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This study utilizes satellite data to investigate water quality conditions in the San Francisco Estuary and its upstream delta, the Sacramento-San Joaquin River Delta. To do this, this study derives turbidity from the European Space Agency satellite Sentinel-2 acquired from September 2015 to June 2019 and conducts a rigorous validation with insitu measurements of turbidity from optical sensors at continuous monitoring stations. This validation includes 965 matchup comparisons between satellite and insitu sensor data across 22 stations, yielding R 2 = 0.63 and 0.75 for Nephelometric Turbidity Unit and Formazin Nephelometric Unit (FNU) stations, respectively. This study then applies remote sensing to evaluate patterns in turbidity during the Suisun Marsh Salinity Control Gates Action ("Gates action"), a pilot study designed to increase habitat access and quality for the endangered Delta Smelt. The basic strategy was to direct more freshwater into Suisun Marsh, creating more low salinity habitat that would then have higher (and more suitable) turbidity than upstream river channels. For all seven acquisitions considered from June 29 to September 27, 2018, turbidity conditions in Bays and Sloughs subregions were consistently higher (and more suitable) (26-47 FNU) than what was observed in the upstream River region (13-25 FNU). This overall pattern was observed when comparing images acquired during similar tidal stages and heights.

Changes in climate patterns are dramatically influencing some agricultural areas. Arid, semi‐arid and coastal agricultural areas are especially vulnerable to climate change impacts on soil salinity. Inventorying and monitoring climate change impacts on salinity are crucial to evaluate the extent of the problem, to recognize trends and to formulate irrigation and crop management strategies that will maintain the agricultural productivity of these areas. Over the past three decades, Corwin and colleagues at the U.S. Salinity Laboratory (USSL) have developed proximal sensor and remote imagery methodologies for assessing soil salinity at multiple scales. The objective of this paper is to evaluate the impact climate change has had on selected agricultural areas experiencing weather pattern changes, with a focus on the use of proximal and satellite sensors to assess salinity development. Evidence presented in case studies for Californiaʼs San Joaquin Valley (SJV) and Minnesotaʼs Red River Valley (RRV) demonstrates the utility of these sensor approaches in assessing soil salinity changes due to changes in weather patterns. Agricultural areas are discussed where changes in weather patterns have increased root‐zone soil salinity, particularly in areas with shallow water tables (SJV and RRV), coastal areas with seawater intrusion (e.g., Bangladesh and the Gaza Strip) and water‐scarce areas potentially relying on degraded groundwater as an irrigation source (SJV and Murray‐Darling River Basin). Trends in salinization due to climate change indicate that the infrastructure and protocols to monitor soil salinity from field to regional to national to global scales are needed. HIGHLIGHTS: Climate change will have a negative impact on agriculture, particularly in arid regions. Proximal/remote sensors are useful to assess climate change impact on soil salinity across scales. Salt‐water intrusion, shallow water tables and degraded water reuse will increase soil salinity. Infrastructure and protocols to monitor soil salinity across multiple scales are needed.

Severe effects of selenium (Se) occurred among birds feeding and nesting at Kesterson Reservoir (San Joaquin Valley, California, USA) in 1983 to 1985. This paper describes the integration of site monitoring, risk assessment, and management actions conducted after the effects of Se were discovered. Selenium contamination of the site occurred over just a few years, but actions to resolve the contamination issues required >20 y. The reservoir, a series of 12 ponds totaling about 1280 acres (518 hectares), served for storage and evaporation of subsurface agricultural drainage. Selenium concentrations in reservoir inflow in 1983 were about 300 µg/L, primarily as selenate; within the ponds it was biogeochemically reduced to other inorganic and organic forms and bioaccumulated by biota or deposited to sediments. An estimated 9000 kg of Se were delivered to Kesterson in 1981-1986. A 1985 order required cleanup and abatement of the reservoir, so the United States Bureau of Reclamation and the US Department of the Interior undertook actions and studies to reduce hazards to birds. In 1988, about 1 million cubic yards (764 500 m3 ) of soil were used to fill portions of the reservoir, transforming it into terrestrial habitat. Intensive monitoring began in 1989 to assess the impact of the reservoir on wildlife, provide a basis for adjusting site management, verify the effectiveness of cleanup actions, and provide a basis for modifying future monitoring. Monitoring continued until 2014, with modifications and management actions based on results of 2 risk assessments (1993 and 2000). Monitoring results in 2013-2014 showed that Se concentrations were relatively stable over time and risks to wildlife were low. From the initial problem discovery to the conclusion of actions taken to remediate the site, combining responsive, reactive, and adaptive monitoring; modeling; risk assessment; and mitigation actions proved effective in solving the problem so that risks to wildlife were reduced to minimal levels. Integr Environ Assess Manag 2020;16:257-268. © 2019 SETAC.

Since 2007, the global mole fraction of atmospheric methane (CH4) has steadily increased meanwhile the 13C/12C isotopic ratio of CH4 (expressed as δ13C-CH4) has shifted to more negative values. Thi...

