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MAY 1, 1995

Salmon Modeling

Contact Person: Pat Brandes (USFWS) (209) 948-7800

We are proposing to fund a fishery statistician to work in collaboration with statisticians representing CUWA and California Department of Fish and Game. The goal is to develop the best model possible using the coded wire tag data. The new approach using logistic regression (general linear models) would also identify factors important to survival, but would not generate survival indices first. The number of smolts recovered/number released would be used as the dependent variable. Effort would be incorporated as one of the independent variables in the relationship. The three statisticians will be submitting a scope of work within the next few weeks, so that funding can then be procured.

Race Identification

The Department of Water Resources contracted with the University of California to conduct a three year research project to identify nuclear DNA discriminators between CaliforniaÆs Central Valley chinook salmon stocks. Dr. Dennis Hedgecock and staff of the Bodega Marine Laboratory are screening a class of rapidly evolving, non protein coding, selectively neutral DNA polymorphisms, called short Tandem Repeat Polymorphic DNA (STRP), for fixed genetic differences that would hopefully provide unambiguous stock identification of individual juvenile Chinook. If fixed genetic differences might still provide a statistical estimate of the relative contributions of spawning stocks to the mixed-stock juvenile Chinook population in the Sacramento-San Joaquin Delta.

About 2,000 fin tissue samples collected from Chinook of known stock were provided to Dr. Hedgecock in 1994/1995. Tissue sampling from known stock will continue for the next two years. Fin tissue samples from the mixed-stock juvenile Chinook population in the Sacramento-San Joaquin Delta will be collected beginning in the fall of 1995. Permits are being coordinated for collection of fin tissue from winter-run length juveniles. Dr. Hedgecock estimated ten to twenty STRPÆs should provide a statistical estimate of the composition of the mixed-stock juvenile population, of which six have been identified. The mixed-stock analysis should begin in the winter of 1995/1996.


Contact Person: Dale Sweetnam (DFG) (209) 948-7800

At present there are two resident special status fish species in the Bay-Delta region. The delta smelt, a small endemic osmerid inhabiting the upper estuary, was listed as threatened by both the DFG and the USFWS in 1993. The splittail, an endemic minnow living in the upper estuary and its tributaries, is a candidate species for listing as threatened by the USFWS. Information about these species was very limited prior to their consideration for listing and came primarily from IEP's routine monitoring efforts. In the case of both species, the IEP now has dedicated monitoring and research efforts to learn more about the abundance, distribution, life history, and factors affecting these species.

Delta Smelt Studies

Monitoring of Delta Smelt Abundance and Distribution Contact Person: Dale Sweetnam (DFG) (209) 948-7800

The Summer Townet and Fall Midwater Trawl surveys (see Section II.D.) provide abundance and distribution information which has been incorporated into the USFWS Biological Opinion for the operation of the CVP and SWP and the recovery plan for delta smelt created by the Delta Native Fishes Recovery Team. The Suisun Marsh study is used to monitor delta smelt abundance in Suisun Marsh. The Bay Study and USFWS Chipps Island trawl surveys (see Sections II. D. and A., respectively) are additional surveys which provide information on delta smelt abundance. The USFWS beach seine survey (see Section II.A.) provides important distributional information during spawning migrations.

Delta Smelt Spawning Season Monitoring Contact Person: Dale Sweetnam (DFG) (209) 948-7800

Midwater Trawl Surveys (see Section II.D.) extended through the spawning season. The purpose of midwater trawling from January through April is to detect delta smelt spawning migrations and to determine which parts of the Estuary are being used for spawning. This survey was also used in 1994 to trigger pulse flows of water on the San Joaquin River if delta smelt were present.

Artificial substrates to capture delta smelt eggs in order to identify specific spawning locations. Delta smelt eggs are demersal and attach to aquatic vegetation, hence, artificial egg collecting substrates will be used to specifically identify spawning locations. Placement of artificial substrates will occur in response to high abundances of adult delta smelt identified by the trawl and/or seine surveys, suitable habitat, and accessibility of locations.

Larval fish surveys to determine the timing, distribution, and abundance of delta smelt larvae and their food supply. Larval fish surveys are critical to identification of factors controlling survival and abundance of young smelt and their food supply. Single 10-minute tows using a 505 mm nitex egg and larval net attached to a sled towed in a stepped-oblique fashion are made at 40 to 80 stations throughout the Estuary from Suisun Bay, the Delta, and the Sacramento River. Sampling runs from mid-February through July. Historically, the principal objective of the survey has been to measure the abundance and distribution of striped bass, but in recent years emphasis has shifted to delta smelt and other species. Otoliths to determine age and growth rates and stomachs for diet analysis from delta smelt collected in this survey are used for additional research (see below).

