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BAY-DELTA UPPER LEVEL SYSTEM PRODUCTIVITY DRAFT CMARP PRODUCT MONITORING OBJECTIVES ! To collect biological data to improve management of San Francisco Bay and Delta resident and migratory species. ! To determine whether the CALFED actions improve the abundance, distribution, health, and feeding success of Bay-Delta resident and migratory species. Relevant CALFED Program Goals and Objectives include: Ecosystem Restoration Program Ecological Process Implementation (all sub-programs) Habitat Implementation (all aquatic, wetland, and riparian sub-programs) Species and Species Group Implementation (all aquatic sub-programs except salmon, steelhead, and delta smelt) Stressor Implementation (all aquatic sub-programs) Water Quality Program Mine Drainage Wastewater and Industrial Discharge Water Management Toxicity of Unknown Origin Watershed Management Coordination CONCEPTUAL MODEL AND/OR LISTING OF HYPOTHESES AND ASSUMPTIONS OF THE SYSTEM The monitoring program for higher level system productivity is based on the following set of assumptions: ! Implementation of CALFED Goals and Objectives will affect the abundance, distribution, health, and feeding success of higher trophic level aquatic species. ! Increases in abundance, distribution, health, and feeding success indicate a positive effect of the CALFED program. ! Suitable monitoring data will help CALFED to develop specific restoration projects for specific species and ecosystems. ! Collection of long-term monitoring data for these fish species will provide an opportunity for adaptive management. This workteam focused on 3 management goals associated with the geographic area of the Bay and Delta: 1) management of harvested populations; 2) monitoring status and trends of a representative array of estuarine species; and 3) assessing general trophic dynamics among estuarine species. The basis for the selection of species within these groups is as follows: I. Management of harvested populations emphasizes particular species. Harvested 10/14/98 Draft 1 species included in this category are summarized in Table 1 along with adequacy of existing monitoring programs for different life history stages. The species addressed by this team include: striped bass, American shad, white and green sturgeon and various catfishes. Also included are some macroinvertebrates, as Dungeness crabs and crayfish. Species which fall within this category, but are addressed by other workteams include centrarchids, salmon, steelhead, and the edible clams of the estuary. Population management requires in-depth knowledge of the full life cycle of the species of interest, unless it can be ascertained that some life-cycle stage is never limiting. II. Monitoring status and trends of estuarine species requires tracking abundance and distribution of a broad array of Arepresentative@ species throughout the estuary. In contrast to managing harvested species, this management goal can be satisfied by sampling a single, sensitive life stage of each species. To meet this goal, a broad geographic area should be sampled with a diverse array of sampling gears so that no habitat or type of species is omitted. Over 165 species of fishes have been collected from the estuary (Appendix 1); however, target species for status and trends sampling comprise only a subset of the most common fishes and invertebrates (Table 2). Common species which are addressed by other workteams include tule perch, inland silverside, rainwater killifish and mosquitofish (Shallow Water Habitat Team), wakasagi (Delta Smelt Team) and hardhead, Sacramento sucker and hitch (River Resident Fishes Team). III. Assessing general trophic dynamics among estuarine species requires knowledge of dietary patterns and selection of species that represent common feeding strategies. Conceptual food web models for the Delta, Brackish and Polyhaline regions are provided in Figures 1-3. Selected species should be abundant enough to be sampled reliably and to have a significant effect within the ecological community. Some monitoring might also include generic measures such as isotope ratios. Lower trophic levels are included in the charge of other workteams. We include 5 categories of species that feed directly upon the lower trophic levels: 1) planktivores such as northern anchovy and American shad; 2) nearshore piscivores such as centrarchids; 3) open channel piscivores such as striped bass; 4) benthic feeders such as splittail, crayfish, starry flounder and caridean shrimps and 5) Apickers@ such as juvenile centrarchids and inland silverside. Species associated with edge habitats such as salmon, tule perch, shiner perch, and inland silverside are covered by the Shallow Water Habitat Team. As a result, nearshore Apickers@ were included in the conceptual model of the food chain, but were not considered for monitoring by this team. 10/14/98 Draft 2 MONITORING PLAN ELEMENTS Measurement of abundance is the primary element of the monitoring plan. Depending on the fish species, the abundance of one or more life stages would be monitored. In addition, distribution, diet/feeding success and health would also be used as indicators for some species. For the purposes of this monitoring plan, the system would be divided into sub-areas (e.g., west Delta, central Delta, north Delta) and distribution would be examined based on the changes in abundance of a given species before and after the CALFED program is implemented. The following summarizes existing programs that would be included as part of the core sampling program and new monitoring that would be required to measure abundance, range and health and to describe food web relationships. Existing Monitoring Monitoring for existing programs is summarized in Table 3. Details about these elements are provided below. The California Department of Fish and Game (CDFG) Fall Midwater Trawl Survey (FMWT) samples 87 stations from San Pablo Bay to Rio Vista on the Sacramento River and Stockton on the San Joaquin River (Stevens and Miller 1983). Currently 116 stations are sampled of which 100 are used for indexing abundance and 16 are sampled to detect the limits of delta smelt distribution. Each station is sampled monthly from September through December using a 17 m-long midwater trawl with a 3.7 m2 