Cat gene frequencies in the San Francisco Bay region,California

A recent cat gene frequency survey undertaken in the San Francisco Bay region has not reconciled all the discrepancies in the two previous studies reported from this area. The only mutants for which reliable frequency estimates exist are long hair, dominant white and piebald spotting. For several alleles, the reasons for the dissimilar results reported by different workers are not clear.     

Cryptic genetic diversity in Rattus of the San Francisco Bay region, California

Invasive species can have complex invasion histories, harbor cryptic levels of diversity, and pose taxonomic problems for pest management authorities. Roof rats, Rattus rattus sensu lato, are common invasive pests of the San Francisco Bay Area in California, USA. They are a significant health risk and pest management efforts impose a large financial investment from public institutions and private individuals. Recent molecular genetic and taxonomic studies of black rats in their native range in Asia have shown that the species is a complex of two karyotypic forms and four mitochondrial genetic lineages that may represent four distinct species. We used mtDNA sequences and nuclear microsatellite variation to identify which mitochondrial lineages of the R. rattus group are present in the San Francisco Bay Area and to test for gene flow among them. We recovered specimens with mtDNA sequences representing two of the major mtDNA lineages of the R. rattus group. Microsatellite variation, however, was not structured in concordance with mtDNA lineages, suggesting a more complex history involving hybridization and introgression between these lineages. Although Aplin et al. (2011) and Lack et al. (2012) reported R. rattus Lineage II in North America, this is the first detailed examination of possible gene flow amongst lineages in this region.     

Notes on a Mesodinium rubrum red tide in San Francisco Bay (California, USA)

Discrete red patches of water were observed in South San FranciscoBay (USA) on 30 April 1993, and examination of live samplesshowed that this red tide was caused by surface accumulationsof the pigmented ciliate Mesodinium rubrum. Vertical profilesshowed strong salinity and temperature stratification in theupper 5 m, peak chlorophyll fluorescence in the upper meter,and differences in the small-scale density structure and fluorescencedistribution among red patches. Events preceding this Mesodiniumred tide included: (i) heavy precipitation and run-off, allowingfor strong salinity stratification; (ii) a spring diatom bloomwhere the chlorophyll a concentration reached 50 mg m^–3;(ii) depletions of dissolved inorganic N and Si in the photiczone; and (iv) several days of rapid warming and stabilizationof the upper surface layer. These conditions may be generalprerequisites for M.rubrum blooms in temperate estuaries. ¹Present address: Station Marine d'Endoume, Centre d'Oceanologiede Marseille, rue Batterie des Lions, 13007 Marseille, France     

Distribution and toxicity of a new colonial Microcystis aeruginosa bloom in the San Francisco Bay Estuary,California

The first distribution, biomass and toxicity study of a newly established bloom of the colonial cyanobacteria Microcystis aeruginosa was conducted on October 15, 2003 in the upper San Francisco Bay Estuary. Microcystis aeruginosa was widely distributed throughout 180 km of waterways in the upper San Francisco Bay Estuary from freshwater to brackish water environments and contained hepatotoxic microcystins at all stations. Other cyanobacteria toxins were absent or only present in trace amounts. The composition of the microcystins among stations was similar and dominated by demethyl microcystin-LR followed by microcystin-LR. In situ toxicity computed for the >75 m cell diameter size fraction was well below the 1 g l^–1 advisory level set by the World Health Organization for water quality, but the toxicity of the full population is unknown. The toxicity may have been greater earlier in the year when biomass was visibly higher. Toxicity was highest at low water temperature, water transparency and salinity. Microcystins from the bloom entered the food web and were present in both total zooplankton and clam tissue. Initial laboratory feeding tests suggested the cyanobacteria was not consumed by the adult copepod Eurytemora affinis, an important fishery food source in the estuary.     

Observations of fallout from the Fukushima reactor accident in San Francisco Bay area rainwater

We have observed fallout from the recent Fukushima Dai-ichi reactor accident in samples of rainwater collected in the San Francisco Bay area. Gamma ray spectra measured from these samples show clear evidence of fission products--(131,132)I, (132)Te, and (134,137)Cs. The activity levels we have measured for these isotopes are very low and pose no health risk to the public.     

