### ATTACHMENT III:

BASELINE STATUS AND CUMUL ATIVE EFFECTS FOR THE

SAN FRANCISCO BAY LISTED SPECIES

1TABLE OF CONTENTS

1: ALAMEDAWHIPSNAKE ............................................................................................ 5

1.1 CUMULATIVE EFFECTS ...................................................................................... 5

1.2 ENVIRONMENTAL BASELINE ........................................................................... 5 1.2.1 Factors affecting species within the action area ............................................... 5 1.2.1.1 Urban development .................................................................................... 6 1.2.1.2 Fire suppression ......................................................................................... 8

1.2.1.3 Predation .................................................................................................... 8 1.2.1.4 Grazing practices ....................................................................................... 9 1.2.1.5 Non-native species ..................................................................................... 9

1.2.2 Baseline Status ................................................................................................ 10

1.3 REFERENCES ...................................................................................................... 12

2: BAY CHECKERSPOT BUTTERFLY ....................................................................... 14

2.1 CUMULATIVE EFFECTS ................................................................................... 14

2.2 ENVIRONMENTAL BASELINE ......................................................................... 14 2.2.1 Factors affecting species e nvironment within the action area ........................ 14 2.2.1.1 Habitat loss and degradation .................................................................... 15 2.2.1.2 Invasive plants and air pollution .............................................................. 17

2.2.1.3 Overutilization for rese arch and private purposes ................................... 17 2.2.1.4 Gopher control and vehicular disturbance ............................................... 18 2.2.1.5 Fire and grazing practices ........................................................................ 18 2.2.1.6 Climate change and climate extremes ...................................................... 19

2.2.2 Baseline Status ................................................................................................ 19

2.3 REFERENCES ...................................................................................................... 22

3: CALIFORNIA CLAPPER RAIL ................................................................................ 25

3.1 CUMULATIVE EFFECTS ................................................................................... 25

3.2 ENVIRONMENTAL BASELINE ......................................................................... 25 3.2.1 Factors affecting species within the action area ............................................. 25 3.2.1.1 Habitat Loss and Fragmentation .............................................................. 26 3.2.1.2 Hunting .................................................................................................... 27

3.2.1.3 Predation .................................................................................................. 27

3.2.1.4 Disease ..................................................................................................... 28

3.2.1.5 Climate Extremes ..................................................................................... 28

3.2.1.6 Habitat Protection and Restoration .......................................................... 29

3.2.2 Baseline Status ................................................................................................ 29

3.3 REFERENCES ...................................................................................................... 30

4: CALIFORNIA FRESHWATER SHRIMP .................................................................. 34

4.1 CUMULATIVE EFFECTS ................................................................................... 34

4.2 ENVIRONMENTAL BASELINE ......................................................................... 34 4.2.1 Factors affecting species e nvironment within the action area ........................ 35

4.2.1.1 Urbanization .............................................................................................. 35

4.2.1.2 Stream Maintenance .................................................................................. 36 4.2.1.3 Water Resource Needs: Imp oundments and Water Diversions ................ 36 4.2.1.4 Gravel Mining ........................................................................................... 37 4.2.1.5 Agriculture Developments ........................................................................ 37

24.2.1.6 Predation ................................................................................................... 38

4.2.1.7 Environmental Extremes ........................................................................... 39

4.2.1.8 Restoration Efforts .................................................................................... 40

4.2.2 Baseline Status .............................................................................................. 40

4.3 REFERENCES ...................................................................................................... 41

5: CALIFORNIA TIGER SALAMANDER: CENTRAL CALIFORNIA DISTINCT

POPULATION SEGMENT ............................................................................................. 42

5.1 CUMULATIVE EFFECTS ................................................................................... 42

5.2 ENVIRONMENTAL BASELINE ......................................................................... 42 5.2.1 Factors affecting species conti nued existence with in the action area ............. 43 5.2.1.1 Rangeland Conversion and Habitat Fragmentation ................................. 43

5.2.1.2 Disease ..................................................................................................... 45 5.2.1.3 Predation, Competition, and Hybridization ............................................. 45 5.2.1.4 Other Factors affecting th e species continued existence ......................... 47

5.2.2 Baseline Status ................................................................................................. 49

5.3 REFERENCES ...................................................................................................... 50

6: CALIFORNIA TIGER SALAMANDER: SANTA BARBARA COUNTY DISTINCT

POPULATION SEGMENT ............................................................................................. 51

6.1 CUMULATIVE EFFECTS ................................................................................... 51

6.2 ENVIRONMENTAL BASELINE ......................................................................... 51 6.2.1 Factors affecting species conti nued existence with in the action area ............. 52 6.2.1.1 Conversion of rangeland for urban and agricultural uses ........................ 52

6.2.1.2 Contaminants ........................................................................................... 54

6.2.1.3 Pest control ............................................................................................... 55 6.2.1.4 Grazing and Water drawdown ................................................................. 56 6.2.1.5 Predation, Competition, and Hybridization ............................................. 56

6.2.1.6 Disease ..................................................................................................... 58

6.2.2 Baseline Status ................................................................................................ 59

6.3 REFERENCES ...................................................................................................... 61

7: CALIFORNIA TIGER SALAMANDER: SONOMA COUNTY DISTINCT

POPULATION SEGMENT ............................................................................................. 63

7.1 CUMULATIVE EFFECTS ................................................................................... 63

7.2 ENVIRONMENTAL BASELINE ......................................................................... 63 7.2.1 Factors affecting species conti nued existence with in the action area ............. 63 7.2.1.1 Habitat Destruction, Degr adation, and Fragmentation ............................. 64

7.2.1.2 Disease ...................................................................................................... 65 7.2.1.3 Predation, Competition, and Hybridization ............................................. 66 7.2.1.4 Other Factors affecting th e species continued existence ......................... 68

7.2.2 Baseline Status ................................................................................................. 70

7.3 References .............................................................................................................. 73

8: DELTA SMELT .......................................................................................................... 75

8.1 CUMULATIVE EFFECTS ................................................................................... 75

8.2 ENVIRONMENTAL BASELINE ......................................................................... 75 8.2.1 Factors affecting species e nvironment within the action area ........................ 75 8.2.1.1 Habitat alteration, curt ailment, and degradation ...................................... 76 8.2.1.2 Changes in food Organisms ..................................................................... 79

38.2.1.3 Toxic Substances ..................................................................................... 79 8.2.1.4 Disease, Predation, and Competition ....................................................... 80 8.2.1.5 Loss of genetic integrity ........................................................................... 80

8.2.2 Baseline Status ................................................................................................ 81

8.3 REFERENCES ...................................................................................................... 82

9: SALT MARSH HARVEST MOUSE .......................................................................... 84

9.1 CUMULATIVE EFFECTS ................................................................................... 84

9.2 ENVIRONMENTAL BASELINE ......................................................................... 84 9.2.1 Factors affecting species e nvironment within the action area ........................ 84

9.2.1.1 Habitat loss and alteration ........................................................................ 85

9.2.1.2 Predation .................................................................................................. 86

9.2.1.3 Conservation actions................................................................................ 87

9.2.2 Baseline Status ................................................................................................ 87

9.3 REFERENCES ...................................................................................................... 88

10: SAN FRANCISCO GARTER SNAKE ..................................................................... 92

10.1 CUMULATIVE EFFECTS ................................................................................. 92

10.2 ENVIRONMENTAL BASELINE ...................................................................... 92 10.2.1 Factors affecting species e nvironment within the action area ...................... 92 9.2.1.1 Habitat Loss and Degradation .................................................................. 93 10.2.1.2 Overutilization for Recreational, Scientific, Commercial, and Educational Purposes ............................................................................................ 97

10.2.1.3 Disease and Predation ............................................................................ 97 10.2.1.4 Other natural and anthropoge nic factors affecting existence................. 98

10.2.2 Baseline Status .............................................................................................. 99

10.3 REFERENCES .............................................................................................. 103 11: SAN JOAQUIN KIT FOX ...................................................................................... 110

11.1 CUMULATIVE EFFECTS ............................................................................... 110

11.2 ENVIRONMENTAL BASELINE .................................................................... 110 11.2.1 Factors affecting species e nvironment within the action area .................... 110 11.2.1.1 Habitat Destruction, Degr adation, and Fragmentation ........................ 111 11.2.1.2 Invasive Species, Predation, and Competition ..................................... 112

11.2.1.3 Disease and Climatic Extremes ........................................................... 112

11.2.2 Baseline Status ............................................................................................ 113

11.3 REFERENCES .................................................................................................. 114

12: VALLEY ELDERBE RRY LONGHORN BEETLE ............................................... 118

11.2 CUMULATIVE EFFECTS ............................................................................... 118

11.2 ENVIRONMENTAL BASELINE .................................................................... 118 12.2.1 Factors affecting species e nvironment within the action area .................... 118 12.2.1.1 Habitat Loss and Degradation.............................................................. 119 12.2.1.2 Predation, Invasive Species, and Other Issues ..................................... 120

12.2.1.3 Habitat Protection and Restoration ...................................................... 121

12.2.2 Baseline Status ............................................................................................ 125

12.3 REFERENCES .................................................................................................. 127

41: ALAMEDAWHIPSNAKE

1.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the Alameda whipsnake ( Masticophis lateralis euryxanthus ) that are reasonably certain to occur in the acti on area. Future federa l actions not directly related to the proposed action are not cons idered because they require additional consultation under Section 7 of the Endangere d Species Act (Act). The numerous nonfederal actions that are reasona bly certain to occur within th e action area consist of urban and suburban development, construction a nd recreational use of paved and unpaved roads, fire suppression, inadequacy of regul atory mechanisms, and inappropriate grazing practices. Many of these fact ors are linked or act synergis tically and create complex consequences for the Alameda whipsnake. For example, suburban developments often impede dispersal and movement of species, as well as contribute to habitat loss and degradation. Housing developments can increase public presence in local parks and trails, as well as increase the number of do mestic and feral cats. These potential impacts further degrade Alameda whipsnake suitable habitat by promoting human interference and increased predatory pressures. Co mpounded with the other non-federal actions, populations become more susceptible to the accu mulation of adverse effects.

1.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the combined effects of past and ongoing human induced and natural factors leading to the status of the speci es, its habitat, and ecosystem, within the action area. The envi ronmental baseline is a snapshot of the Alameda whipsnake’s status at this time. Ho wever, the baseline condition of the assessed whipsnake’s habitat varies across locations a nd within each critical habitat unit. Details of the Alameda whipsnake’s habitat descri ption and known locations are included in Attachment III. Given the large amount of ha bitat and extent of the action area included in this assessment, the discussion of envir onmental baseline includes a general discussion of factors that may affect the Alameda whipsnake within the action area. This information is presented in Section 1.2.1. The baseline status and population dynamics of the species is provided in Section 1.2.2.

1.2.1 Factors affecting species within the action area

At the time of the Alameda whipsnake’s list ing in 1997, failure to implement appropriate fire management practices on public lands a nd rate of habitat loss on private lands was determined to place the Alameda whipsnake in most endangerment (USFWS, 1997). By

the time critical habitat was finalized in 2006, continued urban deve lopment resulting in

5fragmentation and removal of essential features had been determined to be the greatest

threat to all six critical habitat units (USFWS, 2006). Additi onal anthropogenic and natural factors listed as directly and indirectly affecting the species included the effects of fire suppression, inappropriat e grazing practices, predat ion, and non-native species invasions (USFWS, 2006). Sections 1.2.1.1 through 1.2.1.5 provide details on each of these major issues affecting the Alamed a whipsnake in the action area.

1.2.1.1 Urban development

Urban development is determined to be the gr eatest threat to all six critical habitat units (USFWS, 2006). Urban development and a ssociated highway and road construction cause rapid habitat loss, degr adation, and fragmentation, the primary reasons for the Federal and State listing of the species (U SFWS, 2003). Urbanizati on removes features essential to the conservation of the species and is heaviest in the central and western portions of Alameda and Contra Costa Counties (USFWS, 1997; USFWS, 2006).

Urbanization and road constructi on also result in habitat frag mentation and has led to the almost complete disseverment of the fi ve remaining subpopulations by preventing movement and migration (USFWS, 1997).

McGinnis (1992) and the United States Fi sh and Wildlife Service (USFWS) have documented colonies throughout the species’ rang e that are subject to the pressures of residential developments (USFWS, 1997) . In the Hayward-Pleasanton Ridge population, there are a number of housing de velopments that coul d potentially cause destruction, modification and/or fragmentation to the species’ suitable habitat range (USFWS, 1997). These developments incl ude the proposed 500 acre (ac) (200 hectare (ha)) Schaefer Ranch Project with approximately 474 homes, and the proposed Hansen Ranch Project of 146 ac (58 ha) (USFWS, 1997) . The Schafer Ranch development is located on Alameda whipsnake suitable habi tat, while the Hansen Ranch Project is located nearby a sighting of an Alameda whipsnake (USFWS, 1997). Due to 161 ac (64 ha) of Schaefer Ranch Proj ect land being dedicated to the East Bay Regional Park District (EBRPD), increased public use and related activities w ill compound the potential effects on suitable habitat (USFWS, 1997). Towards the south of the HaywardPleasanton Ridge population are the sites of two proposed housi ng developments: the 1,580 ac (632 ha) Hayward 1900 project and th e 391 ac (156 ha) Bailey Ranch project (USFWS, 1997). Both of the project site s were occupied by the Alameda whipsnake when the developments were proposed, a nd contiguous habitat exists between known occupied habitat to the west and east of these future developed areas (USFWS, 1997). Although the Bailey Ranch project includes mitigation measures to alleviate potential impacts toward the species, the development is still expected to result in habitat fragmentation of the Hayward-Pleasant on population (USFWS, 1997). Undeveloped areas such as trails and vineyards are pr oposed for the Hayward 1900 project, but these open areas could also result in habitat fragmentation for the Alameda whipsnake (USFWS, 1997).

6Several developments are proposed for th e Oakland-Las Trampas population that may impact Alameda whipsnakes and their ha bitat (USFWS, 1997). Several of these proposed projects abut the eastern margin of Las Trampas Regional Wilderness and contain habitat known to be occupied by the Alameda whipsnake (USFWS, 1997). Two of these projects include the Rossmoor Ne ighborhood Nine Project of 22 ac (9 ha) and the proposed expansion of the Oakland Zoo (USFWS, 1997). These and other projects in the Oakland-Las Trampas population may result in direct loss of or impacts to the species’ suitable habita t (USFWS, 1997). Although some of these projects have or may

reserve habitat suitable for the Alameda wh ipsnake, the undeveloped hillsides that support chaparral growth will be subject to increased fire suppression due to the close proximity of urban development (USFWS, 1997) . This fire suppression would result in habitat degradation and an increased likelihood of severe wildfires (USFWS, 1997).

Urbanization indirectly impacts the Mount Di ablo-Black Hills, Tilden-Briones, and Sunol-Cedar populations (USFWS, 1997). Th e expanding cities of Pittsburg, Oakley, Brentwood, and Antioch are expected to increas e the degree of public visitation, and thus disturbance, to the nearby EBRPD parks a nd Mount Diablo State Park (USFWS, 1997). In particular, the eastern flank of the Mount Diablo-Black Hills population will be exposed to these indirect impacts associat ed with the 115-unit Clayton Ranch (1,030ac (412 ha)) and the 5,200-unit Cowell Ranch (4,272 ac (1,709)), among others (USFWS, 1997). The southern portion of the Mount Diablo-Black Hills population will see increased urbanization pressure and its asso ciated impacts from the proposed Dougherty Valley (6,000 ac (2,400 ha)) and Tassajara Va lley (4,000 ac (1,600 ha) projects (USFWS, 1997). Increased population pressure from th e north will be caused by the approved 800- unit Franklin Canyon (980 ac (392 ha)) pr ojects (USFWS, 1997). Additional developments are approved or proposed ad jacent to the Sunol-Cedar population in the rapidly growing centers near Dublin and Pl easanton in Alameda County (USFWS, 1997).

Fragmentation has been determined to be of serious concern, including impacts from urban development and associated highway and road construction (USFWS, 2003). The ecological consequences of fr agmentation include the loss of native plants and animals, invasion of exotic species, increased soil er osion, and decreased water quality (USFWS, 2003). Fragmentation leads to ha bitat loss and isolat ion, which increase the likelihood of genetic complications, such as genetic drif t and imbreeding depression (USFWS, 2003). These consequences place species living in fragmented habitats at highest risk of extinction if they (1) depend on native vegetation; (2) require combinations of different habitat types; (3) require larg e territories; and (4) exist at low densities (USFWS, 1997). The Alameda whipsnake is confronted with pa rticularly high risk because the species can be characterized by all of thes e attributes: the species is know n to associate with native Diablan sage scrub (attribute 1), to forage in adjacent grasslands (attribute 2), and to migrate along riparian corri dors (attribute 3) (USFWS, 1997). Although the home range of the Alameda whipsnake is typically betw een 5 and 20 ac (2 and 9 ha), not large in comparison to some animal ranges, the na rrow habitats in some areas may impose significant constraints on the species (USF WS, 1997). Because the Alameda whipsnake is currently listed as threatened, low densit ies (attribute 4) are also expected (USFWS,

71997). Due to the disproportionate effects of urbanization, some populations of the species are more prone to low de nsities than others (USFWS, 1997).

1.2.1.2 Fire suppression

Increasing urbanization prompted the state of California to a dopt an avid fire suppression policy over 50 years ago (USFWS, 2003). The policy has disrupted the natural disturbance regime of the chaparral/scrub co mmunity, and many chaparral habitats in the east Bay area have not burned for severa l decades (USFWS, 2003). To provide the necessary stimulus for new sprouting, seedling re cruitment, and seed di spersal, a cyclical fire regime of 10 to 30 years is required (USFWS, 1997). In the absence of reoccurring disturbance, these chaparral/scrub commun ities are becoming decadent (in a state of decline) and senile (reduced to a featur eless plain) (USFWS, 2003). Other natural disturbances affecting the chaparral/scrub communities include landslides, droughts, and herbivory, although to a lesser degree (USFWS, 2003).

Fire suppression directly and indirectly affects the Alamed a whipsnake (USFWS, 1997). Fire suppression exacerbates the effects of wildfires through the buildup of fuel (underbrush and woody debris), creating c onditions for slow-moving, hot fires (USFWS, 1997). Conditions for the most intense fires occur in summer and early fall when accumulated fuel is dry and abundant (USFWS, 1997). During this period, hatchling and adult Alameda whipsnakes are aboveground a nd populations are likely to sustain the heaviest losses (USFWS, 1997). Fire suppr ession indirectly affects the Alameda whipsnake by altering plant compositions a nd structure of suitable habitat (USFWS, 1997). Infrequent fires allow the establishm ent of closed canopies and thus cooler understory environments. Both the Alameda whipsnake and its lizard prey base are potentially affected by cooler habitats, w ith Alameda whipsnakes being particularly sensitive because of their higher mean active body temperature (33.4°C) and higher degree of body temperature st ability (stenothermy) compar ed to other snake species (USFWS, 1997; USFWS, 2006). Alameda whipsn akes maintain a higher temperature by using partially open and low growing shrub co mmunities that provide predator protection and allow sunlight penetration (USFWS, 1997). This preference is supported by survey studies showing that Alameda whipsnakes ar e less likely to be found in closed canopy environments (USFWS, 1997). Fi re suppression has also led to the encroachment of nonindigenous and ornamental trees into grassland habitats, furt her increasing fu el loads in and around Alameda whipsnak e habitat (USFWS, 2006).

1.2.1.3 Predation

A number of native and nonnative mammals and birds are known or likely to be predators of the Alameda whipsn ake: the California kingsnake ( Lampropeltis getula califoniae ), northern raccoon ( ProcyonProcyon lotor ), striped skunk ( Mephitis mephitis ), Virginia opossum ( Dideplhpis virginianus ), coyote ( Canis latrans ), gray fox ( Vulpes cinereoargenteus ), red fox ( Vulpes vulpes ), and hawks ( Buteo species) (USFWS, 2003).

8Increased predatory pressure may become excessive in situations where the Alameda whipsnake habitat has become fragmented, isolated, and otherwise degraded (USFWS, 2003). Alameda whipsnakes living adjacent to urban developments are at heightened risk

because of the associated loss of cover habita ts and an increase in predators using these areas (USFWS, 2006). For example, predati on and harassment from domestic and feral cats ( Felis domesticus ) increases as urban development infringes upon Alameda whipsnake habitat (USFWS, 2003). The grow ing movement to maintain feral cat populations in parklands inte nsifies this threat (USFWS , 2003). Although predatory impacts on whipsnakes from cats have not been studied, cats are known to prey on the yellow-bellied racer ( Coluber constrictor ), a closely related snake species, as well as have significant impacts on lizard populations (USFWS, 2003). Additional introduced predators include rats ( Rattus species), feral pigs ( Sus scrofa ), and dogs ( Canis familiaris ) (USFWS, 2003). Impacts from these speci es may be especially acute if urban developments directly abut Alameda whipsnake habitat (USFWS, 2003). Special management of nonnative predators may be requi red within all six cr itical habitat units (USFWS, 2006).

1.2.1.4 Grazing practices

Livestock grazing and inappr opriate grazing practices may threaten the Alameda whipsnake (USFWS, 1997; USFWS, 2006). Stud ies have suggested that grazing east of the Coast Range has impacted suitable habitat for the Alameda whipsnake (USFWS, 1997). Livestock grazing becomes detrimenta l to the species wh en it significantly reduces or eliminates shrub and grass cove r (USFWS, 1997). According to these studies, the Alameda whipsnake along with other snake species avoid such ope n areas because of magnified predatory risk and lack of pr ey (USFWS, 1997). In appropriate grazing practices include overgrazing a nd burning or bulldozing to rem ove scrub prior to grazing (USFWS, 2006). These practices affect the scrub component of the vegetation mosaic, and reduce grass height or density to such levels that expose Alameda whipsnakes to greater predation from hawks (USFWS, 2006).

1.2.1.5 Non-native species

In addition to the increased predatory pre ssure from introduced species described in section 1.2.1.2., the Alameda whipsnake is also threatened by nonnative flora and fauna altering California’s native grassland and coastal prairie (USFWS, 2003). Introduced plant species include Genista monspessulana (French broom), Carpobrotus spp. (iceplant), Eucalyptus (Eucalyptus), and Ulex europaeus (gorse) (USFWS, 2003). These species often outcompete and supplant native vegetation to the point of potentially degrading the habitat, increas ing fire risk, and reducing wh ipsnake prey base (USFWS, 2003). Hybridization, which could decrease gene tic variability, is al so a consequence of nonnative invasions (USFWS, 2003). For example, Arctostaphylos pallida , a native member of California’s chaparral ecosystems, can easily hybridize with ornamental Arctostaphylos spp. planted by homeowners (USFWS, 2003). Non-native fauna species

9can also affect native vegetation (USFWS, 2003) . Studies of impacts from feral pigs on natural habitat have shown effects to plant species diversity, total herbaceous cover, and soil chemistry (USFWS, 2003). These vegetatio n alterations incrementally affect the

distribution and abundance of small animals and amphibian species (USFWS, 2003).

1.2.2 Baseline Status

At the time of the species’ “threatened” listing in 1997, the USFWS concluded that the Alameda whipsnake was likely to become e ndangered within the foreseeable future (USFWS, 1997). The USFWS cited the failure to implement adequate fire management practices and sustain suitable ha bitat as key factors in the co ntinued decline of the species (USFWS, 1997). Degradation of suitable habitat is a consequence of urbanization, fragmentation, grazing practices, and mining, each affecting the species’ subpopulations to a different degree. The Population D ynamics section will cover these factors threatening the survival of each subpopulati on and the potential alterations to the currently designated species’ critical habitat. The following Habitat Conservation Plan section will provide detail on authorized take of the species.

Population Dynamics Currently, the Alameda whipsnake inhabits th e Inner Coast Ranges in western and central Contra Costa and Alameda Counties, with occurrences additionally recorded in San Joaquin and Santa Clara Counties (U SFWS, 1997, 2003, and 2006). The current distribution of the subspecies has been re duced to five separated ranges within a fragmented regional metapopulation, all occu rring on private or publ ic, non-Federal land, with little or no interchange due to habitat loss, altera tion, and fragmentation (USFWS, 2003). These ranges correspond to the designate d recovery units in the draft recovery plan for chaparral community species (USFWS , 2003) that preceded the determination of critical habitat (USFWS, 2006).

1. Sobrante Ridge, Tilden/Wildcat Regional Parks area to the Briones Hills, in Contra Costa County (Tilden-Briones population)

2. Oakland Hills, Anthony Chabot area to Las Trampas Ridge, in Contra Costa County (Oakland-Las Trampas population)

3. Hayward Hills, Palomares area to Pleasanton Ridge, in Alameda County (Hayward-Pleasanton Ridge population)

4. Mount Diablo vicinity and the Black Hills, in Contra Costa County (Mount Diablo-Black Hills population)

5. Wauhab Ridge, Del Valle area to the Ceda r Mountain Ridge, in Alameda County (Sunol-Cedar Mountain populati on) (USFWS, 1997 and 2003).

The Tilden-Briones population is currently threatened by ha bitat loss and fragmentation due to suburban/rural growth (USFWS, 2003). While the periphery of the range is impacted most from urbanization, developments within the interior are also promoting fragmentation (USFWS, 2003). The Tilden-Bri ones population is further at risk from catastrophic wildfire and from nonnative invasion (eg. Eucalyptus ) into chaparral and

10scrub communities (USFWS, 2003). Due to par tial overlap of the habitat with regional parklands and municipal watersheds, regiona l preservation and land management to the benefit of the Alameda whipsnake may be possible (USFWS, 2003).

The Oakland-Las Trampas population is impe riled by the decadence of chaparral/scrub stands, high risk of catastrophic wildfires, a nd habitat loss and frag mentation from urban development (USFWS, 2003).

The Hayward-Pleasanton Ridge population is most susceptible to exti rpation. Similar to the other subpopulations, the Hayward-Pleasa nton Ridge population is threatened by urbanization (USFWS, 2003). Unlike any of the other five areas, however, the open space and conservation land within this habita t range is the most disconnected (USFWS, 2003). The northern and southern parts of the range are at immediate risk of isolation, which would increase the susceptibility to genetic drift and chance events (USFWS, 2003).

The Mount Diablo-Black Hills population is threatened by a high potential for catastrophic wildfire, suburban/r ural development, and land us es (eg. mining) that are at odds with Alameda whipsnake suitable habi tat (USFWS, 2003). Th is population is a good candidate for recovery considering the location of public lands, the actions of private nonprofit organizations regarding wildlife corri dors, and the potential for improved fire and grazing practices (USFWS, 2003).

. The Sunol-Cedar Mountain population is threatened by catastrophic wildfires and incompatible land uses, including mining and off-road vehicle use. Currently the pressure from urbanization is relative ly low, although the demand for housing developments is increasing. Unauthorized co llection may be most acute in the southern region of the population. The ar ea attracts reptile enthusiasts and collectors because of its remote roads and diversity of native reptiles.

The Caldecott Tunnel co rridor links the Tilden-Brione s and Oakland-Las Trampas populations, and the Niles Canyon-Sunol corr idor connects the Hayward-Pleasanton Ridge and Sunol-Cedar Mountai n populations. The Caldecott Tunnel corridor is heavily developed and highly fragmented (USFWS, 2003). Much of the vegetation was eradicated from a catastrophic firestorm on October, 20 1991, a nd revegetating the area is still in progress (USFWS, 2003). Future pl ant communities may not promote movement of the Alameda whipsnake because vegetation with low volatility is being discouraged (eg. Artemesia californica, California sagebrush) (USFWS , 2003). The Niles CanyonSunol corridor contains vari ous physical barriers that co uld impede movement of the Alameda whipsnake: Alameda Creek; a 0.3- to 0.6-meter (12- to 24-inch) high concrete barrier; railroad tracks; and heavy vehicular traffic along Niles Canyon Road (USFWS, 2003). Much of the land is also under cul tivation or mining (ie. gravel) and suitable vegetation for the Alameda whipsnake is limited (USFWS, 2003).

Habitat Conservation Plans

11Habitat Conservation Plans are defined in S ection 10 of the Endange red Species Act and target the actions of non-Federal entities in relation to listed species (USFWS, 2005). These plans authorize the take of listed species through Incide ntal Take Permits and help minimize or mitigate the effects of the action (USFWS, 2005). Two Habitat

Conservations Plans are listed on the USFWS species profile webpage for the Alameda whipsnake (Species Profile). The first Plan is the East Bay Municipal Utility District and covers 28,000 ac between Alameda and Contra Coast Counties (Species Profile). The second plan is the East Contra Costa County HCP/NCCP (Species Profile). A permit was

issued for this Plan in 07 /25/07 for 175,435 ac of Contra Co sta County for the duration of 30 years (Species Profile).

1.3 REFERENCES

Literature Cited

Species Profile: Alameda Wh ipsnake (=striped racer) ( Masticophis lateralis euryxanthus ). U.S. Fish and Wildlife Servi ce (USFWS). Available online at: http://www.fws.gov/sacramento/es/animal_spp_acct/alameda_whipsnake.pdf (Accessed on December 10, 2008).

United States Fish and Wildlife Service (USFWS). 1997. Endangered and Threatened Wildlife and Plants; Determination of Endangered Status for the Callippe Silverspot Butterfly and the Behren's Silv erspot Butterfly and Threatened Status for the Alameda Whipsnake. Available online at: http://ecos.fws.gov/docs/ federal_register/fr3183.pdf (Accessed on December 10, 2008).

United States Fish and Wildlife Service (U SFWS). 2003. Draft Recovery Plan for Chaparral and Scrub Community Species East of San Francisco Bay, California. U.S. Fish and Wildlife Service, Region 1, Portland, Oregon. 306 pages. Available

online at: http://ecos.fws.gov/docs/recovery_plans/2003/030407.pdf (Accessed on April 17, 2008).

United States Fish and Wildlife Service (U SFWS). 2005. Habitat Conservation Plans: Section 10 of the Endangered Species Act. Available online at : http://ecos.fws.gov/docs/conservati on_plans/HCP_Incidental_Take.pdf (Accessed on December 22, 2008).

United States Fish and Wildlife Service (USFWS). 2006. Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for the Alameda Whipsnake;

Final Rule. Available online at: http://edocket.ac cess.gpo.gov/2006/pdf/06- 8367.pdf (Accessed on December 10, 2008).

12132: BAY CHECKERSPOT BUTTERFLY

2.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the bay checkerspot butterfly ( Euphydryas editha bayensis ) (BCB) that are reasonably certain to occur in the action area. Future federal actions not directly related to the proposed action are not considered because they require additional consultation under Section 7 of the Endangere d Species Act (Act). The numerous nonfederal actions that are reasona bly certain to occur within th e action area consist of urban and suburban development, infrastructure expansions, commercial and private construction, agriculture, research, pest (gophe r) control, and activities related to climate change. Many of these factor s are linked or act synergis tically and create complex consequences for the BCB. For example, urban and suburban developments encourage the expansion of infrastructure and intens ify the effects of climate change. These developments contribute to habitat loss and facilitate ha bitat fragmentation, weakening the strength and stabili ty of populations. Compounded with the other non-federal actions, populations become even more su sceptible to the accumulation of adverse effects.

2.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the effects of past and ongoing human induced and natural factors leading to th e status of the species, its habitat, and ecosystem, within

the action area. The environmental baseline is a snapshot of the bay checkerspot butterfly’s status at this time. However, th e baseline condition of the assessed butterfly’s

habitat varies across locations and within each critical habi tat unit. Details of the bay checkerspot butterfly’s habitat descripti on and known locations are included in Attachment III. Given the large amount of ha bitat and extent of the action area included of this assessment, the discussion of envir onmental baseline includes a general discussion of factors and a few listed projects that may affect the BCB w ithin the action area. This information is presented in Section 2.2.1. The baseline status and population dynamics of the species is provided in Section 2.2.2. Th e majority of information included in the

environmental baseline section is a summar y of information on the bay checkerspot butterfly presented in the Recovery Plan fo r Serpentine Soil Species of the San Francisco Bay Area (USFWS, 1998), and the Designa tion of Critical Habitat for the Bay Checkerspot Butterfly ( Euphydryas editha bayensis ); proposed rule (USFWS, 2007).

2.2.1 Factors affecting species envi ronment within the action area

A number of factors affect th e species environment, define d by a habitat comprised of serpentine, or serpentine-like or -derived so il. This soil is formed from weathered ultramafic rocks, serpentinite, dunite, and peridotite, and pres ents harsh environments for

14plant growth: 1) a low calcium/magnesium ratio ; 2)lack of essential nutrients such as nitrogen, potassium, and phosphorus; and 3) high concentrations of heavy metals (mineral toxicity) (Kruckenberg, 1984a). Th is native environment is primarily affected by destruction and degradation, and infestat ions of native species (accompanied by air pollution). Factors affecting the species incl ude overutilization for research and private purposes, control of gophers, vehicular dist urbance, fire and grazing practices, and climate change. Sections 2.2.1.1 through 2.2.1.6 provide details on the major issues facing bay checkerspot butterfly populations within the entire action area.

2.2.1.1 Habitat loss and degradation

Habitat loss and degradation is one of the two most influe ntial factors affecting the BCB and is caused primarily by urban and suburba n development (Murphy and Weiss. 1988a). Reducing suitable habitat for the BCB decreases the size and number of populations and increases vulnerability to stochastic environmental events. Elimination of serpentine habitats also destroys steppi ng-stone areas, small patches in between suitable habitat, and makes recolonization and pers istence of metapopulations di fficult (USFWS, 1998). Prior to BCB listing, two primary habitats thought to support persistent “core” populations were lost to housing and infras tructure developments. This habitat conversion occurred around the Hillsborough and San Mateo areas, and included losses to secondary and tertiary habitats (secondary habitat refers to small serpentine outcrops, while tertiary habitat refer to areas where host plants occu r but not on serpentine so il). Extirpation was

recorded to affect 29 of 32 probable secondary habitats, 5 of 8 known secondary habitats, at least 5 of 6 known margin al habitats, and over 9 othe r likely areas (USFWS, 1987). Over the past couple of decades, development in the city of San Francisco has occurred on top of several serpentine habitats (Hunters Point), although whether the areas supported the BCB with quality habitat is unknown. By the time of its listing in 1987, the BCB occupied as few as 2 out of its 16 known historic localities with persistent populations. Only two locations at present, the Edgewood Natural Preserve in San Mateo County and Coyote Ridge in Santa Clara C ounty, support large populations of BCBs. Rates of loss in recent years have slowed considerably but have yet to fully subside (USFWS, 1998).

Habitat fragmentation is documented and is a concern for the BCB because of its limited dispersal ability and distribution within a metapopulation structure. Four patches of

suitable habitat once found within San Mate o County have now been divided into 11 smaller units (Ehrlich, 1961, 1965). Some of th ese units are separated by a 6- or 8-lane freeway, which greatly hinders trans-patch move ment and promotes populations to live in isolation. A BCB population on Sa n Francisco Water Department land first declined, and then went extinct, after it was divided by the construction of I-280 from the Edgewood Natural Preserve population (A. Launer, pers. comm., 1997). The Edgewood Natural Preserve is the largest of the 11 fragmented habitats in San Mateo County, and the only one still supporting a sign ificant population (Ehrlich and Murphy, 1987).

15Urban and suburban developments continue to threaten BCB survival since the time of its original listing in 1987. The growth of the San Francisco Bay Area plus the expanding human population threatens the species into the near future. The U.S. Fish and Wildlife Service (USFWS) has been involved in a num ber of urbanization projects potentially impacting the BCB. Technical assistance was required for eight projects in 1995 and 1996, and 5 projects required informal consu ltations with the USFW. At the time the Recovery Plan for the Serpentine Soil Sp ecies (including the BCB) was released, four projects were proposed or currently proposed that would adversely affect serpentine grassland. These four projects were Cerro Plata, Metc alf Road widening, Richmond/Young Ranches, and Calero Lake Estates.

Cerro Plata

The Cerro Plata project in eastern San Jose was proposed on the Silver Creek Hills bay checkerspot population area. Th e project area incorporated 23 2 hectares (575 acres) of a housing development and golf course on mostly serpentine habitat. According to the USFWS, the Environmental Impact Report for the project underestimated the amount of bay checkerspot habitat at the site, and consequently underestimates the potential impacts. A Habitat Conservation Plan (H CP) (a conservation plan developed by nonFederal parties applying under section 10 of th e Act for a permit for incidental taking of listed species) is being crafted by the s ite owner and consultants to revise the development proposal for the site (USFWS, 1998).

Metcalf Road

The proposed project in the City of San Jo se would widen and st raighten a portion of Metcalf Road. The impacted area would incl ude serpentine habitats and affect the associated serpentine plant and animal speci es that are threatened or rare, and would

increase road kills of the BCB. The Federall y listed species, including the California redlegged frog ( Rana aurora draytonii ), would also be vulnerabl e to the effects of the project. The expanded road would facilitate human access to bay checkerspot core habitat: the Kirby, Metcalf, and San Felip e populations. The USFWS has recommended that the U.S. Army Corps of Engineers c onsult under section 7 of the Act (USFWS, 1998).

Richmond/Young Ranches

The proposed project would extend the City of San Jose Urban Growth Boundary to include portions of Young Ranch, Richmond Ranch, and smaller adjacent properties. The project is the result of combined intere sts of the YCS Investments of San Francisco and the owners of the Richmond Ranch, that toge ther wish to create a planned residential community not exceeding 2,450 housing units , a golf course, resort, and other miscellaneous developments. The extens ion of the 735-hectare (1,817-acre) includes suitable serpentine habitat for the BCB Me tcalf population (City of San Jose, 1997).

Calero Lake Estates

16Not much information has been provided on the Calero lake Estates project. The available information states that the projec t is an incomplete housing subdivision in the southern Santa Teresa Hills, situated in cont act with the Santa Teresa County Park. Bay checkerspot are known to occur in the serp entine habitat in th is location and are vulnerable to the past and future developments (USFWS, 1998).

In addition to the well-described urbaniza tion projects above, other developments in serpentine areas could potentially impact th e BCB as well. Developments in Santa Clara County are predicted to increase into the near future. Developments in San Jose are continuing and are guided under a general plan until 2020. However, this is a separate measure from the proposed Santa Clara C ounty HCP, and the Court of Appeals 6 th
district found that the City’s zoning did not have to be cons istent with the general plan (Juarez et al. v. City of San Jose et al. (6 th District, Case no, CV736436 H014755)). This

means that current habitat not within the urban growth boundary may still be proposed for development. Other projects include the Coyote Valley Specific Plan, residential and industrial developments, the Coyote Valley Research Park project, numerous proposals under the Santa Clara County HCP, and projects including single family residential units and road grading (USFWS, 2007).

