uid=iep,o=EDI,dc=edirepository,dc=org all public read United States Fish and Wildlife Service Claudia Macfarlane United States Fish and Wildlife Service claudia_macfarlane@fws.gov https://orcid.org/0009-0009-5022-3775 Denise Goodman United States Fish and Wildlife Service denise_goodman@fws.gov Kate Erly United States Fish and Wildlife Service kate_erly@fws.gov https://orcid.org/0009-0000-0258-4239 Ryan Cook United States Fish and Wildlife Service john_cook@fws.gov Paula Higginson United States Fish and Wildlife Service Jonathan Speegle United States Fish and Wildlife Service jonathan_speegle@fws.gov https://orcid.org/0000-0002-1780-8351 Gershom Bigham United States Fish and Wildlife Service Eric Huber United States Fish and Wildlife Service eric_huber@fws.gov Trevor Hope United States Fish and Wildlife Service Gabriela Garcia United States Fish and Wildlife Service Adriana Arrambide United States Fish and Wildlife Service Vivian Peck United States Fish and Wildlife Service Savannah Valdez United States Fish and Wildlife Service Jessica Falcon United States Fish and Wildlife Service Mia Adreani United States Fish and Wildlife Service contributor Alison Arntz United States Fish and Wildlife Service contributor Adriana Arrambide United States Fish and Wildlife Service contributor Lucia Arreola United States Fish and Wildlife Service contributor Pamella Asnata United States Fish and Wildlife Service contributor Olivia Bertelsen United States Fish and Wildlife Service contributor Phoebe Bertran United States Fish and Wildlife Service contributor Jordan Besson United States Fish and Wildlife Service contributor Gershom Bigham United States Fish and Wildlife Service contributor Kristie Braken-Guelke United States Fish and Wildlife Service contributor Benjamin Brewster United States Fish and Wildlife Service contributor Selena Cao United States Fish and Wildlife Service contributor Megan Carmen United States Fish and Wildlife Service contributor Ben Charpentier United States Fish and Wildlife Service contributor David Cole United States Fish and Wildlife Service contributor Ryan Cook United States Fish and Wildlife Service john_cook@fws.gov https://orcid.org/0000-0003-0081-6627 contributor John Craig United States Fish and Wildlife Service contributor Clifford Dobias United States Fish and Wildlife Service contributor David Dominguez United States Fish and Wildlife Service contributor Samantha Downs United States Fish and Wildlife Service contributor Justin Dummitt United States Fish and Wildlife Service contributor Nicholas Elsberg United States Fish and Wildlife Service contributor Kate Erly United States Fish and Wildlife Service contributor Jessica Falcon United States Fish and Wildlife Service contributor Isabella Ferruzzi United States Fish and Wildlife Service contributor Jackson Fimrite United States Fish and Wildlife Service contributor Autumn Fisher United States Fish and Wildlife Service contributor Gabriela Garcia United States Fish and Wildlife Service contributor Paul Gary United States Fish and Wildlife Service contributor Erik Geertsma United States Fish and Wildlife Service contributor Andrew Goodman United States Fish and Wildlife Service contributor Jacob Haertel United States Fish and Wildlife Service contributor Alex Haner United States Fish and Wildlife Service contributor Patrick Hapgood United States Fish and Wildlife Service contributor Rebecca Heisey United States Fish and Wildlife Service contributor Benny Her United States Fish and Wildlife Service contributor Michael Higginbotham United States Fish and Wildlife Service contributor Paula Higginson United States Fish and Wildlife Service contributor Erika Holcombe United States Fish and Wildlife Service contributor Trevor Hope United States Fish and Wildlife Service contributor Eric Huber United States Fish and Wildlife Service contributor Brian Hutchinson United States Fish and Wildlife Service contributor Interagency Ecological Program associate Maddie Johnson United States Fish and Wildlife Service contributor Evan Kinnett United States Fish and Wildlife Service contributor Shanna Kowalewski United States Fish and Wildlife Service contributor Kiana Lindblad United States Fish and Wildlife Service contributor Carissa Long United States Fish and Wildlife Service contributor Christopher Lopez United States Fish and Wildlife Service contributor Eric Louwerens United States Fish and Wildlife Service contributor Claudia Macfarlane United States Fish and Wildlife Service claudia_macfarlane@fws.gov https://orcid.org/0009-0009-5022-3775 contributor Robert Manos United States Fish and Wildlife Service contributor Donald Marcetti United States Fish and Wildlife Service contributor Mike Marshall United States Fish and Wildlife Service contributor Jeffrey McLain United States Fish and Wildlife Service associate Andres Mendoza United States Fish and Wildlife Service contributor Diego Meneses United States Fish and Wildlife Service contributor Anna Merrens United States Fish and Wildlife Service contributor Clayton Miller United States Fish and Wildlife Service contributor Lara Mitchell United States Fish and Wildlife Service https://orcid.org/0000-0002-8439-8508 contributor Matt Murphy United States Fish and Wildlife Service contributor Adam Nanninga United States Fish and Wildlife Service adam_nanninga@fws.gov https://orcid.org/0000-0002-2140-0439 contributor Ken Noble United States Fish and Wildlife Service contributor Matt Nobriga United States Fish and Wildlife Service associate Eric Ojerholm United States Fish and Wildlife Service contributor Vivian Peck United States Fish and Wildlife Service contributor Britany Perry United States Fish and Wildlife Service contributor Leo Polansky United States Fish and Wildlife Service associate Lauren Puffer United States Fish and Wildlife Service contributor Taylor Rohlin United States Fish and Wildlife Service contributor Shawn Sanders United States Fish and Wildlife Service contributor Gabriel Santana United States Fish and Wildlife Service contributor Taylor Senegal United States Fish and Wildlife Service taylor_senegal@fws.gov https://orcid.org/0000-0001-7344-2879 associate Joshua Slocum United States Fish and Wildlife Service contributor Garrett Smith United States Fish and Wildlife Service contributor Lori Smith United States Fish and Wildlife Service associate Joe Sonnenberg United States Fish and Wildlife Service contributor Keegan Spencer United States Fish and Wildlife Service contributor Ryan Sprague United States Fish and Wildlife Service contributor Jacob Stagg United States Fish and Wildlife Service contributor Geoffrey Steinhart United States Fish and Wildlife Service contributor Charles Strasser United States Fish and Wildlife Service contributor Michelle Szeto United States Fish and Wildlife Service contributor Vanessa Tobias United States Fish and Wildlife Service https://orcid.org/0000-0003-4872-1643 contributor Savannah Valdez United States Fish and Wildlife Service contributor Kandi Vargas United States Fish and Wildlife Service contributor Nicholas Veal United States Fish and Wildlife Service contributor Erich Von Hasseln United States Fish and Wildlife Service contributor Phil Voong United States Fish and Wildlife Service contributor John Wainwright United States Fish and Wildlife Service contributor Robert Weiland United States Fish and Wildlife Service contributor Jennie Wiggins United States Fish and Wildlife Service contributor 2026-03-25 The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. The main purpose of EDSM is to provide information about endemic Delta Smelt (Hypomesus transpacificus) population sizes and distributions within the upper San Francisco Estuary. To track the life cycle of this annual species, larval trawling with a fine-mesh (20 mm) net is conducted during the spring months, and Kodiak trawling for juveniles and adults occurs during the summer, fall, and winter months. Sampling sites are chosen via a stratified random sampling design. A minimum of two tows are conducted at each site, and field staff typically sample between 18 and 41 sites weekly. All fish collected are identified and enumerated, and a subset are measured for body length. Environmental data (water temperature, conductivity, dissolved oxygen, turbidity, depth) are also measured. In addition to Hypomesus spp., this long-term monitoring dataset can also be useful in evaluating the status and trends of other species of interest, especially pelagic fishes. For more information: https://www.fws.gov/office/lodi-fish-and-wildlife aquatic ecosystems distribution ecology estuaries brackish water freshwater rivers fishes abundance endangered species invasive species water quality LTER controlled vocabulary 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 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. San Francisco Estuary California USA -122.423 -121.289 38.601 37.775 2016-12-15 2025-11-30 ongoing Claudia Macfarlane United States Fish and Wildlife Service claudia_macfarlane@fws.gov https://orcid.org/0009-0009-5022-3775 Denise Goodman United States Fish and Wildlife Service denise_goodman@fws.gov Kate Erly United States Fish and Wildlife Service kate_erly@fws.gov https://orcid.org/0009-0000-0258-4239 Ryan Cook United States Fish and Wildlife Service john_cook@fws.gov Gershom Bigham United States Fish and Wildlife Service Savannah Valdez United States