To characterize the effect of precipitation events, management practices, and soil type on vineyard carbon (C) dynamics, we monitored CO₂ emissions and labile C pools from nine vineyards in Lodi Wine Grape District, California, from April 2011 to December 2012. These commercial vineyards are replicates of three soil series (Redding, San Joaquin, and Tokay), representing a spectrum of soil texture and degree of soil development. We hypothesized that soil characteristics would influence the magnitude of CO₂ efflux occurring in response to precipitation and management events in a Mediterranean climate. During each field visit—bimonthly (April–October) and monthly (November–March)—we measured CO₂, soil temperature, and gravimetric water content (GWC) from vine and intervine (alleys) rows. Monthly, we collected soil samples for dissolved organic C (DOC), which tended to be greater in the alleys of San Joaquin and Redding than Tokay in summer but decreased after the onset of precipitation. In mid-May and mid-October 2012, CO₂ efflux was higher in Tokay than in San Joaquin or Redding. Carbon dioxide efflux across all soils increased as a result of seasonal management practices (i.e., tillage and mowing of cover crops). Management practices distinguished soil DOC between vine rows and alleys from June to October 2012. Soil type or clay content influenced CO₂ efflux across these vineyards, as did GWC and soil temperature. This 20-mo study indicated that CO₂ efflux responded to soil disturbance from management practices, precipitation, and irrigation.

AIM: We use current models of species distribution to predict the future habitat suitability for an endangered, keystone rodent (Dipodomys ingens, giant kangaroo rat). We incorporate the possibility of local adaptation and novel competitive interactions to improve the predictive accuracy of our Maxent models. LOCATION: San Joaquin Valley, California, USA. METHODS: We created Maxent models of two isolated populations of D. ingens. Using local surveys and state‐wide data, we also modelled California ground squirrels (Otospermophilus beecheyi), a potential novel competitor. Models included landscape variables (slope and soil composition) and climate variables (temperature, precipitation and climatic water deficit). We used Warren's I to evaluate niche overlap between species as well as between isolated populations of the same species. We then projected each set of models into the future to evaluate D. ingens response to climate change. RESULTS: Niche overlap between the D. ingens populations was moderate (I = 0.44), suggesting that they already experience different climatic regimes and providing support for population‐level modelling. Projecting individual populations separately into the future, under a high emission climate change scenario (CCSM4, rcp8.5), resulted in less predicted range contraction than modelling the species as a whole. However, forecasted distributions showed areas of increasing niche overlap between the Panoche population of D. ingens and O. beecheyi (I = 0.63 to 0.74), indicating competition could be a novel range limit. MAIN CONCLUSIONS: Modelling the distributions of isolated populations separately provides a more accurate estimation of the species’ contemporary niche, capturing not just overlap between the populations, but individually suitable areas as well. Projecting the individual contemporary and historical models into the future allows us to estimate future habitat suitability. Predicting the distribution of a novel competitor characterizes areas of potential competition. Subsequently, management can target suitable areas for preservation and avoid areas of potential novel competition.

The hydrology of the San Francisco Bay‐Delta estuary (the Delta) has been significantly modified over the past 150 years to serve a variety of human needs for water supply and food production, albeit with adverse ecological impacts. These adverse impacts, in concert with evolving societal values, have motivated change in the estuary's water management to promote ecosystem restoration goals while continuing to support human uses. Understanding historical flow patterns, as well as the environmental functions provided by these flow patterns, is critical to restoration planning. Building upon previous work on outflow trends from the Delta to San Francisco Bay, this paper evaluates historical trends in key interior Delta flows spanning nine decades (1922–2016) and presents an attribution of these trends to various anthropogenic drivers. We reconstructed historical time series records at four key locations in the interior of the Delta; these time series represent tidally‐averaged flows that are intensively managed and are of great importance to the beneficial uses of water in the region. We derived several scenario‐based flow time series at these same four locations to assist in attributing change to a variety of drivers, including reservoir and export pumping operations, in‐Delta barrier and gate operations, and upstream water diversions. Flow changes were measured relative to 1920‐level land use and water management conditions. We find the four interior Delta locations to have distinct seasonal flow trends and, in general, unique responses to various drivers of change. Our work highlights the complex nature of historical flow changes in a highly‐managed estuarine ecosystem, and the types of modifications that would be necessary to reverse these changes.

© 2018 John Wiley & Sons, Ltd. Accurate and reliable reservoir inflow forecast is instrumental to the efficient operation of the hydroelectric power systems. It has been discovered that natural and anthropogenic aerosols have a great influence on meteorological variables such as temperature, snow water equivalent, and precipitation, which in turn impact the reservoir inflow. Therefore, it is imperative for us to quantify the impact of aerosols on reservoir inflow and to incorporate the aerosol models into future reservoir inflow forecasting models. In this paper, a comprehensive framework was developed to quantify the impact of aerosols on reservoir inflow by integrating the Weather Research and Forecasting model with Chemistry (WRF-Chem) and a dynamic regression model. The statistical dynamic regression model produces forecasts for reservoir inflow based on the meteorological output variables from the WRF-Chem model. The case study was performed on the Florence Lake and Lake Thomas Alva Edison of the Big Creek Hydroelectric Project in the San Joaquin Region. The simulation results show that the presence of aerosols results in a significant reduction of annual reservoir inflow by 4–14%. In the summer, aerosols reduce precipitation, snow water equivalent, and snowmelt that leads to a reduction in inflow by 11–26%. In the spring, aerosols increase temperature and snowmelt which leads to an increase in inflow by 0.6–2%. Aerosols significantly reduce the amount of inflow in the summer when the marginal value of water is extremely high and slightly increase the inflow in the spring when the run-off risk is high. In summary, the presence of aerosols is detrimental to the optimal utilization of hydroelectric power systems.

Author(s): Hegarty, JM; Del Blanco, IA; Gallagher, L; Dubcovsky, J | Abstract: California has a vibrant and growing craft brewing industry and a nascent malting industry interested in locally sourced products, which has created a demand for malting barley (Hordeum vulgare L.) production in California. ‘UC Tahoe’ (Reg. No. CV-365, PI 678971) is the first malting barley cultivar released by the University of California and is well adapted to California’s Central Valley (Sacramento and San Joaquin Valleys). UC Tahoe is a two-rowed spring barley with good resistance to powdery mildew and tolerance to yellow dwarf viruses. UC Tahoe combines four quantitative trait loci for resistance to Cereal yellow dwarf virus (CYDV) that were previously identified in the cross between ‘Butta 12’ and ‘Madre Selva’. While not currently a cultivar approved by the American Malting Barley Association, UC Tahoe meets the quality needs of a craft malting and brewing industry interested in sourcing locally grown barley.