2.2.1.2 Invasive plants and air pollution

Invasion of exotic species is the second of the two most infl uential factors affecting the BCB. Despite the inhospitable conditions of serpentine environments, non-natives are still capable of colonizing th e area. Non-native grasses have been observed to choke out BCB host plants in the Edgewood Natural Pres erve (USFWS, 1998) and serpentine soils in Silver Creek Hills (R. White, pers. comm.., 1997, A. Launer, pers. comm., 1997, S. Weiss, pers. comm., 1997, D. Murphy, pers. comm., 1997), and include, but are not limited to, the yellow star thistle ( Centaurea solstitialis ) and certain eucalyptus species ( Eucalyptus spp.). Northern California continues to see new introductions of exotics through gardening, landscaping, and accidental means (USFWS, 1998).

Nitrogen deposition from air po llution facilitates th e spread of non-na tive vegetation in serpentine habitats. The usually nutrient- poor serpentine soils are enriched with the addition of atmospheric nitrogen, a typical limiting factor for plant growth (Weiss 1999, p.1477). Nitrogen has been associated with thic k patches of vegetativ e material (thatch) that inhibits growth of the native plant species (Huenneke et al. 1990, p.488). Thatch threatens the host plants of the bay ch eckerspot through competition and crowding (Weiss 1999, p. 1481).

2.2.1.3 Overutilization for research and private purposes

As part of a long-term research and m onitoring program, Stanford University has investigated the biology of the BCB since 1960. The research has been carried out on the

17Jasper Ridge Biological Reserve, and Harrison et al. (1991) has estimated the effects of collection on two BCB populations. From 1960 and 1983, between 0 and 386 (mean 57.3) females per year were removed from the populations for electrophoresis and other purposes. The number removed, on averag e, was 6.1 percent of the populations (Harrison et al. 1991). The study concluded that the effects of individual removal were

much smaller than the effect of natural envi ronmental variability. The study indicated, however, that the removal incr eased the risk of population ex tinction, from a negligible risk to a 15 percent prob ability over 30 years (depe nding on model used) (USFWS, 1998).

Foot-traffic connected with the study of one Jasper Ridge population was found to have a significant impact on the area’s vegetation (Ehrlich and Murphy,1987). According to Ehrlich and Murphy (1987), trampling could have destroyed the BCB eggs, larvae and pupae. Another study by Orive and Baughman (1989) studied the impacts of a mark-andrecapture study on the BCB at Jasper Ridge and found that handli ng did not observably increase wing-wear.

Illegal collecting has been documented to affect the BCB, and the USFWS has prosecuted known cases. Illegal take will mo st likely affect those BCB populations that are small or have been reduced by natural or ar tificial factors, or that are easily accessible by people (USFWS, 1998).

2.2.1.4 Gopher control and vehicular disturbance

A positive correlation exists between the pres ence of gophers and BCB survival. A study by Singer (1972) noted that BCB larvae can survive later in to the spring on Plantago

erecta growing in soil disturbed by gophers ( Thomomus bottae ). Singer suggested that the gophers loosened up the soil and allowed for more root growth and water retention (Singer, 1972). A more recent study found BC B larval host plants to stay green and edible longer when located on or nearby soil s recently tilled by gophers (Singer, 1972, p. 75; Murphy et al. 2004, p. 26). Another suggestion wa s made that gopher disturbance limits the performance of grasses and allows for the persistence of smaller forbs. The prediapause larva may be able to reach the four th instar since the larval host plants stay greener for longer (Huenneke et al. , 1990, p. 490).

A negative correlation exists between vehicl es and BCB individuals. Bay checkerspot mortality results from direct vehicular strike s and associated turbulence. The degree of annual mortality or injury, however , is uncertain (USFWS, 1998).

2.2.1.5 Fire and grazing practices

After a wildfire spread across portions of San Bruno Mountain in 1986, no bay checkerspot butterflies were subsequen tly observed (USFWS, 2007). Although only 50

individuals had been observ ed there in 1984 (CNDDB, 1984), and other factors besides

18fire were implicated in their extirpation, wildfi res are still considered a threat to the BCB. Prescribed burns, however, are regarded as potentially effective tool s to combat invasion of non-natives and stimulate gr owth of species adapted to the disturbance. However, benefits of burn regimes on serpentine grassl ands are not well documented and have been provided by monitoring studies made possibl e after wildfires. An experimental prescribed burn was conducted on a small segment of Coyote Ridge in 2006, but the benefits to the native speci es, including the BCB, are not yet known (USWFS, 2007).

A limited amount of grazing is considered be neficial to BCB habitat, while over- or under- grazing threatens the surviv al of native host plants. If not appropriately managed, overgrazing threatens to reduce the density of native vegetative mass. A study by

Huenneke et al. (1990, p.489) and Weiss et al. (1999, p. 1480) found that undergrazing resulted in an increase of annual grasses, which crowd out native forbs (USFWS, 2007). Sustainable grazing practices are generally recognized as non-threatening to the BCB (Thomas Reid Associates and Murphy 1987; Murphy, 1988; Weiss, 1996).

2.2.1.6 Climate change and climate extremes

The expected climate change in the San Franci sco Bay Area is curren tly disputed, but any

deviation from current conditions would most likely affect the bay checkerspot (Murphy and Weiss, 2002). Forecasted change scen arios impacting the BCB include wetter and warmer, wetter and cooler, drier and colder, a nd changes in the timing of rainfall. The BCB would likely be sensitive to weather extremes because its developmental requirements and host plants’ survival depe nds on the climate. The largest and potentially most viable populat ion, the Kirby Bay population, is not well-buffered against changes in temperature or precipitati on. The drought in 1975 and 1977 caused the disappearance of many small populations in this normally dry area, compared to populations in normally wetter areas (Murphy an d Weiss, 2002). Climate change is also predicted to change the dominance of native vs. non-native serpentine species (USFWS, 1998).

As with the aforementioned drought in 1975 and 1977, other dry periods and weather extremes have been linked to declines in BCB populations; however, clearcut BCB weather responses are hard to define (Ehrlich et al. 1980; Weiss, 1996). There is evidence that northern California has experien ced more severe and long-lasting droughts in the past millennium than were ever re corded in history (S tine, 1994). The BCB high reproduction potential indicates th e species is well-adapted to the area, as the bay region has been its home for a long time, but its poo r resilience after rece nt weather extremes may be due to other, probably hum an-induced, factors (USFWS, 1998).

2.2.2 Baseline Status

The current bay checkerspot butterfly range is much reduced from its historic distribution (USFWS, 2007). The BCB previously occupi ed the area around the San Francisco Bay,

19spanning from San Bruno Mountai n and Twin Peaks in the we st, to Contra Coast County in the east, and south through Santa Clar a County (Murphy and Ehrlich 1980; Opler et
al. , 1985; California Natural Diversity Data Base, 1996). Currently, the BCB has gone extinct in Contra Costa County (Franklin Ca nyon and Morgan Territory areas), Alameda County (Oakland Hills), San Francisco Count y (Twin Peaks and Mount Davidson), San Bruno Mountain, Buri Buri Ridge (Hillsborough) , Pulgas Ridge (or “San Mateo”), and Redwood City in San Mateo County (historic site referred to as Woodside) (Murphy and Weiss, 1988a; California Natural Di versity Data Base, 1996).

The current distribution is an example of a metapopulation, and because of its interdependent extinction and colonization processes, the exact distribution of the butterfly varies throughout time (Wilcox and Murphy, 1985; Harrison et al. 1988). Any site within the proximity of the historic ra nge could potentially be occupied by the BCB. There are reports of checkerspot ecotypes ( Euphydryas editha ) that occur in the south and east of the bay checkerspot distribution, but st atus of these subspeci es is unknown at this time. Even though the BCB is patchily distri buted, two large metapopul ations have been

identified. These occur in Santa Clara and San Mateo Countie s (Murphy, 1988).

Within the two metapopulations, five core areas have also been identified for the BCB:

one on the San Francisco Peninsula in San Mateo County (Edgewood County Park), and four in Santa Clara County. Core areas r oughly correspond to primary habitat, defined as moderate to large areas of suitable habitat that support persistent bay checkerspot populations. These areas supply migrants to unoccupied sites, continuing the repopulation/extinction cycles. The Santa Cl ara core areas are lo cated along a ridge immediately east of Santa Clara Valley, de signated Coyote Ridge (one of its many common names) by the Recovery Plan (USFWS, 1998). The four core areas are entitled Kirby, Metcalf, San Felipe, and Silver Creek Hills, and are discontinuous serpentine areas that are all within butterfly flight distance of ea ch other. The last of the four core areas, Silver Creek Hills, is not considered by the USFWS to be a significant population, although it has a status of a “core” populati on. These four core areas, comprising the Santa Clara County metapopulati on, are thought to have the best chance of long-term persistence (Murphy, 1988; Murphy and Weiss 1988a). The Edgewood Park metapopulation is smaller, probably due to be ing located on a smaller area, with smaller and poorer quality secondary habitats surround ing it. Natural migration between the two metapopulations is uncommon because they are currently separated by 40 kilometers (25 miles) (USFWS, 1998).

Conservation measures emphasize the value of secondary or satelli te populations that generally occur on smaller or of lesser qual ity land than primary habitats. Both core areas and secondary areas are necessary for the natural metapopulation dynamics of the BCB. Specific dynamics of the BCB are partic ularly important to fields of population and conservation biology and ongoing studies from the 1960s have ge nerated significant data. Further, satellite populations act as stepping stones for dispersal. Tulare Hill appears to be a stepping st one habitat for BCB dispersal across Santa Clara Valley. Finally, secondary populations help protect popul ations against complete extirpation after unforeseen environmental disasters: fire, extreme weather, air pollution, or climate

20change. While core areas may be the targets of catastrophic events, secondary populations may survive to recolonize th e formerly inhabited areas (USFWS, 1998).

Population Dynamics Since its listing in 1987, the di stribution and population size of the bay checkerspot has changed dramatically. Since the critical habitat designation in 2001, the number of

known occurrences has continue d to decline. For exampl e, the USFWS designated 15

critical habitats in 2001. A revised critical habitat desi gnation was proposed in 2007 and suggested redefining and reduci ng the number of units to 12. Most of the proposed units correspond to those from 2001. The eliminated areas were unlikely to support the PCEs for the BCB, or had since been developed. For example, the area designated unit six (Communications Hill) was excl uded from the revised version due to developments and degradation from non-native invasions. Un it two (Pulgas Ridge) is a newly proposed area and is currently undeveloped. The unit re sides within the historic range of the species and could potentially serve as a stepping-stone betw een proposed units four and five, the two southern most units in Sa n Mateo County, and San Bruno Mountain. The proposal awaits final ruling (USFWS, 2007).

The San Mateo County subspecies have signi ficantly declined, and populations at San Bruno Mountain, Pulgas Ridge, and Jasper Ridg e have yet to be detected in limited surveys. No BCB individual was detected on a small southeastern portion of Pulgas Ridge where surveys took place from 1989 to1993 and 1994. However, these surveys only covered a section of the much larger area that was historically occupied by the butterfly. The Edgewood County Park population, deemed the only core population in San Mateo County, was last observed in 2002 (CNNDB, 2006). Rest oration efforts in February and March of 2007 reintroduced a pproximately 1,000 post-diapause larvae to

the Park to maintain a viable San Ma teo County population (C NDDB, 2007). The successful fate of this population has yet to be determined.

Population trends have been discerned for limited portions of Coyote Ridge in Santa Clara County. These portions correspond to units 4, 8, 10, 11, 12, and 15 in the 2001 determination (66 FR 21450) (USFWS, 2007). The population at unit eight (Kirby) increased from 20,000 individuals in 1997 to 700,000 in 2004. In 2005, the population fell to about 100,000 individuals (Weiss, 2006, p. 1). The population at unit 10 (Metcalf) increased from 200,000 individu als in 2000 to 400,000 in 2004, but then declined to 45,000 individuals in 2006 (Weiss, 2006, p.1). The population from unit 12 (Silver Creek) was estimated in larval units, a nd increased from 75,000 in 1992 to 128,000 in 1993, but dropped to an estimated 58,000 in 1994 after grazing was removed from sections of the area (Weiss, 1996, p. 93; Wei ss, 1999, p. 1480). No larvae or adults were observed in 1998 (Weiss, 1999, p. 1480). In 2000 and 2001, a residential subdivision was constructed and grazing was reintroduced in unit 12. Annual surveys since this period have shown 11 adults in 2001, up to a maximum of 51 in 2005. Only 40 adults were detected in 2006, but no larva was obs erved (WRA 2006, p. 10). The population in unit 15 (Tulare Hill) contained approximat ely 2,000 individuals in 2002. The population significantly declined in 2003 with only one sighting of a post-diapause larvae (CH2M Hill, 2004, p. 8-6), and five sightings of a dults in 2004 (CH2M Hill, 2005, p. 8-2). Weiss

21(2007, p.1) estimated the Tulare Hill populat ion to total 100 individuals from the 2004 observation. In 2005, seven adults were obser ved, with no detection of post-diapause larvae (CH2M Hill 2006, p. 8-2). Thousands of BCB were observed at unit 4 (Bear Ranch) in 1994, six adults were observed in 1997, and one adult in 1999. The USFWS does not possess any additional studies on the Bear Ranch population after 1999 (USFWS, 2007).

Habitat Conservation Plans

The San Bruno Habitat Conservation Plan was th e first Habitat Conservation Plan for the bay checkerspot butterfly and was adopted in 1983. Set to expire in 30 years, the Plan will discontinue unless renewed by March 31, 2013. The Plan originally covered 1,400 hectares (3,400 acres) in northern San Mateo County and identified seven animal species and 44 plant species. At the time of its publi cation, the plan did not specifically focus on the BCB, but rather on the mission blue and Sa n Bruno elfin butterflies (listed species at the time), the callippe silverspot butterfly (unlisted at the time), and their host plants (USFWS, 1998). The plan is currently undergoing its fifth amendment, and would

include conservation actions th at would benefit both the bay checkerspot and callipe silverspot butterflies. The conservation act ions include: (1) vegetation management (e.g.

, prescribed fire, herbicide application, mowing, and grazi ng); (2) replanting and restoration; and (3) monitori ng. The plan will also s ubstantially protect all bay checkerspot PCEs. A finalized amendment is expected by the USFWS in 2008 (USFWS, 2007).

Two other Habitat Conservation Plans, acces sed online though the Fish and Wildlife Service webpage, have been issued on behalfof the BCB. The first was entitled MetcalfEvendale/Monta-Vista (PG&E) HCP and was issued in 1997. PG&E Metcalf - El Patio,

Metcalf -Hicks/Vasona LE HCP was the second and was issued in 2007. Both extend three years, and the first Plan has since expired in 2000.

2.3 REFERENCES

Literature Cited

California Natural Diversity Data Base (CNDDB). 1996. Natural Heritage Division. California Department of Fish and Game. State of California.

City of San Jose. 1997. UGB modification fo r the Richmond/Young Ranches. Memo from James R. Derryberry, Director of Planning, Building and Code Enforcement, to the Planning Commission, September 17, 1997. City of San Jose, CA. 7 pp.

Ehrlich, P.R. 1961. Intrinsic barriers to disp ersal in checkerspot butterfly. Science

134: 108-109.

Ehrlich, P.R. 1965. The population biology of the butterfly, Euphydryas editha . II. The

22structure of the Jasper Ri dge colony. Evolution 19: 327-336.

Ehrlich, P.R., and D.D. Murphy. 1987. Conserva tion lessons from long-term studies of checkerspot butterflies. C onservation Biology. 1:122-131.

Ehrlich, P.R., D.D. Murphy, M.C. Singer, C.B. Sherwood, P.R. White, and I.L. Brown. 1980. Extinction, reduction, stability and increase: the response of checkerspot butterfly ( Euphydryas ) populations to the California drought. Oecologia 46: 101-105.

Harrison, S., J.F. Quinn, J.F. Baughman, D.D. Murphy, and P.R. Ehrlich. 1991. Estimating the effects of scientific study on two butterfly populations. American

Naturalist 137: 227-243.

Harrison, S., Murphy, and P.R. Ehrlich. 1991. Distribution of the bay checkerspot butterfly, Euphydryas editha bayensis : evidence for a metapopulation model.

American Naturalist 132: 360-382.

Kruckeberg, A.R. 1984. Californi a serpentines: Flora, vege tation, geology, soils, and management problems. University of Ca lifornia Press, Berkeley, California. 180

pp.

Murphy, D.D. 1988. The Kirby Canyon conser vation agreement: a model for the

resolution of land-use conflicts invol ving threatened invertebrates.

Environmental Conservation 15: 45-48.

Murphy, D.D., and P.R. Ehrlich. 1980. Two California checkerspot butterfly subspecies: one new, one on the verge of extinction. Journal of the Lepid opterists’ Society

34: 316-320.

Murphy, D.D. and S.B. Weiss. 1988. Ecological studies and the conservation of the bay checkerspot butterfly, Euphydras editha bayensis . Biological Conservation

46: 183-200.

Opler, P.A., R.A. Banks, M.M. Bentzien, and S.M. Chambers. 1985. Subspecific status of the bay checkerspot butterfly ( Euphydryas editha bayensis ). A panel report to the Associate Director – Federal Assistance, Fish and Wildlife Serv ice, Department

of the Interior.

Thomas Reid and Associates and D.D. Murphy. 1987. Kirby Canyon Landfill conservation plan 1985/1986 monitoring report. Prepared for Kirby Canyon Trustees, February 17, 1987. Unpublished.

U.S. Fish and Wildlife Service (USFWS). 1987. Endangered and threatened wildlife and

23plants; determination of threatened st atus for the bay checkerspot butterfly ( Euphydryas editha bayensis ). Federal Register 52 :35366-35378 (September 18, 1987).

U.S. Fish and Wildlife Service (USFWS). 1998. Recovery Plan for Serpentine Soil Species of the San Francisco Bay Area. Portland, Oregon. 330+ pp.

U.S. Fish and Wildlife Service (USFWS). 2007. Designation of critical habitat for the Bay Checkerspot Butterfly ( Euphydryas editha bayensis ); proposed rule. Federal Register 72 (162): 48177-48218.

Weiss, S.B. 1996. Weather, landscape struct ure, and the populat ion ecology of a threatened butterfly, Euphydryas editha bayensis . Ph.D. dissertation, Stanford, University, Stanford, California. 119 pp.

Wilcox, B.A. and D.D. Murphy. 1985. Cons ervation strategy: the effects of fragmentation on extinction. Am erican Naturalist 125: 879-887.

Personal Communication

Launer, Alan. 1997. Center for Conservation biology, Stanford University, Stanford,

California.

Murphy, Dennis. 1997. Center for Conservation biology, Stanford University, Stanford,

California.

White, Raymond R. 1997. Biology Department, City College of San Francisco, San Francisco, California.

Weiss, Stuart. 1997. Center for Conservation biology, Stanford University, Stanford,

California

243: CALIFORNIA CLAPPER RAIL

3.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the California Clapper Rail (CCR) ( Rallus longirostris

obsoletus ) that are reasonably certain to occur in the action area. Future federal actions unrelated to the proposed action are not c onsidered because they are subject to consultation pursuant to Section 7 of the E ndangered Species Act (Act). Numerous nonfederal actions that could affect the Califor nia Clapper Rail are reasonably certain to

occur within the action area. These activities are associated with modifications to salt

and brackish marsh habitats and typically include urban and industrial developments, filling and diking activities, maintenance of levees, and conversions of salt marsh to

brackish water habitats. These actions coul d compound to create complex consequences for the CCR. For instance, urban development could lead to habitat loss, degradation, and fragmentation. These factors reduce the quality and suitability of CCR habitat by influencing the presence of tidal channel sy stems and the inland ex tent of high and low tides. Encroaching developments change CCR predation zones and affect second order predators that would otherwise benefit the CCR. Predatory impacts on the CCR are further intensified by high marsh and na tural high tide cover.

3.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the effects of past and ongoing human induced and natural factors leading to th e status of the species, its habitat, and ecosystem, within

the action area. The environmental baseline is a snapshot of the California Clapper Rail’s

status at this time. Details of the California Clapper Rail ’s habitat description and known

locations are included in Attachment III. However, the baseline condition of each assessed CCR species and habitat varies acro ss locations. Given the large number of occupied habitats and extent of the ac tion area included of this assessment, the environmental baseline presents a general discussion of factors that may affect CCR

within the action area. This information includes both detrimental and potentially beneficial factors affecting the species a nd is presented in Section 3.2.1. Additional

information on the current distribution and population dynamics of the CCR is presented as part of the baseline status in Section 3.2.2.

3.2.1 Factors affecting species within the action area

Habitat loss and fragmentation present the most significant threat towards the CCR and its environment. Marsh size and habitat qual ity dictate the maximum number of rails in any particular marsh and are impacted by habi tat alteration. The prim ary causes of this

25loss and fragmentation include: erosion, introduction of freshw ater, change in landscape, subsidence, lack of tidal channels, invasive species, and land management practices. Hunting, predation, disease, and climate ex tremes are additional detrimental factors currently affecting the CCR and its habitat. Beneficial factors in clude restoration and protection projects that have been, or are currently being completed, to reconstruct and

enhance the salt marshes of the San Franci sco Bay Area. Sections 3.2.1.1 through 3.2.1.6 provide details on each of the major issues aff ecting the SFGS within the action area.

3.2.1.1 Habitat Loss and Fragmentation

Fragmentation and loss of habitat are th e main factors affecting CCR populations (Albertson, 1996). An 84% reduc tion in the tidal marsh borde ring San Francisco Bay has occurred since 1850 due to urbanization, f illing, and diking of wetland areas (USFWS, 2007; Environmental Impact; Albertson, 1996; and Save the Bay, 2005). Marshes that have been filled have had the upland vege tation and most of the high marsh zones eliminated which leaves no refuge for the CCRs during high tide (USFWS, 1984). Vegetation high in the marsh has also been el iminated in Suisun Marsh due to diking and livestock grazing (USFWS, 1984). Since the mid 1960s, there ha s been little large scale habitat loss; however, the loss of many small habitats has resulted in significant overall wetland loss and degrad ation (Albertson, 1996).

Physical factors that affect the marsh habita t include erosion, fres hwater introduction to the marsh, small size, fragmentation, subsiden ce, and a lack of tid al channels (USFWS, 2007). The shoreline of the East Bay is eroding, from San Leandro to Calaveras Point,

and could lead to the loss of several CCR populations in the ar ea (USFWS, 2007). The vegetation in about 600 acres of marsh that was previously salt marsh in South San Francisco Bay along Coyote Creek, Alviso Slough, and Guadalupe Slough, has been degraded and transformed to freshwater and brackish water vegetation as a result of freshwater input from Sout h Bay wastewater facilities (USFWS, 2007). The vegetation in this area is dominated by alkali bulru sh, which does not provide suitable nesting habitat, and CCR populations in this ar ea have declined (USFWS, 1984). Land

subsidence has also reduced the available CCR nesting habitat (USF WS, 1984). In South Bay, the difference between the high and low tid es is greater than in San Pablo or Suisun Bays, resulting in marshes that become completely submerged during high tides (USFWS, 2007). Marshes that become completely submerged during high tide usually do not have sufficient escape habitat for the CCR which results in high predation rates and also nesting failures (USFWS, 2007).

CCR habitat is lost due to an increase in the presence of steep sided channels which have replaced “gently sloping channel flats” wh ich are used by CCRs when they forage and when needed as escape routes from predators (SFEISP online). Many of the marshes in South San Francisco Bay are bordered by steep levees resulting in a loss of the upper marsh vegetation and less available cove r for the CCR during winter flood tides (USFWS, 1984). The lack of high marsh habitat and steep levees limits the ability of the CCR population to expand (USFWS, 1984). The de struction of CCR ha bitat has allowed

26the upland predators to more easily reach the vulnerable and relatively unprotected CCR and their eggs (Save the Bay, 2005).

Invasive Species CCR habitat is threatened by invasion of non-native cordgrass (CDFG, 2000). CCR depend on pickleweed and gum plant for nesti ng. Both of these plant species can be displaced by the non-native Spartina which invades channels and accretes sediment (SFEISP online). Excessive sedimentation ca n clog tidal sloughs which are used by the CCR for foraging (Goals Project, 2000). Howe ver, it appears that CCR have colonized marshes with this invasive species and used habitat areas that would otherwise not be suitable for this species (Spautz, 2007).

Land Management The land within Suisun Marsh is managed primarily for waterfowl (USFWS, 1984). Although waterfowl management is very importa nt, all native species that depend on this marsh should be protected and managed a ppropriately (USFWS, 1984). The recovery plan suggests that to achieve this goal “op timal freshwater and tidal flows” should be

maintained to simulate historic flow re gimes (USFWS, 1984). In addition, the CDFG and the USFWS should educate “property owne rs and hunters in waterfowl management areas” including Suisun Marsh about the pr esence and importance of CCRs (USFWS, 1984).

3.2.1.2 Hunting

Commercial and sport hunting of CCRs from 1850 to 1913 initially contributed to the depletion of the CCR (SFWS, 1984 and U.C. Berkeley, 2004), although there is no indication that hunting still impacts the CCR. The Migratory Bird Treaty Act of 1913, which restricted the harvest of game sp ecies, including CCR, allowed several rail populations to recover in the San Francisco Bay marshes; however, the CCR never fully recovered (USFWS, 1984; Albertso n, 1996; and Goals Project, 2000).

3.2.1.3 Predation

Throughout their range, CCRs and their eggs are susceptible to mammalian and avian predators (USFWS, 2007). Non-native mamma lian predators of the CCR and their eggs include Norway rats, red foxes, and feral ca ts and dogs (Environmental Impact and Goals Project, 2000). A study publishe d in 1980 showed that rats were responsible for the loss of 24% of eggs in 50 nests, and a study of CCRs in three marshes in south San Francisco Bay, published in 1988 also suggested that Norway rats were responsible for 24% of nest failures (Goals Project, 2000). Another study in 1992 in the South Bay showed that rats took 31% of eggs in 54 nests (Goa ls Project, 2000). Raccoons ( Procyon lotor ) and skunks also prey on CCR adults, juveniles, and eggs (Berkeley, 2004). Gopher snakes ( Pituophis melanoleuces ) have been observed preying on CCR eggs (Schwarzbach et al.,

272006). River otters ( Lutra Canadensis ) are found in Suisun Marsh and should also be considered to be a predator of the CCR (Goals Project, 2000).

Development in the areas surrounding the mars h displaces predators and also negatively affects higher order predator s, including coyotes, which may limit the numbers of CCR predators (USFWS, 2007 and USFWS, 2003). An increase in the red fox population in the tidal marshes of the South Bay since 1986 has had a negative impact on CCR populations in this area and red foxes may pose the most serious threat to adult CCR (USFWS, 2007 and Goals Project, 2000). Th e population decline in several South Bay marshes (Greco Island, Bay Farm Island, Mo wry Marsh, and Faber-Laumeister Marsh) after 1985 is likely due to predation by f oxes and harriers (Foin et al., 1997).

The San Francisco Bay National Wildlife Re fuge (SFBNWR) implemented a predator management program in 1991 (USFWS, 2003), which has reduced the impact of predators on some populations of the CCR (A lbertson, 1996 and Steiner, 1997; Steiner, 1997). Other efforts are also underway to re duce non-native red f ox populations (CDFG, 2000).

Avian predators of adult CCRs include northern harriers ( Circus cyaneus ), red-tailed hawks ( Buteo jamaicensis ), peregrine falcons ( Falco peregrinus ), and owls (USFWS, 1984; Foin et al., 1997). Predation of nests a nd eggs has also been attributed to ravens (Goals Project, 2000). Electric power tran smission lines which cross tidal marshes provide hunting perches for avian predators allowing increased hunting efficiency and intensity of CCRs (USFWS, 2007 and USFWS, 2003). Remains of CCRs have been found under poles that have been used as pe rches (Foin et al., 1997) . One study looking at predation showed that “64% of the rails killed were take n by raptors, primarily during the winter season” (Goals Project, 2000). Another study showed th at 25% of the rail population in one marsh was taken by raptors during the period from April through November (Goals Project, 2000). The prim ary predator during th e latter study was the barn owl ( Tyto alba ) (Goals Project, 2000).

3.2.1.4 Disease

It is currently unclear if the West Nile virus or other avian diseases will have an impact on the CCR (USFWS, 2007).

3.2.1.5 Climate Extremes

Fluctuations in rainfall and flooding, particular ly during El Niño year s, have the potential to affect the reproductive success of CCRs. Ho wever, while not all flooding events occur during El Niño years (and not all El Niño year s cause widespread flooding), the potential for flooding during these years is indeed gr eater (Monteverdi, 1998) . Populations of CCR may cyclically fluctuate with rainfall pa tterns, as do populati ons of the northern clapper rail in New Jersey (USFWS, 1984). In a study by Schwarzbach, et al . (2006),

28flooding was a minor factor in reproductive success, as oppose d to major factors such as predation or contaminants. Fl ooding affected the number of eggs available to hatch by 2.3% (Schwarzbach, et al . 2006).

3.2.1.6 Habitat Protection and Restoration

A number of restoration, re mediation, and habitat pr otection programs are ongoing. These are described in USFWS, 1984; Albe rtson, 1996; Goals Proj ect, 2000; Berkely, 2004. Significant portions of CCR habitat in South San Francisco Bay have been acquired by the National Audubon Society, CDFG, and the USFWS (USFWS, 1984).

3.2.2 Baseline Status

Southern San Francisco Bay Area has historic ally supported the larg est populations of CCRs. Salt marshes of the southern Bay Area included portions of San Mateo, Santa Clara, and Alameda Counties. Smaller popul ations occurred in San Francisco County and western Contra Costa County. Record s indicated populations around Southampton Bay in Solano County, Napa Marsh in western Napa County, next to Petaluma in Sonoma County, and Tomales Bay in Marin County (c ounties all bordering the Bay). CCRs

occurred further south of the San Franci sco Bay Area in Monterey County (Elkhorn Slough). Reports from the 1930s and 1940s i ndicated populations in Humboldt County (Humboldt Bay) and San Luis Obispo C ounty (Morro Bay), respectively (USFWS, 1984).

Currently, known CCR breeding populations are found only in tidal marshes in the San Francisco estuary (USFWS, 2007; Berkeley, 2004; and SFEISP online). The CCR only occurs in coastal wetlands in Alameda, C ontra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, and Sonoma count ies, which form the San Francisco-Suisun Bay complex (CDPR online). Populations of CCRs can be found in all of the larger tidal marshes in south San Francisco Bay; however, the distribution of CC Rs in the north Bay is fragmented (USFWS, 2007). Small popul ations of CCRs are found throughout San Pablo Bay (USFWS, 2007) a nd in the Suisun Marsh and surrounding areas (USFWS, 2007). Attachment III provides more details on the current range of CCR in the Suisan Marsh and Carquinez Strait, North Bay, Central Bay, and South Bay.

Population Dynamics Historically the CCR population may have once been in the tens of thousands (Foin et al., 1997). Estimations of this number are between 4,000 and 48,000 (Foi n et al., 1997). Based on surveys from 1971 to 1975, the entire CCR population was estimated at 4,200 to 6,000 individuals (USFWS, 1984 and Goals Project, 2000). This population was supposedly split with 55% occurring in Sout h San Francisco Bay and 45% occurring in San Pablo Bay (USFWS, 1984). A breeding de nsity of 1.6 CCR/ha in the South Bay was also described during this period (USFWS, 1984). A censu s reported in 1980 of two South Bay marshes supporting major CCR populat ions described a similar density of

29CCR (1.5 CCR/ha) (USFWS, 1984). This cons istency suggests that CCR populations have been stable since the 1970’s (USFWS, 1984). However, CCR counts from the early

to mid-1980’s indicated that the CCR numbers were lower than those obtained in 1979 (USFWS, 1984). Greco Island and other large South Bay ma rshes that historically supported major CCR populations appeared to no longer provide optimal habitat and yielded lower numbers than would be expected by the large area of land (USFWS, 1984).

Censuses performed in the early to mid-1980s in San Pablo Bay established that these marshes do not support significant CCR populati ons even though this area represents 30% to 40% of the total CCR habitat (USFWS, 1984). This decline could be due to the growth of alkali bulrush over cordgrass attributed to above average winter precipitation (USFWS, 1984). The CCR population in the ea rly to mid-1980s was approximately 50% lower than estimates from the early 1970s (U SFWS, 1984). This decrease was attributed to the introduction of the red fox ( Vulpes vulpes regalis ) (Goals Project, 2000).

In 1990-1991, the CCR population was estimated at around 300 to 500 individuals (Save the Bay, 2005; and Goals Project, 2000). In 1993, the population was measured at around 800 individuals (Goals Project, 2000). The population increase in the South Bay was attributed to predator management th at was implemented in 1991 (Goals Project, 2000). Surveys of the northern parts of the bay (Suisun and San Pablo bays) performed in 1992-1993 indicated a population of 390- 564 individuals or 195-282 breeding pairs (Goals Project, 2000). CCR counts in the winter of 1997-1998 indica ted that the South Bay population was estimated at 650 to 700 individuals (Goals Project, 2000). The estimated population today is about 1,200 indi vidual animals and still growing (Save the Bay, 2005). It is estimated that the South Bay population is 500-600 individuals and that the population in the North Bay may be similar in size (CDFG, 2000). Another source estimates that the CCR population consists of 500-600 individuals in the southern portion of San Francisco Bay (USFWS, 2003).

3.3 REFERENCES

Literature Cited

Albertson, J. 1996. Restoring salt marsh habitat for the recovery of California clapper rails. Tideline. Vol 16 No. 4 pa ges 1-3. Available online at: http://www.fws.gov/desfbay/Ar chives/Clapper/carail.htm (Accessed on September 2, 2008).

California Department of Fish and Game (CDFG). 2000. California’s Plants and

Animals. Available online at: http://www.dfg.ca.gov/wildlife/spec ies/t_e_spp/new_te_rpt.html (Accessed on September 2, 2008).

30California Department of Pesticide Regulat ion (CDPR online). Endangered Species Project. California Clapper Rail. Available online at: http://www.cdpr.ca.gov/doc s/endspec/espdfs/ccrbio.pdf (Accessed on September 2, 2008).

Foin, T.C., E.J. Garcia, R.E. Gill, S.D. Culberson, and J.N. Collins. 1997. Recovery strategies for the California clapper ra il (Rallus longirostris obsoletus) in the heavily-urbanized San Francisco estuarine ecosystem. Landscape and Urban Planning: 38 (229-243). Available online at: http://www.sciencedirect.com/scie nce?_ob=Publicati onURL&_cdi=5885&_pubT ype=J&_acct=C000001678&_version=1&_ur lVersion=0&_userid=14684&md5= c022652b83fc464948c4770cca3bbc44&jchunk=38#38 (Accessed on September 2, 2008).

Goals Project. 2000. Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plan ts, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosyste m Goals Project. P.R. Olofson, editor. San Francisco Bay Regional Water Quality Control Board, Oakland, California.

Available online at: http://sfep.abag.ca.gov/pdf/speciescommunity/Species_and_Community_Profiles.pdf (Accessed on September 2, 2008).

Monteverdi, John, and Jan Null, 1998. El Ni ño and California Preci pitation. Western Regional Technical Attachment, No 97-37, November 21, 1997. Accessed online

at: http://tornado.sfsu.edu/geosci ences/elnino/elnino.html#Not (Accessed on September 2, 2008).

San Francisco Estuary Invasive Spartin a Project (SFEISP online). Coastal Conservancy. California clapper rail ( Rallus longirostris obsoletus ). Available

online at: http://www.southbayrestoration.or g/pdf_files/CLRAhandout_final3.18.05.pdf (Accessed on September 2, 2008).

Save the Bay Classroom. 2005. California Cl apper Rail and Saving the California Clapper Rail. Available online at: http://www.savesfbay.org/site /pp.asp?c=dgKLLSOwEnH&b=886761 and http://www.savesfbay.org/site /pp.asp?c=dgKLLSOwEnH&b=947939 (Accessed on September 2, 2008).

Schwarzbach, S.E. 2006. Limited Reproductive Success for California Clapper Rail in San Francisco Bay. Sound Waves. USGS. Available online at: http://soundwaves.usgs.gov/2006/06 (Accessed on September 2, 2008).

Schwarzbach, S.E., J.D. Albertson, and C. M. Thomas. 2006. Effects of predation, flooding, and contamination on reproductive success of California clapper rails (Rallus longirostris obsoletus) in San Francisco Bay. The Auk. Vol. 123, Issue 1.

31pp 45-60. Available online at: http://findarticles.com/p/ar ticles/mi_qa3793/is_200601/ai_n17186959 (Accessed on September 2, 2008).

Spautz, H., J.T. McBroom, N. Nur, J.G. Even s, J. Albertson, S. Bobzien, K. Zaremba, and M. Herzog. 2007. California clapper ra ils in San Francisco Bay: Modeling habitat relationships at multiple scales to guide habitat restoration and eradication

of non-native Spartina . ESA/SER Joint Meeting. Available online at: http://eco.confex.com/ eco/2007/techprogram/P8922.HTM (Accessed on September 2, 2008).

Steiner, J. 1997. Don Edwards San Francisco Bay National Wildlife Refuge Celebrates its Silver Anniversary. Tideline. Vol. 17 No. 4: pp 1-3. Available online at: http://www.fws.gov/desfbay/ Archives/25th/Silver.htm (Accessed on September 2, 2008).

U.S. Geological Survey (USGS). Western Ec ological Research Center (WERC). The Project: What We Are Doing and Why? and Methods. Available online at: http://www.werc.usgs.gov/dixon/rails/planB.html (Accessed on September 2, 2008).

U.S. Fish and Wildlife Service (USFWS) . 1984. Salt Marsh Harvest Mouse and California Clapper Rail Recovery Plan. U.S. Fish and Wildlife Service, Portland, Oregon. 141 pp. Available online at: http://ecos.fws.gov/docs/recovery_plans/1984/841116.pdf (Accessed on September 2, 2008).

U.S. Fish and Wildlife Service (USFWS). 2003. Evaluation of the Clean Water Act Section 304(a) Human Health Criterion fo r Methylmercury: Protectiveness for Threatened and Endangered Wildlife in California. U.S. Fish and Wildlife Service, Environmental Contaminants Division, Sacramento Fish and Wildlife

Office. Available online at: http://www.fws.gov/sacramento/ec/Met hylmercury%20Criterion%20Evaluation% 20Final%20Report%20October%202003.pdf (Accessed on September 2, 2008).