Fish and Wildlife Service Jessica Falcon United States Fish and Wildlife Service Vivian Peck United States Fish and Wildlife Service Eric Huber United States Fish and Wildlife Service eric_huber@fws.gov Trevor Hope United States Fish and Wildlife Service Gabriela Garcia United States Fish and Wildlife Service Adriana Arrambide United States Fish and Wildlife Service Jonathan Speegle United States Fish and Wildlife Service jonathan_speegle@fws.gov https://orcid.org/0000-0002-1780-8351 Enhanced Delta Smelt Monitoring Program (EDSM) Methods 1. PROGRAM OVERVIEW ====================================================================== The Enhanced Delta Smelt Monitoring Program (EDSM) is conducted by the U.S. Fish and Wildlife Service Lodi Office and 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. EDSM arose from concerns regarding the implementation of the 2008 Biological Opinion (BiOp) for Delta Smelt (Hypomesus transpacificus), the Reasonable and Prudent Alternative (RPA) actions in the BiOp related to reducing the entrainment of adult and juvenile Delta Smelt. EDSM, which began in December 2016, samples year-round using Kodiak trawls or larval gears to collect data on nearly all life stages of endangered Delta Smelt. The EDSM sampling year is divided into three phases of implementation that correspond with Delta Smelt life stages and management goals. The primary objective of all phases of EDSM is to provide abundance and distribution data for the corresponding life stages of Delta Smelt. Phase 1 of EDSM runs from approximately December through March and focuses on adult Delta Smelt. Phase 2 sampling runs from approximately April through June and targets post-larval and juvenile Delta Smelt. Phase 3 runs from approximately July through November and targets juvenile and sub-adult Delta Smelt. In general, the EDSM study area is defined as the waters of the San Francisco Estuary occupied by Delta Smelt. The study area is divided into spatially defined, temporally dynamic strata. In 2016–2017 during phase 1 and 2, there were four spatial strata, two falling into a perceived High-Risk Zone (high risk of entrainment) and two falling into a Low-Risk Zone (low risk of entrainment). As the program evolved, strata were modified to better reflect geographic boundaries and historical Delta Smelt distribution. Within each stratum, sampling locations are selected each week 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 a stratum. (Note: Weekly crew schedules, the number of sites sampled per week, and adaptive effort adjustments are detailed in Section 2 to keep the Overview focused on design and scope.) ====================================================================== 2. FIELD SAMPLING METHODS ====================================================================== 2.1 KODIAK TRAWLS Kodiak trawls are performed from approximately July through March to target juvenile, sub-adult, and adult Delta Smelt throughout the sampling area. A minimum of two replicate tows are conducted at each site. When the first two tows fail to catch Delta Smelt, additional replicate tows are repeated until at least one Delta Smelt is caught, or the maximum limit of four uncompromised tows is reached. This stopping rule approach simultaneously controls take and allows for greater precision in estimating Delta Smelt population parameters. The target duration of each tow is 10 minutes; however, the tow number and duration may vary due to debris, weather, or other sampling constraints. The Kodiak trawl consists of two boats, a net boat and a chase boat, each attached with a rope leading to a single net that is spread open between the two vessels. The net is towed in the top few meters of the water column at a necessary speed and distance apart to ensure that the net mouth remains fully extended and submerged. The net is towed against the current at speeds between 0.45–0.67 m/s. Vessels are maintained at approximately 15 feet apart during towing to ensure the net mouth remains fully extended and submerged. A calibrated mechanical flow meter (General Oceanics, Model #2030) is fixed to the sampling vessel to calculate the distance traveled during each tow. During Kodiak net sample retrieval, the two towing vessels maneuver alongside each other, and the chase boat transfers its tow rope to the net boat to close the mouth of the net and end the tow. The chase boat travels to the live box connected to the cod-end of the net and retrieves, secures, and pulls the live box from the water onto the boat. All fishes collected from the cod end or live box are placed in a holding container filled with water for processing (see Section 3). Lastly, the crew assigns a condition code for each tow as normal (no twists/snags/tears; <5% debris/blockage), fair (partial twists/snags/small tears; 5–25% debris/blockage), or poor (complete twists/snags/large tears; >25% debris/blockage). Poor condition tows are considered compromised and are not counted toward the maximum limit of tows. Field crews sample three to five days per week to sample between 18 and 41 total sites per week (2–15 sites per stratum). Sampling at a chosen location consists of a minimum of two tows to allow estimation of between-tow variability. The cumulative level and distribution of effort are adaptively managed and can shift between phases and years depending on hydrology, fish population status, and management needs. 2.2 LARVAL (20‑mm) TRAWLS Sampling of post-larval and juvenile Delta Smelt occurs from approximately April through June using nets with a 1600 micrometer square mesh, referred to as 20‑mm nets. Generally, two tows are completed at each site, with a target tow duration of 10 minutes each; however, tow duration can range from 3 to 10 minutes due to debris, weather, or other sampling constraints. The 20‑mm net consists of a D‑shaped opening attached to a frame on a weighted sled, towed by a single boat just below the surface of the water. The sled is deployed and retrieved using a hydraulic winch. A calibrated mechanical flow meter (General Oceanics, Model #2030) is fixed to the net opening to calculate distance traveled during each tow. Boat‑mounted flow meters for 20‑mm tows were discontinued after completion of 2024 sampling; beginning in 2025, only net‑mounted flow meters are used. At the end of each tow, the sled is retrieved, and the net is washed down towards the cod‑end using filtered water. Sample contents are preserved in the field and returned to the laboratory for processing (see Section 3). 2.3 WATER QUALITY SAMPLING Water quality measurements are collected prior to each sampling tow from the top 1m of the water column. Temperature is recorded to the nearest 0.1 °C, dissolved oxygen to the nearest 0.01 mg/L, specific conductance to the nearest 0.01 μS/cm (freshwater), and turbidity to the nearest 0.01 FNU. A Secchi disk is used to measure water clarity; Secchi disk measurements are always taken in the shade with sunglasses off and measured in meters (m). Between 2017 and 2020, additional water quality samples were collected from the bottom of the water column prior to each larval sampling tow using a LaMotte Horizontal Water Sampler; this practice was discontinued in May 2020. Starting in August 2024, NTU turbidity collection was discontinued; turbidity continues to be collected in FNU. Because EDSM sampling has not met saltwater thresholds within the Western Delta, saltwater units (mS/cm) are not reported in routine methods. Instrumentation: The YSI ProDSS is the current instrument used for field measurements. Historical instruments (reference only) include the YSI PRO2030 and the Hach 2100Q turbidimeter. Secchi disks are used to measure water clarity. Calibration and maintenance procedures are detailed in Section 4.3. ====================================================================== 3. LABORATORY & FISH PROCESSING METHODS ====================================================================== 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 six species that are readily identified at ≥20 mm FL: Sacramento Splittail (Pogonichthys macrolepidotus), Three‑spine Stickleback (Gasterosteus aculeatus), Western Mosquitofish (Gambusia affinis), Rainwater Killifish (Lucania parva), Bluefin Killifish (Lucania goodei), and Sacramento Sucker (Catostomus occidentalis). Prior to release at the site of capture, fish FL is measured to the nearest mm. If fish do not have a forked caudal fin, standard length is measured. If greater than 50 individuals of a Chinook Salmon race 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 (plus count; measured length of zero). Unmeasured fish transferred for broodstock, or other special studies will have their life stage estimated for take reporting. 