Facing the difficulty of accurately measuring pollution from agriculture, economists have recommended regulatory approaches using proxies such as management practices to reduce agricultural pollution. Using farm‐level cost data on a panel of dairy farms, I estimate the effects of a practice‐based air quality regulation for dairy farms in the San Joaquin Valley in California. As opposed to ex ante analyses, my econometric results indicate that the air quality regulation has not significantly affected the total costs of milk production. Estimates also suggest that the regulation might have differential effects on different elements of costs. I support the econometric findings with evidence on how dairy farms comply with the regulation. Calculated adoption rates of different pollution‐mitigation practices using administrative data reveal that dairy farms have mainly adopted labor‐intensive practices to comply with the regulation.

Ethnohistoric accounts and archaeological research from Central California document a shift from the use of lower-cost, high-ranked resources (e.g., large game) toward the greater use of higher-cost, low-ranked resources (e.g., acorns and small seeds) during the Late Holocene (4500-200 BP). The subsistence transition from higher consumption of large game toward an increased reliance on acorns was likely associated with increases in levels of logistical mobility and physical activity. This study predicts that mobility and overall workload patterns changed during this transition to accommodate new food procurement strategies and incorporate new dietary resources during the Late Holocene in Central California.Osteoarthritis prevalence was scored in the shoulder, elbow, hip, and knee of adult individuals (n = 256) from seven archaeological sites in the Sacramento-San Joaquin Delta region. Comparisons were made between osteoarthritis prevalence, sex, age-at-death, and time period using ANCOVAs.The results of this study indicate significant increases in osteoarthritis prevalence in the hip of adult males and females during the Late Period (1200-200 BP), even after correcting for the cumulative effects of age. No differences were observed between the sexes or between time periods for the shoulder, elbow, and knee joints.The temporal increase in hip osteoarthritis supports the hypothesis that there was an increasing need for greater logistical mobility over time to procure key resources away from the village sites. Additionally, the lack of sex differences in osteoarthritis prevalence may suggest that females and males likely performed similar levels of activity during these periods.

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.

Organic matter amendments supply crop nutrients and enhance soil health, yet information specific to orchards is lacking. A survey was conducted to analyze use of these materials by California almond [ (Mill.) D.A. Webb] growers. Significant differences were observed for benefits, concerns, and accessibility to manure and green waste sources and between users and nonusers. Use patterns were significantly influenced by heavy and light users, farm size, and geographic region. Enhanced soil biology was the main benefit attributed to organic matter amendments by both users and nonusers. Nonusers showed greater concern for food safety compared to users, and all growers reported greater concern for food safety from manure. The greatest adoption of organic matter amendments occurred on small farms (≤170 ha) located in the north San Joaquin Valley in California. Greater accessibility to manure correlated with presence of dairy farms. Poorer accessibility ratings by nonusers suggest access is a barrier to adoption, as opposed to nonusers having an undesirable view of the practice. Common management included applying organic matter amendments during tree dormancy from manure sources in composted forms with no-till. Heavy users on small farms exhibited the greatest year-to-year consistency and were more flexible with selection of sources and diverse in application methods. Large farms (>170 ha) were less likely to use organic matter amendments every year and less likely to apply them on all their farm area. This study identifies a number of strategies to fill knowledge gaps, increase practice awareness, and overcome barriers to adoption.

We used coded wire tag data to compare spawner age structure and seasonal patterns of age-specific size at date among fish harvested in the ocean from the four seasonal run timings (fall, late-fall, winter, and spring) of Chinook Salmon Oncorhynchus tshawytscha from the Central Valley, California, and we examined differences between the fall-run fish (the most abundant run) from the Sacramento and San Joaquin River basins. The runs varied in their ocean size at a common age and date, and within each run, monthly mean ocean sizes appeared to stop increasing when spawners began to return to freshwater. Despite support for multiple hypotheses, no single factor explained all of the variation among and within runs. Ocean size at a common date was well explained by a “juvenile head-start” hypothesis, predicting larger sizes for the spring and fall runs due to earlier ocean entry. Month of spawner return was well explained by a “premature adult migration” hypothesis, predicting earlier returns (within ye...

There is currently only a limited understanding of the relationship between water quality and predation on Pacific salmon Oncorhynchus spp. smolts. We addressed the hypothesis that poor water quality will decrease a smolt’s swimming performance and presumably its predator evasion capabilities. Predation is a major factor affecting salmon smolt survival throughout the San Joaquin River and the Sacramento–San Joaquin Delta of California. Prior studies have quantified predation rates, but the effect of water quality on predator evasion capability has not previously been evaluated. We quantified the swimming performance of juvenile Chinook Salmon O. tshawytscha in relation to water quality variables. The maximum swim speeds (Umax) of 45 hatchery-reared smolts (7.1–9.9 cm FL) were measured in controlled (laboratory) and field environments by using a mobile swim tunnel respirometer; measurements were obtained before and after the fish received a 2-d exposure to the lower San Joaquin River while being he...