mouth. An annual abundance index is calculated as the sum of monthly indices for subareas of the system. To calculate monthly indices, catch per trawl is averaged for stations within each subarea, multiplied by a volumetric estimate for the subarea, then summed across all subareas. The CDFG Bay Study samples 52 stations from south San Francisco Bay to the western Delta using both midwater and otter trawls; 35 of these stations are used for indexing abundance (Armor and Herrgesell 1985). The midwater trawl is the same as used by the FMWT; the otter trawl has a 4.9 m head rope and 3mm mesh codend. Annual abundance indices are calculated for each net as the average of monthly indices. Monthly indices are calculated similarly to the FMWT, except that average catch per 10,000 m3 and average catch per 10,000 m2 were calculated for the midwater and otter trawls, respectively, rather than average catch per trawl. The University of California at Davis samples 7 sloughs in Suisun Marsh using an otter trawl similar to that of the CDFG Bay Study survey (Moyle et al. 1986). For splittail, a monthly abundance index is calculated as the sum of the mean catch per trawl for each of the seven sloughs in the Marsh. Annual abundance indices are calculated as the mean of the monthly values. The USFWS Chipps Island survey samples a single location in the channel at 10/14/98 Draft 3 Chipps Island using a midwater trawl towed at the surface. Ten 20-minute tows are made each day, but the number of days sampled per week varies by month. The Central Valley and State Water projects operate louver facilities to direct fish away from the export pumps (Brown et al. 1996). Salvaged fish are counted year-round at 2-hour intervals when the pumps are operating. Fish salvage data from these facilities are considered a valuable source of abundance data for the system (Stevens and Miller 1983). For splittail, abundance indices are based on the total salvage divided by the volume of water exported during the time periods when each life stage is most abundant at the facilities. The USFWS beach seine survey is used to develop both abundance and distribution indices for salmon and other species. Beach seine sampling began in 1976. It is presently conducted on a year-round basis, with single hauls of a 50-foot, 1/8" mesh minnow seine taken on each sampling date at (in 1998) 46 shore stations throughout the Sacramento-San Joaquin Delta and at shore stations along the Sacramento River as far north as Red Bluff. In the early years, routine sampling at most stations was done only during the late winter/early spring months. All fishes taken in a haul are identified to species and, in most cases, measured for fork length. The panel of stations visited in the beach seine program has changed substantially since the program's inception in 1976. A core set of 13 stations has been visited at least once during January -- March in each year the program has operated, and an additional 13 stations have been visited at least once during the first quarter of each year since 1982. In addition, approximately 100 other stations have been sampled during at least one year, and some of these stations have a sampling history spanning a substantial part of the full life of the program. Several of the core stations have been moved a short distance from their original locations because of riprap construction. The core set of stations is widely distributed, with most stations lying on the lower Sacramento River, the North Delta, the Central Delta, and, more recently, on the San Joaquin River, where the number of stations was substantially increased in 1994. Adult striped bass abundance is monitored by the CDFG with a mark-recapture study in which 5,000-10,000 legal-sized (> 18 inches TL) striped bass are tagged with disk-dangler tags and released during their annual spring spawning migration to fresh water. Gill nets in the western Delta and fyke traps in the Sacramento River near Knights Landing are used to capture the fish. All legal-sized bass caught are counted and all tag recaptures from tagging in previous years are recorded. All tagged fish are aged from annuli on the scales. Recapture samples obtained during tagging are augmented by a year-round creel census which samples throughout the estuary. A sample of striped bass observed in the creel census is measured, sexed, and scale sampled and all tag recaptures are recorded. Fish seen in the creel census are aged from annuli on the scales. A computer-generated age-length key is used to estimate the age composition of all legal-sized striped bass caught during tagging and observed in the creel census. The tagged:untagged ratio in the recapture samples and the number of striped bass tagged is used to calculate mark-recapture Petersen population estimates 10/14/98 Draft 4 stratified by sex and age. Legal-sized age 3 and age 4 abundance is used to estimate recruitment to the legal-sized population. The past practice of annual tagging changed to alternate-year tagging in 1995 as the result of an evaluation of the adequacy of biennial population estimates for monitoring trends in legal-sized striped bass abundance. 10/14/98 Draft 5 Sturgeon abundance is monitored by the CDFG with a mark-recapture study in which 250-2,500 legal-sized (46B72 inches TL) sturgeon are captured in trammel nets in San Pablo Bay in the fall and tagged using disk-dangler reward tags. Tagging is not conducted every year; the most recent tagging was in 1998 and is not planned again until 2001. Sturgeon are measured and release location, tagger, date, and condition of the fish recorded. All tag recaptures in the trammel nets are recorded and used, in conjunction with the number tagged, to estimate sturgeon abundance using a multiple census (for same-year recaptures) or Petersen (for recaptures from previous years' tagging) technique. Juvenile sturgeon abundance is monitored by the CDFG using baited set-lines to capture ages 1-7 (12-36 inches TL) juvenile sturgeon in the delta, Suisun Bay, and San Pablo Bay. Each set-line consists of a 1800-foot ground line along which 80-100 gangions are attached. Each gangion consists of a halibut snap, a 3-4-foot leader, and a single baited hook. Sampling takes place for 3 months between July and November. Each month, three set-lines are fished