uid=EDI,o=EDI,dc=edirepository,dc=org all uid=iep,o=EDI,dc=edirepository,dc=org all public read doi:10.6073/pasta/808043fe9275d010552f00637ebb9d54 United States Fish and Wildlife Service Denise Goodman United States Fish and Wildlife Service denise_goodman@fws.gov https://orcid.org/0000-0002-1710-6122 Brian Mahardja United States Fish and Wildlife Service brian_mahardja@fws.gov https://orcid.org/0000-0003-0695-3745 Catherine Johnston United States Fish and Wildlife Service catherine_johnston@fws.gov https://orcid.org/0000-0002-4416-3771 Jonathan Speegle United States Fish and Wildlife Service jonathan_speegle@fws.gov https://orcid.org/0000-0002-1780-8351 Morgan Gilbert United States Fish and Wildlife Service morgan_gilbert@fws.gov https://orcid.org/0000-0003-0219-3902 Ryan Mckenzie United States Fish and Wildlife Service ryan_mckenzie@fws.gov https://orcid.org/0000-0002-9667-7408 Stephanie Durkacz United States Fish and Wildlife Service stephanie_durkacz@fws.gov https://orcid.org/0000-0003-2768-8215 Stephen Staiger United States Fish and Wildlife Service stephen_staiger@fws.gov https://orcid.org/0000-0002-3777-2421 Adriana Arrambide United States Fish and Wildlife Service adriana_arrambide@fws.gov https://orcid.org/0000-0003-3282-5616 Kate Erly United States Fish and Wildlife Service kate_erly@fws.gov Claudia Macfarlane United States Fish and Wildlife Service claudia_macfarlane@fws.gov 0009-0009-5022-3775 Brynn Perales United States Fish and Wildlife Service brynn_perales@fws.gov David Bridgman United States Fish and Wildlife Service david_bridgman@fws.gov Andreas Raisch United States Fish and Wildlife Service andreas_raisch@fws.gov Justin Dummitt United States Fish and Wildlife Service justin_dummitt@fws.gov Zachary Jessee United States Fish and Wildlife Service zachary_jessee@fws.gov Morgan Gilbert United States Fish and Wildlife Service morgan_gilbert@fws.gov https://orcid.org/0000-0003-0219-3902 contributor Ryan Cook United States Fish and Wildlife Service john_cook@fws.gov https://orcid.org/0000-0003-0081-6627 contributor Stephanie Durkacz United States Fish and Wildlife Service stephanie_durkacz@fws.gov https://orcid.org/0000-0003-2768-8215 contributor Adam Wojtczak United States Fish and Wildlife Service contributor Rick Williams United States Fish and Wildlife Service contributor James Weiler United States Fish and Wildlife Service contributor Phil Voong United States Fish and Wildlife Service contributor Vanessa Tobias United States Fish and Wildlife Service https://orcid.org/0000-0003-4872-1643 contributor Trace Strahle United States Fish and Wildlife Service contributor Jacob Stagg United States Fish and Wildlife Service contributor Joshua Slocum United States Fish and Wildlife Service contributor Timothy Scully United States Fish and Wildlife Service contributor Tom SanFilippo United States Fish and Wildlife Service contributor Tyler Rose United States Fish and Wildlife Service contributor Karena Potter United States Fish and Wildlife Service contributor Leo Polansky United States Fish and Wildlife Service associate Colton Plumb United States Fish and Wildlife Service contributor John Papajohn United States Fish and Wildlife Service contributor Eric Ojerholm United States Fish and Wildlife Service contributor Matt Nobriga United States Fish and Wildlife Service associate Greg Nelson United States Fish and Wildlife Service contributor Matt Myrick United States Fish and Wildlife Service contributor Lara Mitchell United States Fish and Wildlife Service contributor Clayton Miller United States Fish and Wildlife Service contributor Rob Mclean United States Fish and Wildlife Service contributor Justin McClain United States Fish and Wildlife Service contributor Jeffrey McLain United States Fish and Wildlife Service associate James McKenna United States Fish and Wildlife Service contributor Mike Marshall United States Fish and Wildlife Service contributor Sunny Lee United States Fish and Wildlife Service contributor Ryan Kneifel United States Fish and Wildlife Service contributor Harrison Kazik United States Fish and Wildlife Service contributor Baker Holden United States Fish and Wildlife Service associate Luke Hoehn United States Fish and Wildlife Service contributor Debra Henry United States Fish and Wildlife Service contributor Patrick Hapgood United States Fish and Wildlife Service contributor Jackie Hagen United States Fish and Wildlife Service contributor Cory Graham United States Fish and Wildlife Service contributor Andrew Goodman United States Fish and Wildlife Service contributor Paul Gary United States Fish and Wildlife Service contributor David Dominguez United States Fish and Wildlife Service contributor Austin Demarest United States Fish and Wildlife Service associate Emma Davidson United States Fish and Wildlife Service contributor Paul Carrillo United States Fish and Wildlife Service contributor Benjamin Brewster United States Fish and Wildlife Service contributor Aimee Braddock United States Fish and Wildlife Service contributor Angelina Bourandas United States Fish and Wildlife Service contributor Gershom Bigham United States Fish and Wildlife Service contributor Mike Berg United States Fish and Wildlife Service contributor Kenneth Bannister United States Fish and Wildlife Service contributor Interagency Ecological Program associate 2025-12-10 The United States Fish and Wildlife Service’s (USFWS) Experimental Larval Survey was designed and implemented by the Enhanced Delta Smelt Monitoring Program to assess alternative sampling methods for monitoring the larval life stages of the federally endangered Delta Smelt (Hypomesus transpacificus) within the San Francisco Estuary, California, USA. From 2018 to 2019, four different sampling methods (Beach Seine, Manta Trawl Net, 20-mm Surface Trawl Net, 20-mm Midwater Trawl Net) nested in time and space were used to estimate the occupancy rate, relative density, and size distribution of larval Delta Smelt across sampling methods and water depth strata within the San Francisco Estuary. For more information on the Lodi USFWS Office and the Enhanced Delta Smelt Monitoring Program: https://www.fws.gov/lodi/. Interagency Ecological Program for the San Francisco Bay Delta Estuary IEP United States Fish and Wildlife Service USFWS San Francisco Estuary Sacramento-San Joaquin Delta pelagic fish trawl larval fish juvenile fish Chinook salmon Delta Smelt Longfin Smelt Wakasagi Sacramento Splittail Threadfin Shad American Shad aquatic ecosystems distribution ecology estuaries brackish water freshwater rivers fishes abundance endangered species invasive species water quality LTER controlled vocabulary No peer reviewed articles derived from this dataset to date. This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you. https://doi.org/10.6073/pasta/808043fe9275d010552f00637ebb9d54 San Francisco Estuary California USA -122.423 -121.289 38.601 37.775 2018-04-17 2019-05-30 ongoing Claudia Macfarlane United States Fish and Wildlife