	1898	1934	1940-41	1970-71
Native Species
Pacific lamprey	Probably	Probably	Probably	Yes
Pacific brook lamprey	Probably	Probably	Probably	Yes
Rainbow trout	Yes	Yes	Yes	Yes
Chinook salmon	Yes	Yes	Yes	No
Sacramento blackfish	Probably	Yes	Yes	No
Hitch	Yes	Yes	Yes	No
Hardhead	Yes	Yes	Yes	No
Splittail	Yes	No	No	No
California roach	Yes	Yes	Yes	No
Sacramento squawfish	Yes	Yes	Yes	No
Sacramento sucker	Yes	Yes	Yes	Yes
Tule perch	Yes	Yes	Yes	No
Prickly sculpin	Yes	Yes	Yes	Yes
Threespine stickleback	Yes	Yes	Yes	Yes

Introduced Species
Brown trout	No	Yes	Yes	Yes
Carp	No	Yes	Yes	Yes
Brown bullhead	No	No	Yes	Yes
Mosquitofish	No	No	Yes	Yes
Green sunfish	No	No	Yes	Yes
Bluegill	No	Yes	Yes	Yes
Smallmouth bass	No	Yes	Yes	No
Largemouth bass	No	No	Yes	Yes

Total Species	14	17	21	13

Percent Native Species	100	77	62	40

The community of native fishes that once dominated the lakes, sloughs, and rivers of the Valley floor has been largely replaced by nonnative sunfishes, catfishes, and carp (see Table ) (Moyle 1976). These introduced species have proven more successful in disturbed and artificially-created freshwater habitats than the native species. At least two native species are no longer found in their original habitat: the thicktail chub is believed to be extinct, and the Sacramento perch is restricted to some farm ponds (Moore et al. 1990).

Relatively little information is available about the historical fishery of the large lakes of the Tulare Basin, as they were apparently drained before for farmland before their fish fauna was surveyed (Moyle 1976). However, the lakes were probably important habitat for Sacramento perch, the presumably-extinct thicktail chub, and other native fishes (Moyle 1976).

Conditions in the San Joaquin River, which remains the most valuable fish habitat in the Valley, are detailed in a July 11, 1991, letter from the California Department of Fish and Game. This letter, which also discusses potential mitigation measures along the river, is included as Attachment A. Appendix 3 provides a list of common native and introduced fish species found in the San Joaquin River downstream of Friant Dam.

Fisheries

Fisheries resources within the San Joaquin Valley are affected by water availability and adjacent land uses. In the upper San Joaquin River and tributary streams, snow-fed perennial flows sustain both cold water and warm water fish. Historically, the native fish fauna of the San Joaquin Valley included true freshwater fishes, anadromous fishes, and, in the San Francisco Bay-San Joaquin Delta, fishes of marine origin (Moyle 1976). Today, introduced species, such as striped bass, American shad, largemouth bass, and catfishes, generally out-compete native species in habitats altered by the influences of drainwater, reservoirs, and water diversions. Native fishes have been reduced to a minor part of the fauna. Native freshwater fishes can now be found only in relatively undisturbed reaches of the San Joaquin Valley. The spring run of chinook salmon is now extinct in the San Joaquin drainage, and the fall run now occurs in much reduced and dramatically low numbers in major tributaries to the San Joaquin River as shown in Table , the Merced, Tuolumne, Consumnes, Stanislaus, and Mokelumne rivers (CDFG 1992). W.E. Loudermilk, California Department of Fish and Game, stated that the 1991 salmon count for the Merced River stood at 58 returning salmon, of these salmon most returned to the Merced hatchery, but a few natural spawners remained in the River (exact number of remaining natural spawners was unavailable, personal communication, Loudermilk, June 26, 1992).

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Table . Comparison of recent San Joaquin River Basin chinook salmon escapements to historic high escapement levels (from CDFG 1992).

ÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄ

Year Stanislaus Tuolumne Merced San Joaquin Total

1983 500 14,800 18,200 0^a 33,500

1984 12,000 14,000 23,000 0 49,000

1985 13,000 41,000 16,000 0 70,000

1986 6,000 7,00 5,000 0 18,000

1987 6,400 14,900 3,900 0 25,200

1988 12,300 6,300 3,200 2,300^b 24,100

1989 1,543 1,274 211 322^b 3,028

1990 492 96 73 280^b 941

Historic 35,000 22,000 23,000 6,000 na

high (1953) (1940) (1984) (1945)

^{a. Friant Dam closed in 1945, with inadequate

stream flow requirements.}

^{b. Rough estimate of strays entering channels

upstream of the Merced River confluence with

the San Joaquin River.}

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San Joaquin River

The San Joaquin River extends l90 miles from its origins in the Sierra Nevada to the town of Vernalis; it drains about 5.9 million acres, including 2 million acres of irrigated farmland. Depending on snow conditions in the Sierra Nevada, peak runoff occurs between late April and August. Stream flow in the upstream stretches of the San Joaquin River is regulated, primarily for temporary storage and direct water diversion, by Millerton Reservoir, behind Friant Dam.

Flows into Millerton Reservoir average an estimated l,762,000 acre-feet annually (all water is used for agriculture, municipal, and industrial purposes, but there are some limited, albeit, incidental environmental benefits). At Millerton, water is diverted into the Friant-Kern and Madera Canals for delivery to water users in Tulare, Madera, Fresno, and Kern Counties. Flow in the San Joaquin River below Friant Dam is limited to the amount needed to meet the State's 5 cubic feet per second requirement at Gravelly Ford to supply riparian water right holders and unauthorized San Joaquin River diverters; between Gravelly Ford and Mendota Pool, there is little or no flow during most years because all available water is used for agriculture or is lost to recharge the overdrafted groundwater aquifer.

The quantity and quality of San Joaquin River water is strongly influenced by the discharge of agricultural drainage. During the irrigation season (March through September), water is imported from the Delta and delivered through the Central Valley Project's Delta-Mendota Canal to the Mendota Pool to supply the Friant Unit's "exchange contractors" along the San Joaquin River, and to the San Luis Reservoir and San Luis Canal to supply the majority of the San Luis Unit contractors. The Mendota Pool also receives some intermittent flow from Fresno Slough. Water from the pool is then delivered northward via the San Joaquin River to Sack Dam. This reach between Mendota Pool and Sack Dam (about 30 miles) has perennial flows from Delta-Mendota Canal's Delta export water deliveries. At Sack Dam, the river is diverted into Arroyo Canal for delivery to various irrigation districts (exchange contractors) and to wetlands in the western Grasslands area. During the irrigation season, between Sack Dam and the mouth of the Merced River, flows in the San Joaquin River consist almost entirely of contaminated agricultural drainwater, primarily resulting from CVP water deliveries to the San Luis Unit.

Irrigation return flows enter the San Joaquin River predominantly from Mud and Salt Sloughs. Average annual discharges are 54,000 acre-feet for Mud Slough and 204,000 acre-feet for Salt Slough. Of these totals, the four northern districts discharge 23,000 acre-feet of tile water commingled with 34,000 acre-feet of surface returns. Irrigation drainwater in Mud and Salt Sloughs accounts for 44 percent of the flow in the San Joaquin River above its confluence with the Merced River in a normal water year (e.g., 1979) (Moore et al. l990). In a dry year (e.g., 1981), Mud and Salt Sloughs account for 70 percent of the flow. The historic contribution of Mud and Salt Sloughs (prior to construction of Friant Dam) to the San Joaquin River flows were below one percent of those total annual flows (SJVDP 1990).

Addition of agricultural drainage water to the San Joaquin River results in reduced water quality (due to accumulations of salt, trace elements such as selenium, and nutrients). In contrast, water quality in the Sierra Nevada streams (the source of historic flows in the lower San Joaquin River and wetlands in the valley) is generally very high. From Friant Dam downstream to Mendota Pool, good water quality is maintained when water is available (only during flood flow releases from Millerton Lake). However, as flows move onto the San Joaquin Valley floor, the quality declines. Due to agricultural return flows and other discharges of urban and municipal wastes, the San Joaquin River carries some of the poorest quality water in the Valley. In the reach of the River just downstream of Sack Dam, which is usually dry due to water diversions, the primary sources of stream flow are irrigation return flows and groundwater discharged either directly or via Mud and Salt Sloughs. During a normal water year, Mud and Salt Sloughs contribute 72 percent of the salt load (and 44 percent of flow) in the San Joaquin River above the mouth of the Merced River. The contribution increases to 80 percent of the salt load and 70 percent of the flow during dry years. These two sloughs contribute 82 percent of the selenium load in this reach of the San Joaquin River.

