ATTACHMENT III: 

BASELINE STATUS AND CUMULATIVE EFFECTS FOR THE 

SAN FRANCISCO BAY LISTED SPECIES 

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TABLE 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 environment 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 research 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 environment 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: Impoundments and Water Diversions................ 36 

4.2.1.4 Gravel Mining........................................................................................... 37 

4.2.1.5 Agriculture Developments........................................................................ 37 

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4.2.1.6 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 continued existence within 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 the 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 continued existence within 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 continued existence within the action area............. 63 

7.2.1.1 Habitat Destruction, Degradation, 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 the 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 environment within the action area ........................ 75 

8.2.1.1 Habitat alteration, curtailment, and degradation...................................... 76 

8.2.1.2 Changes in food Organisms..................................................................... 79 

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8.2.1.3 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 environment 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 environment 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 anthropogenic 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 environment within the action area .................... 110 

11.2.1.1 Habitat Destruction, Degradation, 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 ELDERBERRY LONGHORN BEETLE............................................... 118 

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

11.2 ENVIRONMENTAL BASELINE .................................................................... 118 

12.2.1 Factors affecting species environment 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 

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1: ALAMEDAWHIPSNAKE 

1.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 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 (Act). The numerous nonfederal actions that are reasonably certain to occur within the action area consist of urban 

and suburban development, construction and recreational use of paved and unpaved 

roads, fire suppression, inadequacy of regulatory mechanisms, and inappropriate grazing 

practices. Many of these factors are linked or act synergistically 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 domestic and feral cats. These potential impacts 

further degrade Alameda whipsnake suitable habitat by promoting human interference 

and increased predatory pressures. Compounded with the other non-federal actions, 

populations become more susceptible to the accumulation 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 species, its habitat, and 

ecosystem, within the action area. The environmental baseline is a snapshot of the 

Alameda whipsnake’s status at this time. However, the baseline condition of the assessed 

whipsnake’s habitat varies across locations and within each critical habitat unit. Details 

of the Alameda whipsnake’s habitat description and known locations are included in 

Attachment III. Given the large amount of habitat and extent of the action area included 

in this assessment, the discussion of environmental 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 listing in 1997, failure to implement appropriate 

fire management practices on public lands and 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 development resulting in 

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

threat to all six critical habitat units (USFWS, 2006). Additional anthropogenic and 

natural factors listed as directly and indirectly affecting the species included the effects of 

fire suppression, inappropriate grazing practices, predation, 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 Alameda whipsnake in the action area. 

1.2.1.1 Urban development 

Urban development is determined to be the greatest threat to all six critical habitat units 

(USFWS, 2006). Urban development and associated highway and road construction 

cause rapid habitat loss, degradation, and fragmentation, the primary reasons for the 

Federal and State listing of the species (USFWS, 2003). Urbanization 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 construction also result in habitat fragmentation and has led to the 

almost complete disseverment of the five remaining subpopulations by preventing 

movement and migration (USFWS, 1997). 

McGinnis (1992) and the United States Fish and Wildlife Service (USFWS) have 

documented colonies throughout the species’ range that are subject to the pressures of 

residential developments (USFWS, 1997). In the Hayward-Pleasanton Ridge 

population, there are a number of housing developments that could potentially cause 

destruction, modification and/or fragmentation to the species’ suitable habitat range 

(USFWS, 1997). These developments include 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 habitat, 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 Project land being dedicated to the East Bay Regional Park 

District (EBRPD), increased public use and related activities will compound the potential 

effects on suitable habitat (USFWS, 1997). Towards the south of the HaywardPleasanton Ridge population are the sites of two proposed housing developments: the 

1,580 ac (632 ha) Hayward 1900 project and the 391 ac (156 ha) Bailey Ranch project 

(USFWS, 1997). Both of the project sites were occupied by the Alameda whipsnake 

when the developments were proposed, and 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-Pleasanton population (USFWS, 1997). Undeveloped 

areas such as trails and vineyards are proposed for the Hayward 1900 project, but these 

open areas could also result in habitat fragmentation for the Alameda whipsnake 

(USFWS, 1997). 