Most of the water diversions on the Sacramento and San Joaquin Rivers (California, United States) and their tributaries are currently unscreened. These unscreened diversions are commonly used for irrigation and are potentially harmful to migrating and resident fishes. A large flume (test section: 18.29 m long, 3.05 m wide and 3.20 m high) was used to investigate the hydraulic fields near an unscreened water diversion under ecologically and hydraulically relevant diversion rates and channel flow characteristics. We investigated all combinations of three diversion rates (0.28, 0.42, and 0.57 m3/s) and three sweeping velocities (0.15, 0.38, and 0.61 m/s), with one additional test at 0.71 m3/s and 0.15 m/s. We measured the three-dimensional velocity field at seven cross sections near a diversion pipe and constructed regression equations of the observed maximum velocities near the pipe. Because the velocity components in three directions (longitudinal, transverse, and vertical) were significantly greater near the diversion pipe inlet compared with those farther from it, they cannot be neglected in the modeling and design of fish guidance and protection devices for diversion pipes. Our results should be of great value in quantifying the hydraulic fields that are formed around fish guidance devices to design more effective protection for fishes from entrainment into unscreened water-diversion pipes.

To evaluate the effect of precipitation events, management practices, and soil type in wine grape (Vitis vinifera L. ssp. vinifera) vineyard systems and provide data for greenhouse gas (GHG) emissions calculators, we monitored nine vineyards in the Lodi wine grape district, California, from April 2011 to December 2012. These commercial vineyards exist on three soil series (Redding, San Joaquin, and Tokay), representing a spectrum of soil textures and degrees of soil development. We hypothesized that soil characteristics would be a dominating factor affecting GHG fluxes, but the magnitude of fluxes would be influenced by precipitation and management events. We measured N₂O fluxes, soil NO₃–N and NH₄–N, and gravimetric water content (GWC) from vine and intervine (alleys) rows bimonthly (April–October) and monthly (November–March). Monthly, we collected soil samples for dissolved organic C (DOC) and dissolved organic N (DON) determination. Path analysis revealed that the effects of soil type and vineyard zone on N₂O emissions were influenced by soil texture (i.e., gravel and clay contents) but that this effect was mediated by GWC through soil temperature and soil inorganic N content. Management practices such as irrigation, fertigation, cover cropping, and tillage affected differences between vine rows and alleys for soil inorganic pools, DOC, and DON from June to October 2012. This 20-mo study indicated that precipitation events strongly influenced N₂O fluxes.

We examined upstream migration patterns of adult Chinook Salmon Oncorhynchus tshawytscha in relation to environmental factors and two management actions (installation of a rock barrier at a distributary and managed pulse flows). Data was collected using a portable resistance board weir and a Vaki Riverwatcher system that provided accurate daily counts of fall-run Chinook Salmon on their spawning migration. Akaike’s information criterion and multimodel inferential approaches, as well as generalized additive models, were used to assess the relative influence of water temperature, flow, moon illumination, weather, operation of a rock barrier, and managed pulse flows to explain the magnitude of daily counts and proportions of Chinook Salmon observed at the weir. Over the 12-year study period (2003–2014), we observed 38,206 Chinook Salmon. The installation of a rock barrier in the lower reaches of the San Joaquin River had positive and consistent influences on daily counts in the years it was installed...

This study was carried out to develop a model to explore the economic viability of subsurface drip irrigation (SDI) for alfalfa production in the major alfalfa production regions of California. Data from previously published studies on alfalfa under drip irrigation were applied to establish the relationship between hay yield and seasonal water use. A correction factor was defined to adjust the potential impacts of SDI due to regional differences in yield potential. A partial economic analysis was developed to assess economic benefits of SDI in alfalfa. The model predicted an additional 7.9 Mg ha−1 yield as a result of switching from surface flood irrigation to SDI, averaged across the principal alfalfa-growing counties and regions in California. The hay yield improvements predicted by the model are in good agreement with the preliminary reports of improved hay yields from the 12 commercial farmers who have implemented SDI in Sacramento Valley, Low Desert, and Southern San Joaquin Valley regions. While the proposed model illustrated the potential profitability of SDI in alfalfa in several regions, further on-farm experience and analysis would be required to confirm these results in practice. Copyright © 2016 John Wiley & Sons, Ltd.

Knowledge of the habitats occupied by species is fundamental for the development of effective conservation and management actions. The collapse of pelagic fish species in the Sacramento–San Joaquin Delta, California, has triggered a need to better understand factors that drive their distribution and abundance. A study was conducted in summer–fall 2014 in an attempt to identify physical and biological habitat conditions that drive the abundance and distribution of pelagic species in the northern region of the system. The study was conducted in the three largest channels in the northern Sacramento–San Joaquin Delta by dimension, volume, and flow capacity. The pelagic community was dominated by three nonnative species, Siberian prawn Exopalaemon modestus, which comprised 56% of the total number of organisms, and two fish species, Threadfin Shad Dorosoma petenense and Mississippi Silversides Menidia audens, which together comprised 43% of the total number of organisms. Total fish and total shrimp abun...

A multi-year drought has taken a severe toll on the agricultural economy of California’s Central Valley. Index insurance is an instrument with the potential to protect water users from economic losses due to periodic water shortages. An index insurance product based on the Sacramento Index and adapted to the Central Valley Project water supply is proposed. To address the potential for intertemporal adverse selection, three product designs are suggested: (1) “early bird” insurance; (2) variable premium insurance; and (3) variable deductible insurance. The performance of the designs are assessed using loss functions from the Westlands Water District in the San Joaquin Valley.