U.S. Fish and Wildlife Service (USFWS). 2007. Species Account: California Clapper Rail ( Rallus longirostris obsoletus ). Sacramento Fish and Wildlife Office.

Available online at: http://www.fws.gov/sacramento/es/an imal_spp_acct/ca_clapper_rail.rtf (Accessed on September 2, 2008).

U.S. Fish and Wildlife Service (USFWS). No date. The Coastal Program – Success in San Francisco Bay. Available online at: http://training.fws.gov/Divi sionSites/ConservationLibr ary/Pubs1/sfbay_coastal.pd

f (Accessed on September 2, 2008).

32University of California at Berkeley (U.C . Berkeley). June 2004. Richmond Field Station: Western Stege Marsh Restorati on. California Clapper Rail Restoration.

Accessed online at: http://www.cp.berkeley.edu/RFS_Feral_Brochure_final.pdf (Accessed on September 2, 2008).

334: CALIFORNIA FRESHWATER SHRIMP

4.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the California freshwater shrimp (CA Shrimp) ( Rallus longirostris obsoletus ) that are reasonably certain to occur in the action area. Future federal actions unrelated to the proposed act ion are not considered because they are subject to consultation pursua nt to Section 7 of the Enda ngered Species Act (Act).

Numerous non-federal actions that could affect the CA shrimp are reasonably certain to

occur within the action area. These activities are often associated w ith modifications to stream morphology and operate synergistically and/or cumulatively with each other in their effects to the CA shrimp. These activ ities include urban development, instream gravel mining, grazing, agricultural developm ent, impoundments, and water diversions. These activities may simultaneously reduce the qu ality and availability of water, reduce the quality and availability of shelter, and c ontaminate suitable habitat. For instance, urban development may result in the loss of riparian vegetation. This could alter temperature regimes and dissolved oxygen leve ls in streams; incr ease bank erosions; and change the invertebrate species composition, im pacting aquatic food s ource availability. The effects of urban development might th en be compounded by activities that reduce water flow such as diversions and impoundments, which increase sediment and pollutant concentrations, and further decrease oxygen av ailability. As the CA shrimp does not have life history characteristic s that favor quick recovery following disturbances, the CA shrimp is vulnerable to the cumulative effect s of habitat degradation (USFWS, 1998).

4.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the effects of past and ongoing human induced and natural factors leading to th e status of the species, its habitat, and ecosystem, within

the action area. The environmental baseline is a snapshot of the California freshwater shrimp’s status at this time. Details of the California freshwater shrimp’s habitat description and known locations are included in Attachment III. However, the baseline condition of each assessed CA shrimp species and habitat varies across locations. Given the large number of occupied habitats and extent of the action area included of this assessment, the environmental baseline presen ts a general discussion of factors that may affect CA shrimp within the action area. This information includes both detrimental and potentially beneficial factors affecting th e species and is presented in Section 4.2.1.

Additional information on the current dist ribution and population dynamics of the CA shrimp is presented as part of th e baseline status in Section 4.2.2.

344.2.1 Factors affecting species envi ronment within the action area

Since the species’ listing in 1988, there c ontinue to be numerous human-related and natural factors affecting the species’ hab itat (USFWS, 2007). Although there have not been any new threats documented since th e listing, some of the factors have since intensified (USFWS, 1998). Furthermore, th e CA shrimp is most likely affected by multiple factors in a majority of locations, rather than just one (USFWS, 1998). These factors include urbanization, st ream maintenance, gravel mi ning, agriculture, silviculture, impoundments, water diversions, native and in troduced predators, and water pollution (USFWS, 1998; USFWS, 2007). Environm ental extremes, compounded by human disturbance, also present a threat to th e CA shrimp (USFWS, 1998; USFWS, 2007). According to the species’ 5-Year Review, overutilization for commercial, recreational, scientific, or educational purposes was not historically a factor affecting the CA shrimp at the time of its listing and no new informati on has come forward that would indicate a change in the imminence of this factor (USFWS, 2007). No information is available concerning the types of pathogens, parasites, or types of coexisting species that may associate with the CA shrimp (USFWS , 1998). Sections 4.2.1.1 through 4.2.1.8 provide details on each of the major issu es affecting the CA shrimp within the action area.

4.2.1.1 Urbanization

On the heels of already much urban de velopment since the CA shrimp’s listing, urbanization has been increasing in rural areas within the San Francisco Bay region (USFWS, 1998). Development outside trad itional populated centers has led, and will lead, to a larger portion of impacted watershe d ultimately draining into CA shrimp habitat (USFWS, 1998). Urban development indirectly affects the CA shrimp due to the direct effects it has on stream quality (USFWS, 2007). The health of stream water is imperiled by the amount of non-point source pollutant s in runoff, as well as the volume, temperature, and speed of runoff (USFWS, 2007). Urban runoff results from precipitation and from dry weather flows from irrigation (USFWS, 1998). Pollutants vary by locations, and can include sediment, petroleum, paint, household cleaning agents, and chlorine from pool water (USFWS, 2007). The acute and sublethal effects these pollutants may have on the species is unknown (USFWS, 2007).

Wastewater is another type of urban by-product marring stre am health (USFWS, 1998). Wastewater discharges and releases from septic systems contribute to summer algal growth from nutrient loadings (USFWS, 1998) . This growth and ensuing eutrophic conditions threaten the CA shrimp from reduced dissolved oxygen levels (USFWS, 1998). Failures in wasterwater treatment fac ilities may also result in discharges of partially treated effluent or chlorinated effluent (USFWS, 1998). A discharge of this nature, with ammonia and chlorine, occurred in 1993 in the Santa Rosa Creek and killed hundreds of small fish (USFWS, 1998).

354.2.1.2 Stream Maintenance

Stream maintenance activities that affect th e species environment include flood control, bank protection, culvert, and grade control structures (USFWS, 1998). Flood control involves straightening, channelizing, and lining stream banks with concrete, effectively eliminating the flood plains, or riparian ar eas (USFWS, 1998). With such removal, CA shrimp habitat of undercut banks and ripari an vegetation is removed, or at a minimum impaired, by increased water velocities and temperature fluctuations (USFWS, 1998). Bank protection activities result in similar c onsequences for CA sh rimp habitat (USFWS, 1998). Bank protection refers to the practice of reinforcing stream banks to prevent natural erosion, and can be in the form of gabions or riprap providing stability (USFWS, 1998). Gabions, however, displace the herbaceo us vegetation growing in the alluvial zones that provide warm season shelter for the species (USFWS, 1998) . Loss of natural banks has occurred and can be expected to continue due to an increase in urban development (USFWS, 1998). Bank protection is also occurring without the requisite Army Corps of Engineers authorization of a section 404 permit that would include recommended measures to preserve CA shrimp habitat (USFWS, 1998). Other flood control methods degrade CA shrimp habita t though herbicide use, dredging, altering channel and bank configuration, and removi ng instream and riparian woody debris (USFWS, 1998).

Direct elimination of shrimp from certain st reams could occur with barriers impeding the movement of CA shrimp upstream (USFWS, 19 98). Sills, designed to protect bridge footing, have scoured downstream areas and formed ledges which prevent upstream movement (USFWS, 1998). Barriers from culver t or grade control structures also result in fragmented populations, possi bly restricting gene flow a nd increasing the likelihood of extirpation (USFWS, 1998).

4.2.1.3 Water Resource Needs: Impoundments and Water Diversions

Impoundments are prevalent in stream draina ge areas that support CA shrimp (USFWS, 1998). Impoundments, whether permanent or temporary, are constructed to reduce hazards, provide recreational benefits, and provide a water supply (USFWS, 1998). In damning a steam, however, impoundments directly and indirectly affect the CA shrimp by acting as migration barrier s, by eliminating upstream habitat, supporting introduced predators, altering hydrology and sediment transport, reduci ng and altering downsteam flows, and by ushering individuals away from the population and into diverted waterways (USFWS, 1998). Impoundments raise the el evation zone, drown roots of riparian vegetation not adapted to higher inundation, and likely reduce riparian vegetation along the shore (USFWS, 2007). Lack of riparian vegetation harms the species by reducing habitat complexity, reducing detritus producti on, elimination of high flow refugia, and increasing bank scouring (USFWS, 2007). The natural winter flood cycle, needed to maintain undercut banks and pools for the CA shrimp, is also impacted by such water storage facilities (USFWS, 1998).

36Water diversions imperil CA shrimp by di rectly reducing water flow, as well as by intensifying the concentrations , and thus effects, from pollutants (USFWS, 1998). At the time the recovery plan was drafted, there we re substantial demands to appropriate water from many streams containing the CA shrimp (USFWS, 1998). In the Huichica Creek watershed, as an example, estimates of tota l water yield range betw een 1,759 acre-feet to 3,097 acre-feet (USFWS, 1998). If full permission were given to appropriate the 2,019 acre-feet of water that was requested by local landowners, the yearly volume of water in the creek would be reduced by two-thirds (USFWS, 1998). Wit hout instream flow requirements, existing pools could become dry (USFWS, 1998). Such high demands of groundwater are also a concern, although for th e fear of saltwate r intrusion and the corollary stress of competing with shrimp found normally in brackish water (USFWS, 1998).

Since 1998, the USFWS has issued 13 biol ogical opinions under section 7 of the Endangered Species Act authorizing incident al take of the shrimp (USFWS, 2007). However, not all projects are consulted on under section 7 (USFWS, 2007). It was discovered that at least one project since 1998, an illegally constr ucted water diversion (not consulted on), may have impacted the CA shrimp (USFWS, 2007). The water

diversion channel incl uded the removal of riparian vegetation along the bank of Olema Creek, as well as foraging and sheltering habitat for the CA shrimp (USFWS, 2007).

4.2.1.4 Gravel Mining

Gravel mining practices interr upt the supply of gravel dow nstream and can disrupt the natural channel geomorphology (USFWS, 1998). Long-term gravel mining retards the development of appropriate soil conditions for riparian vegetation, which under normal

conditions would be the accumulation of fine sediments and organic materials from overbank flooding (USFWS, 1998). Without n ecessary safeguards, instream gravel mining activities along the historic CA shrimp habitat in Austin and Sonoma Creeks will prevent the reestablishment of suitable habita t conditions for the sp ecies (USFWS, 1998). To date, no specific studies have been conducte d to determine the extent of effects of gravel mining on the CA shrimp (USFWS, 2007).

4.2.1.5 Agriculture Developments

Recent vineyard establishments have caused c oncern for the existence of the CA shrimp (USFWS, 1998). Vineyard coverage in Napa County is anticipated to reach 52,000 acres by 2010, approximately 19,000 acres more th an the area covered in 1989 (USFWS, 1998). Land and surface water resources in no t only Napa, but also Sonoma, counties are being intensively developed, and threats to CA shrimp populations include loss of riparian vegetation, inadvertent introduction of herbic ides and pesticides into creek water, diversion of water, and increas e soil erosion (USFWS, 1998).

37Habitat quality for the CA shrimp is imper iled by livestock grazi ng operations and dairy farming (USFWS, 1998). Effects of these operations include riparian vegetation removal, stream bank and channel changes, decreased water quality, and increased water temperature fluctuations (U SFWS, 1998). Stemple Creek watershed, as an example, supports approximately 30 dairy operations and grazing on 50 pe rcent of its land (USFWS, 1998). Grazing activities typically occurs in the vicin ity of steams and riparian

areas where livestick are offered fresh wa ter and palatable forage (USFWS, 1998). Because of the high concentrati on of livestock, Stemple Creek a nd its tributaries have lost much of their riparian vegetation that s upported CA shrimp habitat (USFWS, 1998). In addition to affecting habitat suitability, loss of riparian vegetation impacts the availability of food sources (USFWS, 1998). Changes in the natural riparian zone s alter invertebrate species composition and production in steam s (USFWS, 1998). Grazed streams are characterized by having a high pr oduction of algae due to hi gh insulation and increased nutrient input, as opposed to the limited instream primary pr oductivity seen in streams with dense riparian vegetation (USFWS, 1998).

Poor water quality results from reduced fo rage cover and increased soil compaction (USFWS, 1998). Groundwater rech arge is diminished from the compaction, as well as base flows during the summer and fall (U SFWS, 1998). Reduced forage cover and compaction also result in higher peak flow s following winter stor ms and high sedimentladen flood flows (USFWS, 1998). Runoff fr om manure lots contribute to raising

nutrient levels and increase the concentr ation of ammonia (USFWS, 1998). Water samples from Americano and Stemple Creeks exceeded the Environmental Protection Agency’s (EPA) ammonia criteria for aqua tic life protection for the years 1991-1994 (recovery). The ammonia present is in an un-ionized form (NH 3 ) and an ionized form (NH 4 + ), both of which cause mortality to aquatic organisms (U SFWS, 2007). The elevated copper concentrations in these two creeks have been linke d to dairy practices,

and levels have been detected that also exceed the EPA’s criterion for aquatic life protection (USFWS, 1998).

Timber harvesting, or silviculture, has and may continue to impact CA shrimp populations, although it is reported to be less of a threat today than it has been historically (USFWS, 1998; USFWS, 2007). Pa rticularly those practices that remove stream side vegetation, timber harvesting reduces ch annel stability, decreases canopy cover (increasing water temperature), and increasi ng instream debris (USFWS, 1998). Timber harvesting also increases peak flows, decr eases base flows, and increases sediment transport and deposition (USFWS, 1998). Au stin creek is noted as having timber harvesting activity near its dr ainage, adding to channel degr adation near the confluence with the Russian River (USFWS, 1998).

4.2.1.6 Predation

It can be inferred that the CA shrimp evol ved in the presence of predators due to its cryptic coloration and behavioral characteristi cs (USFWS, 1998). Some native fish that prey on CA shrimp include the California roach ( Hesperoleucus symmetricus ), threespine

38stickleback ( Gasterostreus aculeatus ), riffle sculpin ( Cottus gulosus ) (USFWS, 1998). It is suspected that the following fish ge nerally prey on shrimp: young coho samlmon ( Oncorhynchus kisutch ), steelhead trout (Oncorhynchus mykiss ), Sacramento squawfish ( Ptchoncheilus grandis ), and northern squawfish ( Ptychocheilus oregonensis ) (USFWS, 1998). Other native aquatic predators may include western pond turtles, salamanders, newts, water scorpions, diving beetles, a nd dragonfly and damselfly nymphs (USFWS, 1998).

Nonnative fish have been introduced to the ha bitat of the CA shrimp and are implicated

in the decline of native fi sh (USFWS, 1998). Nonnative sp ecies presence is correlated

with the levels of human disturbance to a st ream (USFWS, 1998). Introduced fish that potentially prey on the CA shrimp include mosquito fish ( Gambusia affinis ), green sunfish ( Lepomis cyanellus ), smallmouth bass ( Micropterus dolomieui ), largemouth bass ( Micropterus salmoides ), common carp ( Cyprinus carpio ), and certain species of minnows (USFWS, 1998). The introduced Chinese mitten crab ( Eriocheir sinensis ) is an invertebrate predator that is established in tributaries flowing into San Pablo Bay and may potentially prey on the CA shrimp (U SFWS, 2007). Predation from introduced species can be more disruptive to a prey population than from native predators because the prey species have not developed mech anisms for defense or avoidance (USFWS, 1998). Some introduced species are also to lerant of poor water quality conditions, increasing the predation stress on their prey it ems (recovery). Both the mosquitofish and green sunfish persist in cond itions that would otherwise pe rmit CA shrimp to live in isolation of natural predator s (USFWS, 1998). For example, the green sunfish is capable of surviving water temperatures up to 97 de grees Fahrenheit, low oxygen levels down to 3 ppm, and high alkalin ities (USFWS, 1998).

4.2.1.7 Environmental Extremes

Environmental extremes, particularly droughts, spring flooding, and th e consequences of climate change, threaten the persistence and stab ility of CA shrimp populations (USFWS, 2007). Reduced precipitation could result in lower stream flows and thus increase the chance that stream segments dry out duri ng summer months. Natural events can devastate CA shrimp populations because they can cause local extinctions upon which recolonization is difficult (USFWS, 2007). A second, compounding factor of droughts is that with reduced precipitation comes an in creased demand for water resources, further intensifying the fatal effects of stream dry-up (USFWS, 2007).

While not mentioned explicitly in the recove ry plan, climate change induced sea level rise could impact the CA shrimp (USFWS, 2007). Sea level rise may result in increasing salinities in reaches supporting the CA Shrimp (USFWS, 2007). Hodgpeth (1968) observed shrimp surviving at 16 – 17 parts per thousand for up to 13 days, and mortality occurring after 7 hours in higher salinities (Hedgpeth, 1968).

394.2.1.8 Restoration Efforts

Since 1998, the USFWS has issued 13 biol ogical opinions under section 7 of the Endangered Species Act authorizing take of th e shrimp in the form of 1,048 linear feet and 3.05 acres of shrimp habitat (USFWS, 2007). The biological opinions for these projects have included a to tal of 548 linear feet combined with 5.49 acres of habitat restoration and/or protection in compen sation for adverse effect (USFWS, 2007). Watershed plans for many streams sustaining CA shrimp population also strive to protect and restore habitat for the species, but many re storation activities for these plans have yet to be implemented (USFWS, 2007). Stemple Creek has received lots of restoration attention through activities supported by the Ba y Institute and executed by the Students and Teachers Restoring Watershed (STRAW ) program (USFWS, 2007). The projects aim to remove nonnative vegetation, plant native species, erect livestock exclusion fencing, and install cattle bridges (USFWS, 2007). To da te, approximately 50,000 linear

feet of stream bank has been restored through STRAW’s 185 completed projects (USFWS, 2007).

4.2.2 Baseline Status

Long-term population estimates are availabl e for the Lagunitas Creek population, known from an eight mile reach beginning from Sh after Bridge to just downstream of the Balleager Bridge U.S.Geological Survey gage (USFWS, 2007). The number of

individuals collected at six sites increased from approximately 1,878 in 1991 to approximately 4,407 in 2000, the same period when (USFWS, 2007) the stream’s morphology changed allowing increased wate r flows and improving and/or increasing habitat conditions (USFWS, 2007). Howeve r, in some areas these morphological changes worsened and/or decrease d habitat conditions (USFWS, 2007).

Population Dynamics The recovery plan listed populations of the California freshwater shrimp remaining in reaches of 17 streams (USFWS, 1998). These included five streams in Marin County (Lagunitas, Olema, Walker, Keys, and Stempl e), and twelve streams in Sonoma County (Blucher, Jonive, Redwood, Green Valley, Salm on, East Austin, Big Austin, Sonoma, Yulupa, Garnett, Huichica, and Napa (USFWS , 1998). As of the 5-year Review, more recent surveys place the number of known locat ions of the CA shrimp up to 23. In addition to those already mentioned, the five reaches of streams known to support the CA shrimp are “Bud Creek” (Sonoma County), Franz Creek (Sonoma County), Ebabias Creek (Sonoma County), Cheda Creek (Marin County, an unnamed tributary of Huichica Creek (Napa County), and a second location on the Napa River (Napa County) (USFWS, 2007). The majority of new information documenting the existence of the species in these additional streams is a result of recent independent surveys. It should be noted, these findings do not represent a systematic can vassing of habitats for the CA shrimp that examines their full spatial distribu tion and extent (USFWS, 2007).

40It is unknown if shrimp populations still pers ist in Laguna de Santa Rosa or Atascadero Creeks. The Yulupa Creek shrimp population is probably under the greatest threat of extirpation (USFWS, 1998). Lagunitas is the only shrimp stream on federal and state land, all others are in private ownership (S erpa, 1996 and USFWS, 1998). A substantial portion of Lagunitas Creek flows through the Sa muel P. Taylor State Park, managed by the California Department of Parks and Recreation, and the Golden Gate National Recreation Area, managed by the National Park Service (USFWS, 1998). A small segment of Salmon Creek flows through the Wa tson School historic site, managed by the Sonoma County Department of Parks and Recreation (USFWS, 1998). On East Austin Creek, the Austin Creek State Recreation Area lies immediately upstream of shrimp populations (USFWS, 1998).

Preliminary genetic analysis on approximately 12 individuals from eight streams indicates populations can be divided into distinct groups based on gene tic similarities of mitochondrial DNA (USFWS, 2007). These tentative data suggest genetic variation between populations may not correspond to the drainage units identified in the recovery plan (USFWS, 2007). The drainage units identified in the rec overy plan were originally developed in an effort to maximi ze genetic diversity (USFWS, 2007).

4.3 REFERENCES

Literature Cited

Hedgepeth, J.W. 1968. The At yid shrimp of the genus Syncaris in California. Hydrobiol. 53 (4):511-524.

Serpa, L. 1996. California Freshwater Shrimp: A Ghost-like Crustacean We Can’t Afford

to Lose. Tideline. Vol. 16 No. 2 1-3. Available online at: http://www.fws.gov/desfbay/Archives/shrimp/shrimp.htm (Accessed on October 3, 2007).

U.S. Fish and Wildlife Service (USFWS). 1998. California Freshwater Shrimp ( Syncaris pacificus Holmes) Recovery Plan. U.S. Fi sh and Wildlife Service, Portland, Oregon. 94 pp. Available online at: http://ecos.fws.gov/docs/recovery_plan/980731a.pdf (Accessed on April 22, 2008).

U.S. Fish and Wildlife Service (USFWS). 2007. Species Account: California Freshwater Shrimp ( Syncaris pacifica ). Sacramento Fish and Wildlife Office. Available

online at: http://www.fws.gov/sacramento/es/an imal_spp_acct/ca_freshwater_shrimp.pdf (Accessed on April 22, 2008).

415: CALIFORNIA TIGER SALAMANDER: CENTRAL CALIFORNIA DISTINCT

POPULATION SEGMENT

5.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on th e central California distinct population segment (DPS) of the California tiger salamander ( Ambystoma californiense ) (central CTS) that are reasonably

certain to occur in the action area. Future federal actions not directly related to the proposed action are not considered because they require additional consultation under Section 7 of the Endangered Sp ecies Act (Act). The numer ous non-federal actions that are reasonably certain to occu r within the action area consist of intensive agriculture ( i.e

., vineyards, row crops, and, orchards), ur ban development, grazing operations, oil production, and contamination from runoff and spills. Many of these fact ors are linked or act synergistically and create complex consequences for the central CTS. For example, conversions to intensive agricu lture and urban developments have resulted in the loss of breeding habitat from the dest ruction or alteratio n of natural vernal pools and seasonal ponds. If these water bodies are destroyed by de ep ripping, a technique that uses a 4- to 7-foot deep plow to break up the hardpan layer, the once compacted soil will no longer

retain water and will inhibit ponding. Repeated deep-ri pping, in addition to plowing and discing in upland habitats, can alter hydrology of the pools a nd ultimately destroy them. In contrast to destroying water bodies, so me seasonal ponds are being converted into permanent ponds for irrigation. However, these ponds are then frequently stocked with fish to control mosquitoes and other probl ematic insects, and can limit central CTS populating the water edges. Both destruction and reduced suitability of breeding habitat, compounded with increased urbanization, fragment and isolate subpopulations from each other and inhibit potentially benefici al gene flow (USFWS, 2004).

5.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a sn apshot of the central CTS’s status at this time. However, the baseline condition of the central CTS population and habitat varies across locations. Given the larg e number of occupied habita ts and extent of the action area included in this assessment, the environm ental baseline includes a general discussion of factors that may affect central CTS with in the action area. This information is presented in Section 5.2.1. Additional information on the current distribution and population dynamics of the central CTS is pres ented as part of the baseline status in Section 5.2.2 (USFWS, 2004).

425.2.1 Factors affecting species continued existence within the action area

The central CTS’s continued existence is primarily affected by the destruction, modification, or curtailment of suitable habi tat due to rangeland conversion for urban and agricultural uses. Other infl uential factors affecting cen tral CTS include: disease; predation, competition, introduced species; contam inants; pest control; livestock grazing; and vehicular strikes. As opposed to many of these factors that negatively affect the CTS, grazing can, in moderation, have a neutra l to positive impact. While some of these factors are known to specifically affect the California Tiger Salamander population in central California (central CTS), others are known to generally affect the California Tiger Salamander (CTS) population throughout its enti re range. The factors known to affect the larger population are still relevant to th e central CTS, but are referred to as CTS. Sections 5.2.1.1- 5.2.1.4 provide details on each of the major issues affecting central CTS

environment within the ac tion area (USFWS, 2004).

5.2.1.1 Rangeland Conversion and Habitat Fragmentation

A variety of urban and agricultural land us es are implicated in the destruction, modification, and curtailment of central CT S habitat (USFWS, 2004). The United States

Fish and Wildlife Service defines urban uses as including nonagricultural development

activities such as building and maintenance of housing, commercial, and industrial developments; construction and widening of roads and highways; golf course construction and maintenance; landfill opera tion and expansion; operation of gravel mines and quarries; dam building and inundation of habitat by reservoirs; and other infrastructure activities (USFWS, 2004). Ag ricultural land uses are defined as including native habitat conversion by discing and deep-ripping; and cultivation, planting, irrigation, and maintenance of row crops, or chards, and vineyards (USFWS, 2004). Both urban and agricultural conversions have reduc ed or modified natural vernal pools and seasonal ponds used for breeding habitats, as well as reduced upla nd habitat used for aestivation and migratio n (USFWS, 2000).

Urban development in central CTS habitat pro ceeds at an elevated rate. Between the years of 1980 and 1997, 2.8 million new housing un its were constructed in California, and 220,000 units are required each year fo r the next 20 years to accommodate the growing population. Most of this developmen t will be outside of the major metropolitan areas, referring to San Francisco, Los Angele s, and San Diego, and will be occurring in the Sacramento, San Joaquin, and Imperial Valleys. Two of these valleys, the Sacramento and San Joaquin Valleys, are inhabited by the central CTS. Low Density residential housing, found outside major metr opolitan areas, is of gr eat threat to the central CTS. The housing areas and rural deve lopments may result in extirpation of the CTS due to the destruction or degradation of breeding sites, upland di spersal habitat, and migration corridors (USFWS, 2004).

Conversion of rangeland and ve rnal pool grasslands to inte nsive agriculture have been well documented in counties inhabited by the ce ntral CTS. The cumulative loss of vernal

43pool grasslands has been estimated at 78 percent by the later 1990s. Historically, approximately 2.7 million hectares (ha) of va lley and coastal grasslands existed within the range of the central CTS. Today, virt ually all valley grassland and oak savanna

habitat has been eliminated from the Cent ral Valley floor due to urbanization and intensive agriculture. It is estimated that less than 10 percent of California’s Central Valley grasslands remain. Future conversion is difficult to estimate, but it is predicted to be a continuing threat to the central CTS because of the projected increase in human population. Furthermore, there is a financial incentive to convert rangeland into irrigated crops as rangeland in central CTS habitat is valued (value/a cre) at a lower cost. Other factors influencing rangeland conversion incl ude a decline in farm rancher income, the aging of ranchers, tax implications of interg enerational transfers of ranches, and the difficulty of beginning a ranching operation ( e.g ., cost and knowledge). However, the rate of conversion may soon decrease as areas with suitable soils and water availability necessary for intensive agricultu re become scarce (USFWS, 2004).

Changes to vernal pool or pond inundation, duration, or depth can detrimentally affect the reproductive success of the CTS. These cha nges are caused by, among others, digging of drainage or irrigation ditches, construction of permanent ponds or reservoirs, deepening or berming of seasonal wetlands, and redirect ion or runoff from developments (USFWS, 2000). The repercussions of these activi ties on the reproductive success of the CTS include: (1) prematurely drying wetlands a nd desiccating CTS larvae; (2) extending the inundation period and facilita tion invasion of non-native predators; (3) creating conditions that foster the hybr idization with the non-native tiger salamander; and (4) increasing vulnerability to disease from isol ation and fragmentation. Wetland habitats are utilized for reproduction; thus destru ctive activities such as filling, discing, or excavating, are injurious or le thal to the eggs, larvae, or breeding adults. Earthmoving operations and cultivation in upl and habitat also threaten th e CTS, which use the habitat to breed, feed, and seek shelter. CTS are at risk in burrows or on the surface from discing, deep-ripping, or grading of upland hab itat. Indirect impacts to the CTS include increased predation from over-exposure, high temperatures, low humidity, and diminished food sources. Earth moving operati ons may further disturb California ground squirrel burrows and crevices, protected ha bitat utilized by the CTS, and may render upland locations untenable or unavailable (USFWS, 2004).

Fragmentation The widespread conversion of land to reside ntial and agricultural uses has led to the fragmentation and isolation of habitat thr oughout the range of the central CTS. Humancaused fragmentation places the CTS at particul ar risk to local extinctions because its metapopulation structure is distributed across the landscape (USFWS, 2000).

“A metapopulation is a group of spatia lly distinct populations that can occasionally exchange dispersing individuals. The populations in a metapopulation are usually thought of as having interdependent extinction and colonization processes, where individua l populations may be extirpated from a

local area and later be reco lonized from another populati on that is still extant” (FR, 72:48177, p.6).

44A reduction in CTS dispersal greatly inhi bits the dynamics of a metapopulation and reduces the abilities of the CTS to persist over time. Of all fact ors associated with urbanization and land conversion, roads accelera te fragmentation by increasing mortality and preventing recolonization of sites th at would otherwise be only temporarily extirpated (USFWS, 2000).

5.2.1.2 Disease

The direct effect of disease on the CTS is unknown and risks to the central California DPS cannot be precluded (USFWS, 2000). Wh ile no information suggests disease is prolific in existing populations in California, several pat hogenic (disease-causing) agents have been linked to deaths of closely-re lated tiger salamanders and other amphibian species. These pathogens include fungi, viruses, and at least one bacterium ( Acinetobacter spp.) (USFWS, 2000; USFWS, 2004) . Chytrid fungus infections (chytridiomycosis) have been detected specifically in Central California tiger salamanders, although the prevalence and effect on the species is unknown (USFWS, 2004).

The bacterium Acinetobacter is common in soil and animal feces (USFWS, 2000). Affected tiger salamanders showed symptoms of red, swollen hind legs and vents, and hemorrhaging of skin and internal organs. Iridoviruses, (a family, containing the genus

Ranavirus ) are viruses with DNA as th e genetic material that o ccur in insects, fish, and amphibians, including tiger salamanders (H arp, 2006; USFWS, 2000). These viruses can cause a range of symptoms, including skin lesions and mortality, or they can be asymptomatic (USFWS, 2000). Ranaviruses ar e of particular concern because these viruses can be spread through fishing gear , artificial stock ponds, and water birds (USFWS, 2003). Outbreaks of ranavirus in tiger salamanders have been directly

associated with altered habitats and artif icial ponds (USFWS, 2003). Ranaviruses, in addition to the fungus Batrachochytrium dendrobatidis that causes Chytridiomycosis, have been identified as potential threats to the CTS because these pathogens have adversely impacted other amphibians, incl uding tiger salamanders (USFWS, 2004). Non-native species of bullfrogs and tiger sa lamanders are potentia l carriers of these diseases (USFWS, 2004).

A study conducted in 1997 showed that tiger salamanders in Georgia reared in ponds

contaminated with silt were susc eptible to infection by the fungus Saprolegnia parasitica (USFWS, 2003). Die offs associated with western toads and Pacific tree frogs, known prey of the CTS, have been associated with Saprolegnia infections (USFWS, 2000). High nitrogen and silt levels from overgrazing or agricultu ral or urban runoff may also increase susceptibility to disease (USFWS, 2000). High levels of nitrogen have been

associated with bacterial blooms and increa sed silt has been associated with fungal infections (USFWS, 2000).

5.2.1.3 Predation, Competition, and Hybridization

45Native predators of the CTS in clude great blue herons ( Ardea herodias ), egrets ( Casmerodius ), western pond turtles ( Clemmys marmorata ), garter snakes ( Thamnophis spp.), larger CTS larvae, larger spadefoot toads ( Scaphiopus hammondii ), and California red-legged frogs ( Rana draytonii ) (USFWS, 2004). Native as we ll as non-native crayfish also prey on CTS (USFWS, 2003). While nativ e predation and hybridiz ation is probably

a discountable threat in hea lthy populations, these native pr edators may have significant impacts on population viability wh en populations are subjected to the cumulative effects of contaminants, migration barriers, a nd/or habitat altera tion (USFWS, 2003).

Predation by and competition with non-native and introduced species contributes to the decline of the CTS (USFWS, 2003). Non-native predators of both adult and larval CTS include Louisiana red swamp crayfish ( Procambarus Clarkii ), mosquitofish ( Gambusia affinis ), sunfish spp. ( e.g ., large mouth bass ( Micropterus salmoides )) bluegill ( Lepomis

macrochirus ), catfish spp. ( Ictalurus spp.), fathead minnow ( Pimephales promelas ), carp ( Cyprinus carpio ), and American bullfrog ( Rana catesbeiana ) (USFWS, 2004; USFWS, 2007). Bullfrogs are known to prey on CTS larvae and studies have shown that the number of CTS decreases as bullfrog numbers increase (U SFWS, 2000). A study observing the effect of bullfrogs on the CRLF, a prey item of CTS, showed that less than 5% of CRLF tadpoles survived to metamorphos is when they were raised with bullfrog tadpoles (USFWS, 2000). Because bullfrogs are still used for food and sport in California, the threat of transport for intenti onal establishment of bullfrogs in central CTS suitable habitat is sign ificant (USFWS, 2004).

Western mosquito fish, which are used to c ontrol mosquitoes because they eat mosquito larvae, are also known to prey on amphibian species (USFWS, 2003). Incidentally, field and laboratory experiments have shown that mosquito fish will preferentially prey on amphibians even in the presence of mosquito larvae (USFWS, 2003). It is not known if mosquito fish target CTS specifically; however , larval CTS may be particularly at risk due to their external gills which are attractive to mosqu ito fish (USFWS, 2003). A study performed in 1994 found that no CTS had been found in ponds where mosquito fish were located (USFWS, 2003). However, another study performed in 2000 found that CTS numbers were reduced in ponds stocked with mosquito fish at densities similar to those found in many stock ponds (USFWS, 2004a). CTS larvae found in ponds containing mosquito fish were smaller, took longer to metamorphose, and typically suffered injuries, such as shortened tails (USFWS, 2004a). Another study performed in 2003 showed that at low densities mosquito fish did not have a significant impact on larval CTS growth and survival, but that growth and size at metamo rphosis was reduced at high fish densities (USFWS, 2004a). It is thought that large numbers of mosquito fish may also outcompete CTS larvae for food (USFWS, 2000).

Other species of non-native fish, including la rgemouth bass, bluegill, catfish, and fathead minnows may also either be directly responsib le for or have the potential to cause the decline of the CTS (USFWS, 2003). In easte rn Merced County, inhabited by the central CTS, CTS were absent from stock ponds that contained non-native fish, but stock ponds without non-native fish supporte d populations of CTS. Thes e non-native fish may affect the prey base of the CTS or prey on larval CT S, either of which is capable of reducing or

46eliminating CTS populations (USFWS, 2000). Several of these species, including largemouth bass, bluegill, catfish, and bullheads, have been and still are stocked in ponds throughout California for fishing (USWFWS, 2003).

Hybridization Hybridization is a serious threat in the Cent ral Coast region of the CTS. Virtually all CTS populations within this region have hybrid genes; introduced genes have been found from southern Santa Clara County through most of Monterey County down to Fort Hunter Liggett on the San Luis Obispo County Line. Hybridization was studied at a site in Monterey County between the central CTS and non-native tiger salamanders.

Researchers found clear evidence that the CTS was interbreeding in the wild and were producing viable, hybrid offspring. The ex tent of interbreeding, though, was found to depend on habitat quality. Pure central CTS we re found to be most prevalent in natural habitats, rather than artificial or disturbe d ones. According to the study, vernal pools contained a larger percentage of pure CTS la rvae. The authors suggest that more hybrids are found in artificial ponds because of the l ack of barriers preventing gene exchange. In the last decade, hybrid tissue has been documented for the first time in Fort Ord, the upper Carmel Valley, and Merced County, where pure CTS individuals had been originally found. Hybridization and introgression is an important evolutionary component, but it becomes a concern when it is fostered by human disturbance activities (USFWS, 2004).

5.2.1.4 Other Factors affecting the species continued existence

Chemical Contaminants Contaminants from oil production and road runoff ( e.g ., hydrocarbons) directly and indirectly affect the CTS. The runoff from roads ( e.g ., oil and other contaminants) is found in adjacent ponds and is implicated in amphibian deformities, as well as amphibian and invertebrate mortality (USFWS 2000). CTS are particularly vulnerable because they inhabit both aquatic and terrestrial habitats which expose them to a variety of toxins throughout their life cycle. Their permeable skin further increases their vulnerability (USFWS, 2004), and studies have found developmental effects in marbled ( Ambystoma

opacum ) and eastern tiger salamanders ( A. tigrinum ), and limited direct effects in five week old salamanders. Study results indicate d that salamanders from oil-contaminated natural ponds metamorphosed earlier at sm aller sizes and that those from oilcontaminated artificial ponds had slower growth rates than larvae raised in noncontaminated ponds. However, affects to eggs and early life stages were not addressed

where effects could be more severe. Othe r studies have examin ed the toxicity of fluoranthene, a polycyclic aromatic hydrocar bon present in petroleum products and urban runoff, on spotted salamanders ( A. maculatum ), northern leopard frogs ( Rana pipiens ), and African clawed frogs ( Xenopus laevis ). Researchers evaluated concentrations at

levels commensurate to those measured in se rvice stations and ot her urban runoff, and found reduced survival and growth abnormalities in all species under field and laboratory conditions. Effects were worsened when the larvae were exposed to fluoranthene in natural sunlight rath er than in artificia l light (USFWS, 2000).

47Sedimentation from road construction, main tenance, and runoff is a second type of contaminant threatening the CTS. Breedi ng ponds are affected by the altered hydrology near roads, which leads to erosion, gullies, and increased sediment deposits in wetland systems. Increased dust from traffic aff ects aquatic and emergent vegetation and may asphyxiate CTS eggs. Excessive sedimentati on ultimately fills pools otherwise usable by the CTS. Sedimentation may also impair the CTS from detecting food items (USFWS, 2000). The risk factor associated with cont aminants in runoff is of concern and will likely increase in both roadside ditches a nd the rest of CTS su itable habitat (USFWS, 2003).