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, where their identification is confirmed using dichotomous keys and/or with the aid of a microscope. During larval sampling, fish that cannot be identified in the field (the majority of fish sampled using larval gear types) are fixed in a solution of 10% buffered formalin, with Rose Bengal added, and brought back to the lab for identification under a microscope. These samples undergo multiple levels of laboratory processing, starting with the removal of debris and vegetation (sorting), followed by several stages of larval fish identification using dichotomous keys and other published resources. Fish, or photographs of fish, that cannot be confidently identified may be sent to external partners for genetic analysis for further verification. Chinook race assignment (river LDC): The race of all unmarked juvenile Chinook Salmon (i.e., no adipose fin clip indicating a hatchery fish) is 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 occurs between October 1–December 31, (2) late fall‑run occurs between January 1–April 15, (3) winter‑run occurs between April 16–August 15, (4) spring‑run occurs between August 16–September 30, and (5) growth rates are identical among all races (Fisher 1992). Although one or more assumptions are likely violated (Fisher 1994; Yoshiyama et al. 1998), the river LDC is widely used by managers and is the only cost‑effective and logistically feasible field method to differentiate among juvenile Chinook races. Due to habitat changes and hybridization, many Chinook characterized as spring‑run by the river LDC may be fall‑run (Banks et al. 2000; Greig et al. 2003; Banks et al. 2014). We use the river LDC to differentiate between unmarked winter‑run sized, spring‑run sized, fall‑run sized, and late fall‑run sized juveniles; these designations are a rough approximation and not definitive. Marked Chinook: Juvenile Chinook with clipped adipose fins are considered marked; all are brought back to the laboratory for coded wire tag retrieval to acquire information on hatchery origin and release location. ====================================================================== 4. INSTRUMENTS & EQUIPMENT (Reference) ====================================================================== 4.1 KODIAK TRAWL GEAR The Kodiak nets used are identical to those used by the Delta Juvenile Fish Monitoring Program and are composed of five panels, each decreasing in mesh size towards a live box at the cod end. Mesh size ranges from 5.1 cm stretch at the mouth to 0.3 cm stretch just before the live box. The live box (36 cm wide × 36 cm tall × 49 cm long) is composed of 0.18 cm thick aluminum perforated with numerous 0.46 cm diameter holes and contains several internal baffles intended to minimize fish mortality and stress due to flow pressure. The fully extended mouth size of the Kodiak net is 1.83 × 7.62 m. A float line and a lead line enable the net to remain at the top few meters of the water column while sampling. At the front of each wing of the net is a 1.83 m spreader bar with floats at the top and weights at the bottom to keep depth constant while sampling. The net is connected to the boats using a 2.3 m rope bridle (2.4 cm diameter) attached to a 30.5 m tow rope (0.95 cm diameter) on each side of the net. The net is fished approximately 31 m from the boats. Tow distance is measured using a calibrated mechanical flow meter (General Oceanics, Model #2030) deployed alongside the boat. (Volume calculations are consolidated in Section 5 to avoid duplication.) 4.2 LARVAL (20‑mm) GEAR The 20‑mm net consists of 1600 micrometer square mesh (identical to the CDFW 20‑mm survey), is 5.5 m long, with a mouth circumference of 4.9 m and mouth area of 1.51 m². The cod‑end jar consists of a 2 L 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. A calibrated flow meter (General Oceanics, Model #2030) is fixed to the net opening to calculate distance traveled during each tow. (Volume calculations are consolidated in Section 5 to avoid duplication.) 4.3 WATER QUALITY INSTRUMENTS & CALIBRATION Water quality measurements such as temperature, dissolved oxygen, and specific conductance are conducted using the YSI ProDSS (current instrument). Secchi disks are used to measure water clarity. Historic instruments include the YSI PRO2030 and the Hach 2100Q turbidimeter. The dissolved oxygen probe on the YSI PRO2030 was quick‑calibrated before each day of sampling (historic). The YSI PRO2030 probe was serviced monthly, during which dissolved oxygen, conductivity, and temperature were calibrated (historic). The calibration of the Hach 2100Q Turbidimeter was checked monthly and calibrated every three months (historic). Flow meters are cleaned and checked for calibration on a weekly basis; if flow meters do not operate within specified parameters, they are replaced. For YSI ProDSS (current), the dissolved oxygen sensor is calibrated weekly in the office and DO% is checked daily before sampling; turbidity and conductivity sensors are calibrated quarterly or as maintenance is needed. ====================================================================== 5. ANALYSIS & METHODS ====================================================================== Data are provided in their original form; no catch‑per‑effort calculations have been made here. Standard operating procedures (SOPs) for sampling methods and quality checks are available upon request. Volume calculations vary based on gear and sampling type but use a common framework: Volume sampled by each tow is estimated by calculating the difference between the end and starting value of the net flow meter and multiplying it by the flow meter’s factory‑stated K calibration factor (0.026873) and the net mouth area. Net Flowmeter = End − Start. For the 20‑mm large larval net: Volume = Net mouth area (1.51 m²) × Net Flowmeter × K (0.026873). For the Kodiak net: Volume = Mean net mouth area (12.54 m²) × Net Flowmeter × K (0.026873). ====================================================================== 6. QA/QC PROCEDURES ====================================================================== A Quality Assurance/Quality Control (QA/QC) program exists to ensure consistent data generation by following EDSM SOP. 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 identification. 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. The program has a dedicated fish biologist 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 ensure correct identification of the fish species. All unknown fish species captured in the field are returned to the laboratory and/or photographed to ensure correct identification. The QA/QC program also includes returning all Wakasagi Smelt (Hypomesus nipponensis) caught during all sampling to the office to be verified by experienced lab staff under SOP. All personnel are trained following SOP for field sampling, data entry QA/QC, and lab processing during their first weeks of employment and then work with experienced employees for the first three months of their employment. Data systems and checks: Kodiak trawl data are entered into two separate online entry forms linked to separate SQL servers housed at USFWS offices in Denver, CO. The SQL server uses customized code for error‑checking and Lodi and Wildlife staff review flagged data and make necessary edits to field datasheets and databases. 20‑mm data are entered and stored in a locally housed Microsoft Access database. 20‑mm data are entered a second time into a second‑entry Access form within the 20‑mm database. Custom queries are used to compare both databases and flag fields that do not match; staff review the field data sheet and databases to correct errors. For both 20‑mm and Kodiak trawl data, an additional R script is used to double‑check matching between the two databases. Additional data quality checks are performed by the data manager using custom queries, ArcGIS (to check coordinates), and R scripts to check for outliers. Coordinate error corrections are made when possible and Target Coordinates replace those unable to be corrected. Water quality values are retained unless shown to be a machine malfunction or obvious transcription error. All coordinate and water‑quality corrections contain comments that action was taken and follow written QC guidance (available on request). Flowmeter values and volumes are reviewed weekly; suspicious volumes are flagged as potentially incorrect following QC guidance (available on request). Volumes are not edited but are noted as suspicious in the FlaggedVolume field. Prior to October 2017, QA/QC was done by crew line‑by‑line comparison of field datasheets with entered data. The program initiated the new QA/QC protocol in October 2017 (dual entry + matching queries); mismatches trigger review and correction in the main and/or duplicate database. Beginning in 2024, the program added a centralized Flag log to document all water quality and coordinate values that appear unusual during review. ====================================================================== 7. CONTRACTOR INFORMATION ====================================================================== All fish identification and water quality measures are conducted by the Lodi Fish and Wildlife Office for the United States Fish and Wildlife Service. The contributor list is restricted to personnel working on the program for the most recent sample year. ====================================================================== 8. EXTERNAL REVIEW PROCESS ====================================================================== EDSM underwent several collegial reviews. The most recent review by the Interagency Ecological Program (IEP) was completed in 2019. In 2017, EDSM was included as part of the Long‑term Operations Biological Opinions (LOBO) Biennial Science Review; the final report of findings was published in January 2018. ====================================================================== APPENDIX A. PROJECT HISTORY / CHANGES IN METHODS AND LOCATIONS (2016–2025) ====================================================================== Modifications to fish sampling (Kodiak trawls and 20‑mm larval sampling) are made regularly to improve data accuracy, respond to management needs, adhere to permit limitations, and accommodate safety conditions and/or special studies. If more information on EDSM program changes over time is needed, contact the data point of contact. 