Waterfowl managers lack the information needed to fully evaluate the biological effects of their habitat conservation programs. We studied body condition of dabbling ducks shot by hunters at public hunting areas throughout the Central Valley of California during 2006–2008 compared with condition of ducks from 1979 to 1993. These time periods coincide with habitat increases due to Central Valley Joint Venture conservation programs and changing agricultural practices; we modeled to ascertain whether body condition differed among waterfowl during these periods. Three dataset comparisons indicate that dabbling duck body mass was greater in 2006–2008 than earlier years and the increase was greater in the Sacramento Valley and Suisun Marsh than in the San Joaquin Valley, differed among species (mallard [Anas platyrhynchos], northern pintail [Anas acuta], America wigeon [Anas americana], green-winged teal [Anas crecca], and northern shoveler [Anas clypeata]), and was greater in ducks harvested late in the season. Change in body mass also varied by age–sex cohort and month for all 5 species and by September–January rainfall for all except green-winged teal. The random effect of year nested in period, and sometimes interacting with other factors, improved models in many cases. Results indicate that improved habitat conditions in the Central Valley have resulted in increased winter body mass of dabbling ducks, especially those that feed primarily on seeds, and this increase was greater in regions where area of post-harvest flooding of rice and other crops, and wetland area, has increased. Conservation programs that continue to promote post-harvest flooding and other agricultural practices that benefit wintering waterfowl and continue to restore and conserve wetlands would likely help maintain body condition of wintering dabbling ducks in the Central Valley of California. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Effective conservation of migratory shorebirds requires information on their stopover ecology and migratory connectivity in areas such as the Great Basin and interior California, USA, where freshwater is highly managed and maintenance of wetland networks requires planning across multiple regions. We captured long-billed dowitchers (Limnodromus scolopaceus; hereafter dowitchers) to study their molt patterns and length of stay in the Klamath Basin during fall migration and their migratory connectivity and over-winter space use in California's Central Valley. Most dowitchers were in active primary molt when captured (83%, n = 116), and molt stage increased during August and September. Radio-tagged dowitchers had an average length of stay after capture of 31.9 days (n = 54). After departing the Klamath Basin, we located 57% of 81 radio-tagged dowitchers in the Central Valley from December to February; most of the 228 detections occurred in the Sacramento Valley (39%) or Grasslands Ecological Area in the San Joaquin Basin (47%). Space use by radio-tagged dowitchers differed among the Sacramento Valley, San Joaquin Basin, and Sacramento-San Joaquin Delta sub-regions, which demonstrated the influence of varying amounts and distributions of habitat. We recommend that managers in the Klamath Basin provide shallow-water wetlands to support migrant dowitchers for ≥30 days beginning around 1 August, but ideally wetlands should be maintained until 30 September if freshwater supplies are available. We also recommend coordinated management of shallow-water wetlands within and between the Klamath Basin and Central Valley to optimize the use of freshwater, a limited and unreliable resource. © 2015 The Wildlife Society.

Background Environmental pollutants and neighbourhood socioeconomic factors have been associated with neural tube defects, but the potential impact of interaction between ambient air pollution and neighbourhood socioeconomic factors on the risks of neural tube defects is not well understood. Methods We used data from the California Center of the National Birth Defects Study and the Children's Health and Air Pollution Study to investigate whether associations between air pollutant exposure in early gestation and neural tube defects were modified by neighbourhood socioeconomic factors in the San Joaquin Valley of California, 1997–2006. There were 5 pollutant exposures, 3 outcomes, and 9 neighbourhood socioeconomic factors included for a total of 135 investigated associations. Estimates were adjusted for maternal race-ethnicity, education, and multivitamin use. Results We present below odds ratios (ORs) that exclude 1 and a chi-square test of homogeneity P-value of

Analysis of a mass burial of seven males at CA-ALA-554, a prehistoric site in the Amador Valley, CA, was undertaken to determine if the individuals were "locals" or "non-locals," and how they were genetically related to one another.The study includes osteological, genetic (mtDNA), and stable (C, N, O, S) and radiogenic (Sr) isotope analyses of bone and tooth (first and third molars) samples.Isotopes in first molars, third molars, and bone show they spent the majority of their lives living together. They are not locals to the Amador Valley, but were recently living to the east in the San Joaquin Valley, suggesting intergroup warfare as the cause of death. The men were not maternally related, but represent at least four different matrilines. The men also changed residence as a group between age 16 and adult years.Isotope data suggest intergroup warfare accounts for the mass burial. Genetic data suggest the raiding party included sets of unrelated men, perhaps from different households. Generalizing from this case and others like it, we hypothesize that competition over territory was a major factor behind ancient warfare in Central California. We present a testable model of demographic expansion, wherein villages in high-population-density areas frequently fissioned, with groups of individuals moving to lower-population-density areas to establish new villages. This model is consistent with previous models of linguistic expansion.

Volcanogenic sandstones are typically rich in volcanic rock fragments that can provide reactive minerals for CO 2 mineralization in a scenario of CO 2 sequestration. To quantitatively evaluate the extent and time scale of CO 2 mineralization in potential reservoir formations, we characterized example high‐porosity volcanic sand from the San Joaquin Valley of southern Central California. Samples were collected from the volcanic‐rich members of the Etchegoin Formation in the San Joaquin Basin near Coalinga, California. Thin sections made from these samples were examined under petrographic microscope to identify mineral compositions, and then scanning electron microscopy (SEM) and energy dispersive x‐ray spectroscopy (EDX) were used to gather quantitative information on mineral abundances, distribution, and reactive surface areas. Porosity and permeability were also measured using core plugs made from outcrop samples. Results show that the Etchegoin volcanic sandstone has a high percentage (10–15%) of reactive minerals (pyroxenes, Fe‐Ti spinel and clays), and high reactive surface areas at about 1 m-super-2/kg. Reactive transport modeling is conducted and shows that these reactive minerals could mineralize 92% of injected and capillary‐trapped CO 2 within 1000 years of injection. Possible effects of heterogeneity on CO 2 injection and mineralization are also studied using the reactive transport code TOUGHREACT. Vertical heterogeneity of mineralogy and hydrology increases both CO 2 injectivity and mineralization. Available volcanogenic sandstones worldwide like the Etchegoin sandstone are summarized from the literature, with formations from the western USA that have CO 2 sequestration potential emphasized.© 2015 Society of Chemical Industry and John Wiley & Sons, Ltd

