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                    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

                   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

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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

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.

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                      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

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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

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        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

        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

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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

        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

        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

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       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.

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!      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.


      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
!      Studies to analyze and interpret data collected by the previously-described
       monitoring programs.


        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).


      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.

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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.

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       Table 1. Current monitoring of harvestable stocks of recreational and commercial fish
       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

green sturgeon       5               5        5             5

catfishes            4               NA       4             4

centrarchids-        3               NA       4             3                    DFG, resident fish
largemouth                                                                       electrofishing
bass, bluegill, et

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

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sufficient for these species.

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       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

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

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

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.

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

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

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

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.

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
 American shad             planktivor            $      !     !      !    age-0                    3              2
 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
 longfin smelt             planktivor     $      $      !     !      !    all                      2              2
 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.

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.

Tropic Level        Species           Distribution   Abundance        Burdens       Diets
 Planktivores    delta smelt           2             2                          X
                 longfin smelt         2             2                          X
                 juvenile striped      1             1            X             X
 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.

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
 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
 Eggs and larvae    What factors control abundance, distribution,     striped bass
                    mortality and growth of larval fish and egg
 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
 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

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,
                                                                     crayfish, crabs.

                    Mapping of substrate and structures in the       Species not well
                    Estuary                                          covered by
                                                                     existing sampling
                                                                     (e.g. pier piling
                                                                     and potential
                                                                     future invaders
                                                                     (e.g. zebra
 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

                    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
 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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