The distribution and temporal dynamics of the estuarine macroalgal community of San Francisco Bay

Long-term sampling of intertidal macroalgae along permanently marked transects within San Francisco Bay has shown a marked decline in overall species number along the estuarine gradient from the ocean to the river, presumably as a result of decreasing salinity and a progressive lack of hard substrata in the upstream direction. Green algae penetrated further landward than either brown or red species. Seasonally, macroalgal species diversity is lowest during the winter-spring months when salinity, temperature, and irradiance are at yearly minima. Macroalgal abundance as measured by percent cover was maximum during the late spring near the mouth of the estuary and during late summer towards the head. The seasonal increase in algal abundance is related to increasing salinity, temperature, and light availability to the bottom. The summer increase in irradiance is due to the longer photoperiod, increased frequency of day-time low tides, and reduced levels of suspended sediments. The aperiodic occurrence of algal blooms in San Pablo Bay may be caused by a combination of physical factors which are ultimately associated with the river inflow. A hypothesis based on interannual differences in river inflow and the contribution of phytoplankton to nutrient cycles in the benthos is presented to explain the occurrence of nuisance algal blooms.     

Movements of green sturgeon, Acipenser medirostris, in the San Francisco Bay estuary, California

Synopsis The green sturgeon, Acipenser medirostris, is a long-lived, iteroparous, anadromous acipenserid that is native to the San Francisco Bay Estuary, California. Sub-adult and adult fish are oceanic, but enter the estuary during the spring and remain through autumn. Little is known about green sturgeon distribution within the estuary or what, if any, physical parameters influence their movements. We report the results of a telemetry study conducted between September 2001 and November 2002. Five sub-adult and one adult green sturgeon were captured by trammel net in the San Pablo Bay region of the estuary. We implanted depth-sensing, ultrasonic transmitters within the peritoneum of individuals and tracked them from a boat for 1 – 15 h per day over periods ranging from 1 to 12 days. Salinity, temperature, and dissolved oxygen profiles of the water column were measured hourly. Observed movements were categorized as either non-directional or directional. Non-directional movements, accounting for 63.4% of observations, were closely associated with the bottom, with individuals moving slowly while making frequent changes in direction and swim speed, or not moving at all. Directional movements consisted of continuous swimming in the top 20% of the water column while holding a steady course for extended periods. Four of the five sub-adult fish remained within the confines of San Pablo Bay for the duration of their tracking period. The remaining sub-adult moved over 45 km up-river into Suisun Bay before contact was lost. The adult fish exited the bay and entered the ocean 6 h after release near Tiburon, CA, a movement of approximately 10 km. The sub-adult fish typically remained at the shallower depths (<10 m) of the estuary, but there were no apparent preferences for temperature, salinity, or dissolved oxygen, with the fish moving widely and rapidly across the range of these physical parameters. Activity is believed to be independent of light level with no discernable crepuscular, nocturnal, or diurnal peaks in activity.     

Time scales and mechanisms of estuarine variability,a synthesis from studies of San Francisco Bay

This review of the preceding papers suggests that temporal variability in San Francisco Bay can be characterized by four time scales (hours, days-weeks, months, years) and associated with at least four mechanisms (variations in freshwater inflow, tides, wind, and exchange with coastal waters). The best understood component of temporal variability is the annual cycle, which is most obviously influenced by seasonal variations in freshwater inflow. The winter season of high river discharge is characterized by: large-scale redistribution of the salinity field (e.g. the upper estuary becomes a riverine system); enhanced density stratification and gravitational circulation with shortened residence times in the bay; decreased tissue concentrations of some contaminants (e.g. copper) in resident bivalves; increased estuarine inputs of river-borne materials such as dissolved inorganic nutrients (N, P, Si), suspended sediments, and humic materials; radical redistributions of pelagic organisms such as copepods and fish; low phutoplankton biomass and primary productivity in the upper estuary; and elimination of freshwater-intolerant species of macroalgae and benthic infauna from the upper estuary. Other mechanisms modulate this river-driven annual cycle: (1) wind speed is highly seasonal (strongest in summer) and causes seasonal variations in atmosphere-water column exchange of dissolved gases, resuspension, and the texture of surficial sediments; (2) seasonal variations in the coastal ocean (e.g. the spring-summer upwelling season) influence species composition of plankton and nutrient concentrations that are advected into the bay; and (3) the annual temperature cycle influences a few selected features (e.g. production and hatching of copepod resting eggs). Much of the interannual variability in San Francisco Bay is also correlated with freshwater inflow: wet years with persistently high river discharge are characterized by persistent winter-type conditions.Mechanisms of short-term variability are not as well understood, although some responses to storm events (pulses in residual currents from wind forcing, erosion of surficial sediments by wind waves, redistribution of fish populations) and the neap-spring tidal cycle (enhanced salinity stratification, gravitational circulation, and phytoplankton biomass during neap tides) have been quantified. In addition to these somewhat predictable features of variability are (1) largely unexplained episodic events (e.g. anomalous blooms of drift macroalgae), and (2) long-term trends directly attributable to human activities (e.g. introduction of exotic species that become permanent members of the biota).     