Delta Smelt Entrainment at North Bay Aqueduct. Larval samples are taken every other day at 4 stations near the diversion in Barker Slough to monitor entrainment losses required under the 1995 USFWS Biological Opinion for delta smelt on the operation of the Central Valley Project and the State Water Project. Diversions at NBA will be restricted to a 5-day running average of 65 cfs for 5 days when delta smelt are present. Samples are sorted, identified, and larval densities are reported on the World Wide Web within 72 hours.

Estimation of larval delta smelt fish losses at the State and Federal water project diversions, and local agricultural diversions in the Delta. The significance of losses of larval smelt to water project diversions are being assessed through a combination of the estuary-wide larval fish survey and sampling by DWR in the south Delta using the similar sampling methods (see Section II.F.). The DWR has initiated an agricultural diversion study (see Section II.F.) to determine the magnitude of entrainment of both larval and juvenile delta smelt in agricultural diversions in the Delta. There are over 1,800 agricultural diversions within the Delta.

Research on Other Life Stages of Delta Smelt Contact Person: Dale Sweetnam (DFG) (209) 948-7800

Purse Seine Survey. The purpose of the purse seining survey is to determine delta smelt utilization of shallow shoals versus deep water areas in bay and river/slough environments. The utilization of shallow water habitat by delta smelt as both spawning and rearing habitat may have increased importance as more emphasis is placed on restoration of these areas for mitigation or flooding of delta islands as reproductive habitat for delta smelt becomes more important. A 100 X 20 ft miniature purse seine with 1600 micron stretch mesh is utilized to sample shoals and deep areas at approximately 15 sampling sites located in Suisun Bay, Montezuma slough, Honker Bay, Sherman Lake, Cache slough, and San Joaquin River. Sampling is conducted during May through July.

Cohort identification from otoliths. Identification of specific cohorts of delta smelt by examination of daily growth increments (circuli) of otoliths (ear bones) are used in concert with larval and juvenile fish abundance data to determine when and where the majority of the population was spawned. As many as 400 delta smelt larvae/year are analyzed. This information combined with environmental information such as food supply, water temperature, salinity, diversions, and other water quality and quantity factors improves our understanding of how environmental conditions impact delta smelt growth and survival.

Dietary requirements of delta smelt. Gut analysis of larval, juvenile and adult delta smelt are used to determine prey items and then are compared to field prey densities. All delta smelt collected in the ichthyoplankton and townet surveys are used in these analyses.

Evaluation of current and proposed gear types in order to evaluate the best method for sampling delta smelt. Recent results from the net evaluations with the standard midwater trawl and kodiak trawl indicate that the kodiak trawl is more efficient at detecting delta smelt. Additional evaluations based on this preliminary information is needed to further determine appropriate sampling techniques to answer specific research questions. It has been speculated that the boat wake affects the catch of delta smelt in a trawl that is pulled directly behind a boat. Additional testing will allow this hypothesis to be tested. Recent information suggests that delta smelt are highly surface oriented and that the presence of a boat may tend to drive delta smelt away from the sampling gear. On the other hand, a kodiak trawl which is normally fished between two boats may benefit from fish being "herded" into the sampling gear.

Since study emphasis now includes detection of individual delta smelt in specific areas of the Estuary, a different type of sampling program must be devised. A total of 13 different types of gear were initially listed for possible evaluation. To date, only three different gear types have been preliminarily evaluated.

Monitoring the distribution of post-larval/early juvenile delta smelt 20 mm in length. Currently, three specific life stages of delta smelt are sampled extensively. These include; 1) larval stages of delta smelt from 5 -15 mm in length, 2) juvenile stages from 20 -50 mm in length, and adult stages from 50 -100 mm in length. Emphasis has recently been placed on 20 mm fish because this is the length at which the salvage operations at the State and Federal Water Project Diversions become effective at capturing fish. Fish larger than 20 mm are used to estimate the "take" of delta smelt at these diversions. Losses of larval and post-larval delta smelt under 20 mm are not counted as take at these diversions. Losses of young-of-the-year delta smelt usually increase to large numbers in May, June and July. Information on the distribution of this life stage can possibly be used to make water management decisions to reduce losses at the export pumps. Additionally, information on delta smelt distribution in April, May, and June is needed to evaluate the effectiveness of the reasonable and prudent alternatives (RPA's) in the USFWS biological opinion which are designed to move early life stages of delta smelt out of the zone of influence of the export pumps.

