CDFW BIOS GIS Dataset, Contact: Steve Stone, Description: This dataset depicts the general boundaries of the Central California Coast Steelhead distinct population segment (DPS) under the U.S. Endangered Species Act, as well as the historical population structure of the species.

Outmigrating Central Valley Chinook Salmon

Access this data on Dryad (DOI: 10.5061/dryad.280gb5mxx)

This Dryad entry contains data files and scripts used for analyses in Thompson et al. 2024 (Evolutionary Applications). Briefly, the study examines outmigration characteristics of juvenile Chinook salmon collecte d at Chipps Island in the Sacramento/San Joaquine Delta by assigning each sample to a population of origin. The analysis is broken down into three parts: 1) leave-one-out analyses to develop a population assignme nt method and evaluate its expected efficacy; 2) validation of the assignment method using an independent dataset of known-origin samples; 3) population assignment of unknown-origin juvenile samples collected at Chipps Island (and obtained from a tissue archive). This Dryad entry contains files and scripts necessary for that analysis, as well as the resulting output files.

Data Files

The following are descriptions of all data files uploaded here.

(Note: the sin...

CDFW BIOS GIS Dataset, Contact: Charleen Gavette, Description: Depiction of Biogeographic Population Groups (BPG) within the South-Central California Coast Steelhead Distict Population Segments (DPS).

Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is often difficult to distinguish individuals from the different Evolutionarily Significant Units. As such, many of the salmon monitoring and evaluation efforts in the Central Valley and San Francisco Bay-Delta are hampered by uncertainty about population (stock) identification and proportional effects of management actions (Dekar et al. 2013; IEP 2019). Studies have identified that the current identification method (length-at-date models) of juvenile Chinook salmon (Fisher 1992) captured in the watershed vary in their accuracy, particularly for spring-run (NMFS 2013; Harvey et al. 2014; Merz et al. 2014). The inaccuracy of the size-based methods is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in size ranges among stocks. The primary objective of this project was the genetic classification (to race; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program monitoring programs. The population-of-origin was determined for sampled fish by comparing their genotypes to reference genetic baselines. Genetic methods, having less statistical uncertainty that size-based models for population identification, were intended to directly target (and reduce) one source of uncertainty in the estimation of loss (take) from water diversions (operations) and develop the information necessary for understanding stock-specific distribution, habitat utilization, abundance, and life history variation. This project supports recommendations from the Interagency Ecological Program’s Salmon and Sturgeon Assessment of Indicators by Life Stage and Interagency Ecological Program Science Agenda efforts to improve Central Valley salmonid monitoring (Johnson et al. 2017; IEP 2019).

   Literature Cited

   Dekar, M., P. Brandes, J. Kirsch, L. Smith, J. Speegle, P. Cadrett and M. Marshall. 2013. USFWS Delta Juvenile Fish Monitoring Program Review. Background Document. Prepared for IEP Science Advisory Group, June 2013. US Fish and Wildlife Service, Stockton Fish and Wildlife Office, Lodi, CA. 224 p.
   Fisher, F.W. 1992. Chinook Salmon, Oncorhynchus tshawytscha, growth and occurrence in the Sacramento-San Joaquin River system. California Department of Fish and Game, Inland Fisheries Divisions, draft office report, Redding. 
   Harvey, B.N., D.P. Jacobson, M.A. Banks. 2014. Quantifying the uncertainty of a juvenile Chinook Salmon Race Identification Methyod for a Mixed-Race Stock. North American Journal of Fisheries Management. 
   IEP, Interagency Ecological Program. 2019. Interagency Ecological Program Science Strategy 2020-2024: Invenstment Priorities for Interagency Collaborative Science.
   Johnson, R.C., S. Windell, P. L. Brandes, J. L. Conrad, J. Ferguson, P. A. L. Goertler, B. N. Harvey, J.Heublein, J. A. Israel, D. W. Kratville, J. E. Kirsch, R. W. Perry, J. Pisciotto, W. R. Poytress, K. Reece, and B. G. Swart. 2017. Increasing the management value of life stage monitoring networks for three imperiled fishes in California's regulated rivers: case study Sacramento Winter-run Chinook salmon. San Francisco Estuary and Watershed Science 15: 1-41.
   National Marine Fisheries Service (NMFS). 2013. Endangered and Threatened Species: Designation of a Nonessential Experimental Population of Central Valley Spring-Run Chinook Salmon Below Friant Dam in the San Joaquin River, CA. Federal Register 70: 79622, December 31, 2013.