Juvenile Chinook Salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River, California, must negotiate the Sacramento–San Joaquin River Delta (hereafter, the Delta), a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Fish that enter the interior and southern Delta—the region to the south of the Sacramento River where water pumping stations are located—survive at a lower rate than fish that use alternative migration routes. Consequently, total survival decreases as the fraction of the population entering the interior Delta increases, thus spurring management actions to reduce the proportion of fish that are entrained into the interior Delta. To better inform management actions, we modeled entrainment probability as a function of hydrodynamic variables. We fitted alternative entrainment models to telemetry data that identified when tagged fish in the Sacramento River entered two river channels leading to the interio...

In the Sacramento–San Joaquin River Delta, California, tidal forces that reverse river flows increase the proportion of water and juvenile late fall-run Chinook salmon diverted into a network of channels that were constructed to support agriculture and human consumption. This area is known as the interior delta, and it has been associated with poor fish survival. Under the rationale that the fish will be diverted in proportion to the amount of water that is diverted, the Delta Cross Channel (DCC) has been prescriptively closed during the winter out-migration to reduce fish entrainment and mortality into the interior delta. The fish are thought to migrate mostly at night, and so daytime operation of the DCC may allow for water diversion that minimizes fish entrainment and mortality. To assess this, the DCC gate was experimentally opened and closed while we released 2983 of the fish with acoustic transmitters upstream of the DCC to monitor their arrival and entrainment into the DCC. We used logistic regression to model night-time arrival and entrainment probabilities with covariates that included the proportion of each diel period with upstream flow, flow, rate of change in flow and water temperature. The proportion of time with upstream flow was the most important driver of night-time arrival probability, yet river flow had the largest effect on fish entrainment into the DCC. Modelling results suggest opening the DCC during daytime while keeping the DCC closed during night-time may allow for water diversion that minimizes fish entrainment into the interior delta. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Published in Agron. J. 107:588–596 (2015) doi:10.2134/agronj14.0415 Copyright © 2015 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. ABSTRACT

Analysis of exposed silage face surface area was conducted to better understand and provide feed management recommendations as well as evaluate potential compliance needs related to volatile organic compound emissions. Policy was developed by the San Joaquin Valley Air Pollution Control District (District) to restrict exposed surface area of silage piles to 199·7 m2 per farm if only one pile was exposed or 399·5 m2 per farm if more than one pile was exposed. Exposed surface area on piles of silages at 20 dairies was quantified to determine impacts of these surface area restrictions. Herd size ranged from 490 to 7,200 milking cows, and the number of exposed piles ranged from one to four per farm as maize and/or wheat silage. Surface area of piles was quantified based on pile measurements and geometric shapes. The measured value was compared to the estimated value using the District ‘online calculator’. The District calculator used inputs for base length and height with assumed constant relationships between base and top lengths. Five of 43 piles had >199·7 m2 of exposed surface area. Sixteen of 20 dairies with more than one exposed surface complied with the exposed surface area restriction. On average, the District calculator overestimated surface areas by 11·6% ± 14·8 (range −57·7 to 38·4%). Pile measurements and use of geometric shapes provide a more precise method to quantify exposed surface area. This will be of particular use for those operators who utilize the District calculator and find their exposed areas out of compliance.

OBJECTIVE Access to clean and affordable water is a significant public health issue globally, in the United States, and in California where land is heavily used for agriculture and dairy operations. The purpose of this study was to explore the geographic relationships among dairy farms, nitrate levels in drinking water, low birth weight, and socioeconomic data at the ZIP code level in the San Joaquin Valley. DESIGN AND SAMPLE This ecological study used a Geographic Information System (GIS) to explore and analyze secondary data. MEASURES A total of 211 ZIP codes were analyzed using spatial autocorrelation and regression analysis methods in ArcGIS version 10.1. RESULTS ZIP codes with dairies had a higher percentage of Hispanic births (p = .001). Spatial statistics revealed that ZIP codes with more dairy farms and a higher dairy cow density had higher levels of nitrate contamination. No correlation was detected between LBW and unsafe nitrate levels at the ZIP code level. CONCLUSION Further research examining communities that use private and small community wells in the San Joaquin Valley should be conducted. Birth data from smaller geographic areas should be used to continue exploring the relationship between birth outcomes and nitrate contamination in drinking water.

Agricultural drainage of organic soils has resulted in vast soil subsidence and contributed to increased atmospheric carbon dioxide (CO2) concentrations. The Sacramento-San Joaquin Delta in California was drained over a century ago for agriculture and human settlement and has since experienced subsidence rates that are among the highest in the world. It is recognized that drained agriculture in the Delta is unsustainable in the long-term, and to help reverse subsidence and capture carbon (C) there is an interest in restoring drained agricultural land-use types to flooded conditions. However, flooding may increase methane (CH4) emissions. We conducted a full year of simultaneous eddy covariance measurements at two conventional drained agricultural peatlands (a pasture and a corn field) and three flooded land-use types (a rice paddy and two restored wetlands) to assess the impact of drained to flooded land-use change on CO2 and CH4 fluxes in the Delta. We found that the drained sites were net C and greenhouse gas (GHG) sources, releasing up to 341 g C m(-2) yr(-1) as CO2 and 11.4 g C m(-2) yr(-1) as CH4. Conversely, the restored wetlands were net sinks of atmospheric CO2, sequestering up to 397 g C m(-2) yr(-1). However, they were large sources of CH4, with emissions ranging from 39 to 53 g C m(-2) yr(-1). In terms of the full GHG budget, the restored wetlands could be either GHG sources or sinks. Although the rice paddy was a small atmospheric CO2 sink, when considering harvest and CH4 emissions, it acted as both a C and GHG source. Annual photosynthesis was similar between sites, but flooding at the restored sites inhibited ecosystem respiration, making them net CO2 sinks. This study suggests that converting drained agricultural peat soils to flooded land-use types can help reduce or reverse soil subsidence and reduce GHG emissions.