Fish collected from the sloughs during the mid 1980's showed elevated levels of selenium in their tissues. Aggregate geometric mean (dry weight) selenium concentrations in whole bluegill samples ranged from 4.4 ppm at Salt Slough to 10.4 ppm at Mud Slough (North). Selenium concentrations in freshwater fishes in the United States average 0.5 ppm. It has been estimated that selenium concentrations of 2.0 ppm could cause toxic effects in fish (Saiki 1985, in Moore et al. 1990). Based on data collected during the fall of 1986, (Saiki 1989, in Moore et al. 1990) noted that selenium concentrations in bluegill gonads from samples collected in the western Grasslands area were sufficiently elevated to impair the reproduction of this species.

San Joaquin River water quality improves from the mouth of the Merced River to Vernalis, due to the diluting effects of the Merced, Tuolumne, and Stanislaus Rivers. However, the San Joaquin River still receives nutrients from agricultural drainage that promote algal growth.

Merced River

Flows of the lower Merced River are regulated by the multi-purpose New Exchequer Dam, and by McSwain, Merced Falls, and Crocker-Huffman diversion dams. Several additional riparian and pump diversions are located between Merced Falls Dam and the confluence with the San Joaquin River. The Merced River fish facility, located below New Exchequer Dam near the town of Snelling, was established (as part of the New Exchequer Dam project) to enhance the existing salmon resources in the Merced River. Annual production of fall-run chinook salmon at the hatchery is presently 300,000 yearlings and 400,000 smolts. The Merced has adequate, natural spawning habitat to sustain at least 25,000 returning fall-run salmon (Reynolds et al. 1990). The number of returning fall-run salmon averaged 9,800 individuals in the 1980's, but the populations are on a downward trend with populations equal to or less than those of the endangered winter-run chinook salmon (Appendix A, "Chinook Salmon Spawning Estimates: 1940-1989"). California Department of Fish and Game reported that the 1990, escapement in the Merced River was 73 salmon (49 of these fish were spawned at the Merced Fish Facility near Snelling) with a rough estimate of 280 strays entering San Joaquin River channels upstream of the Merced River. There is no spawning habitat in the San Joaquin River for the stray salmon. Some of these fish are captured at the expense of the State of Calitornia and relocated to the Merced River Fish Facility. The 1992, escapement was reported to be 58 fish (personal communication, Loudermilk 1992).

Because the volume of water (primarily agricultural drainage water) entering the San Joaquin River from Salt Slough can exceed Merced River outflows, many migrating adult salmon are attracted into the sloughs instead of the Merced River. The CDFG installed fish trapping facilities on San Luis Canal in 1988 to handle misguided adult fish, which are transplanted to the Merced River Fish Facility (Moore, et al. 1990). CDFG annually places a barrier across the San Joaquin River channel to provide an additional deterant to misguided salmon.

Stanislaus, Mokelumne, Calaveras, Cosumnes, and Toulumne Rivers salmon population declines are correlated with the construction of Friant Dam, but direct consequences or contributions of Friant Dam construction and water diversions to salmon population declines have not been established. Impoundments and diversions on each river, drainwater discharges, and Delta pumping have likely been much larger factors leading to the abysmal San Joaquin River tributaries' salmon populations. These salmon populations are continuing to decline to the brink of extinction.

Chowchilla and Fresno Rivers - may be addressed by the San Joaquin River Initiative Study, but may be dropped from the Initiative following a determination on the Hidden and Buchanan environmental assessments. The Fresno River no longer connects to the San Joaquin River as the flows have essentially been eliminated and the lower channel has been obliterated due to agricultural conversions.

Friant contractors water supplies other than Millerton: Kings (Fresno Irrigation District - ? AF), Kaweah (Tulare ID - 65,400 AF), Kern (?), and Tule (Porterville ID - 2,500 AF) rivers.

