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25 results for “San Francisco Bay”
San Francisco Estuary Institute Phytoplankton eDNA and Toxin Monitoring, San Francisco Bay, CA, 2014-2023
From late 2014-present, San Francisco Estuary Institute has conducted molecular monitoring of phytoplankton in partnership with the US Geological Survey from several stations stretching from Rio Vista in the North Delta to the Lower South Bay, past the Dumbarton Bridge. These samples have been analyzed for 18S eDNA data in partnership with Timothy Otten at Bend Genetics, targeting the V7 region. The included dataset covers the 2014-2023 period, including data up to 2022, conducted with an Illumina MISEQ platform, and from 2022-2023 using a NEXTSEQ platform, which enabled much greater sampling depth. Two sets of taxonomic assignments are included in this data release, one using the Silva database, and the other using the PR2 database, two of the leading sources of phytoplankton taxonomic data aiding in assignments of OTUs to taxa. Raw sequence data will also be uploaded to NCBI for comparison. Data collection continues and this release will be updated as new time periods are added.
Six decades (1959-2022) of water quality in the upper San Francisco Estuary: an integrated database of 16 discrete monitoring surveys in the Sacramento San Joaquin Delta, Suisun Bay, Suisun Marsh, and San Francisco Bay
The upper San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated water quality data from 16 boat-based long-term monitoring surveys in the upper SFE. This integrated dataset includes measurements of temperature (surface and bottom), conductivity (surface), salinity (surface), Secchi depth, qualitative concentration of the toxic alga Microcystis (surface), Chlorophyll-a concentration (surface), nutrients (surface), and other parameters from 1959 - 2022. The component surveys range in sampling frequency from thrice weekly to monthly and range in duration from 5 – 60 years. Most component surveys sample at fixed stations, but the Enhanced Delta Smelt Monitoring survey uses random sites and some stations (with “EZ” in the station name) of the Environmental Monitoring Program follow the salinity field. It is highly recommended to inspect the documentation of the component surveys for more information on their methods.
InSAR stack of San Francisco Bay, California from Sentinel-1 descending track 42 processed with GMTSAR
<p>A stack of unwrapped interferograms in the San Francisco Bay area, California, USA</p> <p>Sensor: Sentinel-1 descending track 42</p> <p>Processor: <a href="https://github.com/gmtsar/gmtsar" target="_blank" rel="noopener">GMTSAR</a></p> <p>This is an input dataset for the time series analysis with <a href="https://github.com/insarlab/MintPy/">MintPy</a>.</p> <p>The tropospheric delay estimated from ERA-5 using PyAPS is attached.</p> <p><strong>Version 1.x (~2.3 GB)</strong><br>Time: 2014.12.31 - 2024.06.05 (333 acquisitions, 1297 interferograms)</p> <p><strong>Version 0.x (~290 MB; for fast testing of code development)</strong><br>Time: 2020.01.04 - 2021.07.15 (70 acquisitions, 184 interferograms)</p>
Interagency Ecological Program: San Francisco Bay Study Survey for Fish and Mobile Crustaceans 1980-2024
The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans (brachyuran crabs and caridean shrimp) in the San Francisco Estuary, mainly downstream of the Sacramento-San Joaquin Delta. The Bay Study survey currently samples 52 open-water stations monthly from a research vessel with two types of trawl gear: a midwater trawl to sample pelagic fishes, and an otter trawl to sample demersal fishes, crabs, and shrimp. Historically, the study also included plankton sampling (1980-1989) for larval fish and crustaceans. Fish collected by the otter and midwater trawl are identified to species, counted, and a representative subsample is measured. In addition, crabs from the otter trawl are identified, counted, sexed, and measured, and gelatinous zooplankton from the midwater trawl are identified and counted. Shrimp are retained from each otter trawl sample and returned to the laboratory for processing, which includes identification, counts, sex, and length. Additional data collected at each station includes water depth, Secchi, and a water column profile of temperature and conductivity. This data publication includes fish, crab, shrimp, gelatinous zooplankton (jellies), and water quality data. Metadata related to the plankton sampling will be included in the future when this data is published.