Time scales of change in the San Francisco Bay benthos

Results from multi-year investigations in the San Francisco Bay estuary show that large abundance fluctuations within benthic macroinvertebrate populations reflect both (1) within-year periodicity of reproduction, recruitment, and mortality that is not necessarily coincident with seasonal changes of the environment (e.g., the annual temperature cycle), and (2) aperiodic density changes (often larger than within-year fluctuations) following random perturbations of the environment.Density peaks of the small, short-lived estuarine invertebrates that comprise the vast majority of individuals in the bay's relatively homogeneous benthic community normally occur between spring and autumn depending on the species, in large part a reflection of reproductive periodicity. However, because mild winters permit reproductive activity in some of the common species throughout much of the year, other factors are important to within-year density fluctuations in the community. Seasonally predictable changes in freshwater inflow, wind and tidal mixing, microalgal biomass, and sediment erosion/deposition patterns all contribute to observed seasonal changes in abundance. For example, the commonly observed decline in abundance during winter reflects both short-lived species that die after reproducing and the stress of winter conditions (e.g., inundation by less saline, sediment-laden water and the decline in both planktonic and benthic algal biomass — a direct source of food for the shallow-water benthos). On the other hand, data from several studies suggest that observed recruitment and mortality may in fact be the migration of juveniles and adults to and from study sites. For example, the common amphipod Ampelisca abdita apparently moves from shallow to deep water, or from up-estuary to down-estuary locations, coincident with periods of high river runoff in winter. Growth of individuals within the few studied species populations is also highly seasonal, and appears to be coincident with seasonal increases in the abundance of planktonic and/or benthic microalgae.Two multi-year studies have shown that, in addition to within-year periodicity, major restructuring of the benthic community can occur as a result of anomalous (usually climate-related) perturbations of the benthic habitat. For example, during wet years freshwater-intolerant species disappear from the upper part of the estuary and from shallow areas of the bay. During a two-year drought these same species colonized the extreme upper end of the estuary in large numbers. Other aperiodic perturbations include localized instances of sediment erosion or deposition and algal mat accumulations that greatly depress abundance. Additionally, there is evidence (observations that the clam Macoma balthica establishes large populations only when the amphipod A. abdita is not abundant) that species interactions can contribute greatly to interannual variations. Thus, while community composition may change little over the long term, year-to-year predictability of species abundances is low.     

Disease Risk & Landscape Attributes of Tick-Borne Borrelia Pathogens in the San Francisco Bay Area,California

Habitat heterogeneity influences pathogen ecology by affecting vector abundance and the reservoir host communities. We investigated spatial patterns of disease risk for two human pathogens in the Borrelia genus–B. burgdorferi and B. miyamotoi–that are transmitted by the western black-legged tick, Ixodes pacificus. We collected ticks (349 nymphs, 273 adults) at 20 sites in the San Francisco Bay Area, California, USA. Tick abundance, pathogen prevalence and density of infected nymphs varied widely across sites and habitat type, though nymphal western black-legged ticks were more frequently found, and were more abundant in coast live oak forest and desert/semi-desert scrub (dominated by California sagebrush) habitats. We observed Borrelia infections in ticks at all sites where we able to collect >10 ticks. The recently recognized human pathogen, B. miyamotoi, was observed at a higher prevalence (13/349 nymphs = 3.7%, 95% CI = 2.0–6.3; 5/273 adults = 1.8%, 95% CI = 0.6–4.2) than recent studies from nearby locations (Alameda County, east of the San Francisco Bay), demonstrating that tick-borne disease risk and ecology can vary substantially at small geographic scales, with consequences for public health and disease diagnosis.     