The Waterfowl Program annually monitors the waterfowl breeding population in California for conservation and to establish hunting frameworks within the Pacific Flyway, 1992-2022. Data are collected from both a fixed-wing and helicopter with 2 observers in each. The survey is conducted about the third week in April in the Central Valley and second week in May in NE CA. The state is divided into 9 strata for sampling with transects/segments in each stratum. Species, sex, and breeding status collected. Survey has been conducted since 1955 however a revised survey was developed in 1992 and continues annually. The project is funded by Pittman-Roberston Grant and State Duck Stamp funds. This data and metadata were submitted by California Department of Fish and Wildlife (CDFW) Staff though the Data Management Plan (DMP) framework with the id: DMP000455. For more information, please visit https://wildlife.ca.gov/Data/Sci-Data.

U.S. Census Bureau QuickFacts statistics for Valley Center CDP, California. QuickFacts data are derived from: Population Estimates, American Community Survey, Census of Population and Housing, Current Population Survey, Small Area Health Insurance Estimates, Small Area Income and Poverty Estimates, State and County Housing Unit Estimates, County Business Patterns, Nonemployer Statistics, Economic Census, Survey of Business Owners, Building Permits.

The California Central Valley steelhead (Oncorhynchus mykiss) has declined precipitously since Euro-American colonization and has been listed as threatened under the United States Endangered Species Act since 1998. Hatchery-origin fish now dominate the population and hatchery management is a key listing factor. However, scant release metric information is available. We compiled a time series of O. mykiss hatchery release data for all four Central Valley hatcheries releasing O. mykiss between 1948 and 2017. The biocomplexity of released fish has declined since the early 1980s. Individuals have been released at increasingly similar numbers, biomass, body sizes, times, and locations over time. Moreover, yearling fish have been released at larger sizes, leading to the near-exclusive release of age-1 smolts in February and March since the late 1990s and early 2000s. Pervasive reductions in release portfolios have likely occurred for other hatchery-supported Pacific salmonid stocks throughout the Pacific Rim region. In an increasingly variable environment, such reductions in intraspecific diversity could significantly affect population stability and resilience. Methods Release & Return Database Compilation

We compiled release data from 135 annual reports provided by the California Department of Fish and Wildlife (CDFW) for state-operated hatcheries. The state hatchery annual reports spanned one fiscal year from 1 July to 30 June of the following year: NFH (54 reports, 1956–57 to 2009–10), FRFH (40 reports, 1969–70 to 2009–10), and MRFH (41 reports, 1964–65 to 2007–08; no releases were reported for 1976–77, 1988–89, or 2001–02). From 1988 to 2001, release records were obtained for MRFH from the California Hatchery Scientific Review Group (CA HSRG 2012, Appendix VI) instead of annual reports because the former dataset is more detailed and complete. From 2001–2017 for the FRFH and 2003–2017 for the NFH and MRFH, an electronic dataset from CDFW's statewide inventory system was used instead of annual reports or California Hatchery Scientific Review Group data (CA HSRG 2012, Appendix VIII). Hatchery release data were considered “draft” or non-finalized from 1994–2017 for the NFH, 1992–2017 for the FRFH, and 1988–2017 for the MRFH. Release data for the CNFH from 1948 to winter 1975 were obtained from an electronic database provided by the U.S. Fish and Wildlife Service (USFWS) and data from spring 1975 to 2017 were obtained from the Regional Mark Information System (RMIS, http://www.rmpc.org/, retrieved on 21 May 2020).
The basic reporting unit for all data sources was a cohort of similarly sized fish released together in a stated release location over a specified time (hereafter referred to as a “release group”). Information about brood year (same as emergence year for winter-run O. mykiss), total number of fish planted, average or range of fish size(s)-at-release (usually expressed as fish·lb-1), release timing (from single days to months), and descriptions and (or) geographic coordinates of release locations were reported for release groups. Total numbers of returning O. mykiss trapped at state hatcheries were compiled from annual reports and the electronic database provided by CDFW.