Service Data Manager claudia_macfarlane@fws.gov 0009-0009-5022-3775 Denise Goodman United States Fish and Wildlife Service denise_goodman@fws.gov https://orcid.org/0000-0002-1710-6122 Environmental Data Initiative info@edirepository.org https://edirepository.org 0330j0z60 Environmental Data Initiative The Experimental Larval Survey (ELS) was a component of the U.S. Fish and Wildlife Service Enhanced Delta Smelt Monitoring Program (EDSM). EDSM, which began in 2016, contributes to the monitoring of fish species in the San Francisco Estuary, California as part of the Interagency Ecological Program (IEP) for the San Francisco Estuary and arose from concerns regarding implementation of the 2008 Biological Opinion for Delta Smelt, in particular the Reasonable and Prudent Alternative actions related to reducing the entrainment of adult and juvenile Delta Smelt. EDSM samples year-round using Kodiak trawls and larval gears to provide abundance and distribution data for the different life stages of Delta Smelt. During April and May of 2018 and 2019, EDSM conducted the ELS to evaluate the detection efficiency of larval sampling methods and to assess the occupancy rates of post-larval and juvenile Delta Smelt across water depth strata within the San Francisco Estuary. The survey was conducted with four different sampling methods (Midwater Sled Trawl, Surface Sled Trawl, Manta Trawl, Larval Beach Seine) simultaneously deployed within the same geographic regions and time periods. Sampling locations were selected using a generalized random-tessellation stratified (GRTS) design (Stevens and Olsen 2004). The GRTS sampling procedure yields random samples that are spatially well-distributed across the region. Multiple deployments of each sampling method were conducted to allow for spatially dependent detection probability and occupancy estimation. Key water quality and habitat parameters were collected and are included in the dataset. (1.) Data collection methods: MIDWATER AND SURFACE SLED TRAWLS: Midwater and surface sled trawls were used to sample the “deep water stratum” with water depths greater than 4 meters. Both trawls consisted of one large 20-mm net with a rigid D-shaped opening, attached to a weighted sled, and towed by a single boat using a hydraulic winch. During sampling events, midwater and surface sled trawls were conducted side-by-side. Midwater sled trawls were fished at a depth halfway between the starting water depth of the trawl and the surface for the duration of tows and then rapidly retrieved to the surface at the end of sampling. Target fishing depths for the midwater trawl were attained by adjusting the length of the tow line based on the EDSM tow schedules developed for each vessel (See Supplementary Document). Surface sled trawls were conducted with the net in visible contact with the surface for the duration of the tow. Target tow duration was 10-minutes. Calibrated flow meters were fixed to the net opening to calculate sampling volume (See Analysis and Methods Section for calculations). At the end of each tow, the nets were washed down towards the cod-end using filtered water. Sample contents were preserved in the field and returned to the laboratory for processing (see Fish Handling section below). Multiple deployments were conducted to allow for spatially dependent detection probability and occupancy estimation. Key water quality and habitat parameters were collected and are included in the dataset. MANTA TRAWL: Manta trawls were used to sample the “intermediate water stratum” with water depths between 1.2 and 4 meters. The Manta trawl consisted of two modified 1600 micrometer Neuston nets. One net was deployed on the left and right sides of the boat for each tow. The nets were attached to a davit arm to project them over the sides of the boat. Sampling occurred at the top 0.5 m of the water column. Target tow duration was 10-minutes. Calibrated flow meters were fixed to the net opening to calculate sampling volume (See Analysis and Methods Section for calculations). At the end of each tow, the nets were washed down towards the cod-end using filtered water. Sample contents were preserved in the field and returned to the laboratory for processing (see Fish Handling section below). Multiple deployments were conducted to allow for spatially dependent detection probability and occupancy estimation. Key water quality and habitat parameters were collected and are included in the dataset. LARVAL BEACH SEINE: Larval beach seines were used to were used to sample the “shallow water stratum” with water depths less than 1.2 meters. The larval beach seine consisted of an 8 meter x 1.5 meter beach seine with 1600-micron square mesh and a 1 meter x 1 meter bag that funnels into a code end jar. In 2018, larval beach seines were conducted using standard methods developed by the U.S. Fish and Wildlife Service Delta Juvenile Fish Monitoring Program which consisted of a perpendicular pull into the shore. In 2019, larval beach seines were conducted using a modified method to increase the total area sampled. Seines were pulled in a parallel line along the shoreline up to 30 meters followed by a quarter turn and a perpendicular pull into the shore. Seine dimensions were measured during sampling events and used to calculate sampling volume (See Analysis and Methods Section for calculations). At the end of each pull, the net was washed down towards the cod-end using filtered water. Sample contents were preserved in the field and returned to the laboratory for processing (see Fish Handling section below). Multiple deployments were conducted to allow for spatially dependent detection probability and occupancy estimation. Key water quality and habitat parameters were collected and are included in the dataset. FISH HANDLING: Generally, all fish in each sample that are greater than or equal to 25 mm fork length (FL) are identified to species or race, with the exception of five species that are readily identified at greater than or equal to 20 mm FL: Sacramento Splittail (Pogonichthys macrolepidotus), Three-spine Stickleback (Gasterosteus aculeatus), Western Mosquitofish (Gambusia affinis), Rainwater Killifish (Lucania parva), and Sacramento Sucker (Catostomus occidentalis). Prior to release at the site of capture, we measure fish to the nearest 1 mm FL. If greater than 50 individuals of a Chinook Salmon race, as designated by the river length-at-capture-date criteria (LDC, see paragraph below), or other species listed under the Endangered Species Act (ESA) are captured, a subsample of 50 individuals are randomly measured for FL and the rest are counted and not measured (referred to as a plus count). If greater than 30 individuals of a non-listed species are captured, a subsample of 30 individuals is randomly measured for FL and the rest are counted and not measured. Fish that cannot be accurately identified in the field are brought back to the laboratory. Identification is then confirmed with the