simultaneously for about 24 hours until 21 locations are sampled. Juvenile sturgeon captured incidentally by the adult striped bass tagging program (using gill nets in the western delta during April and May) or the adult sturgeon tagging program (using trammel nets in San Pablo and Suisun bays in September and October) are added to the catch to increase the sample size. A subsample of juvenile fish is aged using a section of the pectoral fin and the resulting age-length key is used to assign ages to the entire catch. An index of year-class strength for white sturgeon is calculated from these age composition data to establish long-term trends in white sturgeon production. Juvenile green sturgeon are infrequently captured in this survey and their abundance is not indexed. Abundance of resident nearshore delta fishes (centrarchids, cyprinids, and ictalurids, primarily) is monitored by the CDFG with boat-mounted electrofishing gear at 20 locations in February, April, June, and August in alternate (odd-numbered) years. Sampling is stratified by area of the delta so that five sites are surveyed in the east and central delta, three sites each in the north and west delta, and four sites in the south delta. This stratification of effort corresponds approximately with the relative abundance of resident fishes in each area as determined from random sampling in 1980- 1983. Fishes are collected by habitat type at each sampling site. Population trends and community structure will be determined using univariate and multivariate statistical analyses. The Real Time Monitoring program is conducted to provide data for adaptive management of the export facilities to minimize impacts to aquatic species. The intensive field portion of sampling starts April 1 and continues through June 30 of each year. The real time monitoring program consists of three parts: 1)enumeration of fish salvaged at the CVP (Central Valley Project) and SWP (State Water Project) fish salvage facilities; 2) collection of fish from strategically selected sites within the Delta, and 3) Delta wide fish distribution survey targeting small juvenile fish. Data reported by the program comes from 7 sample sites located throughout the Delta, where fish are 10/14/98 Draft 6 collected using midwater trawls, Kodiak trawls and a 20mm net (See Table 1). Sampling with the 20mm net takes place only when the bimonthly delta smelt 20mm survey indicates the presence of juvenile delta smelt in the central and southern delta. The bimonthly geographic survey targeting small delta smelt using a 1 mm mesh tow net is reported under the 20mm Delta Smelt Study. An integral part of the real time monitoring program is an active feedback loop that adjusts sampling effort based on the collection of the special status species, delta smelt, splittail and winter-run size chinook salmon. Additional monitoring is conducted to support the Vernalis Adaptive Management Plan (VAMP). VAMP is being implemented to provide protective measures for fall-run chinook salmon and to gather scientific information on the effects of various flows in the lower San Joaquin River, Central Valley Project and State Water Project export pumping rates, operation of a fish barrier, and survival of salmon smolts through the Delta. Sampling includes kodiak trawling in the south Delta and releases of coded-wire-tagged juvenile salmon during flow studies. Proposed Additional Sampling The existing programs are exceptionally valuable because they provide a long-term baseline for the evaluation of CALFED actions and management of several sport and commercial species. However, this sampling is insufficient to address the full suite of CALFED monitoring objectives. As a result, we include recommendations for new monitoring associated with the three previously-described management goals. An overall summary of the additional monitoring elements is provided in Table 4. Details about rationale and possible methods are described below. Harvested Species: Data for several species and life stages are inadequate for effective management. These are indicated by bold face numbers in Table 1. Details of the proposed changes in sampling or new sampling efforts are as follows. ! American shad. Measures of the CLUE of American shad adults may be obtained from the new Central Valley and Anadromous Creel Survey which was initiated in 1997, as well as from catches in the gill nets and fyke traps used for capturing adult striped bass for tagging in the spring. Correspondence between these measurements may indicate whether such data are useful annual measures of relative abundance of adults. Some additional resources may be needed to extract these data from existing catch records. ! White sturgeon: More precise estimates of adult fish abundance can be obtained by increasing tagging effort to two consecutive years in each three year period and by doubling the tagging effort by using two boats. Measurement of potential juvenile recruitment and relative year class strength can be improved by increasing the trawling effort in the lower Sacramento River and Suisun Bay for YOU and juvenile sturgeon. ! Green sturgeon: All life stages of green sturgeon are inadequately sampled. It is 10/14/98 Draft 7 unlikely that we can ever capture enough adults to adequately measure abundance. Measurement of spawning success may be possible by using fyke traps for YOU at the Red Bluff Diversion Dam on the Sacramento River. Eggs and larva could be sampled using artificial substrates and nets fished from boats in the upper Sacramento River and Feather River. 