Current sampling by the townet survey which is done June-August samples 20 mm delta smelt although that size range is at the edge of effectiveness of the net. The kodiak trawl now in use with a 1/4" stretch mesh ( 3.318 mm opening) coded probably is inefficient at catching 20 mm delta smelt which are approximately 2 mm in maximum body width or body depth. A fixed frame net (townet) fitted with a net with a mesh of approximately 1600 microns (3 times the size of a larval net) that targets 20 mm fish and allows a large portion of small debris (small larvae that are difficult to identify, Melosira, etc.,...) to pass through the net is used. The sampling locations selected roughly correspond to current summer townet sampling locations (31 stations from Suisun Bay through the Delta) with several modifications. Additional sampling stations have been added in shallow water habitats in Cache Slough, Horseshoe Bend, Franks Tract, Big Break, and Sherman Island which may act as rearing habitat within the delta.

Research on Delta Smelt/Wakasagi

Sampling of both upstream and downstream reservoirs in order to determine geographical distribution of wakasagi. The distribution and abundance of wakasagi in upstream reservoirs is unknown. Identification of sources of invasion to the Estuary are needed as well as collection of individuals of all size ranges for comparison with delta smelt. Lake Almonor as well as Oroville and Folsom reservoirs are sampled at least once a month from February through July.

Morphometric and meristic analyses of delta smelt and wakasagi. In 1994 it appears that there was a significant influx of wakasagi into the Estuary. Whether these fish have taken up residence in the Estuary or are just transported by the large amounts of water that are transferred through the Estuary is under investigation. With the possibility that wakasagi are residents in the Estuary, the threat to the delta smelt population both by the possibility of hybridization and increased competition for resources (food, spawning habitat, etc.) has increased dramatically. The ramifications of not being able to identify delta smelt to species in the field or at the fish salvage facilities are enormous when exports are limited by the ôtakeö of delta smelt at these facilities.

Morphometric and meristic differences between closely related species are well documented. This study takes 35 morphometric and 8 meristic measurements on each individual fish. In addition, individual fish that have been verified to species using electrophoresis have been available for these analyses. The final result of these analyses will be an aid to separate each species in the field.

Research on Delta Smelt by Other Institutions

Development of objective procedures to separate (identify) this species from longfin smelt during early larval stages. Dr. Johnson Wang has developed a key based on taxonomic characteristics such as morphological differences of gas bladder formation and relationship of the gut to the gas bladder. This Interagency technical report (Number 28, dated August, 1991; Wang, 1991) is currently being used in the laboratory for smelt identification. (This project has been completed.)

Modeling of delta smelt population dynamics and persistence. This project applies population dynamics techniques to compute extinction probabilities and evaluate how changes in the environment and water management might alter them. Data is used from current studies to look for spatial relationships that will aid in predicting extinction probabilities. A population dynamics model has also been produced. Dr. Loo Botsford at UC Davis was principal investigator of this project. This project has been completed.

Development of culture techniques for delta smelt. The purpose of this project to develop large-scale culture techniques for delta smelt in order to determine if large-scale hatchery production is feasible. Dr. Joan Lindberg of Biosystems Analysis is principal investigator of this project.

Investigations of the reproductive cycle and gametogenesis of delta smelt. Currently, the majority of information on delta smelt reproduction is based on related species. The purpose of this study is to investigate reproductive development and gametogenisis of delta smelt. Drs. Serge Doroshov and Randy Mager of UC Davis are principal investigators of this projects

Laboratory studies to determine the environmental tolerances of delta smelt to changes in salinity, temperature and flow. The purpose of this study is to determine minimum and maximum tolerances of delta smelt to salinity and temperature. In addition, approach velocities for screens and maximum flows at which delta smelt can maintain for specific time periods will be determined. Drs. Joe Cech and Tina Swanson at UC Davis are the principal investigators.

Investigation of the potential importance of predation by the introduced inland silversides on larval delta smelt. This study will investigate the potential importance of an invasion of inland silversides on delta smelt abundance. Dr. William Bennett is the principal investigator of this project.

Electrophoretic analysis of delta smelt and related species. The purpose of this project is to document genetic differences between delta smelt (Hypomesus transpacificus), wakasagi (Hypomesus nipponensis), and two populations of longfin smelt (Spirinchus thaleichthys). Loss of genetic integrity is considered a threat to the delta smelt population. Results suggest that delta smelt and wakasagi can interbreed, however the viability of the offspring is unknown. Drs. Bradley Schaffer and Peter Moyle are principal investigators of this project.

Condition measures to evaluate effects of toxicity and starvation on larval delta smelt. The purpose of this project is to use histological and morphometric methods to compare condition of larval delta smelt collected in the field with that of larvae held under various conditions in the laboratory. These analyses will allow evaluation of the extent to which delta smelt condition is affected by variations in their food supply, toxicity and parasites. This knowledge is important to an overall evaluation of factors responsible for the population decline and development of a recovery plan. Dr. David Ostrach at UC Davis is principal investigator of this project. This project is proposed for $99,000.