Seasonal and interannual variation in distribution and population abundance of the shrimp Crangon franciscorum in San Francisco Bay

Shrimp are an important component of the San Francisco Bay biota, both as predators on benthic fauna, and as a food source for predatory fish. Of three common species in the bay, Crangon franciscorum is the most abundant. The bay is predominantly a nursery area for maturing shrimp of this species. During the main reproductive period in the early spring, ovigerous females and planktonic larvae are in most years centered outside the bay in the nearshore ocean, although both are also present in the bay. Juveniles move into both the southern reach and the northern reach shortly after settling, and landward-flowing bottom currents are possibly instrumental in this migration. The seasonal cycle of shrimp abundance in the bay, dominated by this spring immigration of newly settled juveniles, is characterized by a progressive migration of the growing shrimp up the estuary coincident with upstream penetration of higher salinity water during summer. Differences in abundance and distribution between the years 1980, 1981, and 1982 suggest that the level of river discharge and accompanying salinity regime are important controlling factors in the distribution, recruitment levels, and subsequent survival and growth of C. franciscorum in the San Francisco Bay.     

Effects of Climate Change on Range Forage Production in the San Francisco Bay Area

The San Francisco Bay Area in California, USA is a highly heterogeneous region in climate, topography, and habitats, as well as in its political and economic interests. Successful conservation strategies must consider various current and future competing demands for the land, and should pay special attention to livestock grazing, the dominant non-urban land-use. The main objective of this study was to predict changes in rangeland forage production in response to changes in temperature and precipitation projected by downscaled output from global climate models. Daily temperature and precipitation data generated by four climate models were used as input variables for an existing rangeland forage production model (linear regression) for California’s annual rangelands and projected on 244 12 km x 12 km grid cells for eight Bay Area counties. Climate model projections suggest that forage production in Bay Area rangelands may be enhanced by future conditions in most years, at least in terms of peak standing crop. However, the timing of production is as important as its peak, and altered precipitation patterns could mean delayed germination, resulting in shorter growing seasons and longer periods of inadequate forage quality. An increase in the frequency of extremely dry years also increases the uncertainty of forage availability. These shifts in forage production will affect the economic viability and conservation strategies for rangelands in the San Francisco Bay Area.     

Pilot study of the Olympia oyster Ostrea conchaphila in the San Francisco Bay estuary: description and distribution of diseases

Olympia oysters Ostrea conchaphila have declined markedly during the last century and are a focus of restoration in many embayments, including the San Francisco Bay (SFB) estuary. Oysters were collected from 17 sites in this estuary and nearby Tomales Bay in an effort to characterize diseases that may impact recovery of this species and captive rearing programs. Three diseases/disease agents including a Mikrocytos-like protist (microcell), a haplosporidian and hemic neoplasia were observed from several sites along the western margins of the SFB estuary suggesting a geographic localization of disease presence. Based on fluoresecent in situ hybridization (FISH) assays, the microcell is distinct from M. mackini and Bonamia spp. These data highlight the need for further elucidation of the haplosporidian and for careful health management of a declining species destined for captive rearing and supplementation.     

Contemporary Land Change Alters Fish Communities in a San Francisco Bay Watershed,California, U.S.A.

Urbanization is one of the leading threats to freshwater biodiversity, and urban regions continue to expand globally. Here we examined the relationship between recent urbanization and shifts in stream fish communities. We sampled fishes at 32 sites in the Alameda Creek Watershed, near San Francisco, California, in 1993–1994 and again in 2009, and we quantified univariate and multivariate changes in fish communities between the sampling periods. Sampling sites were classified into those downstream of a rapidly urbanizing area (“urbanized sites”), and those found in less impacted areas (“low-impacted sites”). We calculated the change from non-urban to urban land cover between 1993 and 2009 at two scales for each site (the total watershed and a 3km buffer zone immediately upstream of each site). Neither the mean relative abundance of native fish nor nonnative species richness changed significantly between the survey periods. However, we observed significant changes in fish community composition (as measured by Bray-Curtis dissimilarity) and a decrease in native species richness between the sampling periods at urbanized sites, but not at low-impacted sites. Moreover, the relative abundance of one native cyprinid (Lavinia symmetricus) decreased at the urbanized sites but not at low-impacted sites. Increased urbanization was associated with changes in the fish community, and this relationship was strongest at the smaller (3km buffer) scale. Our results suggest that ongoing land change alters fish communities and that contemporary resurveys are an important tool for examining how freshwater taxa are responding to recent environmental change.     