Rodent Control CTS utilize ground squirrel and pocket gopher burrows for aestivation (USFWS, 2003). While the CTS is probably not at risk from ingesting the rodenticid es used to control these two species, the CTS may potentially be at risk from indire ct exposure to them

inside the burrows or concen trated in breeding ponds (U SFWS, 2003). Some of these

rodenticides used in central CTS habita t include chlorophaci none, diphacinone, and strychnine (USFWS, 2003). Fumigants are other pesticides used for rodent control, such as aluminum phosphide, carbon monoxide, and met hyl bromide, which are injected into burrows by using a cartridge or by pumpi ng (USFWS, 2003). These fumigants can be both directly and indirectly lethal to the CTS, although th e effects of these poisons on CTS have not been assessed (USFWS, 2003). Be sides the use of rodenticides, control of rodents by means of eliminating burrows result s is a loss of tenabl e habitat for the CTS (USFWS, 2003). Cattle owners, for example, destroy ground squirrel burrows and thus eliminate CTS habitat because the burrows put cattle at risk of breaking their legs (USFWS, 2003).

Livestock Grazing As opposed to many factors that negatively a ffect the CTS, grazing can, in moderation, have a neutral to positive impact on the CT S. Grazing maintains shorter vegetation and promotes the persistence of ground squirrel burrowing, which creates habitat essential for the CTS. In some cases rangelands presen t the only undeveloped habitat in the County, and thus provided the only opportunity for the salamanders to maintain sustainable populations (USFWS, 2000). Ra ngelands not only provide natural vernal pools, but artificial stock ponds whic h have likely saved many populations from extirpation (USFWS, 2004). Although trampling from cattle affect water levels and soil integrity of ponds and banks, grazing is stil l compatible with CTS as long as burrowing rodents are not completely eradicated (USFWS, 2004).

Road-Crossing Mortality

It is well documented that numerous CTS ar e killed by vehicular traffic while crossing roads (USFWS, 2003). In one study, there we re 45 CTS collected during one hour period on a road bordering Lake Lagunita on the Stanford University Campus. Of the 45 collected, 28 had been killed by cars. Estim ations of CTS mortality from vehicular strikes range from 25 to 72 percent. Mortalit y may be increased by the presence of curbs and berms, which allow salamanders to clim b onto the road but can restrict their

48movement off of the road (USFWS, 2003). Vehi cle usage in Californi a is also increasing as the human population continues to grow. From 1972 to 2001, the State highway system total vehicular usage rose from 108.6 kilometers (km) to 270,000,000,000 (270 billion) km. It is believed that the relativ ely high road-use and road-density values make road-kill mortality a threat to the species (USFWS, 2004).

5.2.2 Baseline Status

The CTS is found only in California. The hi storic range of the CTS included large portions of the Central Valley of California from the southern Sacramento Valley (north of the Sacramento River delta) to the sout hern San Joaquin Valley (USFWS, 2002). The CTS was also found in the lower foothills along the eastern side of the Central Valley and in the foothills of the Coast Ranges (USFWS, 2002). CTS have been historically documented in 27 counties but are no longer found in three (USFWS, 2005). The

USFWS believes that the CTS is still f ound in the remaining 24 counties (USFWS, 2005). CTS have been found in 10 of the 17 Ca lifornia vernal pool designations defined by Keeler-Wolf in 1998 (USFWS, 2004).

Although the CTS has been eliminated from mu ch of its former range in the Central Valley, it still occurs throughout most of its overall historical range and can be locally common (Hammerson, 2004). In addition, it has been recently rediscovered on the San Francisco Peninsula (Hammerson, 2004). The quality, connectivity, and distribution of

the habitat within the current range has been degraded, ev en though the current range of the CTS is close in size to its historic range (USFWS, 2004).

Population Dynamics Studies suggest that the present patchy dist ribution pattern of CTS inhabited areas was caused by a combination of extreme anthr opogenic changes in and around the Central Valley and the restrictive breed ing requirements of the species. Geographic Information Systems (GIS) indicate that there are a pproximately 378,882 ha of Central CTS upland and aquatic habitat remaining. Of the total, 28,526 ha fall within planned areas for highdensity residential, medium density residentia l, industrial, or commercial developments. An additional 24,240 ha are slated for low-density residential development, and 45,880 intended for very-low-density residential development (20 to 160 acre parcels). These projected developments may destroy and fragment central CTS upland and aquatic breeding habitat and ultimately reduce the long-term persistence at the affected localities. In contrast to the detrimental development, part of the central CTS habitat is being protected to some degree. There is an estimated 76,501 ha, 20 percent of the total inhabited area, which is protected from further development or land conversion. However, these sites vary in their degree of protection due to land use designation, nonnative predators, agriculture and landscaping contaminants, rodent control, roads, and hybridization. Thus, the determined “protected ” habitat is considered a liberal estimation (USFWS, 2004).

495.3 REFERENCES

Hammerson, G. 2004. Ambystoma californiense . In: IUCN 2007. 2007 IUCN Red List of Threatened Species . Available online at: www.iucnredlist.org (Accessed on October 4, 2007).

Harp, Elizabeth M, and James W. Petra nka. 2006. Ranavirus in wood frogs ( Rana sylvatica ): potential sources of transmission within and between ponds. Journal of Wildlife Diseases, 42(2), 2006, pp. 307-318. Available online at: http://www.jwildlifedis.org/c gi/content/abs tract/42/2/307 (Accessed on February 19, 2009).

United States Fish and Wildlife Service (USFWS). 2000. Endangered and threatened wildlife and plants; final rule to list the Santa Barbara distinct population of the California tiger salamander as endangered; final rule. Fe deral Register 65 (184):57242-57264. Available online at http://ecos.fws.gov/speciesProfi le/SpeciesReport.do?spcode=D01T (Accessed January 25, 2009).

U.S. Fish and Wildlife Service (USFWS). 2002. Recovery Plan for the California Redlegged Frog ( Rana aurora draytonii ). USFWS, Region 1. Portland, Oregon viii+173 pp. Ava ilable online at: http://ecos.fws.gov/doc /recovery_plans/2002/020528.pdf (Accessed on October 3, 2007).

United States Fish and Wildlife Service (USFWS). 2004. Endangered and threatened wildlife and plants: determination of thre atened status for the California tiger salamander. Federal Register 69 (149):47212-47248. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4278.pdf (Accessed on January 25, 2009).

U.S. Fish and Wildlife Service (USFWS). 2005. California tiger salamander critical habitat designated for the central population - Facts and Q&A. August 23, 2005.

Available online at: http://www.fws.gov/sacramento/ea/news_releases/2005%20News%20Releases/ce ntral_CTS_fCH_QA.htm (Accessed on January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2007. Species Account: California tiger salamander ( Ambystoma californiense ). Sacramento Fish and Wildlife

Office. Available online at: http://www.fws.gov/sacramento/es/animal _spp_acct/california_tiger_salamander. pdf (Accessed on January 25, 2009).

506: CALIFORNIA TIGER SALAM ANDER: SANTA BARBARA COUNTY

DISTINCT POPULATION SEGMENT

6.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on th e Santa Barbara County (SB) distinct population segment (DPS) of the California tiger salamander ( Ambystoma californiense ) (SB CTS) that are reasonably certain to occur in the action area. Future federal actions not directly related to the proposed action are not considered because they re quire additional consultation under Section 7 of the Endangered Species Act (Act). The numerous non-federal actions that are reasonably certain to occur within the action area consist of intensive agriculture ( i.e ., vineyards, row crops, and flower), ur ban development, grazing operations, oil production, and contamination from runoff and sp ills. Many of these f actors are linked or act synergistically and create complex consequences for the SB CTS. For example, conversions to intensive agricu lture and urban developments have resulted in the loss of breeding habitat from the dest ruction or alteratio n of natural vernal pools and seasonal ponds. If these water bodies are destroyed by de ep ripping, a technique that uses a 4- to 7-foot deep plow to break up the hardpan layer, the once compacted soil will no longer

retain water and will inhibit ponding. Repeated deep-ri pping, in addition to plowing and discing in upland habitats, can alter hydrology of the pools a nd ultimately destroy them. In contrast to destroying water bodies, so me seasonal ponds are being converted into permanent ponds for irrigation. However, these ponds are then frequently stocked with fish to control mosquitoes and other pr oblematic insects, and can limit SB CTS populating the water edges. Both destruction and reduced suitability of breeding habitat, compounded with increased urbanization, frag ments and isolates subpopulations from each other and inhibits beneficial gene flow.

6.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a snap shot of the SB CTS’s status at this time. However, the baseline condition of each a ssessed SB CTS species and habitat varies across locations. Given the larg e number of occupied habita ts and extent of the action area included in this assessment, the environm ental baseline includes a general discussion of factors that may affect SB CTS within th e action area. This information is presented in Section 6.2.1. Additional information on the current distribution and population dynamics of the SB CTS is presented as part of the baseline status in Section 6.2.2.

516.2.1 Factors affecting species continued existence within the action area

SB CTS’s continued existence is primarily a ffected by the destruction, modification, or

curtailment of suitable hab itat due to rangeland conversi on for urban and agricultural uses, with road construction, intensive ag riculture, and urbaniza tion constituting the major three uses. Other influential factors affecting SB CTS include contaminants; pest control; grazing practic es and water drawdown; preda tion and introduced species; and disease. As opposed to many of these factors that negatively affect the SB CTS, grazing can, in moderation, have a neutral to positive impact on the SB CTS. Some of these factors are known to affect the SB CTS, while others are known to generally affect the CTS population throughout its entire range. The factors known to affect the larger population are still relevant to the SB CTS, but are referred to as CTS. Sections 6.2.1.1- 6.2.1.6 provide details on each of the major issu es affecting SB CTS environment within

the action area.

6.2.1.1 Conversion of rangeland for urban and agricultural uses

A variety of urban and agricultural land us es are implicated in the destruction, modification, and curtailment of SB CTS habitat. The USFWS (2004a) defines urban uses as including nonagricultural devel opment activities such as building and maintenance of housing, commercial, and i ndustrial developments; construction and widening of roads and highways; golf course construction and maintenance; landfill operation and expansion; operation of grav el mines and quarries; dam building and inundation of habitat by reservoirs ; and other infrastructure activ ities. Agricultural land uses are defined as including native habita t conversion by discing and deep-ripping; and cultivation, planting, irrigation, and maintenance of row crops, orchards, and vineyards. Both urban and agricultural conversions have reduced or modified natural vernal pools and seasonal ponds used for breeding habitats, as well as reduced upland habitat used for aestivation and migratio n (USFWS, 2000).

All known locations of the SB CTS are affect ed by railroads, highways, or other roads causing extensive habitat fragme ntation. SB CTS require la rge tracts of unobstructed landscape for dispersal and migr ation. Larger roads, highw ays, and railroads act as permanent physical barriers and can prevent genetic interchange and movement to and from breeding and aestivation sites. The tempor ary construction of road and rail is also

detrimental to the SB CTS. Slow-movi ng animals are unable to escape the initial intrusion and disruption of construction and any SB CTS in underground burrows are likely to be crushed. Once the road is open, th e salamanders are at risk for being run over on their first dispersal runs to the pond. Studi es indicate that up to 9 to 12 SB CTS are killed as they try to cros s roads during migrations betw een breeding and upland sites (USFWS, 2000). Soil compaction and altera tion, including soil density, soil water content, dust, surface-water flow, patterns of runoff, and sedimentation, are other issues

affected the SB CTS in areas underneath and adjacent to the road bed. Harmful ecological effects of roads can extend outward on average of 0.6 km from the road bed and can make burrowing and migrating near th e road difficult for the SB CTS. A study

52on road distances to wetlands indicated th at the number of am phibian species in a wetland was adversely affected by roads being located within a 2 km (1.2mi) range of that wetland (USFWS, 2000). Berms and cu rbs as low as 9 to 12 cm also are of particular concern, as they allow salamanders to climb onto the road but can restrict their movement off of the road (USFWS, 2003). Such berms exist on the State highway and the secondary road in proximity to three ponds in Santa Barbara County (USFWS, 2003)

Intensive agricultural practices began in Santa Barbara County more than 30 years ago, in

the Santa Maria River and San Antonio Creek Valleys, and continue today. Row crop acreage in the Los Alamos and Santa Rita Valleys has increased by more than 9,900 hectares (ha) (more than 25,000 acres ( ac)) between the years of 1986-1997. An installation of 4,000 ha of vineyards fr om 1996-1999 has more than doubled the land cultivated for grapes. Between the nine years from 1992 to 2000, irrigated cropland in Santa Barbara County has increased by 49% , or by 15,700 ha (38,850 ac), and 36% of this growth occurred in between 1997 and 1999 (5,670 ha or 14,000 ac) (USFWS, 2000).

Vernal pools, seasonal ponds, and upland habitat continue to be lost as suitable land is converted for agricultural and urban uses. Changes to vernal pool or pond inundation, duration, or depth can detrimentally impact the reproductive success of the SB CTS. These changes are caused by, among others, digg ing of drainage or irrigation ditches, construction of permanent ponds or reservoirs, deepening or berming of seasonal wetlands, and redirection or runoff fr om developments (USFWS, 2000). The repercussions of these activi ties on the reproductive success of the SB CTS include: (1) prematurely drying wetlands and desiccat ing SB CTS larvae; (2) extending the inundation period and facilita tion invasion of non-native predators; (3) creating conditions that foster the hybr idization between the non-native tiger salamander; and (4) increasing vulnerability to disease from isol ation and fragmentation. Wetland habitats are utilized for reproduction; thus destru ctive activities such as filling, discing, or excavating, are injurious or le thal to the eggs, larvae, or breeding adults. Earthmoving operations and cultivation in upland habitat also threaten the SB CTS, which use the habitat to breed, feed, and seek shelter. SB CTS are at risk in burrows or on the surface from discing, deep-ripping, or grading of upla nd habitat. Indirect impacts to the SB CTS include increased predation from over exposure, high temperatures, low humidity, and diminished food sources. Earth moving operati ons may further disturb California ground squirrel burrows and crevices, protection ut ilized by the SB CTS, and may render upland

locations untenable or unavai lable (USFWS, 2004 a).

Urbanization and rural residen tial development threaten the SB CTS rangeland areas that may contain vernal pool and grassland habitats. Between 1982 and 1997, privately owned rangeland decreased by 252,524 ha ( 624,000ac), and between 1998 and 2000 the state of California lost an additional 21,555 ha (53,263 ac). This loss of rangeland results from a myriad of factors, including a dec line in farm rancher income, the aging of ranchers, tax implications of intergenerationa l transfers of ranches, and the difficulty of beginning a ranching operation ( e.g ., cost and knowledge) (USFWS, 2004 a).

Fragmentation

53The primary factors causing SB CTS frag mentation are discussed above: road construction, urbanization, and intensive ag riculture. Human-caused fragmentation places the SB CTS at particular risk to local extinctions because its metapopulation

structure is distributed across the landscape (USFWS, 2000).

“A metapopulation is a group of spatia lly distinct populations that can occasionally exchange dispersing individuals. The populations in a metapopulation are usually thought of as having interdependent extinction and colonization processes, where individua l populations may be extirpated from a

local area and later be reco lonized from another populati on that is still extant” (FR, 72:48177, p.6).

A reduction in SB CTS dispersal greatly in hibits the dynamics of a metapopulation and

reduces the abilities of the SB CTS to persist over time. Of the three factors, roads accelerate fragmentation by increasing mortalit y and preventing recolonization of sites that would otherwise be only tem porarily extirpated (USFWS, 2000).

6.2.1.2 Contaminants

Contaminants from oil production and road runoff ( e.g ., hydrocarbons) directly and indirectly affect the SB CTS. The runoff from roads ( e.g ., oil and other contaminants) is found in adjacent ponds and is implicated in amphibian deformities, as well as amphibian and invertebrate mortality (USFWS 2000). SB CTS are particularly vulnerable because they inhabit both aquatic and terrestrial habita ts which expose them to a variety of toxins throughout their life cycle. Their permeable skin further increases their vulnerability (USFWS, 2004a), and studies have found developmental effects in marbled ( Ambystoma

opacum ) and eastern tiger salamanders ( A. tigrinum ), and limited direct effects in five week old salamanders. Study results indicate d that salamanders from oil-contaminated natural ponds metamorphosed earlier at sm aller sizes and that those from oilcontaminated artificial ponds had slower growth rates than larvae raised in noncontaminated ponds. However, effects to eggs and early life stages, which could be more severe, were not addressed. Other studies have examined the toxicity of Fluoranthene, a polycyclic aromatic hydrocarbon present in petroleum products and urban runoff, on spotted salamanders ( A. maculatum ), northern leopard frogs ( Rana pipiens ), and African clawed frogs ( Xenopus laevis ). The researchers evaluated concentrations at levels

commensurate to those measured in service stations and other ur ban runoff, and found reduced survival and growth abnormalities in all species under field and laboratory

conditions. Effects were worsened when th e larvae were exposed to Fluoranthene in natural sunlight rath er than in artificia l light (USFWS, 2000).

Sedimentation from road construction, main tenance, and runoff is a second type of contamination threatening the SB CTS. Breeding ponds are affected by the altered hydrology near roads, which lead s to erosion, gullies, and in creased sediment deposits in wetland systems. Increased dust from traffic affects aquatic and emergent vegetation and may asphyxiate SB CTS eggs. Excessive sedi mentation ultimately fills pools otherwise

54usable by the SB CTS. Sedi mentation may also impair th e SB CTS from detecting food items (USFWS, 2000).

6.2.1.3 Pest control

Pesticides and rodenticides ar e heavily used in the agricultu ral areas associated with CTS aquatic and terrestrial habitats. Therefore, CTS are likely exposed to a variety of pesticides in their natural habitat. CTS are particularly sensitive to these chemicals because of the permeability of their skin (USFWS, 2007). Furthermore, the use of pesticides can negatively impact CTS by reducin g their prey availability (USFWS, 2007). For example, some studies have shown that methoprene, used for mosquito control, is

associated with reduced survival rates and increased malformations of some anuran species (USFWS, 2003). The USFWS reporte d that other insecticides besides methoprene have adversely impacted growth rates in gray treefrog ( Rana clamitans ) tadpoles and increased mortality ra tes in southern leopard frogs ( R. sphenocephala ) (USFWS, 2000). Temephos was identified by the USFWS as an example of these

additional insecticid es (USFWS, 2000). Bacillus thuringensis israeli , a bacterium, is also used in Santa Barbara County for mosquito control (USFWS, 2000). The effects of this bacterium on the CTS prey base are currently un known (USFWS, 2000).

CTS are also negatively affected by rodenticides because they are sma ller than the target species (USFWS, 2007). Ground squirrel populati ons were controlled in Santa Barbara County using compound 1080 (sodium fluoroacet ate) until about 1990 (USFWS, 2000). This chemical is highly toxic to non-target species, including fis h, birds, and mammals and it is thought that the use of compound 1080 in some areas may have contributed to the observed reduction in CTS populations (USFWS, 2000). Grain poisoned with anticoagulant substances is the preferre d method to control ground squirrels where children, pets, or poultry might be present, a lthough grains poisoned with strychnine are also used (USFWS, 2003). The rodenticide, zinc phosphide, can indire ctly impact CTS if it is washed into burrows or ponds used by the salamanders (USFWS, 2003). Two commonly used rodenticides, chlorophacinone and diphacinone, both anticoagulants, can be absorbed through the skin and are therefore very t oxic to CTS (USFWS, 2003). Several gasses also used to control rodents, identified as aluminum phosphide, carbon monoxide, and methyl bromide, are introdu ced into the small mammal burrows where CTS may live (USFWS, 2003).

Another threat to CTS includes habitat loss du e to elimination of small mammal burrows. Small mammal control programs have a pr ofound negative effect on CTS because they

reduce the number of burrows available for CTS use. Studies have found that CTS use both occupied and unoccupied burrows; however, burrows typically collapse within 18

months after the burrow has been vacated by the small mammal. It has not been

determined whether CTS are able to us e collapsed burrows (USFWS, 2000 and 2003).

556.2.1.4 Grazing and Water drawdown

As opposed to many factors that negativel y affect the SB CTS, grazing can, in moderation, have a neutral to positive impact on the SBTS . Grazing maintains shorter vegetation and promotes the persistence of ground squirr el burrowing, which creates

habitat essential for the SB CT S. As of the Federal Regist er final rule (2000), grazing land in Santa Barbara County offered the onl y large amounts of suita ble habitat for the SB CTS. Because rangelands presented the only undeveloped habitat in the County, they provided the only opportunity for the salamande rs to maintain sustainable populations (USFWS, 2000). Rangelands not only provide natural vernal pools, but artificial stock ponds, which have likely saved many populat ions from extirpation (USFWS, 2004 a). Although trampling from cattle may impact wa ter levels and soil integrity of ponds and banks, grazing is considered to be compatible with SB CTS, as long as burrowing rodents are not completely erad icated (USFWS, 2004 a).

Water drawdown affects many of the ponds in Northern Santa Barbara County from agricultural practices such as irrigation and fr ost control. Submersible pumps are used to remove the water during frost control; thus, SB CTS larvae and adults may be killed by being sucked into pump mechanisms. Wate r drawdown also puts the pond at risk of prematurely drying in the sp ring or summer, thus desicc ating the un-metamorphosed larvae (USFWS, 2000).

6.2.1.5 Predation, Competition, and Hybridization

At least four of the six SB CTS metapopul ations are subjected to predation and competition by native and non-native species. Native predators of the CTS include great blue herons ( Ardea herodias ), egrets ( Casmerodius ), western pond turtles ( Clemmys

marmorata ), garter snakes ( Thamnophis spp.), larger CTS larvae, larger spadefoot toads ( Scaphiopus hammondii ), and California red-legged frogs ( Rana draytonii ) (USFWS, 2004a). Native as well as non-native cr ayfish also prey on CTS (USFWS, 2003). Predation of CTS by sticklebacks, fish wh ich are native to California, is unknown (USFWS, 2003). While native predation and hybridization is probably a discountable threat in healthy populations, these native predators may have significant impacts on population viability when populations are su bjected to the cumulative effects of contaminants, migration barriers, an d/or habitat alte ration (USFWS, 2003).

Predation by and competition with non-native and introduced species contributes to the decline of the CTS (USFWS, 2003). Non-native predators of both adult and larval CTS include Louisiana red swamp crayfi sh, mosquitofish, sunfish spp. ( e.g ,. large mouth bass ( Micropterus salmoides )) bluegill ( Lepomis macrochirus ), catfish spp. ( Ictalurus spp.), fathead minnow ( Pimephales promelas ), carp ( Cyprinus carpio ), and American bullfrog ( Rana catesbeiana ) (USFWS, 2004 a; USFWS, 2007). L ouisiana crayfish are found in two known CTS breeding locations in Santa Barbara County (USFWS, 2000). Bullfrogs are known to prey on CTS larvae and studies have shown that the number of CTS decreases as bullfrog number s increase (USFWS, 2000). A study observing the effect of

56bullfrogs on the CRLF, a prey item of CTS, showed that less than 5% of CRLF tadpoles survived to metamorphosis when they we re raised with bullfrog tadpoles (USFWS, 2000).

Western mosquito fish, which are used to c ontrol mosquitoes because they eat mosquito larvae, are also known to prey on amphibian species (USFWS, 2003). Incidentally, field and laboratory experiments have shown that mosquito fish will preferentially prey on amphibians even in the presence of mosquito larvae (USFWS, 2003). It is not known if mosquito fish target CTS specifically; however , larval CTS may be particularly at risk due to their external gills which are attractive to mosqu ito fish (USFWS, 2003). A study performed in 1994 found that no CTS had been found in ponds where mosquito fish were located (USFWS, 2003). However, another study performed in 2000 found that CTS numbers were reduced in ponds stocked with mosquito fish at densities similar to those found in many stock ponds (USFWS, 2004a). CTS larvae found in ponds containing mosquito fish were smaller, took longer to metamorphose, and typically suffered injuries, such as shortened tails (USFWS, 2004a). Another study performed in 2003 showed that at low densities mosquito fish did not have a significant impact on larval CTS growth and survival, but that growth and size at metamo rphosis was reduced at high fish densities (USFWS, 2004a). It is thought that large numbers of mosquito fish may also outcompete CTS larvae for food (USFWS, 2000).

Other species of non-native fish, including la rgemouth bass, bluegill, catfish, and fathead minnows may also either be directly responsib le for or have the potential to cause the decline of the CTS (USFWS, 2003). The Los Alamos and West Orcutt metapopulations, in particular, are limited by these non-nativ e fish species and CT S suitable habitat has supported non-native fish populations for a numbe r of years. These fish may affect the prey base of the CTS or prey on larval CTS, either of which is capable of reducing or eliminating CTS populations (USFWS, 2000). Several of these species including largemouth bass, bluegill, catfish, and bullheads have been, and still are, stocked in ponds throughout California for fishing (USWFWS, 2003).

Hybridization Non-native subspecies of tiger salamanders ha ve been brought to California and used for fishing bait (USFWS, 2004 a). Whether by bait-bucket releas e or intentional introduction, non-native tiger salamanders are now established in California (CDFG, 2010). The practice of importing barred tiger salamanders ( A. tigrinum mavortium ) and Arizona tiger salamanders ( A. tigrinum nebulosum ) was legal in California until December of 2000 (CDFG, 2010). At this time, the California Department of Fish and Game (Department) ruled that using A. tigrinum as bait was illegal, as well as possessing any individual in the genus Ambystoma in California without first obtaining a Department-issued permit (CDFG, 2010). Th is regulation was intended to mitigate CTS hybridization with non-native tiger salamanders (CDFG, 2010). As reported by the USFWS, introduced tiger salamanders have been observed in Santa Barbara County at one location west of Santa Rita Valley (U SFWS, 2000). The non-native species have been known to escape in areas where CTS ar e found, and can compete and breed with CTS (USFWS, 2003). The hybrids that are cr eated when non-native tiger salamanders

57and CTS breed were originally thought to be poorly-adapted to surviv e or be sterile past the first few generations (USF WS, 2007). However, more recent data suggest that the hybrids are viable and can breed with the CTS (USFWS, 2003). Pure CTS have been found more frequently in natu ral habitats compared with artificial or disturbed ones (USFWS, 2004 a). It seems that hybrids are less likely to be found in vernal pools, stressing the importance of protecting exis ting natural vernal pools (USFWS, 2004 a).

6.2.1.6 Disease

The direct effect of disease on the SB CT S is not known, and risks to the distinct population segment (DPS) cannot be precluded (USFWS, 2000). Disease potentially

threatens the SB CTS because it is found in relatively few sites and its metapopulation structure is distributed across a small por tion of the County (USFWS, 2000). Several pathogenic (disease-causing) agents have been linked to deaths of closely-related tiger salamanders and other amphibian species, and include fungi, viruses, and at least one bacterium ( Acinetobacter spp.) (USFWS, 2000; USFWS, 2004 a). These pathogens could devastate current SB CTS populations if introduced into the county (USFWS, 2000).

The bacterium Acinetobacter is common in soil and anim al feces (USFWS, 2000). In one study, this bacterium was found to incr ease with increasing nitrogen levels from atmospheric deposition as the study lake in Utah (Desolation Lake ) dried out (USFWS, 2000). Affected tiger salamanders showed symp toms of red, swollen hind legs and vents, and hemorrhaging of skin and internal organs . Iridoviruses, (a family, containing the

genus Ranavirus ) are viruses with DNA as the genetic ma terial that occur in insects, fish, and amphibians, including tiger salamanders (Harp, 2006; USFWS, 2000). These viruses can cause a range of symptoms, including skin lesions and mortality, or they can be asymptomatic (USFWS, 2000). Ranaviruses ar e of particular concern because these viruses can be spread on fishing gear, arti ficial stocking of ponds for fishing, and water birds (USFWS, 2003). Outbreaks of ranavirus in tiger salamanders have been associated

with altered habitats and ar tificial ponds (USFWS, 2003). Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis , and ranaviruses have been identified as potential threats to the CTS because these diseases have adversely impacted other amphibians, including tiger salamanders (USFWS, 2004a). Non-native species of bullfrogs and tiger salamanders are potential carriers of these diseases (USFWS, 2004 a).

A study conducted in 1997 showed that tiger salamanders in Georgia reared in ponds

contaminated with silt were susc eptible to infection by the fungus Saprolegnia parasitica (USFWS, 2003). Die offs associated with western toads and Pacific tree frogs, known prey of the CTS, have been associated with Saprolegnia infections (USFWS, 2000). High nitrogen and silt levels from overgrazing or agricultu ral or urban runoff may also increase susceptibility to disease (USFWS, 2000). Two of the three ponds in the West Orcutt metapopulation area are in overgrazed gr asslands and are at risk of receiving runoff that has both high nitrogen and high si lt levels (USFWS, 2000). Four ponds in the Los Alamos metapopulation and the two ponds in the Santa Rita metapopulation are on grazing lands (USFWS, 2000). High levels of nitrogen have been associated with

58bacterial blooms and increased silt has been associated with funga l infections (USFWS, 2000).

6.2.2 Baseline Status

The CTS is found only in California. The hi storic range of the CTS included, “large portions of the Central Valley of California, from the southern Sacramento Valley north

of the Sacramento River delta to the sout hern San Joaquin Valley” (USFWS, 2002). The CTS was also found, “in the lower foothills along the eastern side of the Central Valley and in the foothills of the Coast Ranges” (USFWS, 2002). CTS have been historically documented in 27 counties but are no longer found in three of thes e counties (USFWS, 2005). The USFWS believes that the CTS is still found in the remaining 24 counties (USFWS, 2005). CTS have been found in 10 of the 17 California vernal pool designations defined by Keeler -Wolf in 1998 (USFWS, 2004 a).

The historical distribution and numbers of the CTS are unknown and the challenges to estimate of the total number of CTS in Santa Barbara County have been noted by a number of biologists (USFWS, 2004b). SB CTS now occur in six scattered metapopulations across the species’ historic range in northern Santa Barbara County (USFWS, 2000; USFWS, 2004b). These metapopulat ions are listed by region as follows, with the critical habitat unit identified in parentheses: (1) West Orcutt (Western Santa Maria/Orcutt); (2) Bradley-Dominion (Easte rn Santa Maria); (3) North Los Alamos (Western Los Alamos/Careaga); (4) East Los Al amos (Eastern Los Alamos); (5) Purisima Hills (Purisima Hills); (6) Santa Rita (Santa Rita Valley) (USFWS, 2000; USFWS 2004b). The threats from agriculture, urbanization, overgrazing, fragmentation, and

roadkill are severe in four of these metapopulations, moderate in one, and nominal in the sixth (USFWS, 2000). Due to limited information on population dynamics, the most significant factors affecting the species conti nued existence are used as a representation of the metapopulation’s current baseline stat us. This information on each metapopulation is discussed by region as follows:

(1) West Orcutt (Western Santa Maria/Orcutt) This critical habitat unit comprises 26 percent of the total area identified in Santa Barbara County containing SB CTS primary constituent elements (PCEs) and containing 12 of the 46 known breeding ponds in Santa Barbara County (USFWS, 2004b). These breeding

habitats include seven vernal pools, and a handful of smaller water bodies that make suitable breeding grounds for the SBTS but ha ve never been surveyed (USFWS, 2004b). These 46 known breeding habitats of the SB CTS are comprised of 23 artificial ponds, four human-altered ponds, and 19 natura l ponds (vernal pools) (USFWS, 2004b). The greatest threat to this metapopulation is human population growth coupled with residential and commercial development (USF WS, 2004b). The city of Santa Maria is the fastest growing city in the county and urbanization pressure on the SB CTS will increase concomitantly as the population (as projected) grows by at least 160,000 inhabitants in the next 30 years (USFWS, 2004b ). The county may need to develop over 15,000 ac (6,070 ha) to support this growth (USFWS, 2004b).

59(2) Bradley-Dominion (Eastern Santa Maria) This unit also covers 26 percent of the tota l area identified containing SB CTS PCEs, as well as containing four known breeding ponds (natural vernal pool s) (USFWS, 2004b). This unit faces increased development pre ssure similar to unit 1, although unit 2 also experiences losses to SB CTS habitat from illegally-conducted ground disturbing activities (USFWS, 2004b). This metapopulation is considered to be at highest risk of perishing due to agriculture intensification (USFWS, 2000).

(3) North Los Alamos (Western Los Alamos/Careaga) This unit supports four known breeding ponds , as well as human-made ponds within dispersal distance of the SB CTS breeding ponds in the western Los Alamos Valley that may be used for breeding (USFWS, 2004b). Th e Careaga Divide pond, determined to be one of the most unique and pristine vernal ponds where SB CTS breed, is found in this regions (USFWS, 2004b). In contrast to many other breeding locations, the Careaga Divide pond is encased on two sides by ex tensive, dense coast live oak woodland, in addition to coastal sage scrub and grassla nds on the others (USF WS, 2004b). This unit requires special management to preserve habita t in the form of fish removal, sediment control, and reduction of threats associated with berm failure and vineyard development (USFWS, 2004b).

(4) East Los Alamos (Eastern Los Alamos) This region is the site of four known br eeding locations for the SB CTS (USFWS, 2004b). However, the property on which the four ponds sit has been excluded from

critical habitat determination due to a c onservation strategy crea ted by landowners to enhance or create SB CTS aquatic hab itat (USFWS, 2004b). Even without these breeding ponds, this site provides essential upl and habitat and acreage needed to foster a self-sustaining population (USF WS, 2004b). This unit requires special management to address the threats of road mortality and upland habitat loss (USFWS, 2004b).

(5) Purisima Hills (Purisima Hills)

This unit is threatened with habitat loss and requires special management (USFWS, 2004b). This habitat is unique in that it has steeper terrain and is more densely vegetated than all other units (USFWS, 2004b). It is the only unit containing breeding ponds completely surrounded by coastal sage chap arral (USFWS, 2004b). This metapopulation

is the least threatened of th e six, and one landowner expresse d interest in working with the Land Trust of Santa Barbara County to establish conservation easements protecting the species (USFWS, 2000).

(6) Santa Rita (Santa Rita Valley) This unit is ‘severely affected’ by agricu ltural grading, conversion to row crops, and

livestock facilities in the west (USFWS, 2000). The eastern part, a nd population of SB CTS, is affected by alterations to breedi ng ponds for use by cattle and threats of road strikes. This region is also used for oil production (USFWS, 2000). SB CTS in the Santa Rita Valley are at risk of contaminati on from toxic water bodies, potentially causing developmental deformities or death (USFWS, 2000).

606.3 REFERENCES

Department of Fish and Game, California Natural Resources Agency (CDFG). 2010. A

status review of the Ca lifornia tiger salamander ( Ambystoma californiense ). Report to the Fish and Game Commisssion. Nongame Wildlife Program Publications. January 11, 2010. Accessed online at http://www.dfg.ca.gov/wildlife/non game/publications/docs/CTS- StatusEvaluation.pdf Accessed on March 22, 2010).

Federal Register (FR) 72:48177; August 22, 2007 . Endangered and threatened wildlife and plants; designation of critical habitat for the bay checkerspot butterfly ( Euphydras editha bayensis ); proposed rule. Accessed online at http://ecos.fws.gov/speciesProfi le/SpeciesReport.do?spcode=I021 . (Accessed on October 16, 2008).

Harp, Elizabeth M, and James W. Petra nka. 2006. Ranavirus in wood frogs ( Rana sylvatica ): potential sources of transmission within and between ponds. Journal of Wildlife Diseases, 42(2), 2006, pp. 307-318. Available online at: http://www.jwildlifedis.org/c gi/content/abs tract/42/2/307 (Accessed on February 19, 2009).

United States Fish and Wildlife Service (USFWS). 2000. Endangered and threatened wildlife and plants; final rule to list the Santa Barbara distinct population of the California tiger salamander as endangered; final rule. Fe deral Register 65 (184):57242-57264. Available online at http://ecos.fws.gov/speciesProfi le/SpeciesReport.do?spcode=D01T (Accessed January 25, 2009).

United States Fish and Wildlife Service (USFWS). 2002. Recovery Plan for the California Red-legged Frog ( Rana aurora draytonii ). USFWS, Region 1. Portland, Oregon viii+173 pp. Available online at: http://ecos.fws.gov/doc /recovery_plans/2002/020528.pdf (Accessed on October 3, 2007).

United States Fish and Wildlife Service (U SFWS). 2003. Endangered and threatened wildlife and plants: determ ination of endangered stat us for the Sonoma County distinct population segment of the California tiger sala mander. Federal Register 68 (53):13498-13520. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4072.pdf (Accessed on January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2004a. Endangered and threatened

61wildlife and plants: determination of thre atened status for the California tiger salamander. Federal Register 69 (149):47212-47248. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4278.pdf (Accessed on January 25, 2009).

United States Fish and Wildlife Service (USFWS). 2004b. Endangered and threatened wildlife and plants; Designa tion of Critical Habitat for the California tiger salamander ( Ambystoma californiense ) in Santa Barbara County; Final Rule. Federal Register 69 (226):68568-68609. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4355.pdf (Accessed on January 25, 2009).

U.S. Fish and Wildlife Service (USFWS). 2005. California tiger salamander critical habitat designated for the central population - Facts and Q&A. August 23, 2005.

Available online at: http://www.fws.gov/sacramento/ea/news_releases/2005%20News%20Releases/ce ntral_CTS_fCH_QA.htm (Accessed on January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2007. Species Account: California tiger salamander ( Ambystoma californiense ). Sacramento Fish and Wildlife

Office. Available online at: http://www.fws.gov/sacramento/es/animal _spp_acct/california_tiger_salamander. pdf (Accessed on January 25, 2009).

627: CALIFORNIA TIGER SALAMANDE R: SONOMA COUNTY DISTINCT

POPULATION SEGMENT

7.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the Sonoma County distinct popul ation segment (DPS) of the California tiger salamander ( Ambystoma californiense ) (STS) that are reasonably certain

to occur in the action area. Future federal actions not directly re lated to the proposed action are not considered because they require additional consultation under Section 7 of the Endangered Species Act (Act). The numer ous non-federal actions that are reasonably

certain to occur within the action area consist of urban development, intensive agriculture ( e.g ., vineyards), grazing operations, oil pr oduction, contamination from runoff and spills, and non-native species introductions. Many of thes e factors are linked or act synergistically and create complex consequences for the STS. For example, conversions to intensive agriculture and ur ban developments have resulted in a reduction in the sizes and connectivity between patches of suitabl e and occupied habitat on the Santa Rosa

Plain. The extent of this habitat reducti on makes recolonization of some sites more difficult following local extinction. As the STS is found in a metapopulation structure, the persistence depends on the combined dynamic of these local extinctions and subsequent recolonization. Both destruction and reduced suitability of breeding habitat, compounded with increased urbanization, frag ments and isolates subpopulations from each other and inhibits potentially beneficial gene flow. Further, habitat loss magnifies the effects of other factors, such as amount of food, availability of rodent burrows, pesticide use, mortality from vehicles, and predators, more pronounced given the smaller area now exposed to such impacts (USFWS, 2003).