Resulting databases: CV_Steelhead_Hatchery_Release_Database.csv

Objective 1: Temporal trends in juvenile releases Number released: We present annual release data according to the California ‘water year’ (WY; 1 October to 30 September) since this period is more relevant to the Central Valley O. mykiss life cycle than calendar years (e.g., upstream migration in fall and winter, spawning and emergence in winter, rearing in spring and summer [Williams 2006]). When the release period spanned two WYs (5.1% of total number released, 90.5% of which occurred before WY 1976), the WY possessing the larger share of the release period was assigned as the release WY. In rare instances when the release period spanned two WYs and was split equally between WYt and WYt+1 (0.2% of all releases), WYt+1 was set as the release year. A three-year moving average was applied to the annual numerical release data to highlight longer-term trends.

Data file used: CVSH_totmill.csv

Biomass released: Release group biomass was calculated as the product of total number of fish released and mean fish mass for that release group. The mean annual fish mass-at-release for a hatchery was used as the mean mass-at-release for any release group’s missing weight, length, or life history stage-at-release information (3.8% of all releases). A three year moving average was also applied to the annual biomass release data to smooth the time series data.

Data file used: CVSH_biom.csv

Release timing: We analyzed release timing at the monthly scale because release day of month was missing for 63.5% of all releases. The release period usually occurred within the same calendar month (80.3% of all releases) but occasionally a range of calendar months were reported (16.7% of all releases). In limited cases, only release year was reported (3.0% of all releases). Due to these inconsistencies, we restrict all release timing and growth rate analyses to cases when the release start and end months were the same.

Data file used: CVSH_RelTot_revised.csv

Release location: Geographic coordinates of release locations and river km distances from the releasing hatchery to the release location were obtained from Sturrock et al. (2019) (92.0% of all releases), RMIS (1.4% of all releases), or the electronic database provided by CDFW (0.7% of all releases). An additional 5.7% of release location coordinates and hatchery distances were newly determined using the methods described by Sturrock et al. (2019). Coordinates and distances are not available for 0.2% of all released fish due to insufficient descriptions of release site locations.

Data file used: CVSH_violin_hatchdist.csv

Size-at-release: Fish sizes were reported as mean mass (75.2% of all releases) or length (19.5% of total) for each release group. To facilitate dataset comparisons, length-at-release was converted to mass-at-release (and vice versa) according to the following relationship for Sacramento River O. mykiss (Hallock et al. 1961):
ln(M) = ln (8.80 ∙ 10 ―6) + 3.06 ∙ ln(FL)
Where mass is in measured grams and fork length is measured in millimeters. Note that this (M) (FL) relationship was determined for fish with FLs equal to or larger than 325 mm but predicts masses for smaller fish within 5% deviation from a similar length-weight transformation reported for California Central Coast O. mykiss (Huber 2018; 53–442 mm FL range; R2=0.99) across nearly the entire O. mykiss size range encountered in this investigation (97.0% of all hatchery fish with reported lengths smaller than 325 mm FL were larger than 53 mm FL). When size ranges were reported, the midpoint was assigned as the mean length or mass for the release group. Occasionally missing size data could be gleaned from written descriptions of the release group’s life history stage (e.g., “fry”, “fingerlings”, “yearlings”). In these cases (1.5% of all releases), the midpoint of the life stage-at-release mass range (see “Life-stage-at-release” below) was used.

Data file used: CVSH_mass_at_release_violin_data.csv

Age-at-release: All age information was estimated based on an assumed 1 February spawn date (Satterthwaite et al. 2010) and, therefore, should be considered apparent ages. Age analyses were restricted to cases when the release group beginning and end months of release are identical (80.3% of all releases). Apparent ages were estimated as the difference between release month midpoint and 1 February of the brood year.

Data file used: CVSH_age_at_rel_violin_data.csv

Life-stage-at-release: We explored both coarse- and fine-scale trends in the composition of life- stages-at-release. We first classified O. mykiss as sub-yearling (y-) or yearling or older fish (y+). We followed hatchery program guidelines (CA HSRG 2012, Appendix VIII) and assumed O. mykiss became yearlings once they grew to 71.2 g (~180 mm FL). We further classified life history stage-at-release diversity according to fish sizes and standardized nomenclature guidelines (IEP Steelhead PWT 1998). “Yolk-sac fry” were defined as fish with masses <0.3 g; “fry”: ≥0.3 to 1.4 g; “parr”: ≥1.4 g to <26.3 g; “silvery parr”: ≥26.3 g to <71.2 g; “small smolts”: ≥71.2 g to <131.6 g; “large smolts”: 131.6 g to <219.6g; “subadults”: ≥219.6 g to <954.0 g; and “adults”: ≥954.0 g. For cases when size data were missing but life-stage-at-release was described, “fed fry” were assumed to be fry, “fingerlings” were assumed to be parr, “advanced fingerlings” were assumed to be silvery parr, and “smolts” were assumed to be small smolts.Data files used: CVSH_fig8_lifehist.csv and CVSH_propyrling.csv Objective 2: Temporal variation in juvenile release metrics Life stage diversity: We characterized life stage diversity by calculating the Reciprocal Simpson’s Index (RSI; Simpson 1949) for each hatchery and all hatcheries combined per release year. The RSI measures the evenness of a community and ranges from 0 (all life stages were equally represented in every release group) to 1 (all fish were planted at the same life stage).