10/14/98 Draft 8 ! Striped bass: Improvements could be made in understanding inshore shallow water distribution and abundance of YOU striped bass and their distribution and abundance downstream in years of high outflow. Status and Trends Species: Some of the Status and Trend species are presently sampled insufficiently due to habitat preferences or gear efficiencies (Table 5). These under sampled species fall into 3 categories: 1) those using the Bay-Delta primarily as large-sized juveniles and adults (e.g., sharks, skates and rays, Sacramento pikeminnow, hitch, Sacramento blackfish); 2) those using rocks, pilings and other structure as habitat (e.g., several species of surfperches, brown rockfish, all centrarchids); and 3) those captured well by present methods, but whose distribution includes large areas Abetween@ present surveys (e.g., benthic species in the Delta and species commonly found at depths from 1 to 3 m downstream of the Delta). Sampling fishes in category 1 can be accomplish through a combination of expanding the focus and protocols of present programs and addition of some new ones. Present adult striped bass and sturgeon sampling employs gill nets and trammel nets in the Delta and San Pablo Bay, respectively (also fyke traps in the Sacramento River). Each of these gears captures a suite of adult fishes, but limited funding precludes collecting data for non-target species. Moreover, for sufficient coverage, gill net and trammel net sampling should be expanded to include locations in all embayments and a broader variety of channel and shoal habitats. Additional monitoring could include health indexing a subset of fishes from the representative species list (i.e., leopard shark, white sturgeon and California halibut) and regular creel census surveys downstream of the Delta. Sampling fishes in category 2 is accomplished in shallow water (<2.5 m) of the Delta by the resident fish survey, but should extend to include deeper water habitats of the Delta and areas downstream of the Delta, as no such sampling takes place in brackish or marine waters. To effectively sample in habitats with structure, additional methods are required such as baited traps in combination with bait angling and creel census surveys. Selected methods should be employed in the Delta and throughout the downstream embayments. Sampling fishes in category 3 may be dealt with by the Shallow Water Habitat Fishes workteam. Present sampling techniques, primarily beach seining and electrofishing, need to extend to deeper water. However, as the survey should be estuary-wide, electrofishing is precluded as a sampling technique for all areas. Longer beach seines or purse seines set by boat can complement sampling for category 2 if employed throughout the estuary. Food Chain Sampling: Recommended sampling for food chain monitoring in three regions of concern is summarized in Tables 6-8. Distribution and abundance data for several species such as splittail, delta smelt, longfin smelt and striped bass are already being collected by existing sampling programs. Although delta smelt and threadfin shad are included as components of monitoring proposed by this team, more comprehensive monitoring would be provided by the Delta Smelt and Shallow Water Habitat Teams, respectively. Body burden data would be used to examine bioaccumulation of toxins through the food chain. Diet monitoring has been ongoing for YOU striped bass since 1973 and for fall caught juveniles since 1996. These data are currently being evaluated. As part of the striped bass stocking management program the diets of subadult age 1 and 10/14/98 Draft 9 age 2 fish will be monitored. Diet monitoring would include techniques such as gut fullness, prey weights and frequency of occurrence. RESEARCH Recommended research topics were developed for each of the 3 species categories (Tables 9-11). Research topics included in this summary include the following: ! Studies to improve the previously-described monitoring programs. ! Studies to develop new monitoring indicators. ! Studies to provide the foundation for the monitoring of future species (e.g., zebra mussels). ! Studies to analyze and interpret data collected by the previously-described monitoring programs. INDICATORS The indicators to be tracked include abundance, distribution, body burdens and diets for species described for the Monitoring Elements (Tables 6-8). Research studies are included to identify the need for additional measurements such as physiological indicators (Table 11). LINKS The monitoring program in the present plan is designed as a system-wide evaluation for selected species. Additional abundance information for other locations and species would be developed from other CMARP groups such as the Shallow Water Habitat, River Resident Fishes, Delta Smelt and Contaminant workteams. 10/14/98 Draft 10 REFERENCES Armor, C., and P.L. Herrgesell. 1985. Distribution and abundance of fishes in the San Francisco Bay Estuary between 1980 and 1982. Hydrobiologia 129: 211-227. Brown, R, S. Greene, P. Coulston, and S. Barrow. 1996. An evaluation of the effectiveness of fish salvage operations at the intake to the California aqueduct, 1979-1993. J.T. Hollibaugh (ed.). 1996. San Francisco Bay: The Ecosystem. Proceedings of the San Francisco Bay Symposium, 75th Annual Meeting, Pacific Division American Association for the Advancement of Science, June 20-24, 1994. Published by Pacific Division, AAAS. Miller, L.W. 1977. An evaluation of sampling nets used for striped bass and Neomysis in the Sacramento-San Joaquin Estuary. California Department of Fish and Game, Anadromous Fisheries Branch Administrative Report, No. 77-3, 29 pp. Moyle, P.B., R.A. Daniels, B. Herbold, and D.M. Baltz. 1986. Patterns in the distribution and abundance of a non-coevolved assemblage of estuarine fishes. U.S. National Marine Fisheries Service Fishery Bulletin 98: 105-117. Sommer, T.R., R. Baxter and B. Herbold. 1997. The resilience of splittail in the Sacramento-San Joaquin Estuary. Transactions of the American Fisheries Society 126: 961-976. Stevens, D.E., and L.W. Miller. 1983. Effects of river flow on abundance of young chinook salmon, American shad, longfin smelt, and delta smelt in the Sacramento-San Joaquin River system. North American Journal of Fisheries Management 3: 425-437. 