2016: • EDSM test sampling began in November 2016; official sampling began December 15, 2016. Initially, only areas considered high density for Delta Smelt were sampled (Dec 15, 2016–Jan 8, 2017). 2016–2019: • Spatial stratification was originally dynamic and evolved as the program progressed. For each phase, the sampling frame and stratification were set by current Delta Smelt distribution, environmental conditions, and management objectives. The maximum number of tows per site and tow duration were also dynamic. Early EDSM sampling completed between 2 and 10 tows per site and tow duration ranged from 2 to 10 minutes. In July 2018, the target tow number and duration were standardized to 2–4 replicate tows per site with a 10‑minute duration each. Questions regarding stratification, tow maxima, or tow duration can be addressed to the data contact. • Larval trawling sometimes used an oblique tow path from the deepest portion of the sample site (up to 10 m) to the surface; since 2020, larval sampling uses a surface tow method only. 2017: • Kodiak data began entry into a second database to allow for better comparison and QC. • In January, lower‑density areas were added to the frame; by January 31, full frame coverage was achieved. • Feb 25–Mar 2017, closures on the San Joaquin River (levy stability) restricted some sampling in High Risk Low Density strata. • During 2017, up to six regular 20‑mm sites were paired weekly with shallow water sampling; within 100 m of a regular site, a small 20‑mm net was used concurrently in shallow water (<2.4 m). The small 20‑mm net (1600 μm square mesh) was approximately one‑third the size of the large net and deployed from the side of the boat without a sled. Volume of the small 20‑mm net: Net mouth area (0.5504 m²) × Net Flowmeter × K (0.026873). Minimum sampling depth was the minimum safe boat‑operating depth depending on bathymetry/slope. The small 20‑mm net was pulled through the top 0.84 m. • Beginning May 5, crews identified and enumerated all crustaceans and jellyfish; earlier numbers are likely underestimated. • Gear comparisons between Kodiak, 20‑mm oblique tow, and 20‑mm surface tow were conducted Jun 26–28 and Jul 24–26, 2017. • After Jul 1, 2017, station codes included DJFMP sample year and week (YY‑Week‑EDSM subregion); before this, codes were based on EDSM subregion. • Collaboration began with Reclamation’s Directed Outflow Project (DOP) studying outflow effects; EDSM retained Delta Smelt for health/condition, diet, and otolith analyses; in some years, lower trophic samples were paired at EDSM sites in DOP regions/timeframes. • A Wakasagi QC program was developed; all Wakasagi Smelt caught were returned to verify species ID by experienced crew or QA/QC biologist. 2018: • Beginning June 2018, QA/QC included double entry of datasheets for data‑entry accuracy. • April–May 2018 experimental larval sampling (beach seine, Manta nets) across depth strata; three official experimental days in May; regular 20‑mm resumed in June to estimate post‑larval abundances and standard errors. Only June 2018 20‑mm data are shared in the core dataset; experimental datasets are available separately on EDI. 2019: • April–May experimental larval sampling continued, same gears plus light trapping. Regular 20‑mm resumed in June to estimate post‑larval abundances and standard errors. Only June 2019 20‑mm data are in the core dataset; experimental datasets on EDI (https://portal.edirepository.org/nis/mapbrowse?packageid=edi.994.3). • Specific conductance is used instead of unspecified conductivity; unclear whether conductivity measurements in prior years were temperature‑adjusted. 2021: • Dec 14: USFWS began experimental releases of cultured (marked) Delta Smelt, with partners. Dec 21: EDSM began catching marked Delta Smelt. • EDSM began retaining live unmarked Delta Smelt for transfer to the UC Davis Fish Conservation and Culture Laboratory (FCCL) for broodstock collections (generally mid‑Nov–Mar when temperatures <17 °C). 2022: • Apr 1: Station code changed from subregion numbering to unique numbers within stratum (YY‑Week‑EDSM stratum number). • EDSM began retaining live Longfin Smelt (>84 mm) for transfer to FCCL for broodstock collections (generally mid‑Nov–Mar when temperatures <17 °C). 2023: • Following the LFS science plan, EDSM partnered with FCCL to supply wild LFS broodstock to establish a refugia population for captive breeding. • Kodiak season extended one month into April; concurrent full‑effort Kodiak and larval sampling occurred in April 2023. • LFWO began taking swabs of Delta Smelt for Sherlock (Specific High-Sensitivity Enzymatic Reporter unlocking) to determine maternal lineage in house. 2024: • During larval (20‑mm) trawling, generally only fish released in the field, Osmeridae, or ESA‑listed species were identified to species. Other fish were not identified and given Organism Code “NOID.” All Delta Smelt and Wakasagi identified in the lab were identified only to genus, Hypomesus, due to uncertainty in morphological identification to species. • Beginning July 2024, EDSM began randomly subsampling approximately five Wakasagi Smelt from each site for potential genetic monitoring of Delta Smelt/Wakasagi hybrids; each fish was frozen individually and assigned a SpecialStudyID. • Starting August 2024, EDSM no longer collects turbidity in NTU; turbidity is collected in FNU. • Bottom water sampling prior to larval tows was discontinued on August 1, 2024. • Boat‑mounted flow meters for 20‑mm were discontinued after 2024; from 2025 forward, only net‑mounted flow meters are used. 2025: • November 5: LFWO staff began in‑house processing for all DSM captured by EDSM and DJFMP (weighing, measuring, photographing, fin clips to UC Davis Genomic Variation Laboratory(GVL); secondary fin clip and carcass retained on LFWO site). • Changes to Sherlock sampling (number of swabs, frozen and fresh) as requested; not SOP‑specific. •Implemented a new Water Quality and Coordinate review log to track suspicious or inconsistent measurements. • Larval sampling experimental EtOH — regular 20‑mm sampling on hiatus to test efficacy of altering preservation from formaldehyde to ethanol. • April spent preparing for and creating sampling preservation/identification. • Kodiak, Phase 3 started a month earlier (June) due to break in 20‑mm • For Phase 2 No morphological identification to species for Hypomesus spp.; HYPOM code used exclusively. ====================================================================== REFERENCES ====================================================================== •Banks MA, Rashbrook VK, Calavetta MJ, Dean CA, Hedgecock D (2000). Analysis of microsatellite DNA resolves genetic structure and diversity of Chinook Salmon in California’s 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, O’Malley KG (2014). Testing advances in molecular discrimination among Chinook Salmon life histories: evidence from a blind test. Animal Genetics 45(3):412–420. • Fisher FW (1992). Chinook Salmon growth and occurrence in the Sacramento–San Joaquin River system. Draft Inland Fisheries Division Office Report, CDFG. • Fisher FW (1994). Past and present status of Central Valley Chinook Salmon. Conservation Biology 8(3):870–873. • Greene S (1992). Memorandum: Daily length tables. DWR, May 1992. • Stevens D, Olsen A (2004). Spatially balanced sampling of natural resources. JASA 99(465):262–278. • USFWS (1998). 1995 Annual progress report: abundance and survival of juvenile Chinook Salmon in the Sacramento–San Joaquin Estuary. Stockton FWO. • USFWS et al. (2023). EDSM Experimental Larval Survey Data 2018–2019 ver 3. Environmental Data Initiative. • Yoshiyama RM, Fisher FW, Moyle PB (1998). Historical abundance and decline of Chinook Salmon in the Central Valley Region of California. NAJFM 18:487–521. EDSM_20mm.csv Fish catch and water quality data from 20-mm sampling by the Enhanced Delta Smelt Monitoring Program. EDSM_20mm.csv 26746498 060f674a6568ebab6d581a1006893756 1 \r\n column , \ RegionCode Highest level of spatial stratification string Far West Sampled from 12/15/2016- present West Sampled from 12/15/2016- present South Sampled from 12/15/2016- present North Sampled from 12/15/2016- present n/p not provided Subregion Finest level of stratification, an abbreviation of the subregion name. Subregion was used as part of station code July 2017-April 2022 string Finest level of stratification, an abbreviation of the subregion name. Subregion was used as part of station code July 2017-April 2022 n/p not provided Stratum Dynamic groupings of subregions used to define core sampling areas. A part of station code up until April 2022 string LRLD Low Risk, Low Density. Used up until 3/31/2017 LRHD Low Risk, High Density Used up until 3/31/2017 HRHD High Risk, High Density. Used up until 3/31/2017 HRLD High Risk, Low Density. Used up until 3/31/2017 Eastern low.risk.low.density used from 4/24/2017 to 6/30/2017 low.risk.high.density used from 4/24/2017 to 6/30/2017 high.risk used from 4/24/2017 to 