Data file used: CVSH_DI.csv

Interannual variation in release metrics: To investigate interannual variation in release practices, we divided the 70-year time series (1948-2017) into seven 10-year intervals and calculated the decadal coefficient of variation (CV) for six metrics associated with hatchery releases summarized CV10 annually at each hatchery and for all O. mykiss hatchery programs combined. The metrics examined included (1) total number released, (2) total biomass released, (3) mean release month, (4) mean release distance downstream of hatchery, (5)

Demographic data for introduced crab from multiple bays along the Central California coast, shallow subtidal (<3 m depth), from 2009-2016.

Well construction data for 11,917 domestic and 2,390 public-supply wells in the Central Valley were compiled as part of the U.S. Geological Survey (USGS) National Water Quality Assessment Project (NAWQA) and California State Water Resources Control Board (SWRCB) Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP). Data were compiled for wells reported in the USGS National Water Information System (NWIS) database and from well information reported to the SWRCB Department of Drinking Water (SWRCB-DDW). Driller’s log data were transcribed from scanned images of well completion reports filed with California Department of Water Resources (DWR). The wells reported in this data release were filtered by water use to select domestic and public-supply wells and omit other water uses. The compilation was then assumed to be representative of the total population of domestic and public-supply wells in the Central Valley. The wells in the compilation were constructed between 1911 and 2008 but are not grouped or separated by date. The data were used to produce two point data sets containing well location and construction information (depth from land surface to the top and bottom of the well screen, hereafter well-screen tops and bottoms; and screen length), and 12 interpolated GIS raster surfaces created by using Empirical Bayesian Kriging on a 1600 by 1600 meter (1 square-mile) grid. The tables are also included in csv format. The 12 rasters comprise predicted values for well screen tops and bottoms and their 10th and 90th quantile values. The interpolated surfaces may also be used to calculate volumes of water-supply in the Central Valley defined by the well-screen tops and bottoms.

VITAL SIGNS INDICATOR Migration (EQ4)

FULL MEASURE NAME Migration flows

LAST UPDATED December 2018

DESCRIPTION Migration refers to the movement of people from one location to another, typically crossing a county or regional boundary. Migration captures both voluntary relocation – for example, moving to another region for a better job or lower home prices – and involuntary relocation as a result of displacement. The dataset includes metropolitan area, regional, and county tables.

DATA SOURCE American Community Survey County-to-County Migration Flows 2012-2015 5-year rolling average http://www.census.gov/topics/population/migration/data/tables.All.html

CONTACT INFORMATION vitalsigns.info@bayareametro.gov

METHODOLOGY NOTES (across all datasets for this indicator) Data for migration comes from the American Community Survey; county-to-county flow datasets experience a longer lag time than other standard datasets available in FactFinder. 5-year rolling average data was used for migration for all geographies, as the Census Bureau does not release 1-year annual data. Data is not available at any geography below the county level; note that flows that are relatively small on the county level are often within the margin of error. The metropolitan area comparison was performed for the nine-county San Francisco Bay Area, in addition to the primary MSAs for the nine other major metropolitan areas, by aggregating county data based on current metropolitan area boundaries. Data prior to 2011 is not available on Vital Signs due to inconsistent Census formats and a lack of net migration statistics for prior years. Only counties with a non-negligible flow are shown in the data; all other pairs can be assumed to have zero migration.