10/14/98 Draft 11 Table 1. Current monitoring of harvestable stocks of recreational and commercial fish species. Adequacy of monitoring is scaled from 1 to 5, where 1 designates monitoring adequate to manage the population, and 5 indicates no monitoring. NA means not applicable because that life stage is not readily sampled. Bold face indicates where more information would be desirable to manage the populations. Species Life Stage Remarks Adult Egg Young-of- Immature (YOU and the-year to adult) larva (YOU) striped bass 2 5 1 4 2 measures in Townet, summer and fall FMWT for YOU American shad 4 5 2 NA DFG, creel census DFG FMWT measure of CLUE white sturgeon 2 5 4 3 DFG tagging Bay Study, DFG longline green sturgeon 5 5 5 5 catfishes 4 NA 4 4 centrarchids- 3 NA 4 3 DFG, resident fish largemouth electrofishing bass, bluegill, et al. crayfish 4 NA 5 4 CLUE, fishery CLUE, fishery leopard shark 4 NA 5 4 MRFSS data embiotocids- 3 NA 4 4 MRFSS data shiner perch, Bay Study et al. flatfishes - 4 5 4 4 California CPFV, DFG Bay Study Bay Study halibut, starry flounder, et al. bay shrimp 2 5 2 2 Bay Study Bay Study Bay Study Pacific herring 1 3 2 5 DFG - Marine 10/14/98 Draft 12 Resources Bay Study Table 2. Common San Francisco Bay and Delta fish and macroinvertebrate species. Status and trends Arepresentative@ species are bolded; current and proposed sampling for these species is detailed in Table 6 and the text. FISHES black bullhead, S arrow goby, S brown bullhead bay goby Pacific lamprey channel catfish, R cheekspot goby, S river lamprey white catfish longjaw mudsucker, S shimofuri goby bat ray, S rainwater killifish, S yellowfin goby big skate brown smoothhound western mosquitofish, S Pacific staghorn leopard shark, S sculpin inland silverside, S prickly sculpin*, S, R white sturgeon jacksmelt, S topsmelt, S California halibut, S American shad California tonguefish Pacific herring threespine stickleback, S English sole Pacific sardine speckled sanddab threadfin shad, S bay pipefish* starry flounder, S northern anchovy brown rockfish* INVERTEBRATES Chinook salmon, S, R striped bass Crangon franciscorum steelhead, R C. nigricauda white croaker C. nigromaculata delta smelt, S Palaemon macrodactylus longfin smelt black crappie, S wakasagi, S bluegill, S, R Cancer antennarius*, green sunfish, S S plainfin midshipman largemouth bass, S, R C. gracilis redear sunfish, S C. magister, S carp, S, R white crappie, S C. productus*, S golden shiner, S, R Carcinus maenas*, S hardhead, S, R bigscale logperch, S, R Eriocheir sinensis, S hitch, S, R Sac. blackfish, S, R pile perch, S Pacifastacus Sac. pikeminnow, S, R shiner perch, S leniusculus* splittail, S, R tule perch, S Procambarus clarkii, S walleye surfperch, S Sacramento sucker, R white seaperch, S * = Juveniles and/or adults are not be sampled effectively by current sampling program due to habitat preferences (e.g. eelgrass, rocky reefs, structure). S = A significant portion of the juvenile or adult population is in shallow water (<3 m). Although all of the life stages would not be sampled effectively by a deeper water survey, older fish of some species do move to deeper water and could be effectively captured by the existing or proposed sampling program. R = Species is distributed in the rivers and Delta; a Delta only monitoring program may not be 10/14/98 Draft 13 sufficient for these species. 10/14/98 Draft 14 Table 3. Fish and invertebrate monitoring by IEP in 1999. Key to schedule symbols: m=monthly b=biweekly w=weekly s= as scheduled 1-7 =days per week Habitat/ species Method Sampling Number of J F M A M J J A S O N D Variables measured Comments history sites or stations Freshwater and townet Since 1959 31, San Pablo b b b Environment: water No changes from historical estuarine YOU fish; (except Bay through transparency (secchi), survey. e.g. striped bass, delta 1966,1983) Delta temperature, tide stage, smelt. EC (surface and bottom). Biol: catch, abundance indices. Freshwater and Midwater Since 1967 about 100 m m m m m m m m Env: water transparency, Fall surveys include San estuarine YOU fishes; trawl (except 1974, current index tide stage, temperature, Pablo Bay. Spring surveys e.g. striped bass, delta 1979) stations, plus EC (surface and bottom), for delta smelt from Suisun smelt, longfin smelt, added delta boat velocity relative to Bay upstream. American shad, smelt stations water. Biol: catch, fish splittail. since 1991 length (subsample), abundance indices. Marine and estuarine otter trawl Since 1980 52 core Bay m m m m m m m m m m m m Environment: water Bay shrimp consists of fishes and Study stations, transparency, water profile Crangon franciscorum, invertebrates; e.g. bay South SF Bay of temperature and EC, C. nigromaculata, shrimp, Dungeness through West tide stage. Biol: catch, fish C. nigricauda, and crab, YOU: English Delta. length, shrimp and crab Palaemon macrodactylus. sole, shiner perch, sex and length, abundance other surfperches, indices. white croaker. Juvenile: white sturgeon and starry flounder. Marine and estuarine midwater Since 1980 52 sites-South m m m m m m m m m Environment: water Overlaps with the Fall fishes; e.g. YOU trawl Bay through transparency, water profile Midwater Trawl Survey. Pacific herring, the West Delta of temperature and EC, September -December jacksmelt. tide stage. Biol: catch, fish from mid-San Pablo Bay to longfin smelt, length, abundance indices. Western Delta. northern anchovy-all. 10/14/98 Draft 15 Table 3. (continued) Fish and invertebrate monitoring by IEP in 1999. Key to schedule symbols: m=monthly b=biweekly w=weekly s= as scheduled 1-7 =days per week Habitat/ species Method Sampling Number of J F M A M J J A S O N D Variables measured Comments history sites Adult striped bass gill nets Since 1969 Lower San 5 5 Env: temperature. Biol: As of 1995, reduced Joaquin R. catch, fish length, sex, tagging in gill nets and fyke release condition. Pop. traps to every other year size, mortality, fishery (even numbered years). contribution -stocked fish. Adult striped bass fyke traps Since 1969 Sacramento 5 5 5 Env: temperature. Biol: Originally fished at river at Same as gill nets, plus Clarksburg 1969-1988; Knight's catch of species other than Freeport, 1989; Knights landing. 1 site. striped bass. Landing 1990-present Adult striped bass creel creel and tag Ports and s s s s s s s s s s s s Biol: catch, sex, age, and Creel census, unlike census: tag recovery since landing length composition, tagging, will be done every recovery 1969; hatchery facilities CLUE, mortality rates, year to evaluate stocking and evaluation since throughout the tagged: untagged ratios program and recover tags. hatchery 1983. estuary and for population estimates evaluation. Sacramento and hatchery evaluation. River. white sturgeon - trammel 1954, 1967, San Pablo Bay 5 5 Biol: catch, length, CLUE, adults net 1968, 1974, mortality rates, 1979, 1984, abundance, movements, 1985, 1987, catch of other species. 