If the EIS analysis defers to the proposed San Joaquin River Initiative Study the following are of concern: The Kings River is no longer connected to the San Joaquin River drainage basin except during extremely wet years and may or may not be included in the Initiative. The Kaweah, Kern, and Tule Rivers are not in the San Joaquin Basin and will probably not be evaluated in the Initiative or any other currently planned Reclamation study.

Freshwater Fishes

The modified environmental conditions in the downstream area, as well as the effects of competition with introduced fishes, have caused considerable changes to the native fish communities. Originally, the San Joaquin drainage (including parts of the Sacramento-San Joaquin Delta) contained at least 25 species of freshwater fish. Today, the fish fauna is dominated by 30 introduced species, while native fishes have been reduced to 24 species by the extinction of one species, the thicktail chub. Although native fishes still persist in remnant undisturbed areas, several introduced species are thriving in the new hydrologic habitats created by water development projects. Introduced species are now more abundant than native species in San Joaquin Valley waterways (Moyle 1976).

Common fishes of the lower San Joaquin River include largemouth bass, striped bass, crappie, bluegill, threadfin and American shad, channel catfish, bullhead, goldfish, and logperch. Some of the more common species found in Mud and Salt Sloughs include mosquitofish, green sunfish, bluegill, black bullhead, carp, Sacramento blackfish, and white catfish. Freshwater clams and crayfish also occur in the area.

All sampled fish and wildlife in or dependent on the San Joaquin River are contaminated to some degree and, at times, the public is cautioned to consume those animals on a limited basis (Moore et al. 1990).

Although the Friant Division does not contribute directly to the San Joaquin River contamination problem, the construction of the Friant Dam following acquisition of the "exchange contractors" water rights in exchange for Delta-Mendota Canal water established the link to the Friant Division's contribution to the lower San Joaquin River contamination problem.

Anadromous Fishes

The native anadromous fishes of the San Joaquin River system include the chinook salmon (Oncorhynchus tshawytscha), steelhead trout (O. mykiss), and white and green sturgeon (Acipenser transmontanus, and A. medirostris). Introduced anadromous fishes include striped bass (Morone saxatilis) and American shad (Alosa sapidissima).

Salmon -- Rapid and widespread development of irrigated agriculture in the San Joaquin Basin has resulted in a dramatic decline in populations of salmon over the past few decades. Historically, the San Joaquin River system supported both a fall run and a spring run of chinook salmon. A smaller population of winter run salmon may have used the northern east-side tributaries to the San Joaquin River. The spring run population was the most abundant race of chinook salmon in San Joaquin Valley (Reynolds et al. 1990). In total, runs exceeded 100,000 fish annually and probably exceeded 200,000 in peak years (Fry 196l). Today however, chinook salmon production in the San Joaquin River drainage has declined by over 90% since the 1940's (Loudermilk et al. 1989). Spring-run chinook salmon in this drainage essentially were extirpated as a result of construction and operation of Friant Dam. Spring-runs on the other tributaries had been eliminated due to water development projects prior to and shortly after 1900. With artificial propagation, fall-run fish continue to exist in five major east-side San Joaquin River tributaries including the Merced, Tuolumne, Stanislaus, Mokelumne, and Cosumnes rivers. Occasionally fall run chinook salmon also ascend the Calaveras River. In addition, the Calaveras River has supported a small run of winter-run chinook salmon; however, the status of this population is currently unknown (Reynolds et al. 1990). Since the completion of Friant Dam, chinook salmon have appeared in the upper mainstem of the San Joaquin River only in extremely wet years, and have successfully spawned in the Kings River only once, during the flood year of 1969 (Brown and Moyle in Moore et al. 1990). Estimated numbers of spawning adult salmon that returned to the major San Joaquin River tributaries from 1940 through 1989 are presented in Appendix A, "Chinook Salmon Spawning Escapement Estimates: 1940-1989" and these figures are updated and summarized in Table .