use of dichotomous keys and/or with the aid of a microscope. During larval sampling, fish that cannot be identified in the field (generally most fish sampled using larval gear types) are preserved in a solution of 10% buffered formalin and Rose Bengal and brought back to the lab. These samples undergo several levels of laboratory processing, beginning with sorting, followed by several stages of larval fish identification using keys and other published materials. Fish that are still unable to be confidently identified are sent out for additional outside verification, including mitochondrial DNA and/or nuclear DNA testing when needed. The race of all unmarked juvenile Chinook Salmon (i.e., no adipose fin clip to indicate that it is a hatchery fish) are determined using the river LDC developed by Fisher (1992) and modified by Greene (1992). The assumptions associated with the river LDC for the Sacramento-San Joaquin River basin are that (1) spawning of fall-run Chinook Salmon occurs between October 1-December 31, (2) spawning of late fall-run Chinook Salmon occurs between January 1-April 15, (3) spawning of winter-run Chinook Salmon occurs between April 16-August 15, (4) spawning of spring-run Chinook Salmon occurs between August 16-September 30, and that (5) the growth rates of fish are identical among all Chinook Salmon races (Fisher 1992). Although one or more of these assumptions are likely violated (Fisher 1994; Yoshiyama et al. 1998), the river LDC is currently widely used by managers, and is the only cost effective and logistically feasible way to differentiate between the different races of juvenile Chinook Salmon in the field. Fisher (1994) noted that Chinook Salmon races within the Central Valley do appear to spawn at distinctly separate time periods except for fall- and spring-run due to the loss of headwater habitats (e.g., resulting from dams), forced coexistence, and subsequent hybridization within the Sacramento River basin (Banks et al. 2000; Greig et al. 2003; Banks et al. 2014). As a result, many of the Chinook Salmon characterized as spring-run by the river LDC may actually be fall-run. We use the river LDC to differentiate between unmarked winter-run sized, spring-run sized, fall-run sized, and late fall-run sized juvenile Chinook Salmon. The race designations used in this dataset should be considered a rough approximation and not interpreted as definitive. Juvenile Chinook Salmon with missing (clipped) adipose fins are considered marked fish. All clipped juvenile Chinook Salmon observed in recent years are considered hatchery-reared and are brought back to the laboratory for coded wire tag retrieval to acquire information on hatchery origin and release location. WATER QUALITY: Water quality measurements were taken before (trawls) or after (larval beach seines) each sampling event from the top 1 m of the water column. Temperature was recorded to the nearest 0.1 C, dissolved oxygen to the nearest 0.01 mg/L, and specific conductance to the nearest 0.01 microsiemen/centimeter for freshwater or millisiemen/centimeter for salt water. A turbidity meter was used to measure turbidity to the nearest 0.01 nephelometric turbidity unit (NTU). For trawls, a Secchi disk was also used to measure water clarity; Secchi disk measurements were always taken in the shade with sunglasses off. During Sled Trawls, water quality measurements were also taken from the bottom of the water column using Van Dorn style samplers before each tow. The sampler was deployed slowly down to the bottom, then 1-2 feet of line is pulled in for the water sample to be taken. LARVAL BEACH SEINE HABITAT MEASUREMENTS: Substrate composition was quantified visually from five samples randomly collected within the sampling area by two or more crew members. Substrate composition was estimated in 5% increments and categorized based on particle diameter as coarse (CR; >64 mm), gravel (GR; 2-64 mm diameter), sand (SN; 0.062–2 mm), mud (MD; < 0.062 mm; includes clay and silt), and “other” which included coarse organic material (e.g., leafs, woody material, algae, peaty soil, clam shells etc.). If more than 5 cm of finer substrate covered larger substrates, only the finer substrates were recorded. Structure (e.g. submerged rocks, wood debris) and vegetation (e.g. emergent and submerged aquatic vegetation) within the sampling area was also visually estimated. Water velocity at 60% of the water depth and depth measurements were also recorded at 5 randomly selected sites. Habitat scores for each parameter were then averaged to calculate the mean habitat parameter score for each site presented in the dataset. (2.) Sampling effort, fish catch, and water quality data were recorded using datasheets based on a modified version of the Delta Juvenile Fish Monitoring Program datasheet (available upon request to the data contact). (3.) Instruments and equipment: MIDWATER AND SURFACE SLED TRAWL: The Sled Trawl net consisted of 1600 micrometer square mesh and was identical to that used by the California Department of Fish and Wildlife 20-mm Survey. The net was 5.5 meters long, with a mouth circumference of 4.9 meters and mouth area of 1.51 square meters. The cod end jar was a 2 liter Nalgene polyethylene bottle screwed into a General Oceanics ring and attached to the canvas collar at the cod end of the net by a hose clamp. Calibrated flow meters (General Oceanics, Model 2030) were fixed to the net opening to calculate distance traveled during each tow. MANTA TRAWL: The Manta trawl net consisted of a trapezoidal net frame with a 1 meter x 0.81 meter opening at the front and a 1 meter x 0.5 meter opening at the rear. Two buoys were attached on each side of the net frame to keep the rear opening of the net frame inline with the surface of the water during tows. The rear net frame opening (0.5 square meters) was used for sampling volume calculations because it was fully submerged in the top 0.5 meters of water during sampling, whereas the front net frame opening was only partially submerged (See Supplementary Document). A 5 meter long 1600-micron square mesh net was attached to the rear of the net frame. In 2018, the cod end jar was a 2 liter Nalgene polyethylene bottle screwed into a General Oceanics ring and attached to the canvas collar at the cod end of the net by a hose clamp. To deal with debris clogs, the cod end jar was replaced in 2019 with a custom 4-inch diameter PVC container attached to the canvas collar at the cod end of the net by a custom screw in mount (See Supplementary Document). Calibrated flow meters (General Oceanics, Model 2030) were fixed to the net opening to calculate distance traveled during each tow. LARVAL BEACH SEINE: Larval beach seines consisted of an 8 meter x 1.5 meter beach seine with a 1600-micron square mesh and a 1 meter x 1 meter bag that funneled into a 2 liter Nalgene polyethylene bottle screwed into a General Oceanics ring and attached to the canvas collar at the cod end of the net by a hose