Author(s): Buck, S; Auffhammer, M; Sunding, D | Abstract: The lack of robust water markets makes it difficult to value irrigation water. Because water rights are appurtenant to land, it is possible to infer the value of water from observed differences in the market price of land. We use panel data on repeat farmland sales in California's San Joaquin Valley to estimate a hedonic regression equation with parcel fixed effects. This controls for sources of omitted variables bias and allows us to recover the value of irrigation water to landowners in our sample. We show that a more traditional cross-sectional regression results in an artificially low value of irrigation water. © The Author (2014).

Freshwater ecosystem health has been increasingly linked to floodplain connectivity, and some river restoration efforts now overtly target reconnecting floodplain habitats for species recovery. The dynamic nature of floodplain habitats is not typically accounted for in efforts to plan and evaluate potential floodplain reconnection projects. This study describes a novel approach for integrating streamflow dynamics with floodplain area to quantify species-specific habitat availability using hydraulic modelling, spatial analysis and statistical measures of flow regime. We used this hydro-ecological modelling approach to examine the potential habitat for splittail (Pogonichthys macrolepidotus), Chinook salmon (Oncorhynchus tshawytscha) and their food resources under two restoration treatments and two climate change flow scenarios for a study site on San Joaquin River in California. Even with the addition of new floodplain through restoration efforts, the modelling results reveal only 13 streamflow events in the past 80 years had the magnitude and duration required for splittail spawning and rearing, and 14 events had flows long enough for salmon rearing benefits. Under climate change, modelled results suggest only 4–17% of the years in the rest of this century are likely to produce required flow-related habitat conditions for splittail and salmon rearing along the study reach. Lastly, we demonstrate by simulating augmented reservoir releases that restoration of fish habitat will require a more natural flow regime to make use of restored floodplain and achieve the desired hydrologic habitat connectivity. Copyright © 2014 John Wiley & Sons, Ltd.

Landscape composition plays an important, but poorly understood, role in the population dynamics of agricultural pest species with broad host ranges including both crops and weeds. One such pest, the generalist plant bug Lygus hesperus Knight (Hemiptera: Miridae), is a key cotton pest that feeds on various hosts differing in quality in California's San Joaquin Valley (USA). We investigated the effects of 15 common crops and uncultivated agricultural land on L. hesperus populations, by correlating the densities of L. hesperus in focal cotton fields with the areas of the 16 crops in surrounding rings. Insect counts were provided by private pest-control advisors, and spatial data were obtained from Kern County records. We first calculated Spearman's partial correlation coefficients on an annual basis for each crop separately, and then performed a meta-analysis of these correlations across years to describe the overall effect of a particular crop on L. hesperus after the effects of the 15 other crops are removed. Consistent with studies conducted in other areas, L. hesperus density was positively correlated with safflower, and negatively with cotton. Lygus hesperus density was also correlated with several other crops that are often not considered in pest management, including grape, oat, and onion (positive correlations), and almond, pistachio, and potato (negative correlations). Lygus hesperus density was also found to be negatively correlated with alfalfa and positively correlated with uncultivated habitats, a relationship that receives mixed support in the literature. Several other crops tested were not significantly correlated with L. hesperus densities in focal cotton fields, suggesting a neutral role for them in L. hesperus dynamics. The improved understanding of the effects of a greater variety of crops on L. hesperus population dynamics will be useful in the design of agricultural landscapes for enhanced management of this important polyphagous pest.

Providing environmentally safe methods for disposal of drainage water containing salt and nutrients is a challenge for irrigated agriculture. A system developed for sequentially using saline drainage water for supplemental irrigation resulted in significant reduction of the drainage water volume. This system dubbed ‘integrated on-farm drainage management’ (IFDM) was demonstrated on four 65-ha fields located on a farm on the west side of the San Joaquin Valley of California. Three of the fields were used to grow salt-sensitive crops (tomato, garlic) and the fourth was used to grow salt-tolerant crops, e.g. ‘Jose’ tall wheatgrass. Subsurface drainage systems were installed on all fields at a maximum depth of 1.8 m and had controls to regulate shallow water table position and drainage flow. The total drainage flow from the site represented 0.7% of the applied water. The area used for salt-tolerant crops was less than 6% of the total area served, compared to using evaporation ponds requiring areas equal to or greater than 10% of the served area. The results demonstrated that the regional groundwater quality masked the concentrating effect of crop water use. Deep percolation from the fields contributing to the reuse area ranged from 6 to 10% of the total applied water. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

The survival of juvenile Chinook Salmon through the lower San Joaquin River and Sacramento–San Joaquin River Delta in California was estimated using acoustic tags in the spring of 2009 and 2010. The focus was on route use and survival within two major routes through the Delta: the San Joaquin River, which skirts most of the interior Delta to the east, and the Old River, a distributary of the San Joaquin River leading to federal and state water export facilities that pump water out of the Delta. The estimated probability of using the Old River route was 0.47 in both 2009 and 2010. Survival through the southern (i.e., upstream) portion of the Delta was very low in 2009, estimated at 0.06, and there was no significant difference between the Old River and San Joaquin River routes. Estimated survival through the Southern Delta was considerably higher in 2010 (0.56), being higher in the Old River route than in the San Joaquin route. Total estimated survival through the entire Delta (estimated only in 2...