Flow reversal in the south Delta, including the lower San Joaquin River, adversely affects migrating adult salmon and outmigrating juveniles. Export pumping by the CVP and SWP has changed the natural flow patterns of the Delta. The pumps are located at the southern edge of the Delta, but pumping rates usually exceed the flow of the San Joaquin River entering the Delta from the south; therefore, most of the water that is exported must come from the Sacramento River. At high export rates (greater than about 3,500 cfs), water is drawn back up the San Joaquin River from its confluence with the Sacramento River near Sherman Island. Such net upstream flows in the San Joaquin River are typical in all but wet springs, and in the summer and fall of all years. The flow reversal disorients both upstream-migrating adult salmon and downstream-migrating juveniles. (Moore, et al. 1990)

Adults return to their "home stream" to spawn using olfactory cues and some form of memory acquired during the latter part of their juvenile freshwater residence (CDFG 1987a). They select specific gravel size, substrate porosity, water depth, and water velocity for redd (nest) sites. Nest excavation and other behavioral activities precede egg deposition. All Pacific salmon adults die after spawning. Seasonal use patterns of fall-run chinook salmon in the San Joaquin River System are presented in Table , "Use of the San Joaquin River by Life Stages of Fall-Run Chinook Salmon." The majority of salmon eggs atch between mid-January and mid-March.

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TABLE . USE OF THE SAN JOAQUIN RIVER BY LIFE STAGES OF FALL-RUN CHINOOK SALMON^a

³ ³ ³ ³ ³ ³ ³ ³ ³ ³ ³ ³ ³ ³

³ Fall-Run ³Jul ³Aug ³Sep ³Oct ³Nov ³Dec ³Jan ³Feb ³Mar ³Apr ³May ³Jun³

ÀÄÄÄÄÄÄÄÄÄÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÄÁÄÄÄÁÄ

Adult

Migration xx xxx xxx xxx

Spawning x xxx xxx xx

Incubation x xxx xxx xxx xxx xxx x

Rearing &

Migration x xxx xxx xxx xxx xxx xxx x

ÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄÄ

^a CDFG 1987b.

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Striped Bass -- The San Francisco Bay and Sacramento-San Joaquin Delta is habitat for an anadromous striped bass population that supports one of California's most important sport fisheries. Depending on current stock size, about 100,000 to 400,000 striped bass are caught by anglers each year. The annual recreational value of this fishery is estimated at $45 million (CDFG 1989). Additional land-locked populations of striped bass exist in several reservoirs in the San Joaquin Valley including a large population in San Luis Reservoir (which is continually replenished with water imported from the Delta through the CVP and SWP pumps and canals [Moyle 1976]).

Striped bass are native to the east coast of the United States. They were introduced into California's Sacramento-San Joaquin Delta in 1879, and again in 1882. These artificial plantings proved so successful that by 1888 a commercial fishery had been established; the annual commercial harvest of striped bass reached 1.2 million pounds by 1899 (Skinner 1962).

Striped bass spawn from early April to mid-June. For spawning, they require water that is fresh or only slightly saline, with a moderate to swift current. Striped bass will not spawn in waters with a salt content in excess of 180 ppm total dissolved solids. Some spawning occurs in the San Joaquin River from an area about 5 miles downstream from Stockton to Antioch; this is limited due to the combination of low flows and high salinity (USFWS-USBSFW 1969). About one-half to two-thirds of the Bay and Delta's striped bass spawn in the lower Sacramento River system (CDFG 1989). Eggs drift with water currents after spawning and hatch in two to three days into larvae that soon require food but have little swimming ability.

In the last 20 years, the population of adult striped bass has declined substantially. Estimates by the CDFG suggest that the 1980 adult bass population had declined by 63-75% from levels in the early 1960's (CDFG 1989). This decline is largely due to lower recruitment from the juvenile population. Major causes of lower recruitment include losses of eggs and larvae due to entrainment in water diversions (e.g., the CVP and SWP Delta pumps), reduced outflows through the Sacramento-San Joaquin Delta, reduced flows and declining water quality (e.g., high TDS) in the San Joaquin River, reduction of populations of Neomysis (an important food item for young striped bass in the Delta), reduction of the adult striped bass population, water pollution (including presence of residues of pesticides, petrochemicals, trace elements, and metals), dredging and spoil disposal, and introduction of exotic aquatic organisms such as the Chinese clam (Potamocorbula amurensis) which may reduce the supply of desirable food for juvenile bass (CDFG 1989; CDFG 1987b).