7.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a sn apshot of the STS’s status at this time. However, the baseline condition of each asse ssed STS species and habitat varies across locations. Given the large number of occupi ed habitats and extent of the action area included in this assessment, the environmenta l baseline includes a general discussion of factors that may affect STS w ithin the action area. This information is presented in Section 7.2.1. Additional information on the current distribution and population dynamics of the STS is presented as part of the baseline status in Section 7.2.2.

7.2.1 Factors affecting species continued existence within the action area

63STS’s continued existence is primarily affected by conti nued destruction, degradation, and fragmentation of suitable habitat. Secondary threats to the DPS include predation and competition from introduced exotic sp ecies; possible commercialization with nonnative salamanders; various chemical cont aminants; road-crossing mortality; rodent control operations; and a small remaining populat ion. Livestock grazing is another factor affecting STSs, although it can in modera tion be a positive rather than negative influential factor (USFWS, 2002; USFWS, 20 03; USFWS, 2004). Some of these factors are known to affect the California Tige r Salamander population in Sonoma County (STS), while others are known to generally affect the California Tiger Salamander (CTS) population throughout its entire range. The f actors known to affect the larger population are still relevant to the STS, but are re ferred to as CTS. Sections 7.2.1.1-7.2.1.4 provide details on the major issues affecting ST S environment within the action area.

7.2.1.1 Habitat Destruction, Degradation, and Fragmentation

As of 2003 when the Sonoma County DPS wa s listed as endangere d, there were eight remaining known breeding sites on the Sant a Rosa Plain. These subpopulations are threatened by construction of high-density housing, office buildings, roads, and other developments. A study conducted in 1990 foun d that 25 percent of a study area of 11,300-hectares (ha) was being used for subdi visions, “ranchettes”, golf courses, and commercial buildings. Seventeen percent of the study area had been converted for agricultural uses. Since 1990, la nd conversion to urban sites and intensive agriculture continue, particularly to vineya rd operations. Other relative ly minor land conversions to roads, storm drains, and road curbs have th e potential to advers ely impact the STS by fragmenting habitat or impedi ng migration. Of the eight kn own breeding sites at the time of listing, five are within 100 meters (m) of major development activities, and all breeding pools are within 450 m of roads a nd residential development (USFWS, 2003).

Urban Development The Santa Rosa County is rapidly urbanizi ng. Since 1980, the city of Santa Rosa has increased 53% in population size. Be tween 1980 and 1997, housing units grew by 66 percent, an increase from 35,403 units to 53,558 units. More recently, five known breeding locations were lost due to commercial and resi dential development between 2001 and 2003. Six of the eight known remain ing breeding sites are located around the former Air Center, in Southwest Santa Rosa. Th is area contains one of the largest blocks of undeveloped lands within the city limits. In the mid-1980s, the ai rport closed and the property was sold to the City. The Southw est Area Plan proposes to development the majority of this area and places STS br eeding grounds in peril (USFWS, 2003).

Roads and Highways Roads and highways act as physical barriers that inhibit successf ul migration of the STS. The CTS needs large tracts of barrier-free la ndscape and roads present an obstacle in the way of moving to new breeding habitat, or re turning to aestivation sites. In worst case scenarios, roads can completely isolate a breeding site or larger portions of a metapopulation and render them unten able for the species (USFWS, 2003).

64As mentioned previously, all breeding pools are within 450 m of a type of road. A study

on road distances to wetlands indicated th at the number of am phibian species in a wetland was adversely affected by roads being located within a 2 km (1.2 mi) range of that wetland. In addition to habitat fragm entation, direct vehicular strikes are of huge concern for the STS caused by roads. In the Central Valley, large numbers of CTS ranging from 15-20 per mile are killed by vehicles. Some estimates place the percentage of breeding population lost to vehicular strikes at 35-72 percent. Between November 21, 2001 and December 5, 2001, 26 STS individuals were found dead on Stony Point Road running between Santa Rosa and Cotati. This road in western Santa Rosa has seen an

increase in vehicular traffi c by about four fold due to its recent support of heavy

commuter traffic. The combination of road s with curbs and berms places even greater threat on the CTS; Curbs and berms as low as 9 to 13 cm allow movement onto a road but can restrict movement off of a road (USFWS, 2003).

Breeding locations Except for the Hall Road Preserve, all of th e known breeding sites of the STS are found in sites being rapidly converted to high-density housing and office buildings. The STS in each breeding location continues to be impact ed from isolation and fragmentation. Only three breeding sites have hydrologic regimes necessary to support the species (Hall Road Preserve, FEMA/Broadmore North Preserve, and Engel Preserve). Five of the breeding locations are on private property, two of wh ich do not allow surveying and the presence of STS there are unknown. Furthermore, th e plans for the development of the old airfield, if completed, will eliminate all existing migration corridors between extant populations (USFWS, 2003).

Fragmentation The primary factors causing CTS fragmentati on are discussed above: road construction, urbanization, and intensive agriculture. Hu man-caused fragmentation places the STS at particular risk to local extinctions becaus e its metapopulation stru cture is distributed across the landscape (USFWS, 2000).

“A metapopulation is a group of spatia lly distinct populations that can occasionally exchange dispersing individuals. The populations in a metapopulation are usually thought of as having interdependent extinction and colonization processes, where individua l populations may be extirpated from a

local area and later be reco lonized from another populati on that is still extant” (USFWS, 2007 a).

A reduction in CTS dispersal greatly inhi bits the dynamics of a metapopulation and reduces the abilities of the CTS to persist over time. Of the three fact ors, roads accelerate fragmentation by increasing mort ality and preventing recoloni zation of sites that would otherwise be only temporaril y extirpated (USFWS, 2000).

7.2.1.2 Disease

65The direct effect of disease on the CTS is not known and risks to the distinct population segment (DPS) cannot be precluded (USFWS , 2000). Several pathogenic (diseasecausing) agents have been linked to deaths of closely-related tiger salamanders and other amphibian species, and include fungi, vi ruses, and at least one bacterium ( Acinetobacter spp.) (USFWS, 2000; USFWS, 2004). These pathogens could devastate current STS populations if introduced into the county (USFWS, 2003).

The bacterium Acinetobacter is common in soil and animal feces (USFWS, 2000). Affected tiger salamanders showed symptoms of red, swollen hind legs and vents, and hemorrhaging of skin and internal organs. Iridoviruses, (a family, containing the genus

Ranavirus ) are viruses with DNA as th e genetic material that o ccur in insects, fish, and amphibians, including tiger salamanders (H arp, 2006; USFWS, 2000). These viruses can cause a range of symptoms, including skin lesions and mortality, or they can be asymptomatic (USFWS, 2000). Ranaviruses ar e of particular concern because these viruses can be spread through fishing gear , artificial stock ponds, and water birds (USFWS, 2003). Outbreaks of ranavirus in tiger salamanders have been directly

associated with altered habitats and artif icial ponds (USFWS, 2003). Ranaviruses, in addition to the fungus Batrachochytrium dendrobatidis that causes Chytridiomycosis, have been identified as potential threats to the CTS because these pathogens have adversely impacted other amphibians, incl uding tiger salamanders (USFWS, 2004). Non-native species of bullfrogs and tiger sa lamanders are potentia l carriers of these diseases (USFWS, 2004).

A study conducted in 1997 showed that tiger salamanders in Georgia reared in ponds

contaminated with silt were susc eptible to infection by the fungus Saprolegnia parasitica (USFWS, 2003). Die offs associated with Western Toads ( Bufo boreas ), Cascades frogs ( Rana Cascadae ), and Pacific Tree frogs ( Psedocris regilla ), known prey of the CTS,

have been associated with Saprolegnia infections (USFWS, 2000). Saprolegnia ferax outbreaks have caused high amphibian embryo mortalities in the Pacific Northwest (USFWS, 2003). High nitrogen and silt levels from overgrazing or agricultural or urban runoff may also increase susceptibility to disease (USFWS, 2000). High levels of nitrogen have been associated with bact erial blooms and incr eased silt has been associated with fungal infections (USFWS, 2000).

7.2.1.3 Predation, Competition, and Hybridization

All of the known STS metapopul ations are potentially affected by native and non-native species predation and competition (USFWS, 20 03). Native predators of the CTS include great blue herons ( Ardea herodias ), egrets ( Casmerodius ), western pond turtles ( Clemmys

marmorata ), garter snakes ( Thamnophis spp.), larger CTS larvae, larger spadefoot toads ( Scaphiopus hammondii ), and California red-legged frogs ( Rana draytonii ) (USFWS, 2004). Native as well as non-native cray fish also prey on CTS (USFWS, 2003). Predation of CTS by sticklebacks, fish wh ich are native to California, is unknown; however, sticklebacks have been present in California for at least 16 million years and

STS establishment in stickleback habitat is thought to be rest ricted (USFWS, 2003).

66While native predation and hybrid ization is probably a disco untable threat in healthy populations, these native predators may have significant impacts on population viability when populations are subjected to the cumu lative effects of contaminants, migration barriers, and/or habitat alteration (USFWS, 2003).

Predation by and competition with non-native and introduced species contributes to the decline of the CTS (USFWS, 2003). Non-native predators of both adult and larval CTS include Louisiana red swamp crayfish ( Procambarus Clarkii ), mosquitofish ( Gambusia affinis ), sunfish spp. ( e.g ., large mouth bass ( Micropterus salmoides )) bluegill ( Lepomis

macrochirus ), catfish spp. ( Ictalurus spp.), fathead minnow ( Pimephales promelas ), carp ( Cyprinus carpio ), and American bullfrog ( Rana catesbeiana ) (USFWS, 2004; USFWS, 2007 b). Introductions of sunfish, largemouth bass, bluegill, catfish, and fathead minnows are thought to be re sponsible for the eliminati on of the STS from several breeding locations in Sonoma County (USFWS, 2003). These fish may affect the prey base of the CTS or prey on larval CTS, e ither of which is capable of reducing or eliminating populations of CTS (USFWS, 2000) . Bullfrogs are known to prey on CTS

larvae and studies have shown that the num ber of CTS decreases as bullfrog numbers increase (USFWS, 2000). A study observing th e effect of bullfrogs on the CRLF, a prey item of CTS, showed that less than 5% of CRLF tadpoles survived to metamorphosis when they were raised with bullfrog tadpol es (USFWS, 2000). One of the pools at the Hall Road preserve and two of the pools at the FEMA/Broadmore North preserve are

located within 46 m of ditches or creeks known to contain bullfrogs or crayfish. Bullfrogs also likely occur in Roseland Creek, near the FEMA/Broadmore North preserve (USFWS, 2003).

Western mosquito fish, which are used to c ontrol mosquitoes because they eat mosquito larvae, are also known to prey on amphibian species (USFWS, 2003). Incidentally, field and laboratory experiments have shown that mosquito fish will preferentially prey on amphibians even in the presence of mosquito larvae (USFWS, 2003). It is not known if mosquito fish target CTS specifically; however , larval CTS may be particularly at risk due to their external gills which are attractive to mosqu ito fish (USFWS, 2003). A study performed in 1994 found that no CTS had been found in ponds where mosquito fish were located (USFWS, 2003). However, another study performed in 2000 found that CTS numbers were reduced in ponds stocked with mosquito fish at densities similar to those found in many stock ponds (USFWS, 2004). CTS larvae found in ponds containing mosquito fish were smaller, took longer to metamorphose, and typically suffered injuries, such as shortened tails (USFWS, 2004). Another study performed in 2003 demonstrated that at low densities mosquito fish did not have a significant impact on larval CTS growth and survival, but that growth and size at metamorphosis was reduced at high fish densities (USFWS, 2004). It is thought that large numbers of mosquito fish may also out-compete CTS larvae for food (USFWS, 2000).

Another confounding impact of mosquito cont rol is the effect of methroprene, an insecticide hormone mimic. This pesticide has been documented to delay the onset of molting in crustacea that had identical mo lting hormones as insects. The use of

67methropene may decrease the availability of prey of aquatic invert ebrates and thus may indirectly affect the STS (USFWS, 2003).

Other species of non-native fish, including la rgemouth bass, bluegill, catfish, and fathead minnows may also either be directly responsib le for or have the potential to cause the decline of the CTS (USFWS, 2003). These fish may affect the prey base of the CTS or prey on larval CTS, either of which is capable of reducing or eliminating CTS populations (USFWS, 2000). Several of these species, including largemouth bass, bluegill, catfish, and bullheads, have been and still are stocked in ponds throughout California for fishing (USWFWS, 2003).

Hybridization Non-native subspecies of tiger salamanders ha ve been brought to California and used for fishing bait (USFWS, 2004). Th is is still legal in Californi a but is restricted to fewer counties and is regulated by the California Department of Fish and Game (USFWS, 2000). Currently, non-native CTS are not known to occur in the range of the Sonoma County CTS population (USFWS, 2004 a); however , the non-natives have been known to escape in areas where CTS are found, and can compete and breed with CTS (USFWS, 2003). The hybrids that are created when non-native tiger salamanders and CTS breed were originally thought to be poorly-adapted to survive or be sterile past the first few generations (USFWS, 2007 b). However, more recent data suggest that the hybrids are viable and can breed with the CTS (USFWS , 2003). Pure CTS have been found more frequently in natural habitats compared with artificial or disturbe d ones (USFWS, 2004). It seems that hybrids are less likely to be found in vernal pools ma king it all that much more important to protect existing natural vernal pools (USFWS, 2004). The loss of any breeding sites of the STS due to hybridizat ion is of serious concern (USFWS, 2003).

7.2.1.4 Other Factors affecting the species continued existence

Chemical Contaminants Contaminants from oil production and road runoff ( e.g ., hydrocarbons) directly and indirectly affect the STS. The runoff from roads ( e.g ., oil and other contaminants) is found in adjacent ponds and is implicated in amphibian deformities, as well as amphibian and invertebrate mortality (USFWS 2000). ST S are particularly vulnerable because they inhabit both aquatic and terrestrial habitats which expose them to a variety of toxins throughout their life cycle. Their permeable skin further increases their vulnerability (USFWS, 2004), and studies have found developmental effects in marbled ( Ambystoma

opacum ) and eastern tiger salamanders ( A. tigrinum ), and limited direct effects in five week old salamanders. Study results indicate d that salamanders from oil-contaminated natural ponds metamorphosed earlier at sm aller sizes and that those from oilcontaminated artificial ponds had slower growth rates than larvae raised in noncontaminated ponds. However, affects to eggs and early life stages were not addressed

where effects could be more severe. Othe r studies have examin ed the toxicity of fluoranthene, a polycyclic aromatic hydrocar bon present in petroleum products and urban runoff, on spotted salamanders ( A. maculatum ), northern leopard frogs ( Rana pipiens ),

68and African clawed frogs ( Xenopus laevis ). Researchers evaluated concentrations at

levels commensurate to those measured in se rvice stations and ot her urban runoff, and found reduced survival and growth abnormalities in all species under field and laboratory conditions. Effects were worsened when the larvae were exposed to fluoranthene in natural sunlight rath er than in artificia l light (USFWS, 2000).

Sedimentation from road construction, main tenance, and runoff is a second type of contaminant threatening the CTS. Breedi ng ponds are affected by the altered hydrology near roads, which lead to erosion, gullies, and increased sediment deposits in wetland systems. Increased dust from traffic aff ects aquatic and emergent vegetation and may asphyxiate CTS eggs. Excessive sedimentati on ultimately fills pools otherwise usable by the STS. Sedimentation may also impair the CTS from detecting food items (USFWS, 2000). Many STS breeding populations inhabi t roadside ditches in place of pools or ponds because these ditches are the last re maining habitats available (USFWS, 2003).

The risk factor associated with contaminan ts in runoff is of concern and will likely

increase in both roadside ditches and th e rest of CTS suitable habitat (USFWS, 2003).

Rodent Control CTS utilize ground squirrel and pocket gopher burrows for aestivation, with the STS most often utilizing the burrows of gophers (USFWS, 2003). It has been found that the presence of STS is significantly correlated with the presence of gophers (USFWS, 2003). While the CTS is probably not at risk from ingesting the rodenticid es used to control these two species, the CTS may potentially be at risk from indire ct exposure to them

inside the burrows or concen trated in breeding ponds (U SFWS, 2003). Some of these rodenticides used in Sonoma County in clude chlorophacinone, diphacinone, and strychnine (USFWS, 2003). Fumigants are other pesticides used for rodent control, such as aluminum phosphide, carbon monoxide, and met hyl bromide, which are injected into burrows by using a cartridge or by pumpi ng (USFWS, 2003). These fumigants can be both directly and indirectly lethal to the CTS, although th e effects of these poisons on CTS have not been assessed (USFWS, 2003). Be sides the use of rodenticides, control of rodents by means of eliminating burrows result s is a loss of tenabl e habitat for the CTS (USFWS, 2003). This is especially true for the Sonoma County DPS where most breeding locations are likely to experience a heightened degree of r odent control due to the landscaping concerns of developed areas (USFWS, 2003). Cattle owners also destroy ground squirrel burrows, and, t hus, eliminate CTS habitat because the burrows put cattle at risk of breaking th eir legs (USFWS, 2003).

Road-Crossing Mortality Although no ‘systematic’ studies of road-cro ssing mortality of CTS in Sonoma County have been conducted, CTS killed by vehicula r traffic have been documented both in Sonoma County and in other portions of the spec ies ranges. In addition to the road kills mentioned previously, in one study there we re 45 CTS collected during one hour period on a road bordering Lake Lagunita on the Stanford University Campus. Of the 45 collected, 28 had been killed by cars. Estim ations of CTS mortality from vehicular strikes range from 25 to 72 percent. Mortalit y may be increased by the presence of curbs

69and berms, which allow salamanders to clim b onto the road but can restrict their movement off of the road (USFWS, 2003).

Livestock Grazing As opposed to many factors that negatively a ffect the CTS, grazing can, in moderation, have a neutral to positive impact on the CT S. Grazing maintains shorter vegetation and promotes the persistence of ground squirrel burrowing, which creates habitats essential for the CTS. Rangelands not only provide natu ral vernal pools, but artificial stock ponds, which have likely saved many populations fr om extirpation (USFWS, 2004). Although trampling from cattle affect water levels a nd soil integrity of ponds and banks, grazing is still compatible with CTS as long as burro wing rodents are not completely eradicated (USFWS, 2004).

7.2.2 Baseline Status

The CTS is found only in California. The hi storic range of the CTS included large portions of the Central Valley of California from the southern Sacramento Valley (north of the Sacramento River delta) to the sout hern San Joaquin Valley (USFWS, 2002). The CTS was also found in the lower foothills along the eastern side of the Central Valley and in the foothills of the Coast Ranges (USFWS, 2002). CTS have been historically documented in 27 counties but are no longer found in three (USFWS, 2005). The

USFWS believes that the CTS is still f ound in the remaining 24 counties (USFWS, 2005). CTS have been found in 10 of the 17 Ca lifornia vernal pool designations defined by Keeler-Wolf in 1998 (USFWS, 2004).

The historical distribution and numbers of the CTS in Sonoma County on the Santa Rosa

Plain are uncertain due to limited informati on collected on this population prior to the 1990s. CTSs are believed to have occupied a much larger region based on habitat requirements of the species for low elevati on, seasonally filled breeding ponds and small rodent burrows, the ecology of the taxon, the general trend of urban development, and

other adverse factors affecti ng the species. The closest CTS populations to Sonoma County are located in Contra Costa, Yolo, a nd Solano Counties, which are separated from the Sonoma County population by the Coast Ra nge, Napa River, and the Carquinez Straits, and distance of a bout 72 km (USFWS, 2003).

Population Dynamics Currently, the Sonoma County CTS and the Sa nta Barbara CTS are considered the most vulnerable populations of Ca lifornia tiger salamanders. Urban development causing habitat loss continues to be the primary fact or affecting their continued existences, and both populations are particularly vulnerable to the risks associated w ith small, restricted populations. Low population numbers amplify the impact of high death and low birth rates, as well as the effects of genetic drift and inbreeding. A reduction in genetic variability can render a species less capable of adapting to fu ture environmental changes, thus reducing overall fitness. Small populati ons are also threatened by the deterioration of environmental quality (USFWS, 2003)

70Although the total number of individual CT S in Sonoma County is unknown, the STS population is scattered in isolated breeding s ites on a small portion of its historic range on

the Santa Rosa Plain. As of the final rule determining endangered status of the STS, there were eight breeding sites known to exist, distributed in and ar ound the City of Santa Rosa. Other sightings of STS had been docum ented in locations south of the Cotati area in roadside ditches and low quality pools, al though these locations were not considered viable breeding sites. The eight viable breeding sites were defined as follows: (1) Hall Road Preserve; (2) Federal Emergency Mana gement Agency (FEMA)/Broadmore North Preserves; (3)Engel Preserve; (4) Northwest Air Center; (5) Southwest Air Center; (6) North Air Center; (7) Wright Avenue; (8 ) South Ludwig Avenue (USFWS, 2003). Specific elements affecting each population are outlined below:

1) Hall Road Preserve This breeding site sits on 76-ha and is the largest pres erved area where STS are currently

known to inhabit. However recent studies have demonstrated the low productivity of breeding occurring. The land surrounding the preserve is slated for urban development. Exotic predators of the salamander possibly impacting this populat ion are the Louisiana crayfish, stickleback fish, and bullfrogs (USFWS, 2003).

2) FEMA/Broadmore North Preserve This breeding site consists of two contiguous properties on 30.5 acres (ac). The FEMA preserve on 24 ac is one of the most producti ve STS breeding sites, and the Broadmore

North Preserve is a conservati on area of the Bellvue School District. Urban development

encroaches on the site from the north a nd east sides, and a new road and housing development on the west partially blocks the migration route to breed ing pools at the Air Center. This construction, as of 2003, was onl y half completed, and it is expected that the final development will entirely block migration between the two sites (USFWS, 2003).

3) Engel Preserve Not many STS individuals are suspected at this site due to low numbers of larvae observed. Lying on 16-ha of privately-owne d preserve, salamanders were not found at this breeding habitat until th e 2001/2002 rainy season. The presence of Todd Road along the southern boundary of the preserve thre atens the population because it obstructs the migration routes to southern aestivation sites (USFWS, 2003).

4) Northwest Air Center This breeding site consists of one pond on private land. The north and west borders are adjacent to roads supporting heavy traffic. To the east and south, housing developments have eliminated migration routes, thus rende ring the breeding area isolated from the remaining seven (USFWS, 2003).

5) Southwest Air Center

71This breeding site also consis ts of one pond on private land. The City of Santa Rosa has issued permits for development that will like ly extirpate the population from this site. The destruction of the breeding area will fu rther isolate this population and all STS populations, although individua ls may still utilize th e breeding areas in the FEMA/Broadmore Preserve (USFWS, 2003).

6) North Air Center This breeding site consists of one pond on private land. Migr ation is restricted on three

sides due to residential and commercial developments: houses to the west, road to the north, and corporate park to the east. More residential developments are approved by the City of Santa Rosa toward the south, and the Army Corps of Engineers has issued permits with the USFWS for the fill of this breeding site. Due to the emergency listing of the species, construction has tempor arily halted (USFWS, 2003).

7) Wright Avenue The condition or existence of this population cannot be confirmed. This breeding site is located on private land, to which access has been denied for many years. Construction on this property is not currently proposed; howev er, no protection exists to prevent breeding sites and upland habitat from being devel oped. The City of Santa Rosa approved residential development along Wright and Ludwig Avenues, which will concomitantly destroy habitat and increase ve hicular traffic (USFWS, 2003).

8) South Ludwig The condition or existence of this populat ion also cannot be confirmed, as it sits on inaccessible, private land. Construction on this property is not currently proposed; however, no protection exists to prevent bree ding sites and upland habitat from being developed. Threats from increased traffic on Ludwig Ave nue threaten this population (USFWS, 2003).

Not long after the STS was listed as endange red, six additional breeding sites were recognized: (1) Gobbi; (2) Duer Road; (3) Ha routunian; (4) Alton Lane; (5) Southwest Community Park; (6) Yuba Drive. All breeding locations with the exception of

Haroutunian and Alton Lane ar e distributed in the City of Santa Rosa and immediate associated unincorporated areas (USFWS, 2004).

Habitat Conservation One habitat conservation plan was issued on September 12, 2008 for the Sonoma County DPS that will help mitigate impacts of a 4.13 acre loss of habitat (Sonoma). A second plan that will help mitigate future deve lopment impacts is the Santa Rosa Plain Conservation Strategy. This strategy was finalized in December of 2005 and aims to mitigate future impacts to listed species from development on the Santa Rosa Plain. The recovery of these species is a second com ponent of the strategy; areas for species conservation are proposed and short- and long-term milestones are formulated to accomplish recovery goals. The result of this strategy is the adoption of eight conservation areas for the STS, along with one STS preserve system (Santa Rosa).

727.3 References

Santa Rosa Plain Conservati on Strategy: Final. 2005. Sacramento Fish & Wildlife

Office. United States Fish and Wild life Service. Available online at http://www.fws.gov/sacramento/es/santa_rosa_conservation_strategy.htm (Accessed on March 9, 2009).

Sonoma County Office of Education LE HCP. 2008. Sacramento Fish and Wildlife

Office. Available online at http://ecos.fws.gov/conserv_plans/servle t/gov.doi.hcp.servlets. PlanReport?plan_i d=4214®ion=8&type=HCP&rtype=1 (Accessed on March 9, 2009).

United States Fish and Wildlife Service (USFWS). 2000. Endangered and threatened wildlife and plants; final rule to list the Santa Barbara distinct population of the California tiger salamander as endangered; final rule. Fe deral Register 65 (184):57242-57264. Available online at http://ecos.fws.gov/speciesProfi le/SpeciesReport.do?spcode=D01T (Accessed January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2002. Endangered and threatened wildlife and plants; listin g the Sonoma County distinct population segment of the California tiger salamander as endang ered. Federal Register 67 (140):47726-

47740. Available online at http://ecos.fws.gov/docs/federal_register/fr3903.pdf (Accessed on March 9, 2009).

United States Fish and Wildlife Service (U SFWS). 2003. Endangered and threatened wildlife and plants: determ ination of endangered stat us for the Sonoma County distinct population segment of the California tiger sala mander. Federal Register 68 (53):13498-13520. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4072.pdf (Accessed on January 25, 2009).

United States Fish and Wildlife Service (USFWS). 2004. Endangered and threatened wildlife and plants: determination of thre atened status for the California tiger salamander; and special rule exemption for existing routine ranching activities; final rule. Federal Register 69 (149):47212-47248. Available online at: http://ecos.fws.gov/docs/ federal_register/fr4278.pdf (Accessed on January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2005. California tiger salamander critical habitat designated for the centr al population - Facts and Q&A. August 23,

2005. Available online at: http://www.fws.gov/sacramento/ea/news_releases/2005%20News%20Releases/ce ntral_CTS_fCH_QA.htm (Accessed on January 25, 2009).

United States Fish and Wildlife Service (U SFWS). 2007 a. Endangered and threatened

73wildlife and plants; designation of critical habitat for the bay checkerspot butterfly ( Euphydras editha bayensis ); proposed rule. Accessed online at http://ecos.fws.gov/speciesProfi le/SpeciesReport.do?spcode=I021 . (Accessed on October 16, 2008).

United States Fish and Wildlife Service (USFW S). 2007 b. Species Account: California tiger salamander ( Ambystoma californiense ). Sacramento Fish and Wildlife

Office. Available online at: http://www.fws.gov/sacramento/es/animal _spp_acct/california_tiger_salamander. pdf (Accessed on January 25, 2009).

748: DELTA SMELT

8.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the Delta smelt ( Hypomesus transpacificus ) that are reasonably

certain to occur in the action area. Future federal actions not directly related to the proposed action are not considered because they require additional consultation under Section 7 of the Endangered Species Act (A ct). The non-federal actions that are reasonably certain to occur within the action area consist of urbanization, toxic substance contamination of Sacramento-San Joaquin Delt a water, and water resource developments for agriculture and municipal demands. Th e water resource developments include, but are not limited to, reservoirs, water facilities , development that fosters increased pumping capacities, and hundreds of small water intake pipes and diversions that supply water for Delta farms. The majority of these actions divert water out of the Sacramento-San Francisco estuary. As the water resource de velopments increase in number, the volume of outflow in the Delta incrementally dimi nishes and causes complex consequences for the delta smelt. Coupled with seasonal fluctuations in precipitation, these water diversions act synergistically to hinder sufficient food resour ces, influence natural flow patterns, physically entrain individuals in pumping facilities, change non-native species abundance, and alter concentra tions of toxic substances.

8.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a sn apshot of the delta smelt status at this time. However, the baseline condition of each assessed delta smelt species and habitat varies across locations. Given the large numbe r of occupied habitats and extent of the action area included of this assessment, the environmental baseline includes a general discussion of factors that may affect delta sm elt within the action area. This information is presented in Section 8.2.1. Additional information on the current distribution and population dynamics of the delta smelt is pres ented as part of the baseline status in

Section 8.2.2.

8.2.1 Factors affecting species envi ronment within the action area

The delta smelt is highly vulnerable to extincti on because of its short life span, present small population size, and restricted distri bution (USFWS, 1993). According to the USFWS Sacramento-San Joaquin Delta Native Fishes Recovery Plan (USFWS, 1996), delta smelt decline has multiple and synergis tic causes (USFWS, 1996). The Plan listed

75the following causes in order of relative impor tance to the species decline: (1) Reduction of outflows; (2) Entrainment losses to wate r diversions; (3) High outflows; (4) Changes in food organisms; (5) Toxic substances; (6) Disease, competition, and predation; (7) Loss of genetic integrity. In approximately the same descending order of importance, these causes are listed below as sections 8.2.1.1 - 8.2.1.5 (USFWS, 1996).

8.2.1.1 Habitat alteration, curtailment, and degradation

The Sacramento-San Joaquin Delta has been significantly altered by human activity and restoration programs targeting Delta fishes, which have influenced spawning habitats, migration corridors, and reari ng areas in upstream locations, the Delta, and Suisun Bay and Marsh (USFWS, 1996). While the trend of building large-s cale water projects upstream that deplete Delta inflows has s ubsided, huge demands on already dwindling water resources will continue as the popul ation of California increases to 50 million people by 2020 (USFWS, 1996). The delta smelt may be particularly sensitive because studies have shown the species to display a w eak stock-recruitment relationship (ie., little evidence of the effect of parent populati on size on subsequent recruitment), which

indicates that environmental or habitat f actors play a significant role in limiting population abundance (USFWS, 1993).

Water Outflow Delta smelt are sensitive to changes in the delta hydrology that result from water resource development in and upstream of the Delta (USFWS, 2004a). Moderately high spring outflows are critical to moving fish downs tream to shallow water areas around Suisun Bay (USFWS, 1996). Production of zooplankton and phytopla nkton are promoted by the

well-mixed shallow water and offer rich f eeding grounds for the delta smelt (USFWS, 1996). Both a reduction and an increase in th e Delta outflow has the potential to disturb the delta smelt’s access to this source of food (USFWS, 1996).

Reduced outflows caused by upstream storage an d diversions are determined to be the primary cause of delta smelt decline, particul arly when in coincidence with dryer years (USFWS, 1996). A reduction in Delta outflow maintains fish larvae and juveniles in the deep, narrow channels of the Delta where productivity of phytoplan kton is lower due to lack of sunlight penetration (USFWS, 1996). In adequate food resources in these habitats result in threats of poor nutrition and st arvation for the delta smelt (USFWS, 1996).

While no statistical relationshi p has been found between outfl ow rate and abundances of delta smelt, Kimmerer (2002) has shown a change in abundance as it relates to historical flow (USFWS, 2004a). Moyle a nd Herbolf (1989) have also found that the lowest delta smelt numbers occurred either in years of low or extremely high outflows: unusually dry years from 1987 to 1991 have coincided with de clines in delta smelt abundance, as well as unusually wet years with exceptionally high outflows during the years of 1982-1983, 1986, and 1998 (USFWS, 2004a). However, there was no outflow-abundance relationship at intermediate outflows (U SFWS, 1996). Years of high delta smelt abundance were strongly correla ted with springtime location and duration of the 2 parts per thousand (ppt) bottom isoha line (X2) demarcation (USFWS, 2004a). This correlation

76is supported by the higher capture s of delta smelt below 2 ppt and in shallow habitats (when waters of 2 ppt are near shallow habita ts). The link between preferred habitat and fall abundance of the delta smelt also suppor ts the notion that suitable habitat (eg. available nursery habitat) may limit population abundance (USFWS, 2004a).

High outflows also change the Delta hydrol ogy, although the resulti ng consequences to
the delta smelt are less severe than thos e resulting from reduced outflows (USFWS, 1996). High outflows may flush delta smelt a nd its spawn out of the system, along with its food source, zooplankton (USFWS, 1996) . These depleted populations of invertebrates reduced the native fish populati ons and allow easier access to the delta by non-native copepods, clams, and fish (USFWS, 1996).

Water Diversions Water is pumped out of the Delta system mainly by large diversions of the Federal Central Valley Project (CVP) and State Water Project (SWP) for agriculture and municipal demands in California (USFWS, 1996, 2004a). Over 1,800 smaller diversions also pump water out of the system for Delta farms and power plants west of the Delta (USFWS, 2004a). Besides reducing the outflow of water, water diversions cause huge entrainment losses to the delta smelt. Especi ally for younger fish that are planktonic and weak swimmers, large numbers of young delta smelt are entrained at the CVP and SWP plants. In addition, when these two large diversions are in operation, the young delta smelt are susceptible to entrainment by hundreds of siphons and pumps throughout the delta that irrigate Delta is lands (USFWS, 1996, 2004a). Efforts are made to salvage the

detained fish and truck them back to the De lta, but only those fish longer than 20 mm are rescued (USFWS, 2004a). Unfortunately, effect iveness of this rescue operation has not been well-assessed, and a majority of delta smelt are too fragile to survive through the process (USFWS, 2004a).

Larvae are more likely to be entrained during dry years due to thei r higher concentration in river channels and the changes in Delta hydraulics (USFWS, 2004a). High export pumping in dry years shifts small delta smelt upstream to Delta channels rather than in Suisun Bay where they are relatively free fr om entrainment (USFWS, 2004a). Studies have quantified the losses of en trained larvae and juvenile de lta smelt and have estimated numbers to be around several million (USF WS, 2004a). More studies are being conducted, as the season, location, and size of the diversion ar e all major factors influencing entrainment (USFWS, 2004a). Th e California Department of Fish and Game (CDFG) has pinpointed the CVP and SWP as a major source of population impacts to the

delta smelt under certain conditi ons (USFWS, 2004a). They have estimated the loss of juvenile smelts to the CVP and SWP opera tions to range between 11 to 46% annually (USFWS, 2004a). Other major diversions affecting delta smelt habitat are the power generation facilities near Antioch and Pittsburg owned by the Pacific Gas and Electric Company (USFWS, 1996).

Entrainment data has been collected for years at the CVP and SWP operations and reveals that a large number of delta smelt are annually subject to mortality (USFWS, 2004a). Furthermore, optimal rearing conditi ons within the Delta have been removed

77since the 1970s due to water exports: delta sm elt were more abundant in the delta and less abundant in Suisun Marsh in pre-decline peri od, and delta smelt are now less abundant in

the Delta and more abundant in Suisun Marsh 1 (USFWS, 2004a). The possible decision to switch temporary barriers to permanent barriers in the Delta that maintain water levels

for in-delta diverters results in additional impacts to the delta smelt (USFWS, 2004a). The temporary barriers operate from April of each year to November, where upon they are removed, and prevent smelt movement and alter water hydraulics (USFWS, 2004a). Permanent barriers could increase the ope rating period, as well as introduce other influences on the delta smelt (USFWS, 2004a). Computer simulations by the California Department of Water Resources (2003) have shown that the permanent barriers change south delta hydrodynamics, incr easing central delta flows to ward the state and federal export facilities (USFWS, 2004a). These barr iers are currently be ing proposed by the California Department of Water Resources (CDWR) and U.S. Bureau of Reclamation (USFWS, 2004a).

Proposed Modifications to the Water System Increasing water resource demands go hand- in-hand with an increasing population. Specifically for the Central Valley in Californi a, six new projects are proposed that would greatly increase the amount of water dive rged and would likely result in lower Delta outflows and increased entrainment (USFWS, 2 004a). These projects are listed below in Table 8.1. The CALFED Bay-Delta Program proposes to increase their surface water storage capacity through the following projects: (1) north of the delta off stream storage; (2) Shasta enlargement; (3) Los Vaqueros E xpansion; (4) in-delta storage; and (5) additional storage in the Upper San Joaquin (Friant) (USFWS, 2004a). Management of the Delta’s resources by State and Federal ag encies, along with stakeholders, has helped alleviate some of the dangers of diverting too much water, although how effective these management tools will be in future years remains unclear (USFWS, 2004a).

Table 8.1: Proposed Projects for Central Valley, California (USFWS, 2004a) Project Capacity Increase 1 Location Freeport Regional Water Project Project diverts up to 185,000 acre-feet(af)/year

of water. Located at a point of diversion north of the delta at Freeport.

Los Vaqueros Reservoir Expansion Project entails additional 400,000 af of off-stream

storage. New and existing facilities used

at Old River and/or Middle

River.

Reclamation and California Department

of Water Resources (CDWR) Pumping capacity will be increased from 6,680 ft 3 /s, to 8,500 ft 3 /s, eventually reaching 10,300 ft 3 /s. State Water Projects (SWP) Banks pumping plant

1 This “decline” period refers to the years of 1982-1 983 when the delta smelt population took a precipitous decline, and populations numbers stayed consistently low though the years 1984-1992 (USFWS, 1995, 2004a, 2004b).

78Reclamation and CDWR Construction of a 400 ft 3 /s intertie connecting their aqueducts, increasing pumping ability from 4,200 to 4,600 ft 3 /s. Increased pumping at Tracy Pumping Plant.

CALFED 2 Bay-Delta Program Expansion of surface water storage capacity by 3.5 million af (including the 400,000 af project at Los Vaqueros. Project located at existing

reservoirs and off-stream sites.