1990, 1991, 1993, 1994 1997,1998 white sturgeon - setline, 1991,1995 Western Delta, Biol: catch, length, age, Otter trawl sampling done juveniles otter trawl 1980-1998 Suisun Bay, CLUE. by Bay-Study. Additional San Pablo Bay. bottom trawl sampling planned if feasible. 10/14/98 Draft 16 Table 3. (continued) Fish and invertebrate monitoring by IEP in 1999. Key to schedule symbols: m=monthly b=biweekly w=weekly s= as scheduled 1-7 =days per week Habitat/ species Method Sampling Number of sites J F M A M J J A S O N D Variables measured Comments history Resident fish Electro- 1980-1984, Presently: m m m m Env: Temperature, EC, As of 1995, survey centrarchids, fishing boat 1995, 1997 East delta: 5 water transparency, alternates every other cyprinids, West Delta: 3 turbidity, habitat year with adult striped catostomids, North Delta: 3 description. Biol: catches bass tagging program ictalurids, etc. South Delta: 4 and length composition of (odd numbered years). Central Delta: 5 fish at randomly selected transects. Largemouth bass movements and mortality rates. chinook salmon- Midwater Clarksburg, Sacramento 3 3 3 3 3 3 Environment: smolts trawl Hood; 1976- (MWT) temperature, secchi. Biol: American shad (MWT), 1981, small Sacramento catch, length, annual small MWT MWT; (Kodiac trawl) 4 4 3 abundance index. is 6' x 15'; Sacramento, 4 4 4 large MWT 1988-1995, Chipps Island 3 3 3 3 is 10'x30' small 7 5 Kodiac trawl Mossdale 3 3 5 7 3 MWT; 7 Chipps island 1976-1999, 3 3 large MWT. 3 chinook salmon-fry Beach seine 1976-1995 Sacramento- Environment: Sampling targets inland silverside-all Colusa : 9 w temperature.. chinook smolts, but also splittail-YOU, North D: 10 w w w w w w w w w w w w Biol: catch, length, is the likely best Delta smelt Central D: 9 w w w w w w w w w w w w indicator of YOU Since 1991 South D: 10 w w w w w w b b w w w splittail and inland Since 1993 San Joaquin: 8 w w w w w w b b w w w silverside. S.F. Bay m w w w w w b b m m m m m m m m m m m 10/14/98 Draft 17 Table 4. Summary of new monitoring elements to supplement the existing core sampling program. Species shown in italics would be addressed in more detail by other CMARP teams. Body Tropic Level Species Distribution Abundance Burdens Diets Planktivores delta smelt X juvenile striped X bass X American shad X X X threadfin shad X northern anchovy X X jacksmelt/topsmelt X Pacific herring Bottom splittail X X Feeders carp X prickly sculpin X X X white catfish X white sturgeon X X X X green sturgeon X X gobies X X X starry flounder X X X leopard shark X white croaker Pelagic striped bass>2 X X Predators years centrarchids X Benthos Potamocorbula X X X Others X X X Plankton X X Epibenthos crayfish X X X crabs X X X Bay shrimp X 10/14/98 Draft 18 Table 5. Current monitoring of status and trends fishes and macroinvertebrates. Adequacy of current monitoring is scaled from 1 to 5, where 1 designates monitoring adequate evaluate the status of a population, and 5 indicates no monitoring. Bold face indicates where more information would be desirable. Species Trophic Distribution Age classes most Adequacy of sampling role effectively sampled by current fishery SoB CB SPB SuB Del monitoring programs Distribution Abundance leopard shark benthic ! ! $ age-1 - subadults 4 4 white sturgeon benthic $ $ ! ! ! age-3+ subadults=3 subadults= adults=2 3 adults=2 American shad planktivor $ ! ! ! age-0 3 2 e Pacific herring planktivor ! ! ! $ age-0, adults age-0=2 age-0=2 e adults=2 adults=1 northern anchovy planktivor ! ! ! $ age-0, age-1 2 2 e longfin smelt planktivor $ $ ! ! ! all 2 2 e plainfin midshipman benthic ! ! ! $ age-0 2 3 splittail benthic $ ! ! age-0 3 3 white catfish benthic ! age-0 - age-6 4 4 jacksmelt picker ! ! ! $ age-0 3 3 10/14/98 Draft 19 brown rockfish benthic ! ! $ age-0, age-1 4 4 striped bass planktivor $ $ ! ! ! age-0, adult age-0=2 age-0=2 e, predator adult=1 adults=2 white croaker benthic ! ! ! $ all 2 2 shiner perch picker ! ! ! $ age-0, age-1 3 4 bay goby benthic ! ! ! $ all 2 2 shimofuri goby benthic $ $ ! none 5 5 yellowfin goby benthic $ $ ! ! ! age-0, age-1 3 3 Pacific staghorn sculpin benthic ! ! ! ! $ age-0, age-1 3 3 prickly sculpin benthic $ $ ! all 4 4 California halibut benthic ! ! ! $ age-0 - age-2 4 4 English sole benthic ! ! ! $ age-0 2 2 starry flounder benthic $ $ ! ! ! age-0 - age-2 3 3 Crangon franciscorum benthic ! ! ! ! $ all 2 2 Cancer antennarius benthic ! ! $ age-0 4 4 Cancer magister benthic $ ! ! ! age-0 3 2 Eriocheir sinensis benthic ! $ ! ! age-1+ 3 3 Pacifastacus leniusculus benthic ! none 5 5 10/14/98 Draft 20 Table 6. Summary of species suggested for Delta food chain studies. The adequacy of existing sampling to monitor distribution and abundance is indicated on a 1 (adequate)- 5 (inadequate) scale. Bold numbers indicates that additional distribution or diet monitoring is proposed. Species shown in italics would be addressed in more detail by other CMARP teams. DELTA Body Tropic Level Species Distribution Abundance Burdens Diets Planktivores delta smelt 2 2 X juvenile striped bass 1 1 X threadfin shad 3 4 X X longfin smelt X Bottom splittail 3 2 X X Feeders carp ? ? X prickly sculpin 5 5 X white catfish 2 2 X white sturgeon 4 4 X X Pelagic striped bass>2 3 2 X X Predators years Benthos 5 5 X Plankton 4 4 Epibenthos crayfish 5 5 X crabs 5 5 X 10/14/98 Draft 21 Table 7. Summary of species suggested for brackish water food chain studies. The adequacy of existing sampling to monitor distribution and abundance is indicated on a 1 (adequate)-5 (inadequate) scale. Bold numbers indicate that additional distribution or diet monitoring is proposed. Species shown in italics would be addressed in more detail by other CMARP teams. BRACKISH Body Tropic Level Species Distribution Abundance Burdens Diets Planktivores delta smelt 2 2 X longfin smelt 2 2 X juvenile striped 1 1 X X bass Bottom prickly sculpin 4 4 X Feeders gobies 4 4 X starry flounder 3 3 X X Pelagic striped bass>2 3 2 X X Predators years Benthos gobies 3 4 X starry flounder 4 5 X Plankton 3 3 Epibenthos Bay shrimp 3 3 ? 