clamp. Each net had a float line and lead line attached to 1.8 m-long wooden poles at each end. WATER QUALITY: Water quality measurements such as temperature, dissolved oxygen, and conductivity are conducted using the YSI PRO 2030 Meter. Turbidity is collected using Hach 2100Q turbidity meters. Secchi disks are also used to measure water clarity. During 20-mm larval sled sampling, a LaMotte Horizontal Water Sampler model 1077 or 1087 is used to retrieve water from the bottom of the water column for water quality. The dissolved oxygen probe on the YSI PRO 2030 is quick-calibrated before each day of sampling and if a calibration fails, the instrument is no longer used until the necessary repairs have been made. The YSI probe is serviced monthly and dissolved oxygen, conductivity, and temperature are calibrated. The Hach 2100Q Turbidity Meter calibration is checked monthly and calibrated every three months. Flow meters are cleaned and checked for calibration weekly. If flowmeters do not spin within specifications, they are swapped out. Water velocity measurements taken during larval beach seines were conducted using a OTT MF Pro velocity meter in conjunction with a top-set rod. Velocity measurements were taken by rotating the velocity meter orientation to find the peak water velocity at a given location and then taking the average across a 30 second interval at 60% of the water depth. (4.) Analysis and methods: Standard operating procedures for sampling methods and quality checks are available upon request. MIDWATER AND SURFACE SLED TRAWL VOLUME: Volume sampled by each tow was estimated by calculating the difference between the end and starting value of the net flow meter (i.e. total rotations), and multiplying it by the factory-stated K calibration factor (0.026873) and the Sled Trawl net mouth area of 1.51 m2. ELS Dataset Equation: FlowMeterDifference x 0.026873 x 1.51 MANTA TRAWL VOLUME: Volume sampled by each tow was estimated by calculating the difference between the start and end value of the net flow meter (i.e. total rotations), and multiplying it by the factory-stated K calibration factor (0.026873) and the Manta Trawl net mouth area of 0.5 m2. ELS Dataset Equation: FlowMeterDifference x 0.026873 x 0.5 2018 LARVAL BEACH SEINE VOLUME: Larval beach seines in 2018 were conducted with a perpendicular pull into shore. We assumed a 45-degree bank slope in volume calculations. Triangular Prism Volume Equation: Length x Width x Water Depth ÷ 2 ELS Dataset Parameters: SeineLength x SeineWidth x SeineDepth ÷ 2 2019 LARVAL BEACH SEINE VOLUME: Larval beach seines in 2019 were conducted with a parallel pull along the shore (Section 1) followed by a quarter turn (Section 2) and a perpendicular pull into shore (Section 3). We assumed a 45-degree bank slope in volume calculations for the perpendicular pull into shore (Section 3). Volume= Section 1 Volume + Section 2 Volume + Section 3 Volume Section 1 Volume: Cube Volume Equation: Width x Average Length x Average Water Depth ELS Dataset Equation: MiddleTotalWidth x ((StartABLength + MiddleABLength)/2) x (StartADepth+StartBDepth+MiddleADepth+MiddleBDepth)/4) Section 2 Volume: Quarter Cylinder Volume: 0.25 x π x (Major Radius x Minor Radius) x Average Water Depth ELS Dataset Equation: 0.25 x 3.14957 x (MiddleABLength x EndABWidth) x ((MiddleADepth+MiddleBDepth)/2) Section 3 Volume: Triangular Prism Volume: Length x Width x Water Depth ÷ 2 ELS Dataset Equation: (StartTotalLength-MiddleABLength) x EndABWidth x MiddleBDepth ÷ 2 (5.) Project history (change in methods and locations): 2019: Larval beach seining methods were changed to increase the sampling area. 2019: Custom PVC collection jars were fabricated and deployed on manta trawls. (6.) QA/QC: A Quality Assurance/Quality Control (QA/QC) program exists to ensure consistent data generation by following the EDSM standard operating procedures. The program ensures accurate identification of fish species in the field and accurate collection of environmental data. For early life stage fish identification, two or more experienced identifiers examine every fish until consensus is reached on species. Double entry of datasheets is used to check the accuracy of all data entry. Additional proofing (e.g., outlier searches) occurs weekly and as needed ahead of reports and data sharing. METHODS: The program has a dedicated fish biologist that is responsible for training field personnel in fish identification and implementing a field QA/QC program. The QA/QC program consists of testing the fish ID skills of the field crew using preserved and wild specimens at least twice a year, reviewing preserved fish samples that are brought back from the field, and accompanying field personnel when sampling to assure correct identification of the fish species. All unknown fish species found in the field are brought back to the laboratory to ensure correct identification. All personnel are trained following standard operating procedures (SOP) for field sampling, data entry and QA/QC, and lab processing during their first weeks of employment and then work with experienced employees for the first 3 months of their employment. DATA: Data are entered into and stored in a locally housed Microsoft Access database. Data are entered twice into Microsoft Access forms with customized error-checking and data validation checks. QA/QC is conducted with a custom Access query that attempts to match the two datasets. When a mismatch is found, the field data sheet is reviewed, and errors are corrected in the first or second data entry datasets. Additional data quality checks are performed by the data manager using custom queries, ArcGIS (to check coordinates), and custom QA/QC R Scripts. While data have undergone an established QA/QC process, we still suggest assessing data for outliers based on your intended use of the data. (7.) Contractor information: All fish identification and water quality measures are conducted by the field staff of the Delta Juvenile Fish Monitoring Program, Lodi Fish and Wildlife Office, United States Fish and Wildlife Service. Genetic testing was conducted by external laboratories and contact information of the principal investigators are included in the dataset. (8.) External review process: The development of the ELS survey design was assisted by an Independent Review Panel for the Long-term Operations Biological Opinions’ (LOBO) Reasonable and Prudent Alternative (RPA) actions for the Central Valley water operations and received review by staff from the U.S. Fish and Wildlife Service Bay-Delta Office and California Department of Fish and Wildlife. (9.) Methods references: Banks MA, Rashbrook VK , Calavetta MJ, Dean CA, Hedgecock D (2000) Analysis of microsatellite DNA resolves genetic structure and diversity of Chinook Salmon (Oncorhynchus tshawytscha) in Californias Central Valley. Canadian Journal of Fisheries and Aquatic Sciences, 57:915-927. Banks MA, Jacobson DP, Meusnier I, Greig CA, Rashbrook VK, Ardren WR, Smith CT, Bernier-Latmani J, Van Sickle J, OMalley KG (2014) Testing advances in molecular discrimination among Chinook Salmon life histories: evidence from a blind test. Animal Genetics, 45(3):412-420. Fisher, F. W. 1992. Chinook Salmon, Oncorhynchus tshawytscha, growth and occurrence in the Sacramento-San Joaquin River system. Draft Inland Fisheries Division Office Report. California Department of Fish and Game. Sacramento, California. Fisher, F. W. 1994. Past and present status of Central Valley Chinook Salmon. Conservation Biology 8(3):870-873. Greene, S. 1992. Memorandum: Daily length tables. California Department of Water Resources. Environmental Services Office Sacramento, California. May 1992. Stevens, D., and A. Olsen. 