InSAR stack of San Francisco Bay in California from Sentinel-1 descending track 42 processed with ARIA
<p>A stack of unwrapped interferograms in San Francisco Bay, California, USA from Sentinel-1descending track 42</p> <p>Processor: ARIA (processed using ISCE and prepared using <a href="https://github.com/aria-tools/ARIA-tools">ARIA-tools</a> as shown below)</p> <p>Tropospheric delay estimated from ERA5 using PyAPS is attached.</p> <p>This is an input dataset for the time series analysis with <a href="https://github.com/insarlab/MintPy/">MintPy</a>.</p> <p><strong>Version 1.2 (~5 GB):</strong><br> Time: 2015.03.01 - 2022.06.04, 189 acquisitions, 961 interferograms<br> Used ARIA-tools and MintPy commands:</p> <pre><code>ariaDownload.py -b '37.25 38.1 -122.6 -121.75' --track 42 ariaTSsetup.py -f 'products/*.nc' -b '37.25 38.1 -122.6 -121.75' --mask Download prep_aria.py -s ../stack/ -d ../DEM/SRTM_3arcsec.dem -i ../incidenceAngle/*.vrt -a ../azimuthAngle/*.vrt -w ../mask/watermask.msk</code></pre> <p><strong>Version 0.2 (~280 MB; for fast testing of code development)</strong><br> Time: 2016.01.31 - 2017.05.10, 23 acquisitions, 91 interferograms<br> Used ARIA-tools commands (access date Jun 18th, 2022):</p> <pre><code>ariaDownload.py -b '37.35 38.00 -122.45 -121.80' --track 42 --start 20160101 --end 20170510 ariaTSsetup.py -f 'products/*.nc' -b '37.35 38.00 -122.45 -121.80' --mask Download</code></pre> <p> </p>
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California
<p>This repository contains the pertinent datasets used in the manuscript, <em>Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California</em>.</p>
Figures 1-7 in Confirmation of the existence of Heliophanus apiatus (Araneae: Salticidae) in the San Francisco Bay Area of California, USA, first records for North America
Figures 1-7. Heliophanus apiatus from the San Francisco Bay area of California. 1, Male feeding on Drosphila melanogaster. Note the deep black coloration with four white spots, and the white spots on the black palpi. 2, Female on retreat. Note the brown-black coloration and the lack of white spots or bands on the appendages. 3, Anterior view of female feeding on D. melanogaster, displaying the typical brilliant yellow palpi typical of all instars except mature males. 4, Early instar immature, ~2 mm long. Note the white abdominal markings or bands (not spots) that resemble early instars of Salticus. 5, Same specimen as (4) after the next molt, ~2.5 mm long. Subsequent instars resemble the adult female in coloration. 6, Adult male on edge of planter box. 7, Two immatures on a composite flower.
San Francisco Bay Area Kappa
<p>This dataset contains....</p>
Sea level rise, groundwater rise, and contaminated sites in the San Francisco Bay Area, and Superfund Sites in the contiguous United States
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Data from: Contemporary land change alters fish communities in a San Francisco Bay drainage, 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.
Compound coastal flooding in San Francisco Bay under climate change
<p>These files provide the data that are used for the compound coastal flooding analysis in San Francisco Bay under climate change.</p> <p>If you have used this dataset, please cite our papers:<br>"Wang, Z., Leung, M., Mukhopadhyay, S. <em>et al.</em> Compound coastal flooding in San Francisco Bay under climate change. <em>npj Nat. Hazards</em> <strong>2</strong>, 3 (2025). https://doi.org/10.1038/s44304-024-00057-0<em>"</em> . </p> <p>"Wang, Zhenqiang, et al. "A hybrid statistical–dynamical framework for compound coastal flooding analysis." <em>Environmental Research Letters</em> 20.1 (2024): 014005."</p>
Subspecies and Distribution. Z.t.trinotatusRhoads,1895—SWCanada(extremeSWBritishColumbia)andNWUSA(WWashington,andalongthePacificcoastofOregontoextremeNWCalifornia). Z.t.eurekaA.B.Howell,1920—WUSA(coastalNCalifornia). Z.t.montanusMerriam,1897—NWUSA(inlandNW&WCOregon). Z. t. orarius Preble, 1899 — W USA (small area of coastal California just N of San Francisco Bay). in Zapodidae
Subspecies and Distribution. Z.t.trinotatusRhoads,1895—SWCanada(extremeSWBritishColumbia)andNWUSA(WWashington,andalongthePacificcoastofOregontoextremeNWCalifornia). Z.t.eurekaA.B.Howell,1920—WUSA(coastalNCalifornia). Z.t.montanusMerriam,1897—NWUSA(inlandNW&WCOregon). Z. t. orarius Preble, 1899 — W USA (small area of coastal California just N of San Francisco Bay).
Subspecies and Distribution. R.r.raviventrisDixon,1908—SportionofSanFranciscoBay,California(USA). R. r. halicoetes Dixon, 1909 — N portion of San Francisco Bay, California (USA). in Cricetidae
Subspecies and Distribution. R.r.raviventrisDixon,1908—SportionofSanFranciscoBay,California(USA). R. r. halicoetes Dixon, 1909 — N portion of San Francisco Bay, California (USA).
Data from: Contemporary land change alters fish communities in a San Francisco Bay drainage, California, U.S.A.