10/14/98 Draft 22 Table 8. Summary of species suggested for polyhaline food chain studies. The adequacy of existing sampling to monitor distribution and abundance is indicated on a 1 (adequate)-5 (inadequate) scale. Bold numbers indicate that additional distribution or diet monitoring is proposed. POLYHALINE Body Tropic Level Species Distribution Abundance Burdens Diets Planktivores northern anchovy 1 2 X jacksmelt/topsmelt 3 3 X X Pacific herring 3 4 Bottom white croaker 2 2 X Feeders starry flounder 3 3 X X Pelagic striped bass>2 yrs 2 2 X Predators Benthos Potamocorbula 3 4 X Others 5 5 X Plankton 3 3 Epibenthos rock crabs 4 4 X Dungeness crab 3 3 X Bay shrimp 10/14/98 Draft 23 Table 9. Research topics for harvestable species. Topic Research question Species Various species Refine/develop techniques to monitor All distribution and abundance. Microhabitat Develop sampling techniques for habitat types striped bass not adequately sampled, e.g., marshes, downstream areas in high flow years, shallow water. Eggs and larvae What factors control abundance, distribution, striped bass mortality and growth of larval fish and egg survival? YOU What are the relative importance of white sturgeon environmental factors and spawning stock size green sturgeon on year class strength? What factors are responsible for much lower striped bass than expected abundance indices in recent high-flow years? Juveniles What is the cause of the apparent density- striped bass dependent relationship? Develop sampling techniques to adequately measure abundance during the first year of white sturgeon life. Adults What are acceptable harvest rates and are All present harvest rates sustainable? To what extent is variability in white sturgeon white sturgeon population estimates due to sampling error and to migration and extended residence outside the estuary? 10/14/98 Draft 24 Table 10. Research topics for status and trends species. Topic Description of need Species Quantitative Develop gear and techniques to better assess fish numbers per all Sampling m2 or m3, including fixed mouth trawls and studies to assess avoidance (information needed to estimate absolute abundance of small, short-lived species and to facilitate comparison with restoration monitoring). Microhabitat Develop gear and techniques for habitat types not adequately To be sampled: rocks/riprap, eel grass, emergent and submerged determined vegetation, pier pilings etc. Fish Growth Assess and/or develop techniques to monitor growth and To be and condition factor: otolith to total length growth relationships; determined Condition length-weight relationships; RNA/DNA ratios; feeding success (i.e., stomach fullness) etc. Such techniques will be necessary to assess the condition of a species at a point in time, possibly before a decline in abundance, and to assess the benefits of habitat restoration sites relative to monitoring sites at a point in time (necessary because target species may be transient at site). Sampling Develop gear and techniques suitable for sampling in restored All Restored habitats that may be added to monitoring surveys to allow Habitats comparison of density or relative abundance between sites. Seasonal Develop studies to assess the impact of seasonal variation in All Variation in distribution on abundance indices, and develop hypotheses and Distribution studies to detect factors affecting changes in seasonal distribution. 10/14/98 Draft 25 Table 11. Research topics for food chain issues. Topic Research question Species Distribution Refine/develop techniques to monitor threadfin shad, and Abundance distribution and abundance. Examples include prickly sculpin, studies of temporal, spatial and geographic white sturgeon, variation. benthos, plankton, crayfish, crabs. Mapping of substrate and structures in the Species not well Estuary covered by existing sampling (e.g. pier piling communities) and potential future invaders (e.g. zebra mussels) Diets Studies on seasonal, temporal and geographic delta smelt, variation. striped bass, threadfin shad, Examine physiological techniques to analyze splittail, prickly feeding success: histology, DNA, lipids, etc. sculpin, white sturgeon. Carbon studies on sources, mobilization. Possible techniques include isotope ratios and To be microbial studies. determined. Develop a conceptual model of carbon pathways from studies described above. To be determined. Body burdens Analyze mechanisms of uptake, pathways for Threadfin shad, trophic accumulation. splittail, carp, white catfish, Develop conceptual or quantitative models for white sturgeon, trophic accumulation. striped bass, benthos, crayfish, Examine physiological effects: e.g. disease, crabs. feeding and reproductive success. 10/14/98 Draft 26 Appendix 1. Fish species collected from San Francisco Bay and Delta. COMMON NAME SCIENTIFIC NAME FAMILY American eel Anguilla rostrata Anguillidae American shad Alosa sapidissima Clupeidae arrow goby Clevelandia ios Gobiidae barred surfperch Amphistichus argenteus Embiotocidae bat ray Myliobatis californica Myliobatididae bay goby Lepidogobius lepidus Gobiidae bay pipefish Syngnathus leptorhynchus Syngnathidae big skate Raja binoculata Rajidae bigscale logperch Percina macrolepida Percidae black bullhead Ameiurus melas Ictaluridae black crappie Pomoxis nigromaculatus Centrarchidae black perch Embiotoca jacksoni Embiotocidae black rockfish Sebastes melanops Scorpaenidae blackeye goby Coryphopterus nicholsi Gobiidae blue catfish Ictalurus furcatus Ictaluridae blue lanternfish Tarletonbeania crenularis Myctophidae blue rockfish Sebastes mystinus Scorpaenidae bluegill Lepomis macrochirus Centrarchidae bonehead sculpin Artedius notospilotus Cottidae brown bullhead Ameiurus nebulosus Ictaluridae brown Irish lord Hemilepidotus spinosus Cottidae brown rockfish Sebastes auriculatus Scorpaenidae brown smoothhound Mustelus henlei Carcharhinidae brown trout Salmo trutta Salmonidae cabezon Scorpaenichthys marmoratus Cottidae calico surfperch Amphistichus koelzi Embiotocidae California halibut Paralichthys californicus Bothidae California lizardfish Synodus lucioceps Synodontidae California roach Hesperoleucus symmetricus Cyprinidae California skate Raja inornata Rajidae California tonguefish Symphurus atricauda Soleidae chameleon goby Tridentiger trigonocephalus Gobiidae channel catfish Ictalurus punctatus Ictaluridae cheekspot goby Ilypnus gilberti Gobiidae chinook salmon (king) Oncorhynchus tshawytscha Salmonidae chub mackeral (Pacific) Scomber japonicus Scombridae 10/14/98 Draft 27 chum salmon (dog) Oncorhynchus keta Salmonidae C-O sole (turbot) Pleuronichthys coenosus Pleuronectidae coho salmon (silver) Oncorhynchus kisutch