2004. Spatially balanced sampling of natural resources. Journal of the American Statistical Association, 99(465): 262-278. United States Fish and Wildlife Service (USFWS) (1998) 1995 Annual progress report: abundance and survival of juvenile Chinook Salmon in the Sacramento-San Joaquin Estuary. Stockton Fish and Wildlife Office, United States Fish and Wildlife Service, Stockton, California. Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of Chinook Salmon in the Central Valley Region of California. North American Journal of Fisheries Management 18:487-521. ELS_Seine_Data.csv Fish catch and water quality data from Experimental Larval Beach Seines conducted by the Enhanced Delta Smelt Monitoring Program. ELS_Seine_Data.csv 1237386 b26efa7e8f45e064725b3b021a7741cc 1 \r\n column , " https://pasta.lternet.edu/package/data/eml/edi/994/5/c12f9ec4d7357c4d23c2bea369a3562b StationCode The unique station identifier for each randomly-generated sampling site; denotes subregion along with an unique number for sites within that subregion. After July 1, the station code also began to include sample year and sample week (YY-Sample week-Subregion number) string text NA Data not available DepthStratum Water depth stratum in which sampling took place string text NA Data not available SampleDate The date a sample was completed reported in MM/DD/YYYY date YYYY-MM-DD NA Data not available SampleTime Time a trawl was started recorded as HH:MM:SS using 24-hour time and obtained from a Lowrance unit on the sampling boat date hh:mm:ss NA Data not available MethodCode Sampling method used to collect sample string text NA Data not available NetMeshSize Size of net mesh openings measured in micrometers float micrometer natural 1600 1600 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroM Latitude Latitude of sampling location. Sampling locations were selected at seinable sites within a 0.5 mile range of GPS coordinates generated by the generalized random-tessellation stratified sampling design. float degree real 38.02774 38.47053 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG Longitude Longitude of sampling location. Sampling locations were selected at seinable sites within a 0.5 mile range of GPS coordinates generated by the generalized random-tessellation stratified sampling design. float degree real -122.08106 -121.50168 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG GearConditionCode Code used to indicate condition of sampling event string text NA Data not available Disturbance Indicator of whether site has been disturbed string text NA Data not available HaulNumber Number of sample during sequential sampling events float dimensionless natural 1 2 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/UNITLESS Volume Estimated volume of water in sample. See methods for full calculation details. float meterCubed real 16 302.14527 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M3 WeatherCode Code for weather conditions at time of sampling, the code recorded should represent 51% or more of the observed sky conditions by visual observation string text NA Data not available Tide Tide at start of sampling based on tide stage using the closest tidal gauge information string text NA Data not available DO Water dissolved oxygen level in sampling area float milligramPerLiter real 7.52 12.59 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliGM-PER-L SpecificConductance Water Conductivity (or specific conductance) standardized to 25 degrees Celsius float microSiemensPerCentimeter real 94.3 899 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroS-PER-CentiM WaterTemp Water temperature within sampling area float celsius real 13.9 22.1 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG_C Turbidity Water turbidity measured in sampling area float nephelometricTurbidityUnit real 3.71 266 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/NTU SubstrateCode Dominant substrate observed at 5 randomly selected points within sampled area string text NA Data not available WaterVelocityDepth Mean water depth recorded at 5 water velocity sampling points within the sampled area float meter real 0.14 6 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M WaterVelocity Mean water velocity at 60% water depth recorded at 5 points within the sampled area float meterPerSecond real 0.0024 0.0934 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M-PER-SEC StructureCover Visually estimated percent area coverage of structure within the sampling area float percent whole 0 80 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/PERCENT VegCover Visually estimated percent area coverage of vegetation within the sampling area float percent whole 0 80 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/PERCENT SeineLength Length of beach seine during 2018 sampling float meter real 4 25 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M SeineWidth Width of beach seine during 2018 sampling float meter natural 4 8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M SeineDepth Mean starting depth of beach seine during 2018 sampling float meter real 0.4 1.2 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M StartTotalLength Dimension of beach seine during 2019 sampling float meter natural 7 30 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M StartABLength Dimension of beach seine during 2019 sampling float meter natural 7 8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M MiddleTotalWidth Dimension of beach seine during 2019 sampling float meter natural 5 25 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M MiddleABLength Dimension of beach seine during 2019 sampling float meter natural 4 8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M EndTotalWidth Dimension of beach seine during 2019 sampling float meter natural 9 33 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M EndABWidth Dimension of beach seine during 2019 sampling float meter natural 4 8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M StartADepth Dimension of beach seine during 2019 sampling float meter real 0.4 1.3 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M StartBDepth Dimension of beach seine during 2019 sampling float meter real 0 1 