City of Stockton Proposal Construction of new intake

with an ultimate diversion capacity of 371 ft 3 /s. Intake located at the southwestern tip of Empire Tract on the San Joaquin River.

1 af = acres/feet.

8.2.1.2 Changes in food Organisms

A reduction of phytoplankton has occurred in the past few decades, in part due to the Asiatic clam invasion (USFWS, 2004a). Wh ile a study by Kimmer (2002) demonstrated

that the delta smelt declined in abundan ce prior to any changes in phytoplankton, lower phytoplankton numbers suggests a limitation on the Delta system’s capacity to support higher levels of the food web (USFWS, 2004a ). In effect, key zooplankton abundance has been tied to the reduction in pl ankton numbers, although correlations to food

reduction for fish are not as strong (USFWS, 2004a).

While a general reduction in plankton has been documented, the diatom Melosira has instead grown more abundant (USFWS, 2004a). This particular diatom grows in long chains and is difficult for zooplankton to gr aze on (USFWS, 2004a). Thus, the growth of this diatom may also be implicated in z ooplankton declines (USFWS, 2004a). The cause

of Melosira increase is unknown (USFWS, 2004a).

8.2.1.3 Toxic Substances

The waters of the estuary are contaminated w ith a variety of toxic substances, including agricultural pesticides, heavy metals, and other products of urbanized society (USFWS, 1996). Although the effects of these substances on the delta smelt is poorly known at this time, planktonic organisms serving as prey it ems may be affected during periodic flushes of certain chemicals (USFWS, 1996).

2 The CALFED Bay-Delta Program is a collaboration among 25 State and Federal agencies to improve California’s water supply and the ecological health of the San Francisco Bay/Sacramento-San Joaquin Delta (CALFED, 2007).

798.2.1.4 Disease, Predation, and Competition

Disease

The bacterium Mycobacterium ssp. and its correlated disease, mycobacteriosis, has been identified as potentially impacting the de lta smelt (USFWS, 2004a). In a study by

Antonio et. al. (2000), presence and infections fro m this bacterium were examined on wild and captive delta smelt (USFWS, 2004a). No detections of Mycobacterium spp. were made after fish were collected from the Sacramento-San Joaquin Estuary, nor as the

fish were maintained as broodstock at wa ter temperatures of 9-12°C (USFWS, 2004a).

Abundance of Mycobacterium spp. was found among frequently handled broodstock, as well as those more stressed (USFWS , 2004a). The study concluded that Mycobacterium spp. may be lying dormant in the wild popul ation, with infections breaking out under

intensive culture cond itions (USFWS, 2004a). The releva nce and threat to wild delta smelt populations remain unknown at th is time (USFWS, 2004a).

Predation and Competition The non-native silverside ( Menidia beryllina ) population may be an important predator of larval delta smelt and a competitor for copepod prey (USFWS, 2004a). The silversides’ population expanded rapidly in the 1990s af ter an accidental introduction in 1975, and estimates of silverside population abundance are inversely correlated with that of the delta smelt (USFWS, 2004a). Further, shallo w water areas specifically restored for the delta smelt are being occupied by dense schools of silversides, detracting from the value of this habitat. Another potential planktivor e competitor of delta smelt is threadfin shad ( Dorosoma petenense ) (USFWS, 1996). Effects on the delta smelt, however, have not been studied (USFWS, 1996).

Larval fish predators to the delta smelt th at have seen populati on increases since the 1980s include coded-wire-tagged chinook salmon smolts ( Oncorhynchus tshawytscha ), Chameleon gobies ( Tridentiger trigonocephalus ), yellowfin goby ( Acanthogobius flavimanus) , non-native centrarchids, and striped bass ( Morone saxatilis ) (USFWS, 1996, 2004a). Northern pike ( Esox lucius ) introduced into Lake Davis are also of concern; the delta smelt would surely be affected if this fish ever escaped or was introduced into the Sacramento River System (USFWS, 2004a).

8.2.1.5 Loss of genetic integrity

Interbreeding between the delta smelt and wakasagi (Japanese pond smelt) ( Hypomesus nipponensis ) is of potential concern because it may re sult in loss of valuable gametes of felta smelt and hinder the population fr om recovering (USFWS, 2004a). While hybridization is possible, the threat of introgression at the population level is believed to be low due to the sterility or lack of vi able offspring (USFWS, 2004a). According to

Swanson et al . (2000), temperature, salin ity, and flow tolerances of the delta smelt place it at a disadvantage to the wakasagi agai nst suboptimal conditions (USFWS, 2004a).

808.2.2 Baseline Status

The delta smelt currently occupies its histor ic range, although abundance is considerably lower in the south Delta (USFWS , 2004a). Delta smelt of all sizes are found in the main channels of the Delta and Suisun Marsh and the open waters of Suisun Bay where the waters are well oxygenated and temperatures ar e relatively cool, usua lly less than 20-22 degrees Celsius in the summer (68-72 degr ees Fahrenheit) (USF WS, 1996 and 2004b). A substantial population size is ne cessary to compensate for a life history that is at a disadvantage in current Delta conditions: pe lagic life style, short life span, spawning habits, weak swimming ability compared w ith other Delta fishes, and relatively low fecundity (USFWS, 2004a).

Population Dynamics The Summer Tow Net Survey data show an al most complete disappearance of juvenile delta smelt in the south delta sampling st ations by the mid-1970s (USFWS, 2004a). Additional studies have shown that the populat ion has not rebounded to its original size, although a general rise in abundance has been observed in the aftermath of the long drought (USFWS, 2004a). The two-year runnin g average of Delta Smelt Recovery index for 2003, as determined from the Fall Midwater Trawl (FMWT), is the second lowest it has been since the species was listed (USFWS, 2004a). Entrainment at the CVP and SWP continues to destabilize the population and the species will remain threatened in the foreseeable future due in part to continui ng demands for water exports (USFWS, 2004a). According to Moyle (2003), delta smelt will be in danger of extinction until permanent and reliable changes are made to flow a nd temperature regimes that favor the smelt (USFWS, 2004a). Thus, the USFWS has conc luded that the delta smelt abundance has not recovered to its pre-decline (prior to 1982) levels and that the overall population trend is negative (USFWS, 2004a).

Population estimates provided by the San Luis and Delta-Mendota Water Authority

indicate an abundance of delta smelt indi viduals between 1 million and 12 million (USFWS, 2004a). The USGWS an d others have identified flawed methods with this estimation, specifically in the reinterpretation of the Fall Midwater Trawl (FMWT) index (USFWS, 2004a). The USFWS acknowledge s that this estimate is limited by uncertainties, and notes uncertainties with other estimates provided by the Summer Townet Survey and the Kodiak Trawl (USFWS , 2004a). Species, like delta smelt, whose distributional patterns are unknown but whic h are likely to demonstrate different abundances and distributional patte rns in different parts of th eir range are unlikely to be estimated with any useful degree of accur acy (USFWS, 2004a). Efforts to continue

future research to determine more reliable population size estimates are encouraged by the USFWS (USFWS, 2004a).

The San Luis and Delta-Mendota Water Authority (2002) used the population estimates

discussed above to estimate th e probability of extinction of delta smelt (USFWS, 2004a). They estimated that if the sub-adult populat ion is 12 million, then the probability of extinction of delta smelt by 2050 is less than one percent (USFWS, 2004a). However, the USGS (2003) indicated that the use of their population estimates as a basis for

81estimating extinction probability would re sult in a severe underestimate (USFWS, 2004a). Bennett (2003) provided another t ype of analysis (USFWS, 2004a). He

evaluated the likelihood of de lta smelt populations falling below an “effective population size” (ie. a Fall Midwater Trawl index of le ss than 100 for two straight years) (USFWS, 2004a). Using this methodology, he determined there was a 13% chance that the delta smelt’s population size could fall below an effective size within 10 years, and a 33%

chance that the delta smelt’s population size could fall below an effective population size by 2025 (USFWS, 2004a).

8.3 REFERENCES

Literature Cited

Antonio, Dolores B., Christina Swanson, Joes eph J Cech Jr., Randy C. Mager, Sergei Dorshov, and Ronald P. Hedrick. 2000. Prevalence of Mycobacterium in Wild and Captive Delta Smelt. Califor nia Fish and Game 86(4): 233-243.

CALFED Bay Delta Program (CALFED). 2007. About CALFED. California. Available

online at: http://www.calwater.ca.gov/calfed/about/index.html (Accessed on Jan 13, 2009).

Kimmerer, W.J. 2002. Effects of freshwater fl ow on abundance of estuarine organisms: physical effects or trophic linkages? Marine Ecological Progress Series 243: 39-

55.

Moyle, P.B. and B. Herbold. 1989. Status of the delta smelt, Hypomesus transpacificus. Unpublished final report prepared for U.S. Fish and Wildlife Service, Sacramento Field Office, Habitat Conservation Divi sion, Sacramento, California. 42 pp.

U.S. Fish and Wildlife Service (USFWS). 1993. Endangered and Threatened Wildlife

and Plants: Determination of Threatened Status for the Delta Smelt. Federal Register 58 (42):12854-12864. Available online at: http://ecos.fws.gov/docs/ federal_register/fr2235.pdf (Accessed on January 09, 2009).

U.S. Fish and Wildlife Service (USFWS). 1996. Sacramento-San Joaquin Delta Native Fishes Recovery Plan. U.S. Fish a nd Wildlife Service, Portland, Oregon.

Available online at: http://ecos.fws.gov/doc s/recovery_plan/961126.pdf (Accessed on January 09, 2009).

U.S. Fish and Wildlife Service (USFWS). 2004a. 5-Year Review. U.S. Fish and Wildlife Service, Sacramento Field Office, Sacramento, California. 50 pp. Available

online at: http://www.fws.gov/sacramento/es/documents/DS%205- yr%20rev%203-31-04.pdf (Accessed on January 09, 2009).

82U.S. Fish and Wildlife Service (USFWS). 2004b. Formal Programmatic Consultation on

the Issuance of Section 10 and 404 Perm its for Projects with Relatively Small Effects on the Delta Smelt ( Hypomesus transpacificus ) and its Critical Habitat

within the Jurisdiction of the Sacramento Fish and Wildlife Office of the U.S. Fish and Wildlife Service, California. U.S. Fish and Wildlife Service, Sacramento Field Office, Sacramento, Califor nia. 29 pp. Available online at: http://www.fws.gov/sacramento/es/ consultations/coe_delta_smelt.pdf (Accessed on January 15, 2009).

U.S. Fish and Wildlife Service (USFWS). 1995, Formal Consultation and Conference on Effects of Long-Term Operation of the Ce ntral Valley Project and the State Water Project on the Threatened Delta Smelt, De lta Smelt Critical Habitat, and Proposed Threatened Sacramental Splittail.

Personal communications, comment letter, white papers, workshop summaries, federal register publications, and all other information

Bennett, William A. 2003. The population ecology of delta smelt in the San Francisco Estuary. 44 pp.

Moyle, Peter B. 2003. Comment Letter on the Fi ve Year Status Review of the Delta Smelt. 3 pp.

839: SALT MARSH HARVEST MOUSE

9.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the Salt Marsh Harvest Mouse (SMHM) ( Reithrodontomys

raviventris ) that are reasonably certain to occur in the action area. Future federal actions unrelated to the proposed action are not c onsidered because they are subject to consultation pursuant to Section 7 of the E ndangered Species Act (Act). Numerous nonfederal actions that could affect the SMHM are reasonably certain to occur within the

action area. These activities ar e associated with modifications to salt and brackish marsh habitats and typically include urban and industrial developments, filling and diking activities, maintenance of levees, and c onversions of salt marsh to brackish water habitats. Many of these activities are linke d and create complex consequences for the listed species in the action area. These f actors reduce the quality and suitability of SMHM habitat by influencing the presence of tidal channel systems and the inland extent of high and low tides. Encroaching developmen ts exacerbate the inla nd extent of tides by reducing SMHM escape cover from predator s. Moreover, predatory impacts are intensified as urbanization displaces predat ors farther into marshland habitat.

9.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the effects of past and ongoing human induced and natural factors leading to th e status of the species, its habitat, and ecosystem, within

the action area. The environmental baseline is a snapshot of the SM HM’s status at this

time. Details of the SMHM’s habitat description and know n locations are included in Attachment III. However, the baseline c ondition of each assessed SMHM species and

habitat varies across locations. Given the large number of occ upied habitats and extent of the action area included in this assessment, th e environmental baseline presents a general discussion of factors that may affect the SMHM within the action area. This information includes both detrimental and potentially beneficial factors affecti ng the species and is presented in Section 9.2.1. Additional information on the current distribution and population dynamics of the SMHM is presented as part of the baseline status in Section

9.2.2.

9.2.1 Factors affecting species envi ronment within the action area

In the US Fish and Wildlife Service (USFWS ) Recovery Plan (1984), SMHM decline is attributed to five primary f actors: habitat loss, marsh fragmentation, loss of high marsh zone due to backfilling, land subsidence, and vegetational change. These factors continue to affect the species today, with habitat loss and fragmentation contributing

84most significantly to SMHM decline. These f actors all relate to habitat alteration and are discussed together in Secti on 9.2.1.1. Predatory impacts also affect the SMHM and its environment. Predators include cats, non-na tive red foxes, and the Norway rat, among others. Predatory impacts are discussed in Section 9.2.1.2. Conservation actions include restoration and protection projects that have been, or are currently being completed, to

reconstruct and enhance the salt marshes of th e San Francisco Bay Area. These projects are aimed at the SMHM, as well as other San Francisco Bay species, and are presented in

9.2.1.3.

9.2.1.1 Habitat loss and alteration

Fragmentation and loss of habitat are the main factors affecting SMHM populations (USFWS, 1984). An 84% reduction in the tid al marsh bordering Sa n Francisco Bay has occurred since 1850, with the greatest degree of destruction occurring in the southern Bay region (USFWS, 1984). This destruction is attr ibuted to urbanizati on, and the filling and diking of wetland areas (USFWS , 2007a). Diked wetlands on ly provide marginal to inappropriate habitat for the SMHM, with most in the Bay region specifically managed as waterfowl habitats (USFWS, 1984 and Goals Project, 2000). Recently, however, diked wetlands adjacent to the Bay have become mo re important as the tidal marshes have decreased in size and quality (Goals Project, 2000), although they too are threatened by urban and industrial development (Goals Project, 2000).

Two physical factors that affect marsh habitat include erosion and freshwater introduction (USFWS, 2007a; and Goals Project, 2000). The shoreline of the East Bay is eroding, from San Leandro to Calaveras Point, and could lead to the loss of several SMHM populations in the area (USFWS, 2007a ). Fresh water introduction along Coyote Creek, Alviso Slough, and Guadalupe Slough (S outh San Francisco Bay) has caused salt water vegetation to be degraded and conve rted to freshwater and brackish water vegetation. The South Bay wastewater facili ties in the Alviso and Sunnyvale areas are responsible for the freshwater input into a bout 600 acres of previ ous salt marsh, and the converted marsh areas probably no longer support SMHM (USFWS, 1984 and 2007a). The San Jose sewage treatment plant, one of these facilities, pumps more than 120 million gallons a day of treated water into San Francisco Bay, while diluting the salt content in the marsh and changing the ma rsh ecology (Rendon, 1999). This freshwater intrusion kills the pickleweed on which the SMHM depends and benefits plant species like cattails and bulrush which are not used by the SMHM (Rendon, 1999 and Shellhammer, 1998).

Subsidence (up to 10 feet) is a third physical factor affecting SMHM habitat. Caused by groundwater pumping, subsidence has occurred fr om Palo Alto to Alviso during the last hundred years. Consequently, many marshes, including Palo Alto marsh, have changed from pickleweed to cordgrass, resulting in a decline in SMHM (USFWS,1984). Four species of non-native cordgrass ( Spartina spp. ) are rapidly establ ishing in the salt

marshes and mud flats in the San Francisc o Estuary and threaten the physical and biological ecology of the estuary (SFEISP website). Three of these species, “ S.

85densiflora

, S. patens and S. alterniflora -hybrids can all displace native pickleweed (Salicornia spp.), which provi des critical habitat for the salt marsh harvest mouse” (SFEISP website). Non-native Spartina populat ions were first introduced 25 years ago and have now spread to more than 1000 acres (SFEISP website).

Subsidence and diking throughout the SMHM’s range, but especia lly in South San Francisco Bay, have eliminated the periphera l halophyte zone which is important to the SMHM (USFWS, 1984). The upper peripheral ha lophyte zone of most marshes has been filled in, covered over, or converted to salt ponds. Certain marshes are completely submerged during high tides, leaving insuffici ent escape habitat for the SMHM (USFWS, 2007a). SMHM disappear from marshes without escape cover because, during the highest tides, they either expose themselves to predators by moving into the open, or they drown (USFWS, 1984). Development and subs idence have reduced the upper marsh to strips that are “just a few feet wide on the steep sides of levees” (Wong, 2004). These strips are often separated from each other by distances too great for the SMHM to travel (USFWS, 1984). In addition, the southern s ubspecies of SMHM is also endangered due to commercial and residential development around San Francisco Bay which has caused a decrease in the available pickleweed habita t (Brylski, 1999). These habitat changes have led to the loss of SMHM from many marshes and the small numbers of animals seen in most other marshes (Goals Project, 2000).

9.2.1.2 Predation

In addition to its native predators, including snakes, owls, hawks, eg rets, herons, clapper rails, and other raptors, the SMHM also has non-native predators such as cats (house and feral), dogs (feral) and red foxes (USF WS, 1984; Shellhammer, 1998; CDFG, 2000; Rendon, 1999; CDPR online; Goals Project, 200 0; and eNature, 2007). Other predators may include gulls, weasels, and other mamma ls (Brylski, 1999). Predators typically

strike when the SMHM is forced out into the open during high tide. However, very little is known about the effects of predators on th e SMHM (Goals Project, 2000). Predator control, usually for red foxes, has been implemented in several marshes containing California clapper rails and SMHM; however, pr edator control is not typically found in marshes that may only contain SMHM (Goals Project, 2000). Non-native predators have gained access to the SMHM ha bitat because most remaining marshes share an upper side with a leveed salt pond, business park, or s ubdivision (Shellhammer, 1998). The amount of upland buffer necessary to protect the SMHM from predators (especially cats) is currently unknown (Goals Proj ect, 2000). The USFWS recommends 100 feet; however, 100 feet of grassland may not be sufficient to protect the SMHM from feral cats and dogs (Goals Project, 2000).

Little is known about the inte ractions between rodent specie s within the diked marshes; however, one study in 1988 showed that SM HM were seasonally displaced from “optimal habitat by California voles” (Goals Project, 2000). In a ddition, little is known

about the interaction between SMHM and non- native rats. The non-native Norway and roof rats are considered potential predator s of the SMHM and are known to occur with

86the SMHM in several marshes (Goals Proj ect, 2000). Rat control has not been implemented and is especially difficult because there is no poison specific to rats that is concurrently safe for the SM HM (Goals Project, 2000).

9.2.1.3 Conservation actions

The Recovery Plan (USFWS, 1984) proposed five actions required to secure the status of the SMHM: (1) manage existing marsh and poten tial habitat; (2) create new habitat; (3) restore upper portions of marshes; (4) conduc t additional biological research; and (5) continue ongoing management. The Plan doc umented several recovery actions by the USFWS and the California Department of Fi sh and Game (DCFG) that had addressed these goals, involving the San Francisco Bay National Wildlife Refuge (SFBNWR), the San Pablo Bay State Wildlife Area (SPBWA ), the Suisun and San Pablo Bay marsh areas, the Palo Alto City Nature Center Ma rsh, and other smaller marshes and bays along the San Francisco Bay coast.

Conservation plans have continued to be im plemented in the 24 years since the Recovery Plan was publicly released. One Habitat C onservation Plan (HCP) was issued for the SMHM on February 23, 1999 for the duration of three years (HCP). The Zanker Road Resource Mgmt., Ltd. HCP is an 0.83 acre parcel of land located in Santa Clara County consisting of “ruderal grassland on levees of diked wetland” (HCP). Other plans have

included restorations of dike d and salt water-degraded marshe s, acquisitions of private property for wetland restoration, the South Ba y Restoration Project involving the Cargill Company, and conversions of agricultural la nd to marsh habitat. These conservation actions are described in Winton, 200 1; Sunnyvale, 2005; Wong, 2004; USFWS 2001;

USFWS 2006.

9.2.2 Baseline Status

SMHM evolved with the creation of San Francisco Bay about 8,000 to 25,000 years ago and were historically found in most of the marshes throughout San Francisco Bay (USFWS, 1984). SMHM are currently found in tidal and non-tidal salt marshes in San Francisco, San Pablo, and Suisun bays (USF WS, 2007a and CDFG website). It is thought that the wetlands and marshes of the Sacramento-San Joaquin Delta were probably too fresh to support the SMHM and that the Collinsville-Anitoch area was, and likely remains, the eastern limit of th eir distribution (USFWS, 1984 and 2007a). Populations of SMHM occur in the diked mars hes near Collinsville and in both diked and tidal marshes along the Contra Costa County coast (USFWS, 1984). Th e western limit of the northern subspecies is the marshes bordering the mouth of Gallinas Creek on the upper Marin Peninsula (USFWS, 1984).

The southern subspecies of the SMHM historically had two populations in San Pablo Bay (USFWS, 1984). One population could be found on the CDFG Ecological Reserve at Corte Madera (USFWS, 1984). In 1980, trapping at this location was unable to confirm

87the presence of SMHM (USFWS, 1984). Howe ver, the other population is moderate in

size and exists near the Richmond landfill (USFWS, 1984). Populations of southern subspecies can also be found south of th e San Mateo Bridge (USFWS, 1984).

Population Dynamics There are few accurate density figures for SMHM because their numbers are so low (hence errors of sampling are high) (USF WS, 1984). In 1980, SMHM populations in several of the larger mars hes around the Bay, including Peta luma Marsh, Corte Madera Ecological Reserve, Benecia State Park (S outhampton Bay), areas west of Pittsburg, Belmont, New Chicago Marsh near Alviso, along Mowry Slough, and along the Alameda

Flood Control Channel were either extrem ely low or completely missing (USFWS, 1984). Major SMHM populations were found at the mouth of Tolay Creek, Lower Tubbs Island, Fagan Marsh, and the marshes near the San Francisco Ba y National Wildlife Refuge headquarters in Newark, near the m outh of Old Alameda-Mt. Eden Creek, and the Collinsville marshes (USFWS, 1984). In th e mid-1980s, there appeared to be a few thousand animals at the peak of their nu mbers each summer, distributed around the Bay in small, disjunct populations, of ten in marginal vegetation and almost always in marshes without an upper edge of upland vegetati on (USFWS, 1984). A population estimate from 1993 put the wild SMHM population at 2000 (Massicot, 2005).

More recently, the highest consistent SMHM populations are found in “large marshes along the eastern edge of San Pablo Bay and in old dredge spoil disposal ponds on former Mare Island Shipyard property” (Goals Project , 2000). “Most of these marshes are in or will be included in the San Pablo Bay unit of the San Francisco Bay National Wildlife Refuge” (Goals Project, 2000). Some parts of the Contra Costa County coastline and some parts of the Petaluma Marshes as well as the Calaveras Point Marsh in South San Francisco Bay also support large populations of SMHM (Goals Project, 2000). However,

the habitat at Calaveras Point Marsh is dete riorating due to the d ecreasing salinity and corresponding vegetation changes (Goals Proj ect, 2000). The SMHM is thought to be sustaining itself in a few marsh areas in the SFBNWR, including Calaveras and Dumbarton Points, Greco Island, and Ne w Chicago Marsh (Shellhammer, 1998).

9.3 REFERENCES

Literature Cited

Brylski, P. 1999. M114-Salt-marsh Harvest Mouse. California Wildlife Habitat Relationships System, a database of the Ca lifornia Department of Fish and Game (CDFG), in cooperation with the Califo rnia Interagency Wildlife Task Group.

Database version 8.1. Available online at: http://www.dfg.ca.gov/bioge odata/cwhr/lha/lha_M114.pdf and http://sibr.com/mammals/M114.html (Accessed on September 9, 2008).

88Buffa, J. 2007. U.S. Fish and Wildlife Serv ice – Journal Entry: “Honeymoon Suite” at Don Edwards NWR Shows Road to Recovery for Salt Marsh Harvest Mouse.

Available online at: http://www.fws.gov/arsnew/print/print_report.cfm?arskey=21836 (Accessed on September 9, 2008).

California Department of Fish and Game (C DFG). 2000. The Status of Rare, Threatened, and Endangered Animals and Plants of California 2000. Available online at http://www.dfg.ca.gov/wildlife/spec ies/t_e_spp/new_te_rpt.html (Accessed on September 30, 2008).

California Department of Pesticide Regulation (CDPR online). Salt Marsh Harvest Mouse ( Reithrodontomys raviventris ). Available online at: http://www.cdpr.ca.gov/docs/endspec/espdfs/smhm1.pdf and http://www.cdpr.ca.gov/docs/endspec/espdfs/smhmall.pdf (Accessed on September 9, 2008).

(eNature) Salt Marsh Harvest Mouse ( Reithrodontomys raviventris ). 2007.

eNature.com. Nature Guides. Available online at: http://www.enature.com/flashcard/sh ow_flash_card.asp?recordNumber=MA0463 (Accessed on September 9, 2008).

Goals Project. 2000. Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plan ts, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosyste m Goals Project. P.R. Olofson, editor. San Francisco Bay Regional Water Quality Control Board, Oakland, California.

Available online at: http://sfep.abag.ca.gov/pdf/species-community/ (Accessed on September 9, 2008).

Habitat Conservation Plan (HCP). Zanker Road Resource Mgmt., Ltd. Conservation Plans and Agreements Database. Available online at: http://ecos.fws.gov/conserv_plans/servle t/gov.doi.hcp.servlets. PlanReport?plan_i d=1®ion=8&type=HCP&rtype=1 (Accessed on September 9, 2008).

Kay, 2007. Bay cleanup efforts expanding – Linger ing consequences: Spill will have farranging effects on plants and animals in and around bay for years, scientists fear.

San Francisco Chronicle. Available online at: http://www.sfgate.com/cgibin/article.cgi?file=/ c/a/2007/11/11/MNFSTA5L9.DTL (Accessed on September 9, 2008).

Massicot, P. 2005. Animal Info – Saltmarsh Harvest Mouse ( Reithrodontomys

raviventris ). Available online at: http://www.animalinfo.org/spec ies/rodent/reitravi.htm#IUCN (Accessed on September 9, 2008).

Rendon, Jim, 1999. Mouse Pad. Metro. Metr o Publishing Inc. November 24-

89December 1, 1999. Available online at: http://www.metroactive.com/papers /metro/11.24.99/cover/species6-9947.html (Accessed on September 29, 2008).

San Francisco Estuary Invasive Spartina Project (SFEISP onlin e). Coastal Conservancy. Salt Marsh Harvest Mouse ( Reithrodontomys raviventris ). Available online at: http://www.southbayrestoration.or g/pdf_files/HarvestMouseHandout.pdf (Accessed on September 9, 2008)

Shellhammer, H. 1998. A Marsh is a Marsh is a Marsh...But not Always to a Salt Marsh

Harvest Mouse. Tideline. Vol 18 No. 4. Available online at: http://www.fws.gov/desfbay/ Archives/Salty/salty.htm (Accessed on September 9, 2008).

Sunnyvale Website. 2005. Available online at: http://sunnyvale.ca.gov/Dep artments/Parks+and+Recreat ion/Parks/Baylands/Natu

re+and+Preservation/Salt MarshHarvestMouse.htm(Accessed on September 9, 2008).

U.S. Fish and Wildlife Service (USFWS) . 1984. Salt Marsh Harvest Mouse and California Clapper Rail Recovery Plan. U.S. Fish and Wildlife Service, Portland, Oregon. 141 pp. Available online at: http://ecos.fws.gov/docs/recovery_plans/1984/841116.pdf (Accessed on September 9, 2008).

U.S. Fish and Wildlife Service (USFWS). 2001. The Coastal Program – Success in San Francisco Bay. Available online at: http://library.fws.gov/pubs3.html#C http://training.fws.gov/Divi sionSites/ConservationLibr ary/Pubs1/sfbay_coastal.pd

f (Accessed on September 9, 2008).

U.S. Fish and Wildlife Service (USFWS). 2006. U.S. Fish and Wildlife Service – Journal Entry: Converting Commercial Sa lt Ponds to Wetlands for Wildlife at Don Edwards San Francisco Bay National W ildlife Refuge. Available online at: http://www.fws.gov/arsnew/print/print_report.cfm?arskey=20176 (Accessed on September 9, 2008).

U.S. Fish and Wildlife Service (USFWS). 2007a. Species Account: Salt Marsh Harvest Mouse ( Reithrodontomys raviventris ). Sacramento Fish and Wildlife Office.

Available online http://www.fws.gov/sacramento/es/anim al_spp_acct/salt_marsh_harvest_mouse.h

tm (Accessed on September 9, 2008).

U.S. Fish and Wildlife Service (USFWS). 2007b . Species Profile: Salt Marsh Harvest

90Mouse ( Reithrodontomys raviventris ). U.S. Fish and Wildlife Service. Available

online at: http://ecos.fws.gov/speciesProfile /SpeciesReport.do?spcode=A03Y (Accessed on September 9, 2008).

Winton, B. 2001. San Pablo Bay and Marin Isla nds National Wildlife Refuges – Refuges in the North Bay. Tideline. Vo l 21 No. 4. Available online at: http://www.fws.gov/desfbay/Archives/SanPablo/San_Pablo_Marin.pdf (Accessed on September 9, 2008).

Wong. K.M. 2004. Voices From the Field. Ba y Nature. Special Section, OctoberDecember 2004. Available online at: http://www.baynature.com /2004octdec/v04n04s_voices.html (Accessed on September 9, 2008).

9110: SAN FRANCISCO GARTER SNAKE

10.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the San Francisco garter snake ( Thampnophis sirtalis

tetrataenia ) (SFGS) that are reasonably certain to o ccur in the action area. Future federal actions not directly related to the proposed action are not considered because they require

additional consultation under S ection 7 of the Endangered Species Act (Act). The

numerous non-federal actions th at are reasonably certain to occur within the action area consist of expansion of u tility matrices, residential and commercial developments, recreational facilities, land management, agriculture, dredging, channelization, flood control, and overutilization. Many of these factors are linke d or act synergistically and create complex consequences for the SFGS. For example, roads often impede dispersal and movement of species. Highways with h eavy traffic can be a physical deterrent for snake mobility and cause direct mortality from vehicular strikes. Highways may also concurrently impede or inhibit SFGS anuran prey species from dispersal and movement. If close to wetlands, these highways might further reduce th e water quality from chemical

run-off and thus affect the recru itment of anuran prey species.

10.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a sn apshot of the SFGS status at this time. However, the baseline condition of each asse ssed SFGS species and habitat varies across locations. Given the large number of occupi ed habitats and extent of the action area included of this assessment, the environmenta l baseline includes a general discussion of factors that may affect SFGS within the action area. This information is presented in Section 10.2.1. Additional information on the current distribution and population dynamics of the SFGS is presented as part of the baseline status in Section 10.2.2. The majority of information included in the envi ronmental baseline section is a summary of information presented in the 5-Year Re view: Summary and Evaluation of the San Francisco Garter Snake (USFWS, 2006b).

10.2.1 Factors affecting species envi ronment within the action area

SFGS are primarily affected by habitat loss a nd degradation. In the USFWS Recovery Plan for the SFGS, habitat alteration has been cited as the primary threat of species decline (USFWS, 1985). Habitat loss and degr adation continues to be the primary cause today. Other influential factor s include overutilization, diseas e, predation, and invasive

92species. Additional anthropogenic and natural f actors considered to be of a lower threat include reservoir hydrology and topography, vehicular strikes, hybridization with the redsided garter snake (RSGS), and interspecific congenors (other Thamnophis species and subspecies). An overall measure of these lo wer level impacts has yet to be determined due to a lack of accurate population estimates. Sections 10.2.1.1 through 10.2.1.4 provide details on each of the major issues affecting the SFGS within the action area.

9.2.1.1 Habitat Loss and Degradation

Habitat loss and degradation are caused by three main factors. In the order of most to least influential, these factors include expans ion of infrastructure, management practices, and fluctuating water levels. The expansion of infrastructure causes habitat fragmentation by increasing residential and co mmercial developments such as new roads, utility matrices, and recreational activities a nd facilities. Manageme nt practices, such as seral succession, use of perch ponds (e.g., sh allow man-made ponds for irrigation often used in San Mateo County), decreased us e of stock ponds, and practice of dredging waterways may result in SFGS habitat loss and degradation. In a ddition, fluctuating water levels in reservoirs, channelization a nd flood control, and sa line inundation events

can also affect habita t degradation.

Infrastructure Urban areas are currently expanding in San Mateo County. As of 2005, the human population in the San Francisco Peninsula has increased by over 500,000 people since the end of World War II (US Census Bureau in litt. , 2006). Large ranches within this area have been replaced by high density urban de velopment as well as intense agriculture operations (San Mateo County Department of Agriculture, 2004) . Table 10.1 shows a number of proposed urbanization projects w ithin San Mateo County that potentially threaten known populations of the SFGS. Th ese five projects are currently undergoing consultation with the USFWS (USFWS 1996b). Other urbanization pr ojects have been completed in recent years with identifiable consequences on the SFGS and its habitat. These three finished projects are summarized in Table 10.2.

Table 10.1: Proposed urbanization projects with in San Mateo County currently under consultation with the USFWS (USFWS, 2006)

Location Party Proposed Action Type Description Location

Oak Avenue Park, City of Half Moon Bay City of Half Moon Bay Recreational Development Clean-up and

restoration construction, and development of a bicycle and pedestrian trail along Pilarcitos

Creek Oak Avenue Park, City of Half Moon Bay

93Pilarcitos

Watershed Pilarcitos Quarry Operations Expansion Expansion of quarry into SFGS

habitat Pilarcitos

Watershed

City of Pacifica, upland area

between Mori Point

and Calera Creek California Department of Transportation (Caltrans) Housing and

Infrastructure Development Housing development, and

Calera Parkway Project that will

widen sections of Highway 1 City of Pacifica, upland area

between Mori

Point and Calera

Creek

Dennison Reservoir

-- Continuation of Activity Potentially continue dredging

activities due to

increased levels of

siltation Dennison

Reservoir

San Francisco Public Utility

Commission Property (SFPUC), San Mateo County SFPUC Development Construction of

wireless facilities

on property San Francisco Public Utility

Commission

Property (SFPUC), San Mateo County

Table 10.2: Completed urbanization proj ects in San Mateo County

Location Party Project Description Citation

Canada Rd. on

San Andreas Ridge down to

Brisbane Pacific Gas and Electric (PG&E) Jefferson-Martin

transmission line project Replacement and rerouting of 27

miles of

transmission line USFWS, 2005

Cupid’s Row Canal, West of Bayshore --- --- Temporary dredging activity USFWS, 1996b

San Francisco

International Airport (SFO),

West of Bayshore California Department of Transportation (CALTRANS) Bay Area Regional Transport Station (BART) Expansion of station, requiring

realignment of

creek and Cupid’s Row

Canal. USFWS, 1996b;

California Department of Fish and Game,

2005

The Jefferson-Martin transmission line proj ect affected 0.38 acres of wetlands that provided foraging and dispersal area for th e SFGS due to substation expansion. The construction also temporarily affected 7.55 acr es of upland habitat suitable for species dispersal and aestivation. Mitigation for these effects is now being established on California Public Utilities Commission (CPUC) property. The dredging activity at Cupid’s Row Canal may have been a tem porary disturbance, but it indicates the continuing threat of habitat destruction for the SFGS (USFWS, 2006a). The expansion of a Bay Area Regional Transportation (BART) st ation at the San Francisco International Airport (SFO) bisected a West of Bays hore SFGS population (USFWS,1996b; California Department of Fish and Game, 2005). Th e BART expansion project required the realignment of a creek and Cupid’s Ro w Canal, and human activity during the

94construction caused the mortality of six SFGS individuals (USFWS, 2006a). Although

construction caused the take of SFGS individu als, the impact of the completed BART expansion project on the SFGS is thought to be low due to the elevated design of the structure. However, the long term impacts of the project are unknown. Mitigation for the detrimental impacts of the BART project included the purchase of Steele Ranch, a suitable habitat for the SFGS, as well as re storation activities at West of Bayshore (USFWS, 1996b). However, both mitigation effo rts were never fully realized (McGinnis, pers.comm. 2006), and no further informa tion on the efforts is available (USFWS, 2006b).

The increased growth in human population has increased the de mand for recreational opportunities and supported the growth of golf c ourses. Recreational activities, such as running and jogging, are not thr eats to the SFGS; however, biking and off-road vehicle (OHV, or off-highway vehicle) usage at the West of Bayshore are known to degrade SFGS habitat and kill individuals (Larson, 1994) . OHVs have led to the degradation and erosion of upland habitat at Mori Point (D . Fong, pers. comm. 2006). More enforcement and regulation are needed to prevent OHV trespass on privat e and protected public land. Chemical and pesticide use at golf courses contaminates nearby lakes and streams that are not usually associated with urban deve lopment. These waterways are important aquatic habitats and movement corridors for th e SFGS and its primary anuran prey base. Chemical applications may potentially cont ribute to the reduction in habitat quality (Sparling et al. 2000; A. Willy, pers, comm. 2006). In one case, over-application of phosphorous to golf course ponds in Solano C ounty resulted in the mortality of the California Red-Legged Frogs ( Rana aurora draytonii ) and their larvae (USFWS, 2002a). Similar events causing direct mortalit y of the SFGS are a possibility.

Management Practices Changes in management practices have encour aged the presence of seral ecosystems in both protected grasslands and aquatic habitats. The word “seral” refers to the successive changes in flora and fauna during the pro cess of ecological succession. These dynamic ecosystems threaten the SFGS in certain areas of the San Francisco Bay Peninsula (H. Mcquillen, pers. comm. 2006; S. Larson, pers . comm.). Grass-dominated uplands are important habitats for the SFGS because rode nt burrows are utilized for hibernation during winter months (Larsen 1994; McGinnis et. al. 1987) and for migration corridors between aquatic habitats. The loss of fire suppression allows for the dominance of woody species over grasslands and potentiall y inhibits rodent burrowing (D. Hankins, in

litt . 2006). The absence of domestic grazing, which results in th ick brush canopies, renders grassland habitat unsuitable for the SFG S. Seral conditions in aquatic habitats also threaten the SFGS and its amphibian pre y. The presence of cattails increase siltation rates and lead to a reduction in open water, a necessity for Pacific tree frog and California red-legged frog reproduction and survival (McGinnis et. al. , 1987).