Anthropogenic alterations to river systems, such as irrigation and hydroelectric development, can negatively affect fish populations by reducing survival when fish are routed through potentially dangerous locations. Non-physical barriers using behavioural stimuli are one means of guiding fish away from such locations without obstructing water flow. In the Sacramento–San Joaquin River Delta, we evaluated a bio-acoustic fish fence (BAFF) composed of strobe lights, sound and a bubble curtain, which was intended to divert juvenile Chinook salmon (Oncorhynchus tshawytscha) away from Georgiana Slough, a low-survival migration route that branches off the Sacramento River. To quantify fish response to the BAFF, we estimated individual entrainment probabilities from two-dimensional movement paths of juvenile salmon implanted with acoustic transmitters. Overall, 7.7% of the fish were entrained into Georgiana Slough when the BAFF was on, and 22.3% were entrained when the BAFF was off, but a number of other factors influenced the performance of the BAFF. The effectiveness of the BAFF declined with increasing river discharge, likely because increased water velocities reduced the ability of fish to avoid being swept across the BAFF into Georgiana Slough. The BAFF reduced entrainment probability by up to 40 percentage points near the critical streakline, which defined the streamwise division of flow vectors entering each channel. However, the effect of the BAFF declined moving in either direction away from the critical streakline. Our study shows how fish behaviour and the environment interacted to influence the performance of a non-physical behavioural barrier in an applied setting. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Chinook salmon (Oncorhynchus tschawytscha) populations within the highly modified San Francisco Estuary, California, have seen precipitous declines in recent years. To better understand this decline, a decade of coded-wire tag release and recovery data for juvenile salmon was combined with physicochemical data to construct models that represented alternative hypotheses of estuarine conditions that influence tag recovery rate in the ocean. An information theoretic approach was used to evaluate the weight of evidence for each hypothesis and model averaging was performed to determine the level of support for variables that represented individual hypotheses. A single best model was identified for salmon released into the Sacramento River side of the estuary, whereas two competitive models were selected for salmon released into the San Joaquin River side of the estuary. Model averaging found that recovery rates were greatest for San Joaquin River releases when estuary water temperatures were lower, and salmon were released at larger sizes. Recovery rate of Sacramento releases was greatest during years with better water quality. There was little evidence that large-scale water exports or inflows influenced recovery rates in the ocean during this time period. These results suggest that conceptual models of salmon ecology in estuaries should be quantitatively evaluated prior to implementation of recovery actions to maximise the effectiveness of management and facilitate the recovery of depressed Chinook populations.

Bracketing the uncertainty of streamflow and agricultural runoff under climate change is critical for proper future water resource management in agricultural watersheds. This study used the Soil and Water Assessment Tool (SWAT) in conjunction with a Latin hypercube climate change sampling algorithm to construct a 95% confidence interval (95CI) around streamflow, sediment load, and nitrate load predictions under changes in climate for the Sacramento and San Joaquin River watersheds in California's Central Valley. The Latin hypercube algorithm sampled 2000 combinations of precipitation and temperature changes based on Intergovernmental Panel on Climate Change projections from multiple General Circulation Models. Average monthly percent changes of the upper and lower 95CI limits compared to the present-day simulation and a statistic termed the “r-factor” (average width of the 95CI band divided by the standard deviation of the 95CI bandwidth) were used to assess watershed sensitivities. 95CI results indicate that streamflow and sediment runoff in the Sacramento River watershed are more likely to decrease under climate change compared to present-day conditions, whereas the increase and decrease for nitrate runoff were found to be equal. For the San Joaquin River watershed, streamflow slightly decreased under climate change, whereas sediment and nitrate runoff increased compared to present-day climate. Comparisons of watershed sensitivities indicate that the San Joaquin River watershed is more sensitive to climate changes than the Sacramento River watershed, which is largely caused by the high density of agricultural land. Copyright © 2012 John Wiley & Sons, Ltd.

Water from the San Joaquin Delta, having chloride concentrations up to 3590 mg/L, has intruded fresh water aquifers underlying Stockton, California. Changes in chloride concentrations at depth within these aquifers were evaluated using sequential electromagnetic (EM) induction logs collected during 2004 through 2007 at seven multiple-well sites as deep as 268 m. Sequential EM logging is useful for identifying changes in groundwater quality through polyvinyl chloride-cased wells in intervals not screened by wells. These unscreened intervals represent more than 90% of the aquifer at the sites studied. Sequential EM logging suggested degrading groundwater quality in numerous thin intervals, typically between 1 and 7 m in thickness, especially in the northern part of the study area. Some of these intervals were unscreened by wells, and would not have been identified by traditional groundwater sample collection. Sequential logging also identified intervals with improving water quality-possibly due to groundwater management practices that have limited pumping and promoted artificial recharge. EM resistivity was correlated with chloride concentrations in sampled wells and in water from core material. Natural gamma log data were used to account for the effect of aquifer lithology on EM resistivity. Results of this study show that a sequential EM logging is useful for identifying and monitoring the movement of high-chloride water, having lower salinities and chloride concentrations than sea water, in aquifer intervals not screened by wells, and that increases in chloride in water from wells in the area are consistent with high-chloride water originating from the San Joaquin Delta rather than from the underlying saline aquifer.