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M MiddleADepth Dimension of beach seine during 2019 sampling float meter real 0.4 1.5 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M MiddleBDepth Dimension of beach seine during 2019 sampling float meter real 0 1.1 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M EndADepth Dimension of beach seine during 2019 sampling float meter real 0 0.7 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M EndBDepth Dimension of beach seine during 2019 sampling float meter real 0 0.7 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M Comments Notes taken during sampling describing issues or other substrate code string text NA Data not available IDLocation Location where species were identified string text NA Data not available OrganismCode A 1 to 4 letter character code unique to each species string text NA Data not available StageCode Life stage code designation of salmonids string text NA Data not available MarkCode Indicator code of whether or not fish has been marked or tagged string text NA Data not available TagCode Character code of coded wire tag or acoustic tag retrieved from individual string text NA Data not available RaceByLength Estimated race of Chinook Salmon based on the length-at-date criteria string text NA Data not available RaceByTag Race of Chinook Salmon based on the coded wire tag or other markings string text NA Data not available SpecialStudyID Identification code assigned to samples by the Delta Fish Monioring Program string text NA Data not available GeneticID_Nuclear Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. string text NA Data not available Genetic_Nuclear_Test The genetic assay used for nuclear genetic analysis string text NA Data not available Genetic_Nuclear_Test_Lab Name of laboratory who conducted genetic analysis string text NA Data not available Genetic_Nuclear_Test_Lab_PI Name of principle investigator who conducted genetic analysis string text NA Data not available GeneticID_Mitochondrial Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string text NA Data not available Genetic_Mitochondrial_Test The genetic assay used for mitochondrial genetic analysis string text NA Data not available Genetic_Mitochondrial_Test_Lab Name of laboratory who conducted genetic analysis string text NA Data not available Genetic_Mitochondrial_Test_Lab_PI Name of principle investigator who conducted genetic analysis string text NA Data not available ForkLength Length of sampled fish measured from the point of the mouth to the fork of the caudal fin float millimeter real 0 300 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliM Dead Mortality of individual resulting from sampling process string text NA Data not available Count Number of fish sampled float dimensionless natural 1 713 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/UNITLESS no 3825 ELS_Manta_Data.csv Fish catch and water quality data from Experimental Manta Trawls conducted by the Enhanced Delta Smelt Monitoring Program. ELS_Manta_Data.csv 390795 21d66594e00981e08cdedeff752975e4 1 \r\n column , " https://pasta.lternet.edu/package/data/eml/edi/994/5/b4a20a7383bc724643745c6bd6ee363f StationCode The unique station identifier for each randomly-generated sampling site; denotes subregion along with an unique number for sites within that subregion. After July 1, the station code also began to include sample year and sample week (YY-Sample week-Subregion number) string text NA Data not available DepthStratum Water depth stratum in which sampling took place string Intermediate 1.2?4 meter water depth stratum NA Data not available SampleDate The date a sample was completed reported in MM/DD/YYYY date YYYY-MM-DD NA Data not available SampleTime Time a trawl was started recorded as HH:MM:SS using 24-hour time and obtained from a Lowrance unit on the sampling boat date hh:mm:ss NA Data not available MethodCode Sampling method used to collect sample string MANT Manta Trawl NA Data not available NetMeshSize Size of net mesh openings measured in micrometers float micrometer natural 1600 1600 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroM NetSide Side of boat in which the net is deployed. Left is the Port side and Right is the starboard side. string Left Net deployed off the Port side of vessel Right Net deployed off the Starboard side of vessel NA Data not available CloserTo Location of net deployment in reference to shore/channel string Channel Net was closer to the channel Shore Net was closer to the shore NA Data not available Latitude Latitude of GPS coordinate assigned for the random sampling site by GRTS procedure float degree real 38.03125 38.45967 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG Longitude Longitude of GPS coordinate assigned for the random sampling site by GRTS procedure float degree real -122.06498 -121.58993 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LatitudeStart Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real 38.03159 38.45972 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LongitudeStart Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real -122.06461 -121.58966 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LatitudeEnd Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real 38.02842 38.46267 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LongitudeEnd Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real -122.06552 -121.58793 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG GearConditionCode Code used to indicate condition of sampling event string 1 Good sample 2 Fair sample 3 Poor sample 4 No sampling done 8 Sea lion caught in sample; sampling cut chort NA Data not available FlowMeterDebris Indicator code of whether or not debris on flowmeter. Users may choose to exclude samples with flow debris present as these can decrease the accuracy of volume measurements string N No, debris absent Y Yes, debris present NA Data not available FlowMeterDifferenceNet Total revolutions of flowmeter recorded during sampling event. Total revolutions are calculated by taking the differnce between the start and end meter values. float meter natural 24 43606 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M TowNumber Number of tow during sequential sampling events string text NA Data not available TowDirection Direction of towing in relation to the river string D Downstream U Upstream NA Data not available TowDuration Number of minutes when towing occurred float minute natural 7 10 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MIN Volume Estimated volume of water in sample. See methods for full calculation details. float meterCubed real 0.322476 585.912019 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M3 WeatherCode Code for weather conditions at time of sampling, the code recorded should represent 51% or more of the observed sky conditions by visual observation string CLD Majority cloud cover at time of sampling CLR Majority direct sunlight at time of sampling RAN