, Lavinia exilicauda, during a Spring Release of Water from Camanche Dam in the Mokelumne River, California

Synopsis We recorded the movement of Sacramento suckers, Catostomus occidentalis, and hitch, Lavinia exilicauda, before and during a controlled flood release on a regulated California Central Valley River, using radio telemetry. Both species made small, local movements (<550 m) during pre-flood flows. During flood releases, some individual suckers made significantly larger movements (>8100 m) both up and downstream of pre-flood flow locations within the main channel while others did not. In contrast, increased flows did not significantly influence hitch movement from a side-channel pool. Sacramento suckers tended to move upstream during flow increases and downstream during flow reductions while no strong relationship for hitch was apparent. These data show that native Central Valley fishes may exhibit a variety of responses to flow change, including schooling and spawning activity, movements to refugia from higher velocities and no marked change. Managers must take into account life history, age and timing associated with specific species when implementing controlled flow strategies.     

An Experimental Study of Competition Between the Native Sacramento Perch (Archoplites interruptus) and Introduced Bluegill (Lepomis macrochirus)

The Sacramento perch (Archoplites interruptus), a sunfish (Centrarchidae) native only to the Central Valley of California, has been eliminated from most of its native range. To examine the role of interspecific competition in this decline, a series of experiments were conducted to assess the growth, aggressive behavior, and habitat use of Sacramento perch in the presence of bluegill (Lepomis macrochirus), an introduced centrarchid. The experiments indicate that (1) Sacramento perch gain less weight and show reduced growth when placed with bluegill, but that this interaction only occurs with food limitation, and is not affected by overall fish density; (2) Sacramento perch demonstrate less aggressive behavior than bluegill, but become more aggressive when they are conspicuously larger than bluegill; (3) Sacramento perch shift their habitat use in the presence of bluegill. Overall the results imply that Sacramento perch and bluegill exhibit interspecific competition where the mechanism of interaction is aggressive dominance by bluegill. It is suggested that long term persistence of Sacramento perch may require a habitat that is free of introduced centrarchid fishes, or one controlled by a naturally variable hydrological regime.     

Spatial and temporal variation of fish communities in secondary channels of the San Juan River, New Mexico and Utah

Spatial and temporal variation of fish communities in four secondary channels of the San Juan River between Shiprock, NM and Bluff, UT were investigated from July 1993 through November 1994. Fish abundance and habitat availability data were collected to determine if physical attributes of sites influenced spatial and temporal variation in their fish communities. Stability of habitat was shown to positively influence the stability of the fish community. Analysis of variance revealed greater spatial than temporal variation in the abundance of red shiner, Cyprinella lutrensis, fathead minnow, Pimephales promelas, and flannelmouth sucker Catostomus latipinnis, while speckled dace, Rhinichthys osculus showed greater temporal variation. Ordination, using detrended correspondence analysis, revealed variation in fish communities by site, date, and sample year. Spatial variation was greatest during low-flow periods when the greatest differences in habitat among the four sites occurred. Spring runoff had the greatest temporal effect on the fish communities in secondary channels and appeared to reset the communities by displacing those species that were less resistant to increased current velocities. This annual event may help maintain native fish species adapted to these conditions in the San Juan River while moderating the abundance of nonnative fish species.     

Decline of Native Freshwater Fishes in a Mediterranean Watershed on the Iberian Peninsula: A Quantitative Assessment

We examined changes in the distribution of 9 native and 18 introduced freshwater fishes in the south-eastern Pyrenees watershed, Iberian Peninsula, using data from 1996, 1984–1988 and historical information. This region suffers many modifications to its freshwater ecosystems that are linked to human activity in the Mediterranean regions. Fish communities, stream physical habitat and environmental degradation were assessed at 168 sites from 11 basins in 1996. Seven native species (78%) showed decline from previous data, one of which became extirpated in the first half of the 20th century. On the other hand, introduced species are expanding. As a consequence, intact native communities are increasingly rare, declining from presence in 22% of river courses in 1984–1988 to 15% in 1996. The most typical community type is a mixture of native and introduced species occupying 30% of river courses. Stream degradation seems to be the main cause of this process because fish communities differed between degraded streams and streams suffering less impact. A principal component analysis showed that water pollution and modifications to the habitat were the two anthropogenic factors that accounted for most changes in the fish community integrity. Habitat alteration, primarily through construction of dams and water diversions, has fragmented habitats and isolated native fish communities in headwater streams. Current protection measures do not offer effective conservation of threatened species and communities. A global conservation and restoration programme from an ecosystem-based approach is essential to reverse the trend affecting native freshwater fishes in this Mediterranean region.     

Co‐varying impacts of land use and non‐native brown trout on fish communities in small streams

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