Sacramento Splittail Studies

Contact Person: Randy Baxter, (DFG) (209) 948-7800

A gill net survey targeting splittail was conducted during August 1994 to determine their summer distribution and relative abundance in Suisun Marsh, Suisun Bay, the Delta and the lower Sacramento and San Joaquin rivers. This survey also investigated some aspects of habitat use. The information gathered is important in determining the summer habitat and evaluating the status of splittail in the system. A reduced version of this study may take place in 1995.

The Summer Townet and Fall Midwater Trawl (see Section II. D.) surveys provide abundance and distribution information which has been incorporated into the recovery plans for delta smelt and splittail. The Suisun Marsh and S.F. Bay Study otter trawl surveys are part of the splittail recovery plan. The Bay Study sampling area has been expanded to include the Delta to follow low outflow distribution shifts of splittail. The USFWS beach seine work (see Section II. A.) provides important distribution information on young-of-the-year splittail.

The importance of the Sacramento and San Joaquin rivers and their tributaries as splittail spawning and early nursery areas necessitates more extensive sampling in the rivers particularly during the winter through spring period. Identification of spawning and nursery "habitats" will be a primary objective and may require additional personnel, especially if larvae or early stage juveniles are collected as evidence of spawning. Due to need for sampling "habitats", electrofishing will probably be the most effective gear. Moreover a habitat based sampling program would provide valuable information for a variety of other species.


Contact Person: Dr. Wim Kimmerer (SFSU) (510) 525-9073 Contact Person, Hydrodynamics: Mr. Larry Smith (USGS) (916) 979-2615 ext. 395

An understanding of the fundamental ecological processes (energy sources, trophic relationships, hydrodynamics, etc.) of the Bay-Delta is an important prerequisite to understanding and predicting the impacts of the estuarine management and protection efforts of IEP agencies. For this reason a significant proportion of IEP resources is devoted to program elements designed to enhance the understanding of these processes.

Hydrodynamic modeling

A new three dimensional (3-D) model of San Francisco Bay and the western Delta is being developed by USGS and USBR staff that is especially suited for the shallow-water environment of San Francisco Bay and that can be used for making long-term (at least seasonal) simulations of Bay hydrodynamics. The model will be available in 1996 for answering questions on gravitational circulation in Suisun Bay, the location of the null- entrapment zone, and the effects of the location of the 2 ppt isohaline (X2 standard) on Suisun Bay hydrodynamics. A detailed report describing the theory, numerics, and testing of the model will be completed in 1995.

The 3-D model has potential specific applicability to the Agreement in that it could be adapted for real time predictions of San Francisco Bay hydrodynamics ,including the location of X2. The anticipated future direction of this modeling effort is to extend the 3-D Bay model to include the entire delta, but not necessarily in three dimensions. A two- dimensional model of the delta is now feasible. A particle tracking component needs to be added to the 3-D model so that larval transport studies can be attempted. Calibration of the 3- D model will be an ongoing task that will continue to be worked on whenever new data is collected.

Hydrodynamic monitoring

Contact Person: Rick Oltmann or Larry Smith, USGS (916) 979-2615 x358 or x395

USGS has established a network of nine monitoring stations in the lower estuary from South Bay to Chipps Island, where water temperature and specific conductance are recorded continuously at 15-minute intervals. At four of these stations, water level is also recorded. Salinity is computed directly from specific-conductance data. Six of the stations -- San Mateo Bridge, Bay Bridge, Point San Pablo, Selby, Martinez, and Mallard Island -- record temperature and specific conductance at two depths, one near the surface and another at approximately mid- depth. In addition to the salinity and water-level stations, three meteorological stations have been operated in San Francisco Bay (San Pablo Bay, Suisun Bay, and Chipps Island) since 1988. Only the Chipps Island stations is presently being operated. It is anticipated that the salinity and water-level monitoring stations will be operated indefinitely into the future so that a long-term data base is formed. There will be an ongoing need for the data for model development and verification purposes.

A network of ultrasonic velocity meter (UVM) flow monitoring stations is being developed and operated in the Delta by USGS. The UVMs are being calibrated using a flow measuring system based on an acoustic Doppler current profiler. The present network includes 10 UVM stations; Old and Middle Rivers at Bacon Island, four sites on the Sacramento River (above the Delta Cross Channel, below Georgiana Slough, Freeport and at Rio Vista), Three Mile Slough, San Joaquin River at Jersey Point, and Dutch Slough. Analysis of UVM data is providing a better understanding of the hydrodynamics of the delta, and the data will be used to calibrate and validate the new DWRDSM 2 1-d flow model. A possible response to the Agreement could include increasing the real time availability of the Delta flow data for management purposes through telemetering. Presently the data from only one site, Old River at Bacon Island, is telemetered.