Precipitation at time of sampling FOG Foggy at time of sampling NA Data not available Tide Tide at start of tow based on tide stage shown by closest gauge in Lowrance string Ebb Ebbing/outgoing tide Flood Flooding/incoming tide HS High slack tide LS Low slack tide NA Data not available DO Water dissolved oxygen measured w float milligramPerLiter real 5.42 11.3 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliGM-PER-L SpecificConductance Water Conductivity (or specific conductance) standardized to 25 degrees Celsius float microSiemensPerCentimeter real 103.9 1745 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroS-PER-CentiM WaterTemp Water temperature at the surface float celsius real 9.3 21 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG_C Turbidity Water turbidity float nephelometricTurbidityUnit real 4.8 237 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/NTU Secchi Secchi depth measured before the start of towing float meter real 0.12 1.65 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M WaterDepth Depth of water recorded via Lowrance and start of tow float meter real 1 7.5 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M IDLocation Location where species were identified string Field Species identification completed in the field Lab Species identification completed in the laboratory NA Data not available OrganismCode A 1 to 4 letter character code unique to each species string text NA Data not available StageCode Life stage code designation of salmonids string 1 Sac fry 2 Fry 3 Parr 4 Silver Parr 5 Smolt 6 Adult NA Data not available MarkCode Indicator code of whether or not fish has been marked or tagged string None No marks Adclipped Adipose fin clipped NA Data not available TagCode Character code of coded wire tag or acoustic tag retrieved from individual string text NA Data not available RaceByLength Estimated race of Chinook Salmon based on the length-at-date criteria string Fall Fall-run Chinook Salmon race based on length Spring Spring-run Chinook Salmon based on length Latefall Latefall-run Chinook Salmon based on length Winter Winter-run Chinook Salmon based on length Not Raced Not categorized to any run Adult Not categorized to any run; adult salmon NA Data not available RaceByTag Race of Chinook Salmon based on the coded wire tag or other markings string text NA Data not available SpecialStudyID Identification code assigned to samples by the Delta Fish Monioring Program string text NA Data not available GeneticID_Nuclear Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. string text NA Data not available Genetic_Nuclear_Test The genetic assay used for nuclear genetic analysis string text NA Data not available Genetic_Nuclear_Test_Lab Name of laboratory who conducted genetic analysis string UCD Genetic Variation Lab UC Davis Genomic Variation Laboratory NA Data not available Genetic_Nuclear_Test_Lab_PI Name of principle investigator who conducted genetic analysis string A. Finger Dr. Amanda J. Finger NA Data not available GeneticID_Mitochondrial Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string DSM Result of mitochondrial genotyping determined to be Delta Smelt (Hypomesus transpacificus) maternal lineage Fail Unsuccessful genetic analysis WAG Result of mitochondrial genotyping determined to be Wakasagi Smelt (Hypomesus nipponensis) maternal lineage NA Data not available Genetic_Mitochondrial_Test The genetic assay used for mitochondrial genetic analysis string PCR Polymerase Chain Reaction NA Data not available Genetic_Mitochondrial_Test_Lab Name of laboratory who conducted genetic analysis string UCD Aquatic Health Lab UC Davis Aquatic Health Laboratory NA Data not available Genetic_Mitochondrial_Test_Lab_PI Name of principle investigator who conducted genetic analysis string S. Teh Dr. Swee Teh NA Data not available ForkLength Length of sampled fish measured from the point of the mouth to the fork of the caudal fin float millimeter real 0 86 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliM Dead Mortality of individual resulting from sampling process string N No Y Yes NA Data not available Count Number of fish sampled float dimensionless natural 1 459 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/UNITLESS no 1389 ELS_Sled_Data.csv Fish catch and water quality data from Experimental Midwater and Surface Sled Trawls conducted by the Enhanced Delta Smelt Monitoring Program. ELS_Sled_Data.csv 1179707 17b9c7769813249d6c3270df7d8df361 1 \r\n column , " https://pasta.lternet.edu/package/data/eml/edi/994/5/4e3ec8d1f8257b94c501983828ea09ea StationCode The unique station identifier for each randomly-generated sampling site; denotes subregion along with an unique number for sites within that subregion. After July 1, the station code also began to include sample year and sample week (YY Sample week-Subregion number) string text NA Data not available DepthStratum Water depth stratum in which sampling took place string text NA Data not available SampleDate The date a sample was completed reported in MM/DD/YYYY date YYYY-MM-DD NA Data not available SampleTime Time a trawl was started recorded as HH:MM:SS using 24-hour time and obtained from a Lowrance unit on the sampling boat date hh:mm:ss NA Data not available MethodCode Sampling method used to collect sample string text NA Data not available TowType Net fishing method. Midwater or Surface tow string text NA Data not available NetMeshSize Size of net mesh openings measured in micrometers float micrometer natural 1600 1600 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroM Latitude Latitude of GPS coordinate assigned for the random sampling site by GRTS procedure float degree real 19.6221 38.46626 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG Longitude Longitude of GPS coordinate assigned for the random sampling site by GRTS procedure float degree real -122.06042 -121.58729 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LatitudeStart Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real 38.03412 38.66325 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LongitudeStart Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real -122.06054 -121.58658 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LatitudeEnd Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real 38.03565 38.47174 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG LongitudeEnd Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real -122.06092 -121.58515 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG GearConditionCode Code used to indicate condition of sampling event string text NA Data not available FlowMeterDebris Indicator code of whether or not debris on flowmeter. Users may choose to exclude samples with flow debris present as these can decrease the accuracy of volume measurements string text NA Data not available FlowMeterDifferenceNet Total revolutions of flowmeter recorded during sampling event. Total revolutions are calculated by taking the differnce