6/30/2017 Western low.risk.low.density used from 4/24/2017 to 6/30/2017 Western Delta Sampled beginning in 7/3/2017- present Southern Delta Sampled beginning in 7/3/2017- present Upper Sacramento Sampled beginning 7/3/2017 until 03/29/2018 Lower Sacramento Sampled beginning in 7/3/2017- present Lower San Joaquin Sampled beginning in 7/3/2017- present Suisun Bay/Marsh Sampled 7/3/2017 through 12/01/2017 Sac DW Ship Channel Sampled beginning in 7/3/2017 - present Suisun Marsh Sampled beginning in 12/04/2017- present Suisun Bay Sampled beginning in 12/04/2017- present Eastern Delta Sampled 12/4/2017 through 3/30/2018 Cache Slough LI Sampled beginning in 7/3/2017 - present n/p not provided DepthStratum Habitat groupings based on water depth, relevant for 2017 sampling. After 2018 all sampling done in deep water string Deep Water Sampling conducted in deep water (>=10 ft water depth) only for 2017 Phase 2 sampling Shallow Water Sampling conducted in shallow water (<=8 ft water depth) only for 2017 Phase 2 sampling NA Not Available PairedDepth Denotes concurrent sampling in multiple depth strata (relevant to 2017 sampling) string Y Both depth strata are sampled at a given station concurrently and within 100m of each other N No other sample taken within 100m at a given station concurrently with sample collection NA Not Available Phase A portion of sampling year using specific gear to target a particular life stage of delta smelt. The year is generally broken into three phases and shown in the format Year_Phase number. string 2017_1 12/12/2016 through 03/31/2017 2017_2 04/24/2017 through 06/30/2017 2017_3 07/03/2017 through 12/01/2017 2018_1 12/04/2017 through 03/30/2018 2018_2 06/04/2018 through 06/29/2018 2018_3 07/02/2018 through 11/30/2018 2019_1 12/03/2018 through 03/29/2019 2019_2 06/03/2019 through 06/28/2019 2019_3 07/01/2019 through 11/29/2019 2020_1 12/02/2019 through 03/27/2020 2020_2 03/30/2020 through 06/26/2020 2020_3 06/29/2020 through 11/27/2020 2021_1 11/30/2020 through 03/26/2021 2021_2 03/29/2021 through 06/25/2021 2021_3 06/28/2021 through 11/26/2021 2022_1 11/29/2021 through 04/01/2022 2022_2 04/04/2022 through 07/01/2022 2022_3 07/04/2022 through 12/02/2022 2023_1 12/05/2022 through 04/28/2023 (April sampling concurrent with 2023_2) 2023_2 04/03/2023 through 06/30/2023 2023_3 07/03/2023 through 12/01/2023 2024_1 12/04/2023 through 03/29/2024 2024_2 04/01/2024 through 06/28/2024 2024_3 07/01/2024 through 11/29/2024 NA Not Available StationCode The unique station identifier for each randomly-generated sampling site; denotes stratum along with a unique number for sites within that stratum. From July 1 2017 to March 31, 2022, the station code began to include sample year and sample week (YY-Sample week-Subregion site number). Since April 1 2022 the station code replaced the subregion number to the stratum number (YY-Sample week-Stratum site number) string The unique station identifier for each randomly-generated sampling site; denotes stratum along with a unique number for sites within that stratum. From July 1 2017 to March 31, 2022, the station code began to include sample year and sample week (YY-Sample week-Subregion site number). Since April 1 2022 the station code replaced the subregion number to the stratum number (YY-Sample week-Stratum site number) PairedStudy If an additional study was conducted concurrently with sample this field will be filled in with the corresponding study's abbreviation string GCP EDSM Gear comparison study HAB Directed Outflow Project habitat sampling eDNA eDNA water sample collection occurred during tow NA Not Available SampleDate The date a sample was completed reported in MM/DD/YYYY date YYYY-MM-DD 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 Latitude GPS coordinate assigned for the random sampling site by GRTS procedure float degree real 37.81979 38.56602 NA Not Available Longitude GPS coordinate assigned for the random sampling site by GRTS procedure float degree real -122.32701 -121.3673851 NA Not Available LatitudeStart Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real 37.81986 38.56541 NA Not Available LongitudeStart Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real -122.32701 -121.36798 NA Not Available LatitudeEnd Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real 37.81979 38.56293 NA Not Available LongitudeEnd Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real -122.32845 -121.3723 NA Not Available MethodCode Sampling method used to collect sample string Sampling method used to collect sample NA Not Available TowType Delineates how net is deployed and where it samples in the water column string Oblique Large net with weighted sled deployed off the back of the boat and sampling the entire water column available Surface Small net deployed off the side of a boat or large net with weighted sled deployed off the back of the boat, sampling just under the surface of the water NA Not Available NetSize Size of net used string L Large 20mm larval net with sled deployed behind boat S Small 20mm larval net deployed from side of boat (used during 2017 sampling) NA Not Available SamplingDirection Direction of towing in relation to river flow string D Downstream U Upstream NA Not Available TowNumber Number identifying the replicate sample taken at a site float dimensionless natural 1 3 NA Not Available TowSchedule Volume of water sampled calculated from flow meter and net dimensions float minute real 2.5 10 NA Not Available TowDuration Number of minutes when towing occurred float minute real 1 15 NA Not Available MaxCableLength Maximum amount of cable let out for a deep water oblique tow recorded. Cable length is determined by minimum depth observed within a trawl lane. This length is static for surface tows. float foot natural 50 225 NA Not Available GearConditionCode Condition code denoting the status of the tow string 1 Good sample defined as no twists, snags, or tears in the net, little to no debris in/on the net (< 5% coverage), and no (<5%) blockage between the mouth of the net to the live box 2 Fair sample defined as partial twists, snags, or small tears in the net, some debris in/on the net (5-25% coverage), or partial (5-25%) blockage between the mouth of the net to the live box 3 Poor, Sampling highly impaired, defined as complete twists, snags, or large tears in the net, heavy debris in/on the net (>25% coverage), or near complete (>25%) blockage between the mouth of the net to the live box 4 Site was visited but no sample attempted 9 Fish captured outside of the live box or cod end, cannot be assigned to specific tow (e.g. fish gilled or caught in net wings) FlowDebris Debris present on flow meter string Yes Debris present on flow meter impairing rotation No No debris present on flow meter NA not available Volume Volume of water sampled calculated from flow meter and net dimensions float meterCubed real 29.54095144 38842.73968 NA Not Available FlaggedVolume Denotes if a volume is flagged as potentially incorrect string TRUE Volume is flagged as potentially incorrect FALSE Volume is not flagged as potentially incorrect Comments Pertinent comments recorded in the field concerning the sample string Pertinent comments recorded in the field concerning the sample NA Not Available Tide Tide determined by crew by observing the immediate waterways and referencing the tide stage shown by the closest gauge on the Lowrance string High Slack High Slack Low Slack Low Slack Ebb Ebb Flood Flood NA Not Available WeatherCode Code for weather conditions directly overhead at time of sampling, the code recorded should represent 51% or more of the observed conditions string CLR Direct Sunlight CLD Overcast RAN Precipitation FOG Foggy NA Not Available BottomDepth Depth observed on the Lowrance at the beginning of a tow float foot real 2.6 314 NA Not Available Secchi Secchi depth taken before the start of towing float meter real 0.07 2 NA Not Available WaterTempTop Water temperature at the surface before the start of towing float celsius real 10.9 26 NA Not Available WaterTempBottom Water temperature at the bottom before the start of towing. Discontinued bottom water quality sampling May 2020 float celsius real 13.2 25.8 NA Not Available SpecificConductanceTop Water conductivity (or specific conductance at 25 degrees celsius) at the surface before the start of towing float microSiemensPerCentimeter real 6.37 27087 NA Not Available SpecificConductanceBottom Water conductivity (or specific conductance at 25 degrees celsius) at the bottom before the start of towing. Discontinued bottom water quality sampling May 2020 float microSiemensPerCentimeter real 36 28431 NA Not Available TurbidityTopFNU Turbidity at the surface before the start of towing float FormazinNephelometricUnit real 0.89 255.58 NA Not Available TurbidityTopNTU Turbidity at the surface before the start of towing. Turbidity sampling in NTU was discontinued August 2024 float nephelometricTurbidityUnit real 1.8 349 NA Not Available TurbidityBottom Turbidity at the bottom before the start of towing. Discontinued bottom water quality sampling May 2020 float nephelometricTurbidityUnit real 2.01 972 NA Not Available DOTop Dissolved oxygen at the surface before the start of towing float milligramPerLiter real 4.76 13.32 NA Not Available DOBottom Dissolved oxygen at the bottom before the start of towing. Discontinued bottom water quality sampling May 2020 float