Salmonidae common carp Cyprinus carpio Cyprinidae curlfin sole (turbot) Pleuronichthys decurrens Pleuronectidae delta smelt Hypomesus transpacificus Osmeridae diamond turbot Hypsopsetta guttulata Pleuronectidae dwarf perch Micrometrus minimus Embiotocidae English sole Pleuronectes vetulus Pleuronectidae fathead minnow Pimephales promelas Cyprinidae fluffy sculpin Oligocottus snyderi Cottidae golden shiner Notemigonus crysoleucas Cyprinidae goldfish Carassius auratus Cyprinidae gray smoothhound Mustelus californicus Carcharhinidae green sturgeon Acipenser medirostris Acipenseridae green sunfish Lepomis cyanellus Centrarchidae halfmoon Medialuna californiensis Kyphosidae hardhead Mylopharodon conocephalus Cyprinidae hitch Lavinia exilicauda Cyprinidae hornyhead turbot Pleuronichthys verticalis Pleuronectidae hybrid sole (forkline) Inopsetta ischyra Pleuronectidae inland silverside (Mississippi) Menidia beryllina Atherinidae jack mackeral Trachurus symmetricus Carangidae jacksmelt Atherinopsis californiensis Atherinidae kelp greenling Hexagrammos decagrammus Hexagrammidae largemouth bass Micropterus salmoides Centrarchidae leopard shark Triakis semifasciata Carcharhinidae lingcod Ophiodon elongatus Hexagrammidae longfin smelt Spirinchus thaleichthys Osmeridae longjaw mudsucker Gillichthys mirabilis Gobiidae medusafish Icichthys lockingtoni Stromateidae monkeyface prickleback Cebidichthys violaceus Stichaeidae night smelt Spirinchus starksi Osmeridae northern anchovy Engraulis mordax Engraulididae northern clingfish Gobiesox maeandricus Gobiesocidae northern lampfish Stenobrachius leucopsarus Myctophidae northern pike Esox lucius Esocidae ocean sunfish Mola mola Molidae onespot fringehead Neoclinus uninotatus Clinidae Pacific argentine Argentina sialis Argentinidae 10/14/98 Draft 28 Pacific barracuda Sphyraena argentea Sphyraenidae Pacific blacksmelt Bathylagus pacificus Bathylagidae Pacific electric ray Torpedo californica Torpedinidae Pacific hake Merluccius productus Gadidae Pacific halibut Hippoglossus stenolepis Pleuronectidae Pacific herring Clupea pallasi Clupeidae Pacific lamprey Lampetra tridentata Petromyzontidae Pacific pompano (butterfish) Peprilus simillimus Stromateridae Pacific sand lance Ammodytes hexapterus Ammodytidae Pacific sanddab Citharichthys sordidus Bothidae Pacific sardine Sardinops sagax Clupeidae Pacific saury Cololabis saira Scomberesocidae Pacific staghorn sculpin Leptocottus armatus Cottidae Pacific tomcod Microgadus proximus Gadidae painted greenling Oxylebius pictus Hexagrammidae penpoint gunnel Apodichthys flavidus Pholidae pile perch Rhacochilus vacca Embiotocidae pink salmon (humpback) Oncorhynchus gorbuscha Salmonidae plainfin midshipman Porichthys notatus Batrachoididae prickly sculpin Cottus asper Cottidae pumpkinseed Lepomis gibbosus Centrarchidae pygmy poacher Odontopyxis trispinosa Agonidae queenfish Seriphus politus Sciaenidae rainbow seaperch Hypsurus caryi Embiotocidae rainbow trout (steelhead) Oncorhynchus mykiss Salmonidae rainwater killifish Lucania parva Cyprinodontidae red brotula Brosmophycis marginata Bythitidae red Irish lord Hemilepidotus hemilepidotus Cottidae red shiner Cyprinella lutrensis Cyprinidae redear sunfish Lepomis microlophus Centrarchidae redeye bass Micropterus coosae Centrarchidae redtail surfperch Amphistichus rhodoterus Embiotocidae riffle sculpin Cottus gulosus Cottidae river lamprey Lampetra ayresi Petromyzontidae rock sole Pleuronectes bilineatus Pleuronectidae rockpool blenny Hypsoblennius gilberti Blenniidae rubberlip seaperch Rhacochilus toxotes Embiotocidae Sacramento blackfish Orthodon microlepidotus Cyprinidae Sacramento perch Archoplites interruptus Centrarchidae Sacramento squawfish Ptychoceilus grandis Cyprinidae 10/14/98 Draft 29 Sacramento sucker Catostomus occidentalis Catostomidae saddleback gunnel Pholis ornata Pholidae sand sole Psettichthys melanostictus Pleuronectidae scalyhead sculpin Artedius harringtoni Cottidae senorita Oxyjulis californica Labridae sevengill shark Notorynchus cepedianus Hexanchidae shimofuri gobi Tridentiger bifasciatus Gobiidae shiner perch Cymatogaster aggregata Embiotocidae shokihaze goby Tridentiger barbatus Gobiidae showy snailfish Liparis pulchellus Cyclopteridae silver surfperch Hyperprosopon ellipticum Embiotocidae smallmouth bass Micropterus dolomieui Centrarchidae sockeye salmon (kokanee, red) Oncorhynchus nerka Salmonidae speckled dace Rhinichthys osculus Cyprinidae speckled sanddab Citharichthys stigmaeus Bothidae spiny dogfish Squalus acanthias Squalidae splittail (Sacramento) Pogonichthys macrolepidotus Cyprinidae spotfin surfperch Hyperprosopon anale Embiotocidae spotted bass Micropterus punctulatus Centrarchidae spotted cusk-eel Chilara taylori Ophidiidae starry flounder Platichthys stellatus Pleuronectidae striped bass Morone saxatilis Percichthyidae striped kelpfish Gibbonsia metzi Clinidae striped mullet Mugil cephalus Mugilidae stripedfin ronquil Rathbunella hypoplecta Bathymasteridae surf smelt Hypomesus pretiosus Osmeridae threadfin shad Dorosoma petenense Clupeidae threespine stickleback Gasterosteus aculeatus Gasterosteidae thresher shark Alopias vulpinus Alopiidae tidepool sculpin Oligocottus maculosus Cottidae tidewater goby Eucyclogobius newberryi Gobiidae topsmelt Atherinops affinis Atherinidae tube snout Aulorhynchus flavidus Gasterosteidae tui chub Gila bicolor Cyprinidae tule perch Hysterocarpus traski Embiotocidae wakasagi Hypomesus nipponensis Osmeridae walleye surfperch Hyperprosopon argenteum Embiotocidae warmouth Lepomis gulosus Centrarchidae western (Pacific) brook lamprey Lampetra richardsoni Petromyzontidae western mosquitofish Gambusia affinis Poeciliidae 10/14/98 Draft 30 white bass Morone chrysops Percichthyidae white catfish Ameiurus catus Ictaluridae white crappie Pomoxis annularis Centrarchidae white croaker Genyonemus lineatus Sciaenidae white seaperch Phanerodon furcatus Embiotocidae white sturgeon Acipenser transmontanus Acipenseridae whitebait smelt Allosmerus elongatus Osmeridae wolf-eel Anarrhichthys ocellatus Anarhichadidae yellow bullhead Ameiurus natalis Ictaluridae yellow perch Perca flavescens Percidae yellowfin goby Acanthogobius flavimanus Gobiidae yellowtail rockfish Sebastes flavidus Scorpaenidae 10/14/98 Draft 31
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