between the start and end meter values. float meter natural 4380 34640 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M TowNumber Number of tow during sequential sampling events string text NA Data not available TowDirection Direction of towing in relation to the river string text NA Data not available TowDuration Number of minutes when towing occurred float minute natural 3 11 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MIN Volume Estimated volume of water in sample. See methods for full calculation details. float meterCubed real 177.7326474 1405.6298872 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M3 WeatherCode Code for weather conditions at time of sampling, the code recorded should represent 51% or more of the observed sky conditions by visual observation string text NA Data not available Tide Tide at start of tow based on tide stage shown by closest gauge in Lowrance string text NA Data not available DOTop Dissolved oxygen measured within the top meter of the water column float milligramPerLiter real 6.65 11.95 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliGM-PER-L SpecificConductanceTop Water Conductivity (or specific conductance) standardized to 25 degrees Celsius measured within the top meter of the water column float microSiemensPerCentimeter real 78.5 1848 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroS-PER-CentiM WaterTempTop Water temperature measured within the top meter of the water column float celsius real 13.2 21.1 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG_C TurbidityTop Turbidity measured within the top meter of the water column float nephelometricTurbidityUnit real 6.64 288 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/NTU DOBottom Dissolved oxygen measured from water samples collected within one meter of the bottom float milligramPerLiter real 5.08 11.8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliGM-PER-L SpecificConductanceBottom Specific Conductivity measured from water samples collected within one meter of the bottom float microSiemensPerCentimeter real 78.7 1873 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MicroS-PER-CentiM WaterTempBottom Water temperature measured from water samples collected within one meter of the bottom float celsius real 13.3 21.6 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/DEG_C TurbidityBottom Turbidity measured from water samples collected within one meter of the bottom float nephelometricTurbidityUnit real 7.52 944 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/NTU Secchi Secchi depth measured before the start of towing float meter real 0.19 1.8 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M WaterDepth Depth of water recorded via Lowrance and start of tow float meter real 10.9 74.4 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/M IDLocation Location where species were identified string text NA Data not available OrganismCode A 1 to 4 letter character code unique to each species string text NA Data not available StageCode Life stage code designation of salmonids string text NA Data not available MarkCode Indicator code of whether or not fish has been marked or tagged string text NA Data not available TagCode Character code of coded wire tag or acoustic tag retrieved from individual string text NA Not available RaceByLength Estimated race of Chinook Salmon based on the length-at-date criteria string text NA Data not available RaceByTag Race of Chinook Salmon based on the coded wire tag or other markings string text NA Not available SpecialStudyID Identification code assigned to samples by the Delta Fish Monioring Program string text NA Not available GeneticID_Nuclear Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. string text NA Data not available Genetic_Nuclear_Test The genetic assay used for nuclear genetic analysis string text NA Data not available Genetic_Nuclear_Test_Lab Name of laboratory who conducted genetic analysis string text NA Data not available Genetic_Nuclear_Test_Lab_PI Name of principle investigator who conducted genetic analysis string text NA Data not available GeneticID_Mitochondrial Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string text NA Data not available Genetic_Mitochondrial_Test The genetic assay used for mitochondrial genetic analysis string text NA Data not available Genetic_Mitochondrial_Test_Lab Name of laboratory who conducted genetic analysis string text NA Data not available Genetic_Mitochondrial_Test_Lab_PI Name of principle investigator who conducted genetic analysis string text NA Data not available ForkLength Length of sampled fish measured from the point of the mouth to the fork of the caudal fin float millimeter real 0 285 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/MilliM Dead Mortality of individual resulting from sampling process string text NA Data not available Count Number of fish sampled float dimensionless natural 1 1033 NA Data not available http://qudt.org/schema/qudt/hasUnit http://qudt.org/vocab/unit/UNITLESS no 4503 EDSM_Fish_Taxonomy table of fish taxonomy EDSM_Fish_Taxonomy.csv 19739 486d9d29b6d9bdc69d1e776b60d0ee3c 1 \r\n column , " https://pasta.lternet.edu/package/data/eml/edi/994/5/9502f2d3ad63c395b1b8e326ecd3cac6 OrganismCode OrganismCode A 1 to 4 letter character unique to each species string text NA Not available IEPFishCode IEPFishCode A standardized six letter code used for each species across the Interagency ecological program string text NA not available CommonName CommonName Common name used for species string text NA Not available NonNative NonNative Indicator if the species is native or invasive in the San Francisco Estuary (yes=invasive, no=native) string no Fish is native yes fish is non native NA not available Phylum Phylum Taxonomic Phylum string text NA not available Class Class Taxonomic Class string text NA not available Order Order Taxonomic Order string text NA not available Family Family Taxonomic Family string text NA not available Genus Genus Taxonomic Genus string text NA not available Species Species Taxonomic Species string text NA not available Active Active Indicator if the species is still being recorded as part of the monitoring program string 0 not active 1 active NA not available LengthMeasurementType LengthMeasurementType Type of length measurement taken on juvenile and adult fish (e.g., fork length for fish with forked or heart-shaped caudal fins; total length for square or rounded caudal fins) string FL Fish measured to fork length TL Fish measured to total length NA not available no 193 ELS_Supplementary_Figures.pdf Supplementary Figures ELS_Supplementary_Figures.pdf 326793 f3ef6b8bc87757b516eef2cd0f56cfd0 application/pdf https://pasta.lternet.edu/package/data/eml/edi/994/5/c5e7cb7450e064ab0cbc6fe4eae58b6f unknown conductivity (or specific conductance at 25 degrees celsius) unit NTU- ratio of the amount of light transmitted through a water sample with the amount scattered at an angle of 90 degrees to one side