milligramPerLiter real 2.69 14.42 NA Not Available IDLocation Location of organism identification string Lab Organism was preserved in field and identified and measured in lab Field Organism was identified and measured upon collection in field; released unless noted by SpecialStudy field NA Not Available IDStatus Level of laboratory identification of organism string Complete All levels of lab ID have been completed Primary Report created after 1st ID (not final) Secondary Report created after 2nd ID (not final) NA Not Available CommonName Full common name for organism caught string Full common name for organism caught NA Not Available OrganismCode Code representing organism caught string Code representing organism caught NA Not Available IEPFishCode A standardized six letter code used for each species across the Interagency ecological program string A standardized six letter code used for each species across the Interagency ecological program NA Not Available MarkCode Abbreviation for the type of mark on a fish string Adclipped Adipose fin clipped None No marks None-FCCL No mark present but hatchery origin PlvcRt Pelvic fin clipped right VIE-GS Visible implanted elastomer tag: Green Snout VIE-LBA Visible implanted elastomer tag: Left/ Blue/ Anterior dorsal VIE-LBP Visible implanted elastomer tag: Left/ Blue/ Posterior dorsal VIE-LGA Visible implanted elastomer tag: Left/ Green/ Anterior dorsal VIE-LGP Visible implanted elastomer tag: Left/ Green/ Posterior dorsal VIE-LOA Visible implanted elastomer tag: Left/Orange/Anterior dorsal VIE-LOP Visible implanted elastomer tag: Left/ Orange/ Posterior dorsal VIE-LRA Visible implanted elastomer tag: Left/ Red/ Anterior dorsal VIE-LRP Visible implanted elastomer tag: Left/ Red/ Posterior dorsal VIE-PS Visible implanted elastomer tag: Pink Snout VIE-RBA Visible implanted elastomer tag: Right/ Blue/ Anterior dorsal VIE-RBP Visible implanted elastomer tag: Right/Blue/Posterior dorsal VIE-RGP Visible implanted elastomer tag: Right/Green/Posterior dorsal VIE-RGA Visible implanted elastomer tag: Right/ Green/ Anterior dorsal VIE-ROA Visible implanted elastomer tag: Right/ Orange/ Anterior dorsal VIE-ROP Visible implanted elastomer tag: Right/Orange/Posterior dorsal VIE-RRA Visible implanted elastomer tag: Right/ Red/Anterior dorsal VIE-RRM Visible implanted elastomer tag: Right/Red/Mid dorsal NA Not Available StageCode A code denoting life stage string 1 Yolk sac fry 2 Fry 3 Parr 4 Silver parr 5 Smolt 6 Adult (CHN = 500+ and RBT >300+) A Estimated Osmeridae life stage: Adult (DSM: >58mm; LFS: >84mm) L Estimated Osmeridae life stage: Larvae (DSM and LFS: <20mm) J Estimated Osmeridae life stage: Juvenile (DSM: 20-58mm; LFS 20-84mm) NA Not Available Expression Maturation code, recorded for all Delta or Longfin smelt string E Eggs expressed M Milt expressed X No eggs or milt expressed NA Not Available Dead Mortality due to sampling excluding processing string Yes Fish was a mortality due to sampling excluding processing No Fish was not a mortality due to sampling excluding processing and released alive NA Not Available ForkLength Fish fork length from point of mouth to fork of the caudal fin measured to the nearest millimeter; Larval fish or fish with round or heart shaped caudal fins are measured for total length,when ForkLength is 0, fish were captured and counted but not measured. Larval fish are measured to the tenth of a millimeter float millimeter real 0 630 NA Not Available RaceByLength Race designation assigned to non-adclipped Chinook Salmon based on river length-at-date criteria developed by Fisher (1992) and modified by Greene (1992) string Fall Fall-run Chinook Salmon race based on length Spring Spring-run Chinook Salmon based on length LateFall Late fall-run Chinook Salmon based on length Winter Winter-run Chinook Salmon based on length Adult Not categorized to any run; adult salmon(CHN = 500mm+ RBT <300mm) NA Not Available TagCode If present, code from coded-wire-tag after extraction and reading. NT means no tag was found. LT means tag was lost after extraction. string LT Lost Fish/Tag. No tag code available NT No Tag found in fish. No tag code available NR Not returned; fish not returned for processing. No tag code available NA not available RaceByTag Chinook salmon race designation assigned based on the coded wire tag found string Fall Fall-run Chinook Salmon Spring Spring-run Chinook Salmon LateFall Late fall-run Chinook Salmon Winter Winter-run Chinook Salmon NA not available SpecialStudy A code assigned to denote that this fish was part of a special study. Multiple codes with a / indicate that the fish was used in more than one special study. string DNA Fin clip was collected. If fish was genotyped results may be available. DOP Fish transferred for Directed Outflow Project L Fish intentionally sacrificed and returned to lab for verification OT CHN retained for otolith sample V Fish received outside morphological ID verification NA Not Available SpecialStudyID A unique identifier for a specimen being used in a special study. Some special studies do not have a Special Study ID string A unique identifier for a specimen being used in a special study. Some special studies do not have a Special Study ID NA Not Available FishComments Pertinent comments related to organism identification string Pertinent comments related to organism identification NA Not Available GeneticID_Nuclear Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. string Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. NA not available Genetic_Nuclear_Test The genetic assay used for nuclear genetic analysis string Osmerid panel Nuclear DNA panel used to distinguish Delta Smelt, Wakasagi, Longfin Smelt, or hybrid (Benjamin et al. 2018). This method does not identify the maternal lineage of hybrids(see mitochondrial DNA methods) NA not available Genetic_Nuclear_Test_Lab Name of laboratory who conducted genetic analysis string UCD GVL UC Davis Genomic Variation Laboratory NA not available Genetic_Nuclear_Test_Lab_POC Point of contact for the lab that conducted genetic analysis string A. Finger Dr. Amanda J. Finger NA not available GeneticID_Mitochondrial_Test1 Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string DSM Delta Smelt (Hypomesus transpacificus) Fail Unsuccessful genetic analysis WAG Wakasagi Smelt (Hypomesus nipponensis) LFS Longfin Smelt (Spirinchus thaleichthys) NA not available Genetic_Mitochondrial_Test1 The genetic assay used for mitochondrial genetic analysis string PCR Polymerase Chain Reaction for DNA sequencing to determine maternal lineage qPCR Quantitative Polymerase Chain Reaction for DNA sequencing to determine maternal lineage NA not available Genetic_Mitochondrial_Test1_Lab Name of laboratory who conducted genetic analysis string UCD AHL UC Davis Aquatic Health Laboratory UCD GVL UC Davis Genomic Variation Laboratory NA not available Genetic_Mitochondrial_Test1_Lab_POC Point of contact for the lab that conducted genetic analysis string S. Teh Dr. Swee Teh B. Hammock Dr. Bruce Hammock R. Nagarajan Dr. Raman Nagarajan NA not available GeneticID_Mitochondrial_Test2 Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string DSM Delta Smelt (Hypomesus transpacificus) Fail Unsuccessful genetic analysis WAG Wakasagi Smelt (Hypomesus nipponensis) NA not available Genetic_Mitochondrial_Test2 The genetic assay used for mitochondrial genetic analysis string SHERLOCK (Specific High-Sensitivity Enzymatic Reporter unLOCKing) A CRISPR-based diagnostic tool for real-time Hypomesus species verification using species-specific assays for Delta Smelt and Wakasagi to determine maternal lineage. (Baerwald et al. 2020)� qPCR Quantitative Polymerase Chain Reaction to determine maternal lineage PCR Polymerase Chain Reaction to determine maternal lineage NA not available Genetic_Mitochondrial_Test2_Lab Name of laboratory who conducted genetic analysis string UCD GVL UC Davis Genomic Variation Laboratory NA not available Genetic_Mitochondrial_Test2_Lab_POC Point of contact for the lab that conducted genetic analysis string R. Nagarajan Dr. Raman Nagarajan NA not available Count Number of fish records from the sample with the corresponding fork length float dimensionless natural 1 2697 NA Not Available 69060 EDSM_KDTR.csv Fish catch and water quality data from Kodiak trawling by the Enhanced Delta Smelt Monitoring Program. EDSM_KDTR.csv 91651496 5505a394878ffb10343d16ab0d0d4cea 1 \r\n column , \ RegionCode Highest level of spatial stratification string Far West Sampled from 12/15/2016- present West Sampled from 12/15/2016- present South Sampled from 12/15/2016- present North Sampled from 12/15/2016- present n/p not provided Subregion Finest level of stratification, an abbreviation of the subregion name. Subregion was used as part of station code July 2017-April 2022 string Finest level of stratification, an abbreviation of the subregion name. Subregion was used as part of station code July 2017-April 2022 n/p not provided Stratum Dynamic groupings of subregions used to define core sampling areas. A part of station code up until April 2022 string LRLD Low Risk, Low Density. Used up until 3/31/2017 LRHD Low Risk, High Density Used up until 3/31/2017 HRHD High Risk, High Density. Used up until 3/31/2017 HRLD High Risk, Low Density. Used up until 3/31/2017 Eastern low.risk.low.density used from 4/24/2017 to 6/30/2017 low.risk.high.density used from 4/24/2017 