Given that the vast majority of migration out of the region was to other counties in California, California counties were bundled into the following regions for simplicity: Bay Area: Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, Sonoma Central Coast: Monterey, San Benito, San Luis Obispo, Santa Barbara, Santa Cruz Central Valley: Fresno, Kern, Kings, Madera, Merced, Tulare Los Angeles + Inland Empire: Imperial, Los Angeles, Orange, Riverside, San Bernardino, Ventura Sacramento: El Dorado, Placer, Sacramento, Sutter, Yolo, Yuba San Diego: San Diego San Joaquin Valley: San Joaquin, Stanislaus Rural: all other counties (23)

One key limitation of the American Community Survey migration data is that it is not able to track emigration (movement of current U.S. residents to other countries). This is despite the fact that it is able to quantify immigration (movement of foreign residents to the U.S.), generally by continent of origin. Thus the Vital Signs analysis focuses primarily on net domestic migration, while still specifically citing in-migration flows from countries abroad based on data availability.

This layer depicts areas designated for Steelhead Critical Habitat as well as habitat type and quality in the California Central Valley Evolutionary Significant Unit (ESU - a 'distinct population 'of Pacific salmon defined as a 'species 'under the Endangered Species Act). These data represent the stream segments identified as Critical Habitat by the National Marine Fisheries Service (NOAA Fisheries) Southwest Regional Office (SWR). The linework for this layer is based on the California Department of Fish and Game (CDFG) and Pacific States Marine Fisheries Commission (PSMFC) 1:100,000 scale stream based routed hydrography. SWR biologists divided the routed hydrography into stream segments using the best available information to represent local Steelhead distribution and habitat. As a result, each segment has its own unique identifier (GIS_Link) and related presence and habitat information. The data set is in shapefile format and can be included as a map layer in a GIS. This data set This GIS layer is part of a larger mapping effort to define the anadromous distribution and to designate critical habitat in five steelhead ESU's and two Chinook ESU's in California. Several NOAA Fisheries offices participated in this effort. As a result, although the same issues were addressed within each ESU, the offices chose differing approaches to define and populate the habitat attributes. The consequence is that there are some slight differences in the attribute tables between the coastal ESUs and the Central Valley ESUs. For a complete description of the NOAA Fisheries Critical Habitat Designation project and for links to the final report, frequently asked questions, and other project documents, please visit: http://www.nwr.noaa.gov/1salmon/salmesa/crithab/CHsite.htm .

CDFW BIOS GIS Dataset, Contact: Steve Stone, Description: This dataset depicts the general boundaries of the Central California Coast Coho Salmon evolutionarily significant unit (ESU) (i.e., a distinct population segment (DPS) under the U.S. Endangered Species Act) as well as the historical population structure of the species.

Meek_et_al_EandE_LocusMapNamesAndSequenceFile contains the Sequence ID and corresponding Map ID for loci used in the linkage map. The sequence provided is for one of the two alleles at each locus.Meek_et_al_EandE_Sequence_DataFile contains the sequences for the 24,198 SNP loci discovered. Sequence names are followed by "_1" or "_2" to denote the two different alleles of the same locus.Meek_et_al_EandE_Seq_Count_dataFile contains the sequence counts for each individual in the RAD-seq study at each SNP locus, showing the counts for both allele 1 and allele 2, separated by a comma.

VITAL SIGNS INDICATOR Migration (EQ4)

FULL MEASURE NAME Migration flows

LAST UPDATED December 2018

DESCRIPTION Migration refers to the movement of people from one location to another, typically crossing a county or regional boundary. Migration captures both voluntary relocation – for example, moving to another region for a better job or lower home prices – and involuntary relocation as a result of displacement. The dataset includes metropolitan area, regional, and county tables.

DATA SOURCE American Community Survey County-to-County Migration Flows 2012-2015 5-year rolling average http://www.census.gov/topics/population/migration/data/tables.All.html

CONTACT INFORMATION vitalsigns.info@bayareametro.gov

METHODOLOGY NOTES (across all datasets for this indicator) Data for migration comes from the American Community Survey; county-to-county flow datasets experience a longer lag time than other standard datasets available in FactFinder. 5-year rolling average data was used for migration for all geographies, as the Census Bureau does not release 1-year annual data. Data is not available at any geography below the county level; note that flows that are relatively small on the county level are often within the margin of error. The metropolitan area comparison was performed for the nine-county San Francisco Bay Area, in addition to the primary MSAs for the nine other major metropolitan areas, by aggregating county data based on current metropolitan area boundaries. Data prior to 2011 is not available on Vital Signs due to inconsistent Census formats and a lack of net migration statistics for prior years. Only counties with a non-negligible flow are shown in the data; all other pairs can be assumed to have zero migration.