Agriculture practices contribu te to the loss of suitable SFG S habitat. Although data are available on the relationship between other garter snakes and row crops, information specific for the SFGS is not available. One study found the plains garter snake ( Thamnophis radix ), which has a habitat similar to the SFGS, absent from fields that had

95been plowed, but not from fields that had been grazed or burned (Conant et. al.

, 1945 ). More recent studies have found garter snake numbe rs to be lower than average in suitable

wildlife habitats surrounded by plowed agricultural areas (Keller and Heske, 2000). Scientists attribute these low numbers primar ily to plowing activities and speculate that heavy machinery increases soil compaction, re duces overall soil tilt h (physical condition of the soil in relation to its fitness for gr owth), and leads to soil erosion (A. Allen in litt.

, 1995).

Fluctuating Water Levels Stock ponds in ranges or pastures benefit the SFGS by providing aquatic habitats. However, these types of ponds are decreasi ng. Instead, perch ponds are in high demand in rural areas of San Mateo County and are of little value to the SFGS (J. Howard in litt.

, 2006). Because perch ponds are primarily us ed for irrigation, water levels fluctuate between growing seasons. Rapid draw-dow n for summer crops, a high utilization period,

removes much of the water and renders th e ponds unsuitable for the SFGS and amphibian prey species (McGinnis, 1984; McGinnis, 1987; San Mateo County Department of Agriculture, 2004). Perch ponds further aff ect the SFGS because the water is acquired from nearby waterways. Extracting water from these creeks and streams results in unreliable water levels, potentially extirpati ng the SFGS and its prey species (McGinnis, 1984).

Shallow ponds are important habitats for SFG S prey items, including the California redlegged frog and the Pacific tree frog, because they can provide aquatic habitats through the spring and summer months. Frog egg masse s may become exposed to predation and dry out when water levels drop. In areas wher e their prey species ar e unable to survive, SFGSs will likely disperse and potentially be subject to predation. Rapid draw down also increases the potential for bullfrogs to establ ish themselves where native ranids used to live. Bullfrogs are known to prey on other amphibians, including SFGS prey species, potentially resulting in a decline of native ranids and narrowing th e feeding opportunities of the SFGS (P. Keel, pers. comm. 2006). Bu llfrogs pose a direct threat to the SFGS because they consume juvenile individuals, although the SFGS may also feed on juvenile bullfrogs. While the predatory th reat of bullfrogs to SFGS is thought to be low, the threat to amphibian prey is more consequential (Barry in litt. , 2005). Similar events related to unsuitable habitat and amphibian prey may occur at reservoir systems where rapidly fluctuating water levels are common (F reel and Giorni, 1994).

Degradation of riparian habitats, stream channe lization, and increased levels of salinity in

freshwater habitats also threaten the SFGS (USFWS, 1985; Larsen, 199 4). Alterations in stream and riparian habitats reduce the conn ectivity between sites, limit these habitats from functioning as movement areas, and redu ce the complexity of streams serving as migration corridors (USFWS, 1985). Both the SFGS and its amphibian prey are negatively affected by these alterations (Calif ornia Department of Fish and Game, 2005). Salinity in freshwater is detrimental to anuran s, as concentrations over 7.0 ppt are lethal to Pacific tree frogs and th eir larvae (Larson, 1994). Increased salinity has been

documented in a number of areas used as habi tat by the SFGS, and the presence of salinetolerant plants indicates de gradation in freshwater qual ity (S. O’Brien, pers. comm.

962006). Places affected by sa linization include Cupid’s Row Canal, West of Bayshore, Pescadero Marsh, and Mori Point.

10.2.1.2 Overutilization for Recreational, Scientific, Commercial, and Educational Purposes

Although unauthorized take of the SFGS for r ecreational, scientific, commercial, and educational purposes has decreased in recent year s, it is still considered a threat to the species according to employees with the Calif ornia State Parks (J. Kerbavaz, pers. comm. 2006; P. Keel, pers. comm. 2006). During the 1970s and 1980s, ill egal take was a primary threat occurring at SFG S habitat in West of Bayshore; however illegal take has reportedly subsided in recent years. Several factors, such as speculation towards genetic purity, may have contributed to the decline in illegal take at West of Bayshore (S. Barry

in litt. 2006b); however, the level of reduction an d impact on the species remains unclear (P. Keel, pers. comm. 2006; J. Kerbavaz, pers. comm. 2006). Amateur herpetologists have collected the species for their beautiful coloration and rarit y, and some amount of illegal collection still occurs. Illegal take has also been known to occur at the Pescadero Marsh since the early 1990s as well as at ANSR (J. Kerbavaz, pers. comm. 2006; P. Keel, pers. comm. 2006). Although unauthorized take has reportedly declined in recent years, it should be noted that staffing restrictions within the California State Parks Department prevent further resource allotment to SFG S take enforcement (P. Keel, pers. comm. 2006).

10.2.1.3 Disease and Predation

Disease, parasites, and predation all negativel y affect the SFGS. Of the three, disease caused by the chytrid fungus is the mo st threatening. The chytrid fungus ( Batrachochytrium dendrobatridus ), a lethal paras ite, poses an indir ect threat to the SFGS by drastically affecting its anuran prey base. The fungus has caused an epidemic that has seen prolific growth throughout th e world in recent years, to some degree

attributed to altered weather patterns (Pounds et. al. , 2006). Lethal pandemics are a real possibility for certain frog species that now , due to global warmi ng, inhabit locations where humidity is high and daily temperat ure extremes are minimized (P. Johnson in litt.

, 2006). A chytrid fungus pandemic can spread ra pidly and is capable of wiping out entire amphibian populations on the Peninsula. Comb ined with food shortages, such a situation would have dire consequences for the SFGS, in addition to all other garter snakes in the area (Jennings et. al. , 1992; AmphibiaWeb in litt. , 2006).

Although other parasitic infections of the SFGS are threats, they are not considered ones of catastrophic magnitude. The parasites know n to affect the SFGS include tapeworms, flagellate protists, and nemotode worms (Lar son, 1994). Several juve nile mortalities in the West of Bayshore are attributed to these th ree types of parasites. Parasitic tapeworms and thorny-headed worms may use mosquito fi sh as hosts in the northern Bay area.

97Various ranid species and the SFGS that feed on the mosquito fish are at risk for infection (M. Kolipinski in litt.

, 2006).

Predation by native avian species and bullfr ogs are a threat to the SFGS, although the impact on SFGS individuals is unknown. Of the avian species, the American crow ( Corvus brachyrhynchos) was found to be a significant predator of the SFGS (Shine et
al. , 2001). Other probable avian predat ors include red-tailed hawks ( Buteo jamaicensis ), red-shouldered hawks ( Buteo lineatus ), great egrets ( Ardea alba ), snowy egrets ( Egretta

thula ), black crowned night herons ( Nycticorax nicticorax ), northern harriers ( circus

cyaneus ), and great blue herons ( Ardea herodias ) (Larson, 1994; Freel and Giorni, 1994). Long-tailed weasels ( Mustela frenata ), and large mouth bass ( Micropterus affinis) are also listed as potential pred ators of the SFGS (Larsen 1994).

Bullfrogs are known to prey on SFGS, although the extent of predation is unclear. Bullfrogs have only been observed preying upon juveniles, and it has been suggested that they may not significantly affect the SFGS popul ation and can be discounted as a threat. Alternately, the SFGS preys on bullfrogs as a secondary food source, suggesting that bullfrogs may serve beneficial purposes (Barry in litt. , 2005). As stated previously, bullfrogs prey on the Californi a red-legged frog and the Pacifi c tree frog, two significant food sources of the SFGS (Lawler et al. , 1999; USFWS, 2002b). Bullfrogs may also compete with the California red-legg ed frog for food and habitat (Lawler et al. , 1999; USFWS, 2002b; K. Leyse, pers. comm. 2006; S. McGinnis, pers. comm. 2006; P. Keel, pers. comm. 2006). The degree of competition is debatable because the two frogs may have significantly different diets that precl ude competition. Some scientists argue that

the cooler annual climate on the Peninsula lim its reproduction and prev ent bullfrogs from out-competing native frogs that are better adap ted to the cooler temperatures (Barry, 1994; P. Keel, pers.comm. 2006).

10.2.1.4 Other natural and anthropoge nic factors affecting existence

Invasive species, such as the bullfrog (discuss ed in the preceding pa ragraph), threaten the

continued existence of the SFGS. Other invasi ve species include exotic centrarchid fish, large mouth bass ( Micropterus salmoides) and the sunfish ( Lempomis ). All three of these non-natives prey on tadpoles of the Californi a red-legged frog and Pacific tree frog, prey of the SFGS. In addition, the effects of bullfrogs and non-native fish species may act synergistically (Simberloff a nd Van Holle, 1999). Research has demonstrated that nonnative bluegills ( Lepomis macrochirus) promote the survival of bullfrogs by consuming dragonfly nymphs that prey on bullfrog larvae. Fish also avoid bullfrogs because of their unpalatability (Kruse and Francis, 1977).

Artificial water impoundments and highways may adversely affect the SFGS. The presence of steep banks and absence of leve l areas next to dense vegetation prevents basking areas and hinders thermoregulation of the snakes and prey species. The absence of the vegetation also increases exposure to predators (Barry, 1994). Roads and highways affect the dispersal and movement of the SFGS, and contribute to direct

98mortality from vehicular stri kes. Snakes utilize roads for thermoregulation, and the

SFGS has been observed on dirt roads around the SFO, SFPUC, and Ano Nuevo areas. Amphibian prey is also affected by roads a nd highways. Due to nocturnal habits, roads with activity from 2200 hours to 0400 hours may serve as effective dispersal barriers. Amphibians are sensitive to water pollutant s and are adversely affected by roads in proximity to wetlands. Storm water runoff c ontaminates aquatic habitats and reduces recruitment of anuran individuals, potentially contributing to the decline of the SFGS.

Hybridization and interspecifi c competition have been suggested as possible low level

threats to the SFGS. A broa der range of color variation in wester n populations lends support to the idea of hy bridization (Wharton, 1989; Barry, 1994; Larsen, 1994;

McGinnis in litt. , 2005). Stebbins, 1985, categorized salamanders into single phenotypic traits dictating color pattern; however, others suggest that the variations result from a range of environmental variables (McGinnis in litt. 2005). Barry (1994, in litt. 1996) argues that, because the SFGS and RSGS have remained distinct populations while living in close proximity in La Honda Upland, the possibility and threat of hybridization is low. Interspecific competition between the SFGS and other Thamnophis species, garter and ribbon snakes (Myers et al., 2008), is low and does not pose a significant threat. Dietary

differences between the SFGS and the Santa Cruz garter snake ( T. atratus atratus , SCGS) result in very little habitat overlap between the two species. While the coast garter snake ( T. elegans terrestris , CGS) does overlap in range with the SFGS, its diet of primarily slugs and rodents results in low levels of competition as well.

10.2.2 Baseline Status

The current distribution of the SFGS lies entirely within the limits of San Mateo County, California (USFWS, 1985). Within the Count y, SFGSs are mainly found in the coastal areas, in addition to other small inhabited locations (U SFWS, 2005). A population in San Bruno Mountain once represented the most nor theastern extension of the range, although today it may be extirpated. The San Br uno Mountain population may have been moved to that area for conservation purposes by amat eur herpetologists. The species from the Half Moon Bay region may have had a sim ilar origin from attempted conservation, although no exact records are available for c onfirmation (Barry, 1994). Regardless, the species remain extant at Half Moon Bay (McGinnis, 1988).

The current distribution is not precisely know n because much of the range is comprised of private property; however, studies indicate that the SFGS can still be found within much of its historic range (USFWS, 2006 a nd 2007). The historic distribution of the SFGS extends just north of the San Francisc o-San Mateo County line near Merced Lake

south to Waddell Creek located within th e Big Basin Redwoods State Park. The population at Waddell Creek is questionable beca use of the suspected presence of hybrid species (Goals Project, 2000). Records show that the species may have extended south into Stanford of Santa Clara County and the west coast of the Santa Cruz Mountains. However, SFGS have been extirpated from certa in locales, and field studies in these areas are restricted due to private property (California Natural Di versity Data Base, 2006). The

99historic distribution extends along the western coast of the peninsula south to Ano Nuevo State Reserve (ANSR). On the eastern edge of their range, the SFG S occupied the Buri Buri Ridge along the San Andres Rift and then south, in an arc, from the San GregorioPescadero State Park west to Tunitas Creek (Barry, 1994).

While the current distribution may extend th roughout most of its historic range, the number of SFGS populations has declined in recent years (USFWS, 2007). Habitat destruction due to small projects constantly afflicts the species. Urbanization continues to expand and the prevalent agriculture practi ces of disking and plan ting cycles increases the fragmentation of suitable habitat (Barry, 1994). Sightings of the SFGS have occurred in the Upper Crystal Springs Reservoir a nd Mud Dam in 1998 (San Francisco Planning Department, 2001). Others sightings have b een recorded from “San Andreas Reservoir and in a sag pond between San Andreas and Crystal Springs” (San Francisco Planning Department, 2001). Currently, wild SFGS popula tions are limited to coastal San Mateo County and other small pockets (USFWS, 2005).

Population Dynamics

Some sources state that 65 “permanent” reproductive populations ranging from two to

over 500 adults have been found on the Sa n Francisco Peninsula (Kaplan, 2002 and Goals Project, 2000). The total SFGS popula tion is believed to be around 1500 snakes over one year old (Kaplan, 2002 and Goals Pr oject, 2000). All young under one year old are not included in population counts becau se the population increases when the young

are born and returns to around 1500 the followi ng spring due to insufficient resources (Kaplan, 2002). It is thought th at half of the populations are protected to some degree by refuges including preserves and state parks (Goals Project, 2000).

Six areas are known to contain significant popula tions of SFGS: 1) West of Bayshore, or Milbrae, 2) Laguna Salada (Sharp Park), 3) San Francisco State Fish and Game Refuge (including both Upper and Lower Crystal Sp rings Reservoirs), 4) Pescadero Marsh Natural Preserve, 5) Ano Nuevo State Rese rve (ANSR), and 6) Cascade Ranch (USFWS, 1985). A discussion on baseline status for each of the major populations is provided below. With the exception of West of Bayshore, sufficient information for the other five locales does not exist to discern discrete popul ation trends. Altern atively, these trends are inferred from current habitat dynamics and conditions.

West of Bayshore Sufficient population data exists to reveal a tr end for the West of Bayshore habitat, near the SFO. At one time, this area was cons idered to hold the la rgest SFGS population, and between 1983 and 1985, 695 individuals were captured (USFWS, 1985; Natureserve in

litt. , 2006; Larsen, 1994). Based on another st udy completed in the mid-1990s, only 179 individuals were captured (Larsen, 1994). Although drawin g comparisons between the

studies is difficult due to different methods and sampli ng techniques, both studies indicate that the population has declined. A third trapping occurred in 1997 before the construction of the Bay Area Regional Tran sport (BART) station, and only 25 snakes were captured (Larsen, 1994; S. Larsen, pers. comm., 2006; USFWS, pers. comm.. 2006). While this trapping occurred in a lim ited region of the West of Bayshore habitat,

100the low number of captured individuals was unanticipated considering the much higher numbers observed and caught in prior years (S. Larsen, pers. comm. 2006).

Declines in the West of Bayshore populati on are expected due to ongoing construction and habitat degradation. The reduction in th e open water component of the canal system in recent years has led to a decrease in suita ble habitat for an amphibian prey base. Both increases in vegetation and silt ation reduce the quantity and qu ality of habitat (S. Larsen, pers. comm. 2006). Other negative activities affecting the SFGS in the area include encroaching development, illegal collecting, and limited law enforcement (Larsen, 1994). The SFO and USFWS have recently agreed to improve the habitat quality for the SFGS at the West of Bayshore area.

Laguna Salada The SFGS population at Laguna Sa lada is also thought to have declined. This population

trend can be attributed to two influxes of sa lt water into the snake’s habitat in the 1980s (Steiner and Hafernik, 1992). No salination ev ents have occurred since a protective levee was built, and it has been suggested that the sn akes never historically occupied the site (Barry, 1994). Other detrimenta l activities include off-road vehicle use and illegal trash dumping at the Mori Point area (Steiner a nd Hafernik, 1992; D. Fong, pers. comm. 2006). These habitat degrading actions have been mitigated by the National Park Service (D. Fong, pers. comm. 2006; National Park Se rvice, pers. comm. 2006), although no information on these actions has been pr ovided (USFWS, 2006b). Further relief has come from a partnership between the Nati onal Park Service and the USFWS via an agreement to construct two ponds for amphibi an prey of the SFGS (S. Larsen, pers. comm. 2006; H. McQuillen, pers. comm. 2006). In 1996, volunteers of the National Park Service recorded the SFGS foraging for the California red-legged frog in both of the ponds, demonstrating the benefits of the constructed ponds (S. Gardner in litt. , 2006).

Mori Point is located within the great er Laguna Salada area. Although the SFGS historically occupied Laguna Salda at Mori Po int, the species is not thought to currently exist in this area (McGinnis, 1990; McGinnis, pers. comm. 20 06). The extirpation of the SFGS occurred after ponds in the area were fill ed and agricultural disking practices were implemented in 1990 along Calera Creek. Prior to these landscape changes, high occurrences of SFGS individuals were repor ted in Calera Creek Channel (McGinnis, 1990; McGinnis, pers. comm. 2006). Following these changes, no sightings have been reported at Calera Creek based on inform al walk-through surveys (MsGinnis, pers. comm.; K. Swaim, pers. comm. 2006). Obse rvations from 1978 and 1990 indicate that there may have been SFGS movement between th e Calera Creek corridor and Mori Point, based on SFGS sightings along a ridgeline separa ting the corridor and Mori point (Barry

in litt. , 2006). However, no occurrences of SFGS individuals have been reported

between these two locations since the development in 1990 (K. Swaim pers. comm.. 2006). A proposal for road construction and residential development along Calera Creek further challenge the recovery of the sp ecies (S. Larsen, pers. comm. 2006; H. McQuillen, pers. comm. 2006).

San Francisco State Fish and Game Refuge

101This population of SFGSs lives in proximity to the Crystal Springs and San Andreas

Reservoirs. While this area has been designated a refuge, it is owned and managed by the San Francisco Public Utility Company (SFPUC) (J. Stolz, pers. comm. 2006). This public land provides quality habitat for th e SFGS because of the restricted access designated near the reservoirs (J. Naras pers. comm. 2006). Large quantities and high

densities of individuals have been observ ed (Barry, 1996). However, the population is threatened from human activity because the area is not specifically managed for the SFGS (J. Stolz, pers. comm. 2006). Current trail systems and proposals for additional trails along the waterways of the ref uge increase human presence and possible

disturbances to the SFGS. One SFGS indivi dual was run over by a bi cycle on a road next to the SFCUP property, and other human-related stressful or lethal activities are possible (A.M. McGraw in litt. , 2005). A habitat conservation pl an has been discussed between the USFWS and the SFPUC, although no plan has been implemented to date (S. Larsen, pers. comm. 2006; J. Naras, pers. comm. 2006).

Pescadero Marsh Natural Preserve The population at Pescadero Marsh is t hought to be declining, despite recent improvements in certain habitat conditions (USFWS, 2006b). This population has been deemed genetically signifi cant because the SFGS phenotype in the area more closely resembles the “holotype” (i.e., defined as “the single specimen chosen as a representative type when establishing the taxonomic gr oup) than any other population (Larsen, pers.comm. 2006). Pescadero Marsh has regul ar influxes of salt water that reduce the habitat quality of the area for the SFGS. During the 1990s, several recovery actions improved the fresh water quality, although no in formation on those actions is provided (USFWS, 2006b). The SFGS no w inhabits eastern portions of the marsh and a few artificial ponds that are adjacent to origina lly inhabited areas. Some California State Parks staff believe that the habitat for the SFGS and their anuran prey have markedly improved (McGinnis, 2002; J. Kerbavoz, pers. comm.). However, the high salinity levels continue in much of the marsh resulting in unsuitable habitat for amphibian prey (C. Atkinson, pers. comm. 2006; P. Keel, pers. comm. 2006; J. Smith, pers. comm. 2006).

Recent restoration efforts to lim it salt water influx into the marsh have resulted in little success. However, restoration work aimed at neighboring properties may be benefitting the population. Staff from Pescadero Marsh and Peninsula Open Space Trust (POST) are implementing prescribed burns on Cloverdale Ranch as part of an upland conservation management plan. Further information is n eeded to evaluate the effectiveness of the project; however, it is anticipat ed to help the population (A . Willy, pers.comm. 2006).

Ano Nuevo State Reserve (ANSR) There have been sightings of the SFG S at the ANSF since 1975. In 1987, 13 SFGS individuals were trapped around the h eadquarters’ pond (Barry, 1978; McGinnis et al.

, 1987). In 1988, a more comprehensive surv ey of the ANSR documented 57 individuals (Keel et al. , 1991). The study authors believe that the ANSR may contain one of the largest known SFGS populations, and they attribute these larg e numbers, in part, to the available wetlands and suitable upland foragi ng sites for amphibian prey. Between 2004 and 2005, the California State Pa rks and the USFWS performe d two burns on 45 acres of

SFGS habitat to increase lo cal populations (Halbert, 2005) . According to trapping

102surveys before and after the burn, the number of SFGS individuals increased from 7 to 53. Given differences in survey methodology, it is difficult to draw conclusions from the results of the two studies. Therefore, addi tional information is needed to access the effectiveness of burn disturbance in improvi ng habitat quality for the SFGS (P. Halbert, pers. comm. 2006). According to California State Parks, ANSR may acquire new land from a conveyance of property in the near futu re. The California State Parks is currently discussing acquisition of the land, which woul d provide an area suitable for California red-legged frog restoration ,with a private land owner. The land would also provide more protected land for the SFGS (A. Willy, pers . comm. 2006; V. Roth, pers. comm. 2006).

Cascade Ranch Cascade Ranch is the only pr ivate property discussed in th e Recovery Plan for the SFGS (USFWS, 1985). Little is known about the popu lation distribution on the site. However, overgrazing, in the late 1980s, and a 1989 USFWS-approved construction of a resort lodge, general store, cabins, and camping area may have reduced habitat quality for the SFGS. The project included a recovery plan for the species and a monitoring program to continue for 5 years (Biosear ch Associates, 2003). The fi nal monitoring report in 2005 demonstrated that the recovery plan had su cceeded in providing suitable habitat for the SFGS as well as its amphibian prey (Bios earch Associates, 2005). In 1994, Cascade Ranch was designated as a “high quality” SFG S habitat due to the presence of ANSR breeding ponds nearby. However, the pres ence of Highway 1 and the proximity to agriculture fields in the area may hinder the mobility and dispersal of the species (Freel and Giorni, 1994).

10.3 REFERENCES

Literature Cited

103Goals Project. 2000. Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosys tem Goals Project. P.R. Olofson, editor. San Francisco Bay Regional Water Quality Control Board, Oakland, California. Available

online at: http://sfep.abag.ca.gov/pdf/species- community/Species_and_Community_Profiles%5BPart3%5D.pdf (Accessed on November 5, 2007).

Kaplan, M. 2002. Not-so-common garters. Meli ssa Kaplan’s Herp Care Collection.Last updated April 19, 2007. Available online at: http://www.anapsid.org/garters.html (Accessed on October 16, 2007).

104Myers, P., R. Espinosa, C. S. Parr, T. Jones, G. S. Hammond, and T. A. Dewey. 2008. The Animal Diversity Web (online). Accessed July 23, 2008 at http://animaldiversity.org

105San Francisco Planning Department. 2001. Peninsula Watershed Management Plan – Final Environmental Impact Report (E IR). EIR Certification Date: January 11, 2001.

Available online at: http://sfwater.org/Files/Reports/3-Env_Set_Impacts.pdf (Accessed on November 5, 2007).

USFWS. 1985. Recovery plan for the San Francisco garter snake ( Thamnophis sirtalis

tetraenia ). U.S. Fish and Wildlife Service, Portland, Oregon. 77 pp.

USFWS. 1996. Biological Opinion for BART expansion, San Mateo County. Service file # 1-1-96-F-86. Sacramento, California.

USFWS. 2002a. Formal endangered species section 7 consulation on the proposed orchards at Hiddenbrooks Projects, Solano County, California. Service file # 1-1-02-F-0250.

USFWS. 2002b. Recovery plan for the California red-legged frog ( Rana aurora draytonii ). U.S. Fish and Wildlife Service, Portland, Oregon. Viii+173 pp.

USFWS. 2005. Formal endangered species sectio n 7 consultation for Pacific Gas and

Electric’s Jefferson-Martin 230kV Tr ansmission Line Project, San Mateo County, California. Service file # 1-1-05-F-1226. Sacramento, California. Dated 12 August.

USFWS. 2006a. Formal endangered species section 7 consultation for city of Half Moon Bay’s permit application for co nstruction of a clean-up and restoration and development of a bicycle and pedestri an trail in Oak Avenue Park along Pilarcitos Creek, City of Half Moon Bay, San Mateo County, California. Service file # 1-1-06-

1060197. Sacramento, California. Dated 10 August.

USFWS. 2006b. 5-Year Review: Summary and Evaluation of the San Francisco Garter Snake. Threatened and endangered species system database. Available online at: http://ecos.fws.gov/tess_public/ (Accessed on July 12, 2008).

USFWS. 2007. Species Account: San Francisco Garter Snake ( Thamnophis sirtalis

tetrataenia ). Sacramento Fish and Wildlife Office. Available online at: http://www.fws.gov/sacramento/es/ani mal_spp_acct/sf_garter_snake.pdf (Accessed on October 16, 2007).

Personal Communication

107In Litt. References

10810911: SAN JOAQUIN KIT FOX

11.1 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the San Joaquin kit fox ( Vulpes macrotis mutica ) (SJKF) that are reasonably certain to occur in the action area. Future federal actions not directly related to the proposed action are not cons idered because they require additional consultation under Section 7 of the Endangere d Species Act (Act). The numerous nonfederal actions that are reas onably certain to occur within the action area consist of industrial and petroleum field development, agriculture, surface mining, and urbanization projects related to infrastructure, irri gation canals, wind farms, power lines, and aqueducts. Many of these factors are linked or act synergistically and create complex consequences for the SJKF. More specifica lly, these habitat modifications compress and fragment the species’ range. Combined w ith the high mortality of the SJKF during dispersal, movement between habitats is limited and the long-term viability of the population is threatened.

11.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as combined effects of past and present factors, both natural and anthropogenic, leading to the status of the species, its habitat, and ecosystem. The environmental baseline is a sn apshot of the SJKF status at this time. However, the baseline condition of the assess ed SJKF’s habitat varies across locations. Given the large number of occupied habitats a nd extent of the action area included of this assessment, the environmental baseline include s a general discussion of factors that may

affect the SJKF within the action area. This information is presented in Section 11.2.1.

Additional information on the current distri bution and population dyna mics of the SJKF is presented as part of the baseline status in Section 11.2.2. The majority of information

included in the environmental baseline secti on is a summary of information presented in the Recovery Plan for Upland Species of the San Joaquin Valley, California (USFWS, 1998).

11.2.1 Factors affecting species envi ronment within the action area

The San Joaquin kit fox was listed as “endange red” by the U.S. Fish and Wildlife Service (USFWS) in 1971. More than 90% of its nati ve habitat in the San Joaquin Valley has become fragmented or destroyed as a resu lt of agricultural, industrial, and urban developments. As the human population in California continues to expand, suitable habitat for the kit fox will inevitably decrease . Such land conversions contribute to SJKF

110declines through displacement, reduction in prey abundance, and di rect and indirect moralities. Since the 1950s, the primary factor of SJKF decline is attributed to loss, degradation, and fragmentation of habitats. Less severe threats to the species’ survival are attributed to: (1) non-nat ive invasion, predation, and comp etition; and (2) disease and

climatic extremes. A detailed discussion of th ese three factors is presented in Sections 11.2.1.1 through 11.2.1.3.

11.2.1.1 Habitat Destruction, Degradation, and Fragmentation

The survival of the SJKF is threatened pr imarily by industrial, ag ricultural, and urban developments that readily reduce the size and quality of availa ble habitat (USFWS, 1998). Grazing practices (agriculture ), however, are not considered part of that threat, and may actually benefit the SJKF. Livestock may alter population densities of prey species, but may not harm the SJKF if grazing inte nsity is controlled (Morrell 1975; Orloff et al.

, 1986; Laughrin, 1970; Balestreri, 1981). Excess grazing of shrub cover that affects prey numbers may be detrimental (O’farrell et al., 1980; O’Farrell and McCue, 1981; USFWS, 1983; Kato, 1986).

The major urbanization developments within the SJKF range include cities, towns, aqueducts, irrigation canals, surface mines, road networ ks, non-petroleum industrial projects, power lines, and wind farms. While these actions are detrimental to suitable habitat, the SJKF may still ut ilize adjacent areas to expand prey bases or construct additional den sites. For example, individuals have been observed with dens in a number of urban habitats: along canals and in le vees (Jones and Stokes, 1981; Hansen, 1988), abutting highways (ESA Planning and E nvironmental Services, 1986b, Hansen, 1988), near wind farms (Hall 1983, Orloff et al. , 1986), along power line corridors (Swick, 1973), and at sanitary land fills (R. Faubion, pe rs. comm.). The SJKF have also been documented utilizing habitats adjacent to towns and behaving differently from individuals living in more remote populations . These individuals scavenge for food in dumpsters, forage from smaller areas, dem onstrate diurnal activity patterns, and are comparatively tame. It is thought that this variability in behavior and temperament reflects their degree of ecological plasticity ( e.g ., Grinnell et al. , 1937, p.411; T. Murphy, pers. comm., B.L. Cypher pers. comm.).

Habitat loss due to petroleum field development affects the SJKF in the southern half the San Joaquin Valley. Habitat is lost to construction and grad ing of roads, well pads, tank settings, pipelines, and settling ponds. Hab itat is degraded from noise, ground vibrations, venting of toxic and noxious gases, and th e release of petroleu m products and waste waters. SJKFs are also at higher risks to traffic-related mortalities on oil fields. However, it is thought that as long as mitigation efforts accompany drilling developments, oil sites may provide ade quate habitat for the SJKF (O’Farrell et al. , 1980; Spiegel et al ., in press). The effects of oil activities on SJKF population density, reproduction, dispersal, and mortality were examined at the Elk Hill Naval Petroleum Reserves, California. No differences we re reported between populations living on developed or undeveloped areas of the reserve (Berry et al ., 1987a). Likewise, a

111correlation between population size and habitat disturbance for SJKF populations in Kern County is unclear. Nonethele ss, habitat loss remains the most significant factor affecting SJKF survival on oil fields (Spiegel et al ., in press).

11.2.1.2 Invasive Species, Predation, and Competition

The SJKF is threatened by coyotes, non-native red foxes, domestic dogs( Canis familiaris ), bobcats ( Felis rufus ), and large birds of prey (Hall, 1983; Berry et al., 1987; O’Farrell, et al ., 1987; White et al . 1994, Ralls and White, 1995; CDFG, 1987). Due to land conversions and human activities (White, 2000), the non-native red fox is currently expanding its distribution in central California (Orloff et al ., 1986; Lewis et al ., 1993) and may be a factor in SJKF declines in Sa nta Clara Valley (T. Rado, pers.comm.). Red foxes are also implicated in declines in th e northwestern portion of their range (USFWS, 1998). Red foxes may potentially limit opport unities for the SJKF through competition or predation. Competition arises from the f oxes utilizing similar den sites and preying on the same species. The effects of red foxes have not been well-studied, and neither their historical impacts nor continuing expans ion on the SJKF are clear (USFWS, 1998).

Predation and competition are not listed explicitly as threatening the survival of the SJKF in the Recovery Plan (USFWS, 1998), but th eir effects are noneth eless mentioned as adversely affecting the species. For example, coyote injuries are li sted as the primary factor in the majority of SJKF mortalities (White et al. , 2000). Coyotes will “aggressively dominate encount ers with red foxes and will pursue and kill” red, gray (Sargent and Allen, 1989), and kit foxes. However, a coyote c ontrol program at the Naval Petroleum Reserves in California repo rted no increase in survivorship among the SJKF, nor was there a decreas e in coyote-induced mortalit y (Cypher and Scrivner, 1992; Scrivner and Harris, 1986; Sc rivner, 1987). Incidentally, the coyote may simultaneously benefit the SJKF by reducing the competiti on and predation by the non-native red fox. The gray fox is a native species which ma y compete with the SJKF, although to what degree is unknown (USFWS, 1998).

11.2.1.3 Disease and Climatic Extremes

Both disease and climatic extremes are imp licated in SJFK mortality (USFWS, 1983). At Camp Roberts, rabies caused a 6.3 percent dec line in radio-collared individuals (Standley

et al. 1992), and the disease may be linked to the population decline at Camp Roberts in recent years (P.J. White, pers. comm.). A si gnificant threat is posed by stochastic environmental events, particularly drought and flooding. Drought affects the reproductive success of the SJKF by affecting th e availability of prey (White and Ralls, 1993; Spiegel et al. in press). There is a concern of local extincti ons in certain isolated

areas. Excessive rainfall al so adversely affects prey popul ations. The above-average rainfall in 1994-1995 caused a “rapid and se vere” decline of small mammal populations. Fewer pupping dens were found in the Elk H ills region in 1995, and the proportion of pup rears was relatively small (B.L. Cypher pers. comm., L.K. Spiegel pers. comm.).

11211.2.2 Baseline Status

Though the SJKF has been listed for over 30 ye ars, the status throughout most of its range is poorly known, in part due to limite d access on private properties. Despite the lack of a comprehensive survey, research proj ects, incidental sightin gs, and local surveys indicate that kit foxes currently inhabit some areas of suitable habitat on the San Joaquin Valley floor. Suitable habitat is also found in the surrounding foothills of the coastal mountain ranges, the Sierra Nevada, Tehach api Mountains (from southern Kern County north to Contra Costa, Alameda, and San Jo aquin Counties), near La Grange, Stanislaus County on the east side of the Valley, and some of the larger scattered islands of natural land on the Valley floor in Kern, Tulare, Ki ngs, Fresno, Madera, and Merced Counties.

Kit foxes occur westward into the interior coastal ranges in Mont erey, San Benito, and Santa Clara Counties (Pajaro River watershed) , in the Salinas River watershed, Monterey and San Luis Obispo, and in the upper Cuyama River watershed in northern Ventura and

Santa Barbara Counties and southeastern Sa n Luis Obispo County. Kit foxes are also known to live within the city limits of the city of Bakers field in Kern County (USFWS, 1998).

“The largest extant populations of kit f oxes are in western Kern County on and around the Elk Hills and Buena Vista Valley, Kern County, and in the Carrizo Plain Natural Area, San Luis Obispo County. The kit fox pop ulations of Elk Hills and the City of Bakersfield, Kern County, Carrizo Plain Na tural Area, San Luis Obispo County, CiervoPanoche Natural Area, Fresno and San Benito Counties, Fort Hunter Liggett, Monterey County, and Camp Roberts, Monterey and San Luis Obispo Counties have been recently, or are currently, the focus of various research projects. Though monitoring has not been continuous in the central and northern portions of the range, populations were recorded in the late 1980s at San Luis Reservoir, Me rced County, North Gra sslands and Kesterson National Wildlife Refuge area on the Valle y floor, Merced County, and in the Los Vaqueros watershed, Contra Costa County in the early 1990s. Sma ller populations and isolated sightings of kit foxes are also know n from other parts of the San Joaquin Valley floor, including Madera County and easte rn Stanislaus County” (USFWS, 1998, p.124)

Population Dynamics The SJKF is known for its instability in popul ation size. It is not uncommon for the SJKF population to fluctuate five fold or more from year to year. These large variations

are correlated with the intrinsic fluctuations of desert ecosystems. The volatility in precipitation affects seed bank a nd vegetative biomass, leading to associated fluctuations in leporids (rabbits and ha res) and rodents. Ultimatel y, these density independent

variables lead to fluctuations in kit fox re productive rates. Both extended episodes of drought or rainfall can contri bute to low reproduction a nd population crashes (White et
al. 2000).

The San Joaquin kit fox is found within three or four core populati ons, and approximately nine satellite populations that vary in size and degree of isolation (White et al. 2000).

113These core populations are thought to “anc hor the spine” of the metapopulation (USFWS, 1998). Three core populations are: (1) Carrizo Plain Natural Area in San Luis Obispo County; (2) Natural lands of western Kern County inhabite d by kit foxes (e.g., Elk Hills, Buena Vista Hill, and the Buena Vista Valle y, Lokern Natural Area and adjacent natural land); and (3) the Ciervo-Panoche Natural Area of western Fresno and eastern San Benito Counties. Each core population is distinct and has different envir onmental conditions, as manifested in their unsynchronized populati on dynamics (B.L. Cypher, pers. comm.). Population viability studies suggest that extinc tion probabilities increase dramatically if

either the Carrizo Plain or western Ke rn County population is extirpated. The combination of these three populations is a dvantageous compared to other groupings, because they are all more or less inte rconnected by grazing lands (although steep and rocky in certain places) (USFWS, 1998). An important population, although not a core population, is located in the Salinas-Pajaro Re gion at Camp Roberts and Fort Hunter Liggett. This population has natural connecti ons to the Carrizo Plain Natural Area and the San Joaquin Valley, although the extent of migration between these areas is unknown (K. Ralls pers. comm.).

Safe harbor and other land ow ner incentive programs have b een initiated to reduce the degree of isolation between populations and promote conservation of SJKF populations on agricultural lands. These in itiatives should ensure that farmers are not penalized, farming is not disrupted, and habitats are prot ected that maintain and enhance kit foxes. The American Farmland Trust has already proposed a project addressing the SJKF fragmentation. In addition to the goals listed above, the project also aims to establish small populations of breeding SJKFs on farm lands. These breeding grounds would serve as bridges between isolated patches and th e larger populations “al ong the spine of the metapopulation” (USFWS, 1998). There is one safe harbor agreement listed on the San Joaquin kit fox ( Vulpes macrotis mutica ) species profile USFWS webpage: Paramount Farming SHA, Artificial Escape Den Project. The USFWS issued a permit for 3 years in 2003 for the take of the SJ KF on approximately 1000 acres of land from Paramount Farms, Kern County. Twenty one Habitat Conservation Plans for the SJKF are also listed on the species profile USFWS.