to 6/30/2017 high.risk used from 4/24/2017 to 6/30/2017 Western low.risk.low.density used from 4/24/2017 to 6/30/2017 Western Delta Sampled beginning in 7/3/2017- present. Only Sampled during Phase 1 dependent on location of X2 Southern Delta Sampled beginning in 7/3/2017- present. Only Sampled during Phase 1 Upper Sacramento Sampled until 03/29/2018 Lower Sacramento Sampled beginning in 7/3/2017- present Lower San Joaquin Sampled beginning in 7/3/2017- present Suisun Bay/Marsh Sampled 7/3/2017 through 12/01/2017 Sac DW Ship Channel Sampled beginning in 7/3/2017 - present Suisun Marsh Sampled beginning in 12/04/2017- present Suisun Bay Sampled beginning in 12/04/2017- present Eastern Delta Sampled 12/4/2017 through 3/30/2018 Cache Slough LI Sampled beginning in 7/3/2017 - present n/p not provided Phase A portion of sampling year using specific gear to target a particular life stage of Delta smelt. The year is generally broken into three phases and shown in the format Year_Phase number. string 2017_1 12/12/2016 through 03/31/2017 2017_2 04/24/2017 through 06/30/2017 2017_3 07/03/2017 through 12/01/2017 2018_1 12/04/2017 through 03/30/2018 2018_2 06/04/2018 through 06/29/2018 2018_3 07/02/2018 through 11/30/2018 2019_1 12/03/2018 through 03/29/2019 2019_2 06/03/2019 through 06/28/2019 2019_3 07/01/2019 through 11/29/2019 2020_1 12/02/2019 through 03/27/2020 2020_2 03/30/2020 through 06/26/2020 2020_3 06/29/2020 through 11/27/2020 2021_1 11/30/2020 through 03/26/2021 2021_2 03/29/2021 through 06/25/2021 2021_3 06/28/2021 through 11/26/2021 2022_1 11/29/2021 through 04/01/2022 2022_2 04/04/2022 through 07/01/2022 2022_3 07/04/2022 through 12/02/2022 2023_1 12/05/2022 through 04/28/2023 (April sampling concurrent with 2023_2) 2023_2 04/03/2023 through 06/30/2023 2023_3 07/03/2023 through 12/01/2023 2024_1 12/04/2023 through 03/29/2024 2024_2 04/01/2024 through 06/28/2024 2024_3 07/01/2024 through 11/29/2024 2025_1 12/01/2024 through 03/28/2025 2025_3 06/2/2025 through 11/28/2025 NA not available StationCode The unique station identifier for each randomly-generated sampling site; denotes stratum along with a unique number for sites within that stratum. From July 1 2017 to March 31, 2022, the station code included sample year and sample week (YY-Sample week-Subregion site number). Since April 1 2022 the station code replaced the subregion number to the stratum number (YY-Sample week-Stratum site number) string The unique station identifier for each randomly-generated sampling site; denotes stratum along with a unique number for sites within that stratum. From July 1 2017 to March 31, 2022, the station code included sample year and sample week (YY-Sample week-Subregion site number). Since April 1 2022 the station code replaced the subregion number to the stratum number (YY-Sample week-Stratum site number) PairedStudy If an additional study was conducted concurrently with sample this field will be filled in with the study's abbreviation. string GCP EDSM Gear comparison study HAB Directed Outflow Project habitat sampling eDNA eDNA water sample collection occurred during tow TMS Trawl Mensuration Study NA not available SampleDate The date a sample was completed reported in YYYY-MM-DD date YYYY-MM-DD 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 Latitude GPS coordinate assigned for the random sampling site by GRTS procedure float degree real 37.78277 38.57897 Longitude GPS coordinate assigned for the random sampling site by GRTS procedure float degree real -122.3332 -121.32598 LatitudeStart Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real 37.78277 38.57868 LongitudeStart Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual starting location of a trawl float degree real -122.33647 -121.32271 LatitudeEnd Latitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real 37.78277 38.57891 LongitudeEnd Longitude value recorded from the marked waypoints on the Lowrance unit indicating the actual end location of a trawl float degree real -122.33857 -121.32229 MethodCode Sampling method used to collect sample. KDTR= Kodiak Trawl 20mm= 20mm larval trawl string Sampling method used to collect sample. KDTR= Kodiak Trawl 20mm= 20mm larval trawl SamplingDirection Direction of towing in relation to river flow string D Downstream U Upstream NA not available TowNumber Number identifying the replicate sample taken at a site float dimensionless natural 1 10 NA not available TowMax The pre-assigned maximum number of tows to be completed at a sampling site based on the stopping rules for each stratum float dimensionless natural 1 10 TowDuration Number of minutes when towing occurred float minute real 0.1 15 NA not available GearConditionCode Condition code denoting the status of the tow string 1 Good sample defined as no twists, snags, or tears in the net, little to no debris in/on the net (< 5% coverage), and no (<5%) blockage between the mouth of the net to the live box 2 Fair sample defined as partial twists, snags, or small tears in the net, some debris in/on the net (5-25% coverage), or partial (5-25%) blockage between the mouth of the net to the live box 3 Poor, Sampling highly impaired defined as complete twists, snags, or large tears in the net, heavy debris in/on the net (>25% coverage), or near complete (>25%) blockage between the mouth of the net to the live box 4 Site was visited but no sample attempted 9 Fish captured outside of the live box or cod end, cannot be assigned to specific tow (e.g. fish gilled or caught in net wings) FlowDebris Debris present on flow meter string Y Debris present on flow meter impairing rotation N No debris present on flow meter NA not available Volume Volume of water sampled calculated from flow meter and net dimensions float meterCubed real 0 336983.0392 NA not available FlaggedVolume Volume flagged as potentially incorrect string TRUE Volume is flagged as potentially incorrect FALSE Volume is not flagged as potentially incorrect Comments Pertinent comments recorded in the field concerning the sample string Pertinent comments recorded in the field concerning the sample NA not available Tide Tide determined by crew by observing the immediate waterways and referencing the tide stage shown by the closest gauge on the Lowrance string High Slack High Slack Low Slack Low Slack Ebb Ebb Flood Flood NA not available WeatherCode Code for weather conditions directly overhead at time of sampling, the code recorded should represent 51% or more of the observed conditions string CLR Direct Sunlight CLD Overcast RAN Precipitation FOG Foggy NA not available BottomDepth Depth observed on the Lowrance at the beginning of a tow float meter real 0.6 40.23 NA not available Secchi Secchi depth taken before the start of towing float meter real 0.050000001 2 NA not available WaterTemp Water temperature before the start of towing float celsius real 6.400000095 27.89999962 NA not available SpecificConductance Water conductivity (or specific conductance) at 25 degrees Celsius before the start of towing float microSiemensPerCentimeter real 6.380000114 41942 NA not available TurbidityNTU Water turbidity at the surface before the start of towing. Turbidity sampling in NTU discontinued August 2024 float nephelometricTurbidityUnit real 0 482 NA not available TurbidityFNU Water turbidity at the surface before the start of towing float FormazinNephelometricUnit real 0.280000001 271.5 NA not available DO Water dissolved oxygen at the surface before the start of towing float milligramPerLiter real 3.09 14.87 NA not available CommonName Full common name for organism caught string Full common name for organism caught NA not available OrganismCode Code representing organism caught string Code representing organism caught NA not available IEPFishCode A standardized six letter code used for each species across the Interagency Ecological Program string A standardized six letter code used for each species across the Interagency Ecological Program NA Not available MarkCode Abbreviation for the type of mark on a fish string AdClipped Adipose fin clipped None No marks None-FCCL No mark present but hatchery origin PlvcRt Pelvic fin clipped right VIE-LBA Visible implanted elastomer tag: Left/ Blue/ Anterior dorsal VIE-LBP Visible implanted elastomer tag: Left/ Blue/ Posterior dorsal VIE-LGA Visible implanted elastomer tag: Left/ Green/ Anterior dorsal VIE-LOA Visible implanted elastomer tag: Left/Orange/Anterior dorsal VIE-LOP Visible implanted elastomer tag: Left/ Orange/ Posterior dorsal VIE-LRA Visible implanted elastomer tag: Left/ Red/ Anterior dorsal VIE-LRP Visible implanted elastomer tag: Left/ Red/ Posterior dorsal VIE-RBA Visible implanted elastomer tag: Right/ Blue/ Anterior dorsal VIE-RBP Visible implanted elastomer tag: Right/Blue/Posterior dorsal VIE-RGP Visible implanted elastomer tag: Right/Green/Posterior dorsal VIE-RGA Visible implanted elastomer tag: Right/ Green/ Anterior dorsal VIE-ROA Visible implanted elastomer tag: Right/ Orange/ Anterior dorsal VIE-ROP Visible implanted elastomer tag: Right/Orange/Posterior dorsal VIE-RRM Visible implanted elastomer tag: Right/Red/Mid dorsal VIE-RRA Visible implanted elastomer tag: Right/ Red/Anterior dorsal VIE-RRP Visible implanted elastomer tag: Right/ Red/Posterior dorsal NA not available StageCode A code denoting life stage string 1 Yolk sac fry 2 Fry 3 Parr 4 Silver parr 5 Smolt 6 Adult (CHN = 500+ and RBT >300+) A Estimated