Given that the vast majority of migration out of the region was to other counties in California, California counties were bundled into the following regions for simplicity: Bay Area: Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, Sonoma Central Coast: Monterey, San Benito, San Luis Obispo, Santa Barbara, Santa Cruz Central Valley: Fresno, Kern, Kings, Madera, Merced, Tulare Los Angeles + Inland Empire: Imperial, Los Angeles, Orange, Riverside, San Bernardino, Ventura Sacramento: El Dorado, Placer, Sacramento, Sutter, Yolo, Yuba San Diego: San Diego San Joaquin Valley: San Joaquin, Stanislaus Rural: all other counties (23)

One key limitation of the American Community Survey migration data is that it is not able to track emigration (movement of current U.S. residents to other countries). This is despite the fact that it is able to quantify immigration (movement of foreign residents to the U.S.), generally by continent of origin. Thus the Vital Signs analysis focuses primarily on net domestic migration, while still specifically citing in-migration flows from countries abroad based on data availability.

Species names are shown with number of DPSs in parenthesis. Name, listing status, and recovery domain is also shown for each DPS.

Central California spans a wide variety of urban, agricultural, and natural terrain, including the San Francisco Bay area, the Central Valley, and the Sierra Nevada Mountains. Population within this region is growing rapidly, and there are persistent, serious air pollution problems including fine particulate matter (PM2.5) and ozone. Summertime photochemical air pollution is the focus of the present study, which represents a first phase in the development and application of a modeling capability to assess formation and transport of ozone and its precursors within Central California over an entire summer season. This contrasts with past studies that have examined pollutant dynamics for a few selected high-ozone episodes each lasting 3-5 days. The Community Multiscale Air Quality model (CMAQ) has been applied to predict air pollutant formation and transport in Central California for a 15-day period beginning on July 24, 2000. This period includes a 5-day intensive operating period (July 29 to August 2) from the Central California Ozone Study (CCOS). Day-specific meteorological conditions were modeled by research collaborators at NOAA using a mesoscale meteorological model (MM5). Pollutant emissions within the study domain were based on CARB emission inventory estimates, with additional efforts conducted as part of this research to capture relevant emissions variability including (1) temperature and sunlight driven changes in biogenic VOC, (2) weekday/weekend and diurnal differences in light duty (LD) and heavy-duty (HD) motor vehicle emissions, (3) effects of day-specific meteorological conditions on plume rise from point sources such as power plants. We also studied the effects of using cleaner pollutant inflow boundary conditions, lower than indicated during CCOS aircraft flights over the Pacific Ocean, but supported by other surface, ship-based, balloon and aircraft sampling studies along the west coast.

Link to the ScienceBase Item Summary page for the item described by this metadata record. Service Protocol: Link to the ScienceBase Item Summary page for the item described by this metadata record. Application Profile: Web Browser. Link Function: information

The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for juvenile White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. After two years of this experimental sampling program, it was discontinued due to low catches of White Sturgeon. SJR_Juvenile_WST_Set Data This dataset contains data on an experimental sampling program using trammel nets and setlines to catch juvenile White Sturgeon in the San Joaquin River. Sets were made at targeted locations from November-January in 2016 and 2017. One White Sturgeon (1000 mm fork length) was captured in a trammel net in 2016. SJR_Juvenile_WST_Catch Data This dataset contains data for individual fish caught in trammel nets or setlines in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, and tag information are provided. SJR_Fish_Taxonomy Data This dataset contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.

Ranks are based on case counts and incidence rates of California counties. Antelope Valley, not a county but a large part of Los Angeles County, is included to demonstrate how high incidence rate can be within LA County. Compared to the 57 other counties in California during 2001–2011, LA County had the third highest average annual number of cases and Antelope Valley had a higher incidence rate than all but six counties.*Counties not part of the Central California Valley are Los Angeles, San Luis Obispo, San Diego, Riverside, Ventura, Orange, San Bernardino, Monterey, Santa Clara, and Santa Barbara.Top average annual coccidioidomycosis cases and incidence rates (per 100,000 people) in California, 2001–2011 and 2008–2011.

This page serves data for only the "Quadrat data" dataset. See "Related Datasets" section for access to the other data types mentioned in the study data description below and the Methods & Sampling section.

Study data description:

Abundances and sizes of target invertebrates in quadrat surveys; photos of habitat complexity and a subset of specimens; and GPS coordinates of quadrats.