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Data from: Population structure and genetic diversity among eelgrass (Zostera marina) beds and depths in San Francisco Bay
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Data from: Shared temporal increases in bill size among songbirds of the San Francisco bay area are due to different seasonal selective pressures
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Data from: LiDAR-derived digital elevation model of Whale's Tail Marsh, San Francisco Bay, 2019
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Model code and outputs of "Modeling the Dispersal of the San Francisco Bay Plume over the Northern and Central California Shelf"
<p>- "model_code.rar" contains the model source code.</p> <p>- "model_grid.nc" contains the grid file.</p> <p>- "model_outputs.nc" contains the model outputs.</p>
A paleo-proxy-based reconstruction of still water level in the San Francisco Bay during 1500 - 2000 CE
<p>The dataset contains the following files: </p> <ol> <li>AWT_hisPCs_1880_2017.csv : Three leading annual principal components (APCs) of sea surface temperature anomalies (obtained from ERSSTv4) in the Hovmoller space during 1880 to 2017. </li> <li>APC*_1000sims_500yr.csv : Reconstructions of three APCs using paleo-proxy-based Nino3.4 reconstructions from 1500 to 2000. Each file contains 1000 simulations. </li> <li>TESLA_SF_reconstructed_SWLs_Sims_*_*_wSS.mat : there are four files for total 1000 simulations of reconstructed still water levels (SWLs) at San Francisco Bay. They can be accessed using MATLAB. Each of the files contains the following data: <ul> <li>time_fin : time in matlab format, 1500 - 2000 hourly. Time series starts from June 1st 1500, to account for wave climate. </li> <li>tide_raw_fin : astronomical tide prediction from 1500 - 2000, at hourly resolution. </li> <li>tide_raw_slr_fin : adding ~2.2mm/yr of SLR on to tide_raw_fin starting in 1900. </li> <li>tide_fin : correcting tide_raw_slr_sin with an ~0.09m offset to also account for the mismatch between MSL from ~1900- 2000 and the time before SLR is calculated. </li> <li>mmsl_sim_hourly : monthly mean sea level, anomalies plus seasonality, at hourly resolution. </li> <li>SWL : still water level at hourly resolution (tide_fin + mmsl_sim_hourly)</li> <li>SS_fin : hourly storm surge time series. </li> <li>DSWL : SWL + SS_fin. </li> </ul> </li> <li>MMSLA_100yrsRTs_30sw.RDS : Results of quasi-non-stationary flood risk analysis using annual maxima series (AMS) of MMSLA for a return period of 100yrs. The data set contains the following: <ul> <li>eva: 1000 x 3 array contains GEV estimation of return levels for each of 1000 simulation. Column 2 contains the estimated return levels, columns 1 and 3 contains 2.5 percentiles and 97.5 percentile values around the estimates. </li> <li>swa : contains the results of GEV calculated over a 30 years sliding window. This is a list of 6 components as below: <ul> <li>RTsim : An array of return level estimated for j-th window and i-th simulation </li> <li>RTobs: Return level estimates for last 100years (historical period)</li> <li>ci.lower.delta and ci.upper.delta : these denote the 95% interval of sampling variability in 100yr events using the Delta method. </li> <li>window.size : size of the sliding window. </li> <li>sliding.yrs : starting year of each sliding window. </li> </ul> </li> <li>conf : alpha or significance level (0.05 in this case).</li> <li>return.period : return period (100 years in this case). </li> <li> method: character string denoting which parameter estimation method is used ("MLE"). </li> <li>type: character string denoting which extreme value distribution is used *("GEV" or generalized extreme value distribution in this case). </li> <li>ams.ts : annual maxima series (input) values are saved here in the output. Can be used to reproduce the analysis. </li> <li>cur.ts : NULL. If ams.ts is not supplied, ams.ts is calculated using the input values of cur.ts. Not stored in the output if ams.ts input values are supplied. </li> </ul> </li> <li>MMSLA_100yrsRTs_100sw.RDS: Results of quasi-non-stationary flood risk analysis using annual maxima series (AMS) of MMSLA for a return period of 30yrs, with a sliding window of 100 years. The components of this .rds are same that that for 100yrs sliding window. </li> <li>ams_dswl_1_1000_sim_wSS.rds : Annual maxima series of SWL (MMSL + tide + Storm surge) for 1000 simulations as simulated using TESLA. </li> <li>ams_dswl_1_1000_sim_wSS_no_slr.rds : Annual maxima series of SWL (MMSL + tide + Storm surge) for 1000 simulations after removing SLR trend from 1900 onwards. </li> <li>ams_dswl_1_1000_sim_wSS_all_slr.rds : Annual maxima series of SWL (MMSL + tide + Storm surge) for 1000 simulations after adding a total 0.2 m SLR over 1500 - 2000 CE to superimpose SLR on to full extent of natural variability. All .RDS files are to be accessed using R. </li> </ol> <p>For further details, please contact Sudarshana Mukhopadhyay (sm2798@cornell.edu)</p>
Minimum Depth to Groundwater for the Coastal San Francisco Bay Area
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