Osmeridae life stage: Adult (DSM: >58mm; LFS: >84mm) L Estimated Osmeridae life stage: Larvae (DSM and LFS: <20mm) J Estimated Osmeridae life stage: Juvenile (DSM: 20-58mm; LFS 20-84mm) NA not available Expression Maturation code, recorded for all Delta or Longfin smelt string E Eggs expressed M Milt expressed X No eggs or milt expressed NA not available Dead Mortality due to sampling excluding processing string Yes Fish was a mortality due to sampling excluding processing No Fish was not a mortality due to sampling excluding processing and released alive NA not available ForkLength Fish fork length from point of mouth to fork of the caudal fin measured to the nearest millimeter; Larval fish or fish with round or heart shaped caudal fins are measured for total length,when ForkLength is 0, fish were captured and counted but not measured float millimeter real 0 770 NA not available RaceByLength Race designation assigned to non-adclipped Chinook Salmon based on river length-at-date criteria developed by Fisher (1992) and modified by Greene (1992) string Fall Fall-run Chinook Salmon race based on length Spring Spring-run Chinook Salmon based on length LateFall Late Fall-run Chinook Salmon based on length Winter Winter-run Chinook Salmon based on length Adult Not categorized to any run; adult salmon NA not available TagCode If present, code from coded-wire-tag after extraction and reading. NT means no tag was found. LT means tag was lost after extraction string LT Lost Fish/Tag. No tag code available NT No Tag found in fish. No tag code available NR Not returned; fish not returned for processing. No tag code available NA not available RaceByTag Chinook salmon race designation assigned based on the coded wire tag found string Fall Fall-run Chinook Salmon by coded wire tag Spring Spring-run Chinook Salmon by coded wire tag LateFall Late fall-run Chinook Salmon by coded wire tag Winter Winter-run Chinook Salmon by coded wire tag NA not available SpecialStudy A code assigned to denote that this fish was part of a special study. Multiple codes with a / indicate that the fish was used in more than one special study. string Cage Sent to UC Davis for genetic testing to determine whether they were CDWR Delta Smelt cage study progeny DNA Fin clip collected for genetic analysis SHL Mucous swab taken for Sherlock analysis OT CHN retained for otolith sample Se Fish was brought back for Selenium study DOP Fish transferred for Directed Outflow Project V Fish received outside morphological verification L Fish returned to lab for verification L/U Fish returned to lab for verification & Fish died before release as unintentional mortality NA not available SpecialStudyID A unique identifier for a specimen being used in a special study. Some special studies do not have a Special Study ID string A unique identifier for a specimen being used in a special study. Some special studies do not have a Special Study ID NA not available GeneticID_Nuclear Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. string Most likely species identification based on nuclear genetic analysis. For Chinook Salmon, race is used as identification. NA not available Genetic_Nuclear_Test The genetic assay used for nuclear genetic analysis string Parentage panel A single nucleotide polymorphism panel by the Genomic Variation Laboratory, designed to genetically manage pair-crosses of Delta smelt from available broodstock and is also used to determine wheter wild caught delta smelt are of hatchery origin (recaptured releases). Use of this panel is limited to Delta Smelt Osmerid panel Nuclear DNA panel used to distinguish Delta Smelt, Wakasagi, Longfin Smelt, or hybrid (Benjamin et al. 2018). This method does not identify the maternal lineage of hybrids(see mitochondrial DNA methods) NA not available Genetic_Nuclear_Test_Lab Name of laboratory who conducted genetic analysis string USFWS Abernathy FTC United States Fish and Wildlife Service Abernathy Fish Technology Center UCD GVL UC Davis Genomic Variation Laboratory NA not available Genetic_Nuclear_Test_Lab_POC Point of contact for the lab that conducted genetic analysis string A. Finger Dr. Amanda J. Finger S. Mussmann Dr. Steven M Mussman NA not available GeneticID_Mitochondrial_Test1 Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string DSM Delta Smelt (Hypomesus transpacificus) LFS Longfin Smelt (Spirinchus thaleichthys) Fail Unsuccessful genetic analysis Not HYPOM Determined not to be in the Hypomesus genus through SHERLOCK WAG Wakasagi Smelt (Hypomesus nipponensis) NA not available Genetic_Mitochondrial_Test1 The genetic assay used for mitochondrial genetic analysis string PCR Polymerase Chain Reaction for DNA sequencing to determine maternal lineage qPCR Quantitative Polymerase Chain Reaction for DNA sequencing to determine maternal lineage SHERLOCK (Specific High-Sensitivity Enzymatic Reporter unLOCKing) A CRISPR-based diagnostic tool for real-time Hypomesus species verification using species-specific assays for Delta Smelt and Wakasagi to determine maternal lineage. (Baerwald et al. 2020)� SHERLOCK_Axxin A CRISPR-based assay for ultra-sensitive, non-invasive species identification from environmental samples run on a portable fluorescence reader to determine maternal lineage NA not available Genetic_Mitochondrial_Test1_Lab Name of laboratory who conducted genetic analysis string UCD AHL UC Davis Aquatic Health Laboratory UCD GVL UC Davis Genomic Variation Laboratory Lodi FWO Lodi Fish and Wildlife Office DWR California Department of Water Resources NA not available Genetic_Mitochondrial_Test1_Lab_POC Name of principle investigator who conducted genetic analysis string S. Teh Dr. Swee Teh B. Schreier Brian Schrier R. Nagarajan Dr. Raman Nagarajan D. Goodman Denise Goodman NA not available GeneticID_Mitochondrial_Test2 Most likely species identification based on mitochondrial genetic analysis. For Chinook Salmon, race is used as identification. string DSM Delta Smelt (Hypomesus transpacificus) Fail Unsuccessful genetic analysis WAG Wakasagi Smelt (Hypomesus nipponensis) NA not available Genetic_Mitochondrial_Test2 The genetic assay used for mitochondrial genetic analysis string SHERLOCK (Specific High-Sensitivity Enzymatic Reporter unLOCKing) A CRISPR-based diagnostic tool for real-time Hypomesus species verification using species-specific assays for Delta Smelt and Wakasagi to determine maternal lineage. (Baerwald et al. 2020)� qPCR Quantitative Polymerase Chain Reaction to determine maternal lineage PCR Polymerase Chain Reaction to determine maternal lineage NA not available Genetic_Mitochondrial_Test2_Lab Name of laboratory who conducted genetic analysis string UCD GVL UC Davis Genomic Variation Laboratory NA not available Genetic_Mitochondrial_Test2_Lab_POC Point of contact for the lab that conducted genetic analysis string R. Nagarajan Dr. Raman Nagarajan NA not available Count Number of fish records from the sample with the corresponding fork length float dimensionless natural 1 16174 NA not available 252765 EDSM_Fish_Taxonomy.csv Taxon table for species including native or invasive classification EDSM_Fish_Taxonomy.csv 19851 5fbcf64cf0ce5af7ab782c0523a13bd6 1 \r\n column , \ OrganismCode A 1 to 4 letter character unique to each species string A 1 to 4 letter character unique to each species IEPFishCode A standardized six letter code used for each species across the Interagency ecological program string A standardized six letter code used for each species across the Interagency ecological program NA not available CommonName Common name used for species string Common name used for species NonNative Indicator if the species is native or invasive in the San Francisco Estuary (yes=invasive, no=native) string yes Nonnative and/or invasive species to the San Francisco Estuary no Native species to the San Francisco Estuary NA not available Phylum Taxonomic Phylum string Taxonomic Phylum NA not available Class Taxonomic Class string Taxonomic Class NA not available Order Taxonomic Order string Taxonomic Order NA not available Family Taxonomic Family string Taxonomic Family NA not available Genus Taxonomic Genus string Taxonomic Genus NA not available Species Taxonomic Species string Taxonomic Species NA not available Active Indicator if the species is still being recorded as part of the monitoring program string 1 Species is still currently being recorded as part of the monitoring program 0 Species is not currently being recorded as part of the monitoring program 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 measurement taken as a fork length (heartshaped or forked caudal fin) TL Fish measurement taken as a total length (rounded or square caudal fin) NA not available 194 ChangeLog.csv Log of structural changes to dataset ChangeLog.csv 4269 b97740db88ef8a866095633b62f95d26 text/csv unknown FlagLog.csv Log of Flagged Parameters FlagLog.csv 7022 6e1cdfe9ee57a2cab9252daf20b73374 text/csv unknown FlagLog_metadata.csv Flag Log Metadata FlagLog_metadata.csv 1199 b1b2a3301cf7f93e176c4a22e1f6cd08 text/csv unknown conductivity (or specific conductance at 25 degrees celsius) unit NTU- ratio of the amount of white light transmitted through a water sample with the amount scattered at an angle of 90 degrees to one side FNU-ratio of the amount of infrared light transmitted through a water sample with the amount scattered at an angle of 90 degrees to one side EMLassemblyline 3.6.0