Spread of Exotic Cordgrasses and Hybrids (Spartina sp.) in the Tidal Marshes of San Francisco Bay, California, USA

Four species of exotic cordgrass (Spartina sp.) occur in the San Francisco estuary in addition to the California native Spartina foliosa. Our goal was to map the location and extent of all non-native Spartina in the estuary. Hybrids of S. alterniflora and S. foliosa are by far the most numerous exotic and are spreading rapidly. Radiating from sites of deliberate introduction, S. alterniflora and hybrids now cover ca. 190 ha, mainly in the South and Central Bay. Estimates of rate of aerial increase range from a constant value to an accelerating rate of increase. This could be due to the proliferation of hybrid clones capable of rapid expansion and having superior seed set and siring abilities. The total coverage of 195 ha by hybrids and other exotic cordgrass species is slightly less than 1% of the Bay's tidal mudflats and marshes. Spartina anglica has not spread beyond its original 1970s introduction site. Spartina densiflora has spread to cover over 5 ha at 3 sites in the Central Bay. Spartina patens has expanded from 2 plants in 1970 to 42 plants at one site in Suisun Bay. Spartina seed floats on the tide, giving it the potential to export this invasion throughout the San Francisco estuary, and to estuaries outside of the Golden Gate. We found isolated plants of S. alterniflora and S. densiflora in outer coast estuaries north of the Bay suggesting the likelihood for the San Francisco Bay populations to found others on the Pacific coast.     

Health resources management and physician control in a San Francisco,California, hospital.

The continued escalation in health care spending has caused money to become an increasingly limited resource, which may eventually affect the ability of health professionals to provide complete health care services. Health care payers have stressed efficiency and the appropriateness of health care measures and are putting greater financial pressures on health professionals by making them more accountable for services provided. Hospitals and physicians must take a more active role in monitoring health care delivery and work together to improve performance efficiency. Efficiency can be gained through a comprehensive program that emphasizes high-quality care and the effective use of health care resources. The Health Resource Management Program is a model for carrying out this function that integrates data analysis and physician input and education.     

Discovery of introduced and cryptogenic cochliopid gastropods in the San Francisco Estuary, California

We report the first discovery in the San Francisco Estuary (‘Estuary’)of two cochliopid gastropods, Littoridinops monroensis and Tryoniaporrecta. These identifications were based on morphologicalcriteria and supported by analysis of mitochondrial DNA (cytochromec oxidase subunit I, COI) sequence data. We also report thefirst discovery of males in parthenogenetic T. porrecta. Thenew records represent large range extensions for both of theseNorth American species, which were previously recorded frompredominantly brackish habitats along the western Atlantic-GulfCoast (L. monroensis) and thermal springs in the Great Basinand lower Colorado River region (T. porrecta). The COI haplotypeobserved in Estuary specimens of L. monroensis differed fromthose detected in two western Atlantic populations by only 1–3 bp,suggesting recent divergence which is not consistent with theseparation of these two areas by imposing terrestrial barrierssince at least the Pliocene. We suggest that L. monroensis wasrecently introduced to the Estuary by transoceanic shipping,adding to the large exotic biota that has invaded this highlydisturbed ecosystem. The COI haplotype observed in Estuary specimensof T. porrecta is closely similar to haplotypes detected inNevada and Utah populations and highly divergent relative tothe single haplotype observed in other California populations.The implications of these findings for the status of T. porrectain the Estuary are unclear, because the native range of thisparthenogen has not been established and its scattered distributionin the West may be attributable to natural dispersal acrossland (on birds) and/or anthropogenic spread. Although we suggesttreating T. porrecta as cryptogenic in the Estuary, a nativestatus may be suggested by independent (subfossil) evidencethat this snail was locally present prior to establishment ofthe area as a major centre of human population and commercein the 1850s. (Received 13 April 2007; accepted 25 June 2007)     

Genetic Variants of Hemoglobin and Other Blood Proteins in the San Francisco Bay Area

Studies of blood genetics in “normal healthy” persons and patients of different racial groups in the San Francisco Bay Area were carried out from January 1965 to April 1968. They show that diseases due to genetic abnormalities of blood are fairly common in this region. Frequencies for abnormal hemoglobins and erythrocyte enzyme deficiencies and variants were recorded and it was noted that abnormalities in hemoglobin metabolism that may lead to mild or severe clinical and hematological symptoms proved rather common. Accompanying other disease conditions, they may cause difficulties in diagnosis. Several diseases due to or associated with different enzyme abnormalities were encountered.