11.3 REFERENCES

Literature Cited

Balestreri, A.N. 1981. Status of the San Joaqui n kit fox at Camp R oberts, California, 1981. Unpubl. Rep., U.S. Department of Ar my, Engineering, Environmental and Natural Resources Office. California Polytechnic State University, San Luis Obispo, 30 pp.

Berry, W.H., J.H. Scrivner, T.P. O’Farrell, C. E. Harris, T.T. Kato, and P.M. McCue.

1141987. Sources and rates of mo rtality of the San Joaquin kit fox, Naval Petroleum Reserve #1, Kern County, CA, 1980 -1986. Rep. No. EGG 10282-2154, EG&G Energy Measurements, Goleta, CA, 34 pp.

California Department of Fish and Game (CDFG). 1987. Los Banos Grandes project – 1986 annual progress report. Sacramento, Unpubl. Rep., 28 pp.

Cypher, B.L., and J.H. Scrivner. 1992. Coyote co ntrol to protect enda ngered San Joaquin

kit foxes at the Naval Petroleum Reserves, California. Pp. 42-47, in Proceedings

of the 15 th Vertebrate pest Conference (J.E. Borrecco and R.E. Marsh, eds.). University of California, Davis, 415 pp.

ESA Planning and Environmental Services. 1986. San Joaquin pipeline biological assessment. Unpubl. Rep., San Francisco, CA, 142 pp.

Grinnell, J., J.S. Dixon, and J.M. Linsdale . 1937. Fur-bearing mammals of California. Vol. 2. University of California at Berkeley.

Hall, F.A. 1983. Status of the San Joaquin kit fox, Vulpes macrotis mutica , at the Bethany wind turbine generating site, Alam eda County, California. Unpubl. Rep., California Department of Fish and Game, Sacramento, 34 pp.

Hansen, R.B. 1988. Porterville urban area boundry biotic surv ey. Unpubl. Rep., Hansen’s Biological Consulting, Visalia, CA, 219 pp.

Jones and Stokes Associates, Inc. 1977. Ground s quirrel control, Fort Ord Complex, Fort Ord, California. U.S. Department Army, HQ 7 th Infantry Division, Fort Ord, Sacramento, CA, Final Environmental im pact Statement, Contract No. DACA05- 77-C-0006, 412 pp.

Kato, T.T. 1986. Survey of potential habitat for the endangered San Joaquin kit fox ( Vulpes macrotis mutica ), in the Carrizo Plain, San Luis Obispo County, California. Rep. No. EGG 10282-2124, EG &G Energy Measurements, Goleta, CA, 24 pp. + Appendix.

Laughrin, L. 1970. San Joaquin kit fox: its distribution and abundance. California Department of Fish and Game, Sacramento Wildl. Manage. Branch, Admin. Rep. No. 70-2, 20 pp.

Lewis, J.C., K.L. Sallee, and R.T. Golightl y, Jr. 1993. Introduced red fox in California. California Department of Fish and Game, Sacramento, Nongame Bird and Mammal Sec., Rep. 93-10: 1-70, 70 pp.

Morrell, S.H. 1975. San Joaquin kit fox dist ribution and abundance in 1975. California Department of Fish and Game, Sacram ento, Wildlife Management Branch, Admin. Rep. No. 75-3, 28 pp.

115O’Farrell, T.P., and P.M. McCue. 1981. Inventory of San Joaquin kit fox on USBLM lands in the western San Joaquin Valle y—final report. Rep. No. EGG 1183-2413, EG&G Energy Measurements, Goleta, CA, 36 pp. + Appendices.

O’Farrell, T.P., et al . 1987. Distribution of the enda ngered giant kangaroo rat, Dipodomus ingens , on the Naval Petroleum Reserves, Kern County, California. Rep. No. EGG 10282-2173, Santa Barbar a Operations, EG&G Energy Measurements, Goleta, CA, 30 pp.

O’Farrell, T.P., T.T. Kato, P.M. McCue, and M.L. Sauls. 1980. Inventory of San Joaquin

kit fox on USBLM lands in southern and southwestern San Joaquin Valley—final report. Rep. No. EGG 1183-2400, EG&G En ergy Measurements, Goleta, CA, 74 pp. + Appendices.

Orloff, S.G., F. Hall, and L. Spiegel. 1986. Di stribution and habitat re quirements of the San Joaquin kit fox in the northern extrem e of their range. Trans. West. Sect.

Wildl. Soc. 22:60-70.

Ralls, K., and P.J. White. 1995. predation on en dangered San Joaquin kit foxes by larger

canids. J. Mammal. 276: 723-729.

Sargeant, A.B., and S.H. Allen. 1989. Observed interactions between coyotes and red

foxes. J. Mammal. 70: 631-633.

Scrivner, J.H. 1987. Summary and evaluation of the coyote control program on Naval Petroleum Reserve #1, Kern County, California, 1987. Rep. No. EGG 10282- 2186, EG&G Energy Measurements, Goleta, CA, 13 pp.

Scrivner, J.H., and C.E. Ha rris. 1986. Summary and evalua tion of the coyote control program, Naval Petroleum Reserve #1, Kern County, California, 1986. Rep. No. EGG 10282-2125, EG&G Energy Measurements, Goleta, CA, 28 pp.

Spiegel, L.K., J. Tom, M. Disney, and T. Da o. In press. Reproduction of San Joaquin kit fox ( Vulpes macrotis mutica ) in undeveloped and oil deve loped habitats of kern County, California. In , Studies of San Joaquin ki t fox in undeveloped and oil developed areas. California En ergy Commission, Sacramento.

Standley, W.G., W.J. Berry, T.P. O’Farrell , and T.T. Kato. 1992. Mortality of San Joaquin kit fox ( Vulpes macrotis mutica ) at Camp Roberts Army National Guard Training Site, California. Re p. No. EGG 10617-2157, EG&G Energy Measurements, Goleta, CA, 19 pp.

Swick, C.D. 1973. Setermination of San Joaquin k it fox range in Contra Costa, Alameda, San Joaquin, and Tulare Counties, 19 73. California Department of Fish and Game, Sacramento, Spec. Wildl. Invest., Unpubl. Rep., 15 pp.

116U.S. Fish and Wildlife Servic e (USFWS). 1998. Recovery plan for upland species for the San Joaquin Valley, California. Region 1, Portland, OR. 319 pp.

U.S. Fish and Wildlife Servic e (USFWS). 1983. San Joaquin kit fox recovery plan. U.S. Fish and Wildl. Service, Portland, OR, 84 pp.

White, P.J., K. Ralls, and R.A. Garrott. 1994. Reproduction and spacing patterns of kit foxes relative to changing prey avai lability. J. Wildl. Manage. 57:861-867.

White, P.J., William H. Berry, Julie J. Eliason, and Michael T. Hanson. 2000. Catastrophic decrease in an isolated popul ation of kit foxes. The Southwestern Naturalist 45(2): 204-211.

Personal Communication

Cypher, B.L., Program Manager, Enterprise Ad visory Services, Inc., Endangered Species and Cultural Resources Program, Tupman, CA.

Fabian, R., U.S. Bureau of Reclamation, Fresno, CA.

Murphy, T.D., Department of Biology, California State University, Bakersfield, CA.

Spiegel, L.K., California Energy Commission, Sacramento, CA.

Rado, T.A., Biological Consultant, Riverside, CA.

Ralls, K., Smithsonian Institute, Washington, DC.

White, P.J., California Polytechnic Resear ch Biologist, Camp Roberts Endangered Species Study Group, San Luis Obispo, CA.

11712: VALLEY ELDERBERRY LONGHORN BEETLE

11.2 CUMULATIVE EFFECTS

Cumulative effects include the e ffects of future state, tribal , local, private, or other nonfederal entity activities on the valley elderberry longhor n beetle (VELB) ( Desmocerus californicus dimorphus ) that are reasonably certain to o ccur in the action area. Future federal actions unrelated to the proposed act ion are not considered because they are subject to consultation pursua nt to Section 7 of the Enda ngered Species Act (Act).

Numerous non-federal actions that could affect the VELB are reasonably certain to occur within the action area. These will typically include maintenance of levees and canals, agriculture, park management, grazing activities, and urban development. Many of these activities are linked and create complex effect s on listed species or their habitat in the action area. For example, main tenance of levees and canals facilitate continued farming activities and restrict water flow into downstream riparian habitats. Farming utilizes the fertile soil in riparian habitats and fu rther contributes to its net habitat loss.

11.2 ENVIRONMENTAL BASELINE

The environmental baseline is defined as the effects of past and ongoing human induced and natural factors leading to th e status of the species, its habitat, and ecosystem, within

the action area. The environmental baseline is a snapshot of the valley elderberry longhorn beetle’s status at this time. Details of the valley elderberry longhorn beetle’s habitat description and known locations are included in Attachment III. However, the baseline condition of each assessed VELB speci es and habitat varies across locations. Given the large number of occupied habitats a nd extent of the action area included of this assessment, the environmental baseline include s a general discussion of factors that may

affect VELB within the action area. This information is presented in Section 12.2.1.

Additional information on the current distri bution and population dyna mics of the VELB is presented as part of the baseline st atus in Section 12.2.2. Tables 12.1, 12.2, and 12.3, present restoration and preserva tion projects that have been completed, or are currently being completed, on behalf of the VELB and its habitat. The majority of information

included in the environmental baseline secti on is a summary of information presented in the 5-Year Review: Summary and Evaluation of the Valley Elderberry Longhorn Beetle (USFWS, 2006).

12.2.1 Factors affecting species envi ronment within the action area

The VELB is primarily affected by riparian habitat loss, due to factors such as maintenance of levees and canals, and park management. To a lesser degree, the VELB is also affected by predation and invasive sp ecies. When the species was first listed by

118the United States Fish and Wildlife Service (U SFWS), 90% of the ripa rian habitats that once occupied the Central Valley 150 y ears ago had become obsolete (Barr, 1991; USFWS, 2007a). While the rate of habitat loss has declined within the past 25 years, the lo1ss has yet to fully subside. Urbanization projects continue with in the species range, although for mitigation purposes, adjoining habi tat conservation plans for each action are also underway. These plans are in conj unction with former and ongoing riparian restoration and conservation activities. Proj ects to protect existing land, and enhance or restore current riparian habitats, have been or are currently being completed by private organizations ( ie . land trusts), and by Federal, Stat e or local agencies. Sections 12.2.1.1 through 12.2.1.3 provide details on each of the major issues and actions affecting the VELB within its range of habitats (USFWS, 2006).

12.2.1.1 Habitat Loss and Degradation

Habitat loss is the number one factor contribu ting to VELB decline. In particular, the removal of riparian habitat, and as a conse quence the removal of the elderberry host plant ( Sambucus spp.), has been the primary factor si nce the species was first listed as

“Threatened” in 1980. The overall loss continue s to this day (USFWS, 1984 and 2007a).

This reduction in habitat is linked to urba n development, flood controls, levees and canals, agriculture, and park management. Th ese factors have the potential to remove, degrade or fragment VELB habita t. The species is particularly sensitive to these adverse factors because of its high hab itat specificity and its limited dispersal ability. Isolated subpopulations are vulnerable to extirpation from environmental, demographic, and genetic events (Schonewald-Cox et al. 1983).

The loss of habitat has histor ically been a major threat to the VELB. Between 1900 and 1990, there was a 96% loss of riparian habita t in the southern portion of the Central Valley (Kern to Fresno Counties), with only 16,000 acres remaining. There was an 84% loss with 21,000 acres remaining in the middle Valley (Merced to San Joaquin Counties), and an 80% loss with 96,000 acres remaini ng in the northern Valley (Sacramento and Solano Counties to Shasta County). Loss rates slowed between 1960 and 1990, but were still relatively “high” with 59% loss in the s outh, 65% loss in the middle, and 35% loss in the northern Central Valley (Geographic Information Center, 2003). Quantifying the actual loss of elderberry is di fficult, however. It is uncerta in how much of the riparian habitat contained elderberry, or even if it was occupied by th e VELB (USFWS, 2006).

The VELB “is in long-term decline due to human activities that have resulted in widespread alteration and frag mentation of riparian habita ts, and to a lesser extent, upland habitats, which support the beetl e” (USFWS, 1996 and 2007 a). Historically, riparian habitats in the Central Valley were utilized heavily for their significant quantity

of wood and for their fertile soil. In the last 25 years, the rate of ri parian loss has slowed significantly due to the decrea sing number of existing ripa rian habitats, restoration efforts, and protections provided under the Act for both the VELB and other species. Non-riparian, upland habitats where elderberry occurs have also declined: savanna and grassland adjacent to riparian areas, oa k woodland, and mixed chaparral-woodland.

119Since 1980, the USFWS has allowed an esti mated incidental take of 10,000 to 20,000 acres of beetle habitat, for the purpo ses of urbanization, water management, transportation, and flood control (Talley et al. 2006 ). This area amounts to 12,000 to 15,000 elderberry shrubs or 40,000 to 50,000 elderb erry stems one inch in diameter. Between 1983 and 2005, the USFWS completed 526 formal Section 7 consultations. One jeopardy opinion was issued in the early 19 80s to the U.S. Army Corps of Engineers for the Sacramento River Bank Protection Program. Two other programmatic biological opinions were issued in 1997 to the U.S. Army Corps of Engineers and the Federal Highways Administration (USF WS, 2006). Non-Federal par ties are issued section 10(a)(1)(B) permits for the take of listed species. To date, 18 permits for habitat conservation plans, totaling 970,000 acres for the VELB, have been issued (USFWS, 2006).

The current maintenance of levees and can als for the purposes of flood control and agriculture could resu lt in a loss of habitat for the VELB (Talley et al. 2006). Historically, artificial levees , river channelization, dam c onstruction, water diversion, and heavy groundwater pumping have all been attributed to the destruction of VELB habitat (USFWS, 1984). Flood control levees constr ucted in the lower Sacramento River have apparently reduced the number of elderberry shrubs and associated VELBs compared to the unobstructed upper Sacramento River (Talley et al. 2006). Future restoration potential for the lower Sacramento River is hindered by the availability of suitable sites (USFWS, 2006). Due to concerns of VELB habitat interfering with flood-fighting, or with risking the chance of costly mitigation afterwards, the Reclamation Board has limited the planting of elderberry in flood plains over the past decade (USFWS, 2006). By excluding elderberry from re storation projects, th e potential benefits to the beetle are undermined. However, land owner incentive prog rams, discussed later, offer a means to mitigate the threat to the VELB caused by lev ee and canal maintenance (USFWS, 2006).

12.2.1.2 Predation, Invasive Species, and Other Issues

The potential predators of the VELB are the Argentine ant ( Linepithema humile ),

insectivorous birds and lizards , and the European earwig ( Forficularia auricularia)

. However, little is known of the overall imp acts these predators have on the beetle (USFWS, 2006). The Argentine ant is an aggr essive competitor and appears to be the main predator of the VELB (Huxel, 2000). The ant displaces na tive populations of arthropods and is currently expanding its range throughout riparian habitats in California. Between 1998 and 2002, 30 sites were examined along Putah Creek and American River

and the number of sites infested with the ant during that tim e period increased by a factor of 3 (Huxel, 2000; Holyoak and Talley, 2001). According to Huxel (2000), there was a negative correlation between th e observed presence of the ants and VELB exit holes on elderberry along Putah Creek in 1997. The Argentine ant may affect the success of VELB mating or feeding, or pr ey on eggs and larvae (Way et al. 1992). Due to the moisture requirements of the ants, riparian and irrigation areas may provide suitable habitats for the ant to thrive in (Huxel, 2000).

120Insectivorous birds, insectivorous lizards and the European earwig ar e potential predators of the VELB because they all forage on the stems of elderberry (Klasson et al. 2005). The European earwig is known to be a scave nger and omnivore. It may prey on VELB larvae because the earwig is known to feed on the larvae of tethered mealworms ( Tenebrio monitor) . The earwig is often found in urba n areas, and like the Argentine ant, also in riparian and irrigati on areas because of the availa bility of moisture (Klasson et al. 2005). According to Klasson ( et al. 2005), mitigation sites generally have the highest densities of European earwigs because of the associated irrigation. However, this fact has yet to be proven statistically (Klasson et al. 2005).

The host plant elderberry is threatened by the colonization of invasive species (Talley et al., 2006). Invasive woody speci es include: black locust ( Robinia pseudoacacia ), giant reed ( Arundo donax ), red sesbania ( Sesbania punicea ), Himalaya blackberry ( Rubus

armeniacus ), tree of heaven ( Ailanthus altissima ), Spanish broom ( Spartium junceum ), Russian olive ( Eleagnus angustifolia ), edible fig ( Ficus carica ), and Chinese tallowtree ( Sapium sebiferum )” (Talley et al., 2006). Non-w oody invasive species include ripgut brome ( Bromus diandrus ), foxtail barley ( Hordeum murinum ), Lolium multiflourum , and starthistle/knapweed ( Centaurea spp.). Non-woody species may affect elderberry establishment or germination, and increase fire risk. One study on Robinia pseudoacacia demonstrated a positive correlation between th e VELB and the black locust. However, this positive association wa s thought to be temporary as elderberry would soon be crowded out (Talley et al., 2006).

Other issues attributed to V ELB habitat decline include gr azing animals and park/forest management (Talley et al ., 2006). Browsing deer and cattle are known to feed on elderberry shoots and bark, and according to th e California Department of Fish and Game (CDFG) biologists, cattle “r eadily” forage on new elderberry growth (USFWS, 1984). Additionally, rodents may damage new sap lings, and voles have reportedly girdled elderberry shrubs at two diffe rent conservation banks (Talley et al. 2006). In some State and local parks, the clearing of undergrowth and the institution of lawns has reduced suitable VELB habitat. Similar practices o ccur in the few natural woodlands remaining, further reducing suitable habitat (USFWS, 1980).

12.2.1.3 Habitat Protection and Restoration

The number of riparian restor ation projects and protective ac tions in the Central Valley has increased in recent years (USFWS, 2006). The actions are categorized into one of the following three groups: the protection of existin g riparian habitats, the enhancement or restoration of riparian habitats plus the planting of elderbe rry shrubs, or the enhancement or restoration of riparian ha bitats without the planting of elderberry. Table 8.1 provides a summary of projects in which riparian habi tat was acquired or protected in the Central valley since 1980 (excerpted from Talley et al. 2006). The table shows that 22 agencies and organizations have prot ected approximately 50,000 acres of existing land. Table 8.2 provides a summary of projects in which riparian habitat was restored and elderberry

121were plated in the Central Va lley (excerpted from Talley et al. 2006). Seven agencies are responsible for 19 projects which have or ar e restoring 5,193 acres of habitat and planting 130,345 elderberry saplings. Ta ble 8.3 provides a summary of projects in which riparian habitat was restored, yet no elderberry were planted in the Central Valley (excerpted from Talley et al. 2006). This table reveals that 1,592 acres have been or are being restored.

Table 12.1: Summary of projects in which riparian habitat was acquired or protected in the Central Valley since 1980 (excerpted from Talley et. al. 2006). Project/Program Floodplain acres (approx.) Comments

Sacramento Valley:

Sacramento River Natural Wildlife Reserve (NWR) 11,000 May acquire up to 18,000 acres

The Nature Conservancy (TNC)

Sacramento ~3000 Many projects turned over to the

Sacramento River NWR Big Chico Creek Ecological Preserve, California State University (CSU) Chico

Research Foundation 4000

Fenwood Ranch, Shasta Land

Trust 2160 2.5 miles river frontage. Conservation

easement Gover Ranch/Bloody Island, Bureau of Land Management 800 Conservation Easement

Hamilton City levee setback 1500 [Bobelaine Sanctuary, Audubon] [400] [Acquisition in 1975 pre-dates listing (1978) but was then considered outside VELB range] Feather River Wildlife Area, California Depart. of Fish and Game (SDFG) 2500 Units flank Bobelaine Sanctuary [May predate listing]

American River Parkway 4600 Mu ch park area pre-dates listing

Consumnes River: Consumnes River Preserve, TNC and partners 5500 Approx. 40,000 acres non-floodplain

Stone Lakes NWR 4000 May acquire up to 18,200 acres San Joaquin Valley: San Joaquin River NWR 6600 May acquire up to 12,900 acres Partners for Fish and Wildlife,

Natural Resource Conservation Service (NRCS) 23+ miles river frontage. Conservation

easements

San Joaquin River Parkway ~2000 http://www.sjrc.ca.gov/docs/ Parkway_map_01-06.pdf Bobcat Flat, Friends of the

Tuolumne 300

Big Bend, Tuolumne River,

Natural Resource Conservation Service (easement) 250 Conservation easement

Grayson River Ranch, Tuolumne River, NRCS 137 Conservation easement

Mining Reach-7/11 Segment, Tuolumne River, Turlock Irrigation District 87 2.2 river miles. Don Pedro 1996 Federal Energy Regulatory Commission Settlement Agreement

Merced River Salmon Habitat Restoration Program Mostly for channel restoration

122Fine Gold Creek, CDFG 708 Kaweah River watershed, Sequoia Riverlands Trust 2200+ In fee and conservation easements

Kern River Preserve, Audubon

California 1000 Benefit to VELB not established

Total ~45,000

Table 12.2 Summary of projects in which riparian habitat was restored and elderberry were planted in the Central Valley (excerpted from Talley et al. 2006).
Project/Name Owner/ Manager Planted by River Acres # EB 1
planted Comments

Llano Seco USFWS River

Partners Sacramento 271 1472

Ord Bend USFWS River

Partners Sacramento 111 1616

Turtle Bay McConnell Arboretum, Turtle Bay Exploration Park River

Partners Sacramento 100 1323 Has FWS Biological Opinion 1-1-03- F-189, appears pure restoration Flynn USFWS TNC Sacramento 247 5605 Kopta State

Controller’s

Trust TNC Sacramento 105 2086

Lohman TNC Sacramento 20 882

Ohm USFWS TNC Sacramento 206 7613

O’Connor Lakes Ecological

Reserve CDFG River

Partners Feather 471 900 300-400 more plantings planned

Packer Island USFWS TNC Sacramento 175 7633

Partners for Fish

and Wildlife projects private Sacramento 700 Elderberry planted, # not

recorded

Phelan Island USFWS TNC Sacramento 117 2730

Pine Creek USFWS TNC Sacramento 270 6781 Princeton Ferry USFWS TN C Sacramento 44 2700

Rio Vista USFWS TNC Sacramento 799 36735

River Unit California Department of

Water Resources (DWR) TNC Sacramento 27 486

Ryan USFWS TNC Sacr amento 164 6164 Sam Slough DWR TNC Sacramento 72 7200

Shaw DWR TNC Sacramento 11 383

Southam USFWS TNC Sacramento 65 2574

Sul Norte USFWS TNC S acramento 46 1271

Mohler Tract II USFWS River

Partners Stanislaus 35 520 Anadromous

Fish Restoration Program McHenry Ave

Recreation Area US Army Corps of Engineers River

Partners Stanislaus 32 512

Merced NWR USFWS USFWS San Joaquin 40 160

San Luis NWR USFWS USFWS San Joaquin 210 840 San Joaquin River

NWR USFWS River

Partners San Joaquin 800 32512

123Mining Reach7/11 Segment Turlock Irrigation

District HART

Restoration Group Tuolumne 87 160 2.2 river miles.

Don Pedro 1996 Federal Energy Regulatory

Commission

Settlement Agreement

Totals: 5,193 130,345

1 EB = Elderberry

Table 12.3: Summary of projects in which ripa rian habitat was restored yet no elderberry were planted in the Ce ntral Valley (excerpted from Talley et al . 2006).
Project/Name Owner/ Manager Planted by River Acres Comments

Battle Creek CDFG River

Partners Battle Creek 21

Beehive Bend CDFG River

Partners Sacramento 59

Big Bend Tuolumne R.,

Preservation

Trust River

Partners Tuolumne 250 Planning in 2003

Butler Slough CSU Chico

Restoration

Foundation River

Partners Sacramento 54

Cottonwood Creek CDFG River

Partners Cottonwood

Creek 15

Del Rio CDFG? 1 River

Partners Sacramento 259 Acquisition. Adj. to

Llano Saco NWR unit.

Future SHA? 1

Drumheller Slough USFWS River

Partners Sacramento 135

Gianella Landing/Beard CDFG River

Partners Sacramento 20

Howard Slough, Butte

Basin CDFG River

Partners Butte Creek 51

Jacinto CDFG River

Partners Sacramento 37

Moulton Weir CDFG River

Partners Sacramento 46

Partners for Fish & Wildlife, NRCS projects Private San Joaquin 23+ river miles

Pine Creek CDFG River

Partners Sacramento 235

Princeton CDFG River

Partners Sacramento 34

River Ranch Private River

Partners Sacramento 3

Sacramento R., Big Chico Ck., Mud Ck., [confluence] Cal. Dept. of

Pesticide Regulation (CDPR)? 1

[Bidwell-Sac RSP] TNC Sacramento 217 Acquisition and restoration planning only at this stage? 1

124Thomas CDFG River

Partners Sacramento 19

Merced River Salmon

Enhancement CDWR/CDFG Merced unknow

n Planning stage for vegetation? 1

Grayson River Ranch Natural

Resource

Conservation

Service (easement) Tuolumne 137

Total: 1592

1 Question marks appear in the 5-Year Review (USFWS, 2006), and no explanation is provided regarding their meaning.

Each riparian restoration and enhancement project will not necessarily benefit the VELB. Certain constraints limit the VELB’s ability to disperse to or inhabit certain areas, so actual advantages to the beetle vary with site. Elderberry plants need to be mature enough so that they provide a dependable hab itat from year-to-year. The colonization of the beetle may be difficult to overcome becau se of a barrier or dispersal limitation. The site should also be ecologically suitable for elderberry spec ies over the long term (USFWS, 2006). For example, although some re storation projects do not plan on directly introducing elderberry, the projects may s till serve the VELB if restored areas can support long term recruitment and survival of the hostplant. Elderberries will likely colonize the area, but will do so at a slower ra te than if it had been directly planted (River Partners, 2003, River Partners 2004b). Factor s such as the distance from known beetle locations, suitability of the habitat for el derberry shrubs, and post-placement monitoring of the beetle determine the success of each restoration project (USFWS, 2006).

Safe Harbors Agreement and other land owner incentives The Safe Harbor Agreement was develope d to “encourage landowners to enhance, restore, or otherwise encourage listed species to use their property for foraging, breeding, resting, or other activities” (USFWS, 2006). The program accomplishes this goal by allowing private property owners to restore or maintain thei r property for the benefit of endangered species through issuance of Sec tion 10 permits, without incurring additional regulatory restrictions (EDF, 2008; USFWS, 2006). The lan downer opines to return the property to its “baseline condition”, the mutu ally agreed upon state of property between the USFWS and landowner (USFWS, 2006). Three Safe Harbor agreements have so far been made for the VELB: 7,450 acres from the Burrows and Big Bluff Ranches in Tehama County, a programmatic agreemen t for up to 3,500 acres along the Mokelumne River, and 259 acres in Glenn County (USFWS, 2006). Other landowner incentive programs are available to private owners a nd organizations that want to support the

restoration of VELB habitat without the ensuing negative consequences (USFWS,2006).

12.2.2 Baseline Status

The current distribution of the VELB ranges from the southern portion of Shasta County south to Fresno County in the San Joaquin Vall ey (Barr, 1991). Records primarily based

125on exit holes indicate that there are roughly 190 locations in the Central Valley where the beetle is known to occur (Ca lifornia Department of Fish and Game, 2006). This number is up from less than 10 locations in 1980, along the American River, Putah Creek, and Merced River in the Central Valley (USFWS , 1980). Historically, there have been records indicating the beetle’s presence in Kern County, but current observations of living specimens have yet to be found (Talley et al. 2006). However, an increase in known locations can primarily be attributed to an increased effort to look for the beetle. Also, the number of locations is not repres entative of the known populations, as there are 24 records of VELB occupancy located within 2 miles of the American River (no exact locations specified) (CDFG, 2006).

A suite of occupancy surveys have been conducted to gain a better understanding of VELB population numbers, densities, and lo cations. A survey in 1982 identified one individual at Rossmoor Bar from among “ 1,247 elderberries along the American River from Rancho Cordova to Johnson Industrial Park in Sacramento” (USFWS, 1984). However, emergence holes were found on 27% of the elderberry trees. Similarly, no adults were found from a survey of 228 el derberries along Putah Creek, spanning Solano and Yolo Counties, yet 44% of the trees had exit holes (USFWS, 1984). The frequency of VELB presence along the American River was found to be 20-50%, while the frequency was less than 20% along the Sacramento River (LSA, 2004). “VELB occupancy ranged from 2.9% in a non-ripari an scrub area to 7-11.2% of shrubs in riparian reaches of Putah Creek and the Amer ican River” (Talley et al., 2006). “Beetle density averaged about 2 new exit holes per ‘site’” (Talley et al., 2006). The VELB is generally found “with 1-2 exit ho les per occupied shrub or per site and occupancy rates of 2-10% of shrubs or 25% of sites” (Talley et al. in press; Talley et al., 2006). “Neither pruning nor topping affected the colonization or loss of VELB from shrubs, or the length of time that a shrub was either occupied or unoccupied by VELB” (Talley et al., 2006).

It is worth mentioning the factors that may af fect the accuracy of population estimates. The two main types of survey error include overestim ates due to misidentification of exit holes and underestimates due to difficulty of locating exit holes. Beetle sightings are rare and exit holes provide a proxy for observing beet le presence. These exit holes could be misidentified as being created by the VELB, when they were actually produced by such animals as horntails, wood wasps (Siricidae), or solitary bees. Locating the exit holes proves to be even more difficult because of dense shrubbery and the low number of holes per tree. Along the American River, exit ho les per tree average from 1.6 in non-riparian habitats to 2.2-2.9 in riparian habitats (Talley et al. in press; Talley et al. 2006). Locating the beetle exit holes, as opposed to misidentifying the holes, is thought to have a greater influence on our understanding of the beet le’s distribution and numbers (Talley et al. 2006).

Population Dynamics Little information exists on the range-wide population trends of the VELB. One longterm data set was acquired by Collinge et al. (2001). The data set examined a majority of locations surveyed by Barr (1991). Both st udies observed the VELB at roughly 20% of the sites and on approximately 25% of th e elderberries examined. Although the

126proportions of occupancy between the two studi es appear similar, the study by Corringe

et al. actually found fewer occupied sites and groups of shrubs (Collinge et al. 2001). Elderberry density and the number of examined sites containing elde rberry had decreased since the study conducted by Barr (1991) (Collinge et al. 2001). Another study, although not long-term, recorded occupancy rates at 64% for the Sacramento River between Sacramento and Red Bluff (Lang et al. 1989). However, 64% was an average between the sites. Occupancy rates ranged from 28% between Sacramento and Colusa to 94%

between Chico and Red Bluff. This variati on was attributed to greater flood control efforts along the southern reach of the Sacramento River, reducing the width of the riparian corridor (Lang et al. 1989). However, a straight comparison of occupancy rates is difficult because the methodologies utilized by Corringe et al. (2001) and Barr (1991) are different from those utilized by Lang et al. (1989).

While VELB habitat continues to be lost, today that loss is typically accompanied by compensatory measures (Talley et al. 2006). However, uncertainty remains about the

extent to which natural environments are co mpensated for by restor ed habitats (Talley et
al. 2006). Compared to the historic extent of habitat reduction, the total area of restored and enhanced habitats still remains quite sm all. Restoration and mitigation efforts are valuable, however, with the hope that proactiv e efforts will provide ha bitat for persistent and sustainable metapopulations. Mitigation e fforts to replace elderberry shrubs more than compensate for the number of elderberry lost to development, but the quality, size, and persistence of these shr ubs is questionable (Talley et al. 2006). According to a survey by Talley et al., the VELB occupied 47% of now developed habitat, while the beetle now occupies 43% of the accompanying mitigation habitats. One possibility for the discrepancy in percentages is that a si gnificant, unquantified num ber of elderberries may be planted in upland, non-riparian, area s which are not preferred habitats for the VELB. Incidentally, even with an overall ne t population loss, there is not a strong trend toward decline or recovery (Talley et al. 2006).

12.3 REFERENCES

Literature Cited

Barr, C.B. 1991. The distribution, habitat, and status of the valle y elderberry longhorn beetle, Desmocerus californicus dimorphus. U.S. Fish and Wildlife Service, Sacramento, California. 134 pp. Available online at: http://www.fws.gov/sacramento/es/docu ments/VELB_Report/velb_report.htm (Accessed on July 25, 2008).

California Department of Fish and Game. 2006. California Natural Diversity Database,

Available online at: http://www.dfg.ca.gov/whdab/html/cnddb.html

.

Collinge, S. K., M. Holyoak, C. B. Barr, and J. T. Marty. 2001. Riparian Habitat

127Fragmentation and population persistence of the threatened valley elderberry longhorn beetle in central California. Biological Conservation 100:103-113.

Environmental Defense Fund (EDF). 2008. Pr oviding a safe harbor for endangered species on private land. Environmenta l Defense Fund, New York, NY 10010.

Available online at: http://www.edf.org/article.cfm?ContentID=399 (Accessed on July 28, 2008).

Holyoak, D. A. 1998. Effect of Argentine ant invasions on ground-dwelling arthropods in northern California riparian woodl ands. Oecologia (Berlin) 116:252-258.

Huxel, G. R. 2000. The effect of the Argentin e ant on the threatened valley elderberry longhorn beetle. Biological Invasions 2:81-85.

Klasson, M., M. holyoak, and T.S. Talley. 2005. Valley elderberry longhorn beetle habitat management plan: Phase 2 Annua l Report to the National Fish and Wildlife Foundation. Sacramento County Department of Regional parks, Recreation and Open Space, Sacramento.

Lang, J., J. D. Jokerst, and G. E. Sutter. 1989. Habitat and populat ions of the valley elderberry longhorn beetle along the Sacr amento River. USDA Forest Service General Technical Report PSW 110:242-247.

LSA Associates, Inc. 2004. Valley Elderbe rry Longhorn Beetle. Solano HCP/NCCP. Solano County Water Agency. Species Descriptions. Available online at: http://www.scwa2.com/hcp/Final%2 0Draft%202.0/Appendices/APPX%20BSpecies%20Descriptions/Valley%20 Elderberry%20Longhorn%20Beetle.pdf (Accessed on July 24, 2008).

River Partners. 2003. River Partners 2003 A nnual Report. River Partners, Chico, California. 16 pp.

River Partners. 2004a. Survey of planted elderberry on Sacramento River National Wildlife Refuge riparian restoration site s for use by valley el derberry longhorn beetles, Tehama, Butte and Glenn County, Ca lifornia. Report prepared for: U.S. Fish and Wildlife Service. Helen Swagerty and Scott Chamberlain, authors. River Partners, Chico, Claifornia.

River Partners. 2004b. Riparian habitat restor ation, Sacramento River Wildlife Area, Mouton Weir Unit. Colusa County, Californi a. Final Report. Michelle Cederborg, author. River Partner, Chico California.

River Partners. 2004c. Riparian habitat restora tion, Sacramento River Wildlife Area, Pine Creek Unit. Glenn and Butte County, Calif ornia. Final report. Helen Swagerty and Michelle Cederborg, authors. Ri ver Partners, Chico California.

128River Partners. 2004d. Riparian habitat restor ation, Upper Butte Basin Wildlife Area, Fields 229 and 232 of the Howard Slough Unit. Glenn County, California. Final report. Helen Swagerty, aut hor. Chico, California.

Schonewalk-Cox, C.M., S. M. Chambers, B. McBryde, and L. Thomas (eds.). 1983 Genetics and conservation. Benjamin /Cummings, Menlo Park, CA.

Talley, T.S., E. Fleighman, M. Holyoak, D. Mu rphy, and A. Ballard. In press. Rethinking a rare-species conservation strategy in an urbanizing landscape. The case of the valley elderberry longhorn beet le. Biological Conservation.

Talley, T.S., D. Wright, and M. Holyoak. 2006. Assistance with the 5-Year Review of the Valley elderberry longhorn beetle ( Desmocerus californicus dimorphus ). United States Fish and Wildlife Service, Sacramento. Available online at: http://www.fws.gov/sacramento/es/docu ments/VELB_5yr_review_Talley_etal.pd

f (Accessed on July 24, 2008).

U.S. Fish and Wildlife Service (USFWS). 1980. Listing the Valley Elderberry Longhorn Beetle as a Threatened Species with Cr itical Habitat. Federal Register 45 (155):52803-52807. Available online at: http://ecos.fws.gov/docs/ federal_register/fr449.pdf (Accessed on July 24, 2008).

U.S. Fish and Wildlife Service (USFWS). 1984. Valley Elderberry Longhorn Beetle Recovery Plan. U.S. Fish and Wild life Service, Portland, Oregon. 62 pp.

Available online at: http://www.fws.gov/sacramento/es/re covery_plans/velb_recovery_plan.pdf (Accessed on July 24, 2008).

U.S. Fish and Wildlife Service (USFWS). 1996. Letter to the U.S. Army Corps of Engineers with the Subject - Programmatic Formal Consultation Permitting Projects with Relatively Small Effects on the Valley Elderberry Longhorn Beetle

Within the Jurisdiction of the Sacramen to Field Office, California (Corp File #199600065). U.S. Fish and Wildlife Service, Sacramento Field Office, Sacramento, California. Available online at: http://www.fws.gov/sacramento/es/do cuments/velb_coe_prog_text.htm (Accessed on July 24, 2008).

U.S. Fish and Wildlife Service (USFW S). 2006. 5-Year Review: Summary and Evaluation for the Valley Elderberry Longhorn Beetle ( Desmocerus californicus dimorphus ). U.S. Fish and Wildlife Serv ice, Sacramento Field Office, Sacramento, California. 28 pp. Available online at: http://ecos.fws.gov/docs/five_year_review/doc779.pdf (Accessed on July 24, 2008).

U.S. Fish and Wildlife Service (USFWS). 2007 a. Species Account: Valley Elderberry

129Longhorn Beetle ( Desmocerus californicus dimorphus ). Sacramento Fish and

Wildlife Office. Available online at: http://www.fws.gov/sacramento/es/animal_spp_acct/velb.pdf (Accessed on July 24, 2008).

Way, M.J., M. E. Cammel, and M. R. Paiv a. 1992. Studies on egg predation by ants (Hymenoptera: Formicidae), esp ecially on the eucalyptus borer Phoracantha semipunctata (Coleopteral Cermabycidae) in Portugal. Bulletin on Entomological

Research 82:425-432.

130