Export pumping by the CVP and SWP has changed the natural flow patterns of the Delta. The reverse flows into the southern Delta draw young fish and their food organisms out of the spawning and nursery areas and transport them to the pumps, where they are either captured and transported for release in nursery areas in the western Delta or sucked into the pumps and distributed through the CVP and SWP canals. Many of the salvaged fish are lost due to stress associated with handling and transport, and as a result of predation associated with the CVP and SWP pumps (CDFG 1987b).

Upstream diversions and water storage reservoirs on major east-side streams have reduced outflows through the Sacramento-San Joaquin Delta. Low flows have reduced the transport of bass eggs and larvae, and, combined with degraded water quality, have at times caused the Delta to be saltier than is suitable for striped bass spawning.

Reptiles and Amphibians

Western pond turtles were once abundant in Tulare Lake and supported a commercial fishery there. Early accounts noted that turtles completely covered drift logs and banks around the lake (Werschkull et al. 1984; Moore et al. 1990). These turtles greatly declined in numbers following the draining of Tulare Lake and the alteration of other aquatic habitats within their historic range.

Other reptile and amphibian species have been affected by habitat alteration and possibly the introduction of non-native amphibians. The giant garter snake, which is found in freshwater wetlands and slow-moving streams and sloughs, has apparently been extirpated from the Tulare Basin (though it is still found in the San Joaquin Basin) (Moore et al. 1990; CDFG 1990). This snake has been proposed for Federal listing. The blunt-nosed leopard lizard population has declined due to conversion of alkali desert scrub habitat; the population of California tiger salamanders has decreased due to conversion of California prairie and valley oak woodlands, and associated vernal pools, to agricultural lands. The tiger salamander requires vernal pools or other temporary ponds to reproduce. The California red-legged frog is now absent from the Valley floor; factors leading to its decline probably included habitat conversion and competition and predation by the introduced bullfrog (Moore et al. 1990). Appendix 4 provides a list of typical reptiles and amphibians of the San Joaquin Valley that may be found in the project area.

Birds

The wetlands of the San Joaquin Valley were an important stopping place and wintering habitat for waterfowl of the Pacific Flyway. Millions of waterfowl used these wetlands each year from fall through early spring. Many other species, especially shorebirds, passerines, and some waterfowl, were year-round residents and bred in the wetlands and uplands of the San Joaquin Valley. Appendix 5 provides a list of some of the common bird species of the Valley.

The San Joaquin Valley remains critically important wintering habitat for Pacific Flyway waterfowl; the Central Valley (San Joaquin and Sacramento Valleys) supports about 60 percent of the Pacific Flyway wintering population, a total of 8 to 12 million ducks and geese, as well as hundreds of thousands of shorebirds and other marsh and water birds (CDFG 1983; Moore et al. 1990). In recent years, however, the number of waterfowl wintering in the Central Valley, and the number of Pacific Flyway waterfowl in general, has decreased. These declines have been attributed to loss of both breeding and wintering habitat and successive years of drought (USFWS and Canadian Wildlife Service 1986; USFWS 1987; Moore et al. 1990). Species that have undergone notable declines, especially in recent years, include trumpeter swan (which has been extirpated from the San Joaquin Valley), tundra swan, Pacific white-fronted goose, Aleutian Canada goose (a federally-listed threatened subspecies), fulvous whistling duck (which no longer breeds in the Valley), American wigeon, mallard, and northern pintail (Moore et al. 1990).

At least 25 other bird species have declined in population or range in the San Joaquin Valley due to habitat loss or degradation. Alterations to wetlands or waterways have affected western and Clark's grebes, American white pelican, double-crested cormorant, black-crowned night heron, least bittern, white-faced ibis, northern harrier, osprey, greater sandhill crane, California black rail, western snowy plover, California gull, black tern, short-eared owl, and tricolored blackbird populations. Conversion of riparian forest or valley oak woodland has adversely affected Cooper's hawk, Swainson's hawk, golden eagle, osprey, yellow-billed cuckoo, long-eared owl, willow flycatcher, least Bell's vireo, yellow warbler, yellow-breasted chat, and tricolored blackbird populations (Moore et al. 1990).

In addition, the decline in local populations of nine species has been attributed to pesticide contamination. These species include the bald eagle, Cooper's hawk, Swainson's hawk, merlin, American peregrine falcon, prairie falcon, burrowing owl, yellow-billed magpie, and tricolored blackbird (Moore et al. 1990).

Winter habitat is the single most important limiting factor to waterfowl in the Pacific Flyway. The FWS ranks the Central Valley wetland habitat as second out of 33 locations on its national habitat priority scale.

Mammals

The San Joaquin Valley supported an abundant mammalian fauna (Moore et al. 1990). Tule elk and pronghorn were the dominant large herbivores of the Valley; California mule deer were less abundant. Grizzly bears were common in the riparian and oak woodlands and in wetlands. Other carnivores included coyotes, gray and San Joaquin kit foxes, mountain lions, bobcats, striped and spotted skunks, badgers, raccoons, ringtails, and possibly gray wolves. Woodrats, rabbits, squirrels, pocket gophers, kangaroo rats, shrews, and other small rodents were the prey of many of the carnivore species. Beavers, river otters, and minks were common in streams. Several species of bats were widespread in the Valley. Appendix 6 provides a list of some common mammals of the study area.

The distribution and abundance of many mammal species in the San Joaquin Valley have been affected by habitat alteration and degradation; populations of some species were reduced by market or bounty hunting. Such hunting extirpated grizzly bears and gray wolves from the State of California (Jameson and Peters 1988). Conversion of riparian forest and valley oak woodlands to agricultural land has led to declines of riparian brush rabbit, pale big-eared bat, ringtail, American badger, and San Joaquin Valley woodrat populations. Loss of California prairie and San Joaquin saltbush habitat has led to declines of San Joaquin pocket mouse, pale big-eared bat, American badger, Nelson's antelope ground squirrel, short-nosed kangaroo rat, giant kangaroo rat, Fresno kangaroo rat, Tipton kangaroo rat, San Joaquin kit fox, and pronghorn populations. Declines in populations of the Buena Vista Lake shrew, the greater western mastiff bat, the tule elk, and the golden beaver have been associated with loss of wetland habitat (Moore et al. 1990).

In addition, use of pesticides and especially rodenticides may be at least partly responsible for declines in the populations of some mammal species, including the San Joaquin myotis, greater western mastiff bat, American badger, and Nelson's antelope ground squirrel (Moore et al. 1990). Populations of other species have likely been affected by habitat alteration, hunting, or pesticides; however, data are not available to evaluate any effects.

Threatened and Endangered Species

On October 15, 1991, the Service provided Reclamation with a Biological Opinion for the Friant Division water contract renewals (USFWS 1991); here, we only summarize the findings presented in that Opinion. For more detailed information about the federally-listed species of the project area, please refer to the Biological Opinion. Fifteen federally-listed threatened or endangered species have been found in the project area; these are listed in Appendix 7. In general, the reason for the decline of these species' populations has been habitat loss. In the Friant planning area, agricultural development has been the most important factor leading to conversion and loss of habitat for these species.

Much of the remaining habitat for the listed species is found in isolated fragments that support small, highly vulnerable populations. Fragmented populations of relatively immobile species, including the listed kangaroo rats, blunt-nosed leopard lizard, and all the plants, are especially susceptible to further disturbance. Once extirpated from a site, they may be unable to reestablish in that area if no dispersal corridor exists connecting the site to another population.

To date, recovery plans have been prepared for only the blunt-nosed leopard lizard and the San Joaquin kit fox. The key objective in these recovery plans requires protection and restoration of contiguous habitat over a broad geographic expanse. Similar programs of habitat protection and restoration are likely to be key components of recovery plans for the remaining species; acquisition of the habitat proposed in the leopard lizard and kit fox plans would probably benefit the other San Joaquin Valley species as well. To date, however, habitat acquisition has not kept pace with the habitat losses that continue to eliminate the few remaining wildlands of the Friant planning area and the San Joaquin Valley.