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Several developments are proposed for the Oakland-Las Trampas population that may 

impact Alameda whipsnakes and their habitat (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 Neighborhood 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 habitat (USFWS, 1997). Although some of these projects have or may 

reserve habitat suitable for the Alameda whipsnake, 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 Diablo-Black Hills, Tilden-Briones, and 

Sunol-Cedar populations (USFWS, 1997). The expanding cities of Pittsburg, Oakley, 

Brentwood, and Antioch are expected to increase the degree of public visitation, and thus 

disturbance, to the nearby EBRPD parks and 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 associated 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 associated impacts from the proposed Dougherty 

Valley (6,000 ac (2,400 ha)) and Tassajara Valley (4,000 ac (1,600 ha) projects (USFWS, 

1997). Increased population pressure from the north will be caused by the approved 800-

unit Franklin Canyon (980 ac (392 ha)) projects (USFWS, 1997). Additional 

developments are approved or proposed adjacent to the Sunol-Cedar population in the 

rapidly growing centers near Dublin and Pleasanton 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 fragmentation include the loss of native plants and animals, 

invasion of exotic species, increased soil erosion, and decreased water quality (USFWS, 

2003). Fragmentation leads to habitat loss and isolation, which increase the likelihood of 

genetic complications, such as genetic drift 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 large territories; and (4) exist at low densities (USFWS, 1997). 

The Alameda whipsnake is confronted with particularly high risk because the species can 

be characterized by all of these attributes: the species is known to associate with native 

Diablan sage scrub (attribute 1), to forage in adjacent grasslands (attribute 2), and to 

migrate along riparian corridors (attribute 3) (USFWS, 1997). Although the home range 

of the Alameda whipsnake is typically between 5 and 20 ac (2 and 9 ha), not large in 

comparison to some animal ranges, the narrow habitats in some areas may impose 

significant constraints on the species (USFWS, 1997). Because the Alameda whipsnake 

is currently listed as threatened, low densities (attribute 4) are also expected (USFWS, 

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1997). Due to the disproportionate effects of urbanization, some populations of the 

species are more prone to low densities than others (USFWS, 1997). 

1.2.1.2 Fire suppression 

Increasing urbanization prompted the state of California to adopt an avid fire suppression 

policy over 50 years ago (USFWS, 2003). The policy has disrupted the natural 

disturbance regime of the chaparral/scrub community, and many chaparral habitats in the 

east Bay area have not burned for several decades (USFWS, 2003). To provide the 

necessary stimulus for new sprouting, seedling recruitment, and seed dispersal, a cyclical 

fire regime of 10 to 30 years is required (USFWS, 1997). In the absence of reoccurring 

disturbance, these chaparral/scrub communities are becoming decadent (in a state of 

decline) and senile (reduced to a featureless 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 Alameda whipsnake (USFWS, 1997). 

Fire suppression exacerbates the effects of wildfires through the buildup of fuel 

(underbrush and woody debris), creating conditions 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 and populations are likely to sustain the 

heaviest losses (USFWS, 1997). Fire suppression indirectly affects the Alameda 

whipsnake by altering plant compositions and structure of suitable habitat (USFWS, 

1997). Infrequent fires allow the establishment of closed canopies and thus cooler 

understory environments. Both the Alameda whipsnake and its lizard prey base are 

potentially affected by cooler habitats, with Alameda whipsnakes being particularly 

sensitive because of their higher mean active body temperature (33.4°C) and higher 

degree of body temperature stability (stenothermy) compared to other snake species 

(USFWS, 1997; USFWS, 2006). Alameda whipsnakes maintain a higher temperature by 

using partially open and low growing shrub communities that provide predator protection 

and allow sunlight penetration (USFWS, 1997). This preference is supported by survey 

studies showing that Alameda whipsnakes are less likely to be found in closed canopy 

environments (USFWS, 1997). Fire suppression has also led to the encroachment of nonindigenous and ornamental trees into grassland habitats, further increasing fuel loads in 

and around Alameda whipsnake 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 whipsnake: 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). 

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Increased 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 habitats and an increase in predators using these 

areas (USFWS, 2006). For example, predation and harassment from domestic and feral 

cats (Felis domesticus) increases as urban development infringes upon Alameda 

whipsnake habitat (USFWS, 2003). The growing movement to maintain feral cat 

populations in parklands intensifies 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 species may be especially acute if urban 

developments directly abut Alameda whipsnake habitat (USFWS, 2003). Special 

management of nonnative predators may be required within all six critical habitat units 

(USFWS, 2006). 

1.2.1.4 Grazing practices 

Livestock grazing and inappropriate grazing practices may threaten the Alameda 

whipsnake (USFWS, 1997; USFWS, 2006). Studies have suggested that grazing east of 

the Coast Range has impacted suitable habitat for the Alameda whipsnake (USFWS, 

1997). Livestock grazing becomes detrimental to the species when it significantly 

reduces or eliminates shrub and grass cover (USFWS, 1997). According to these studies, 

the Alameda whipsnake along with other snake species avoid such open areas because of 

magnified predatory risk and lack of prey (USFWS, 1997). Inappropriate grazing 

practices include overgrazing and burning or bulldozing to remove 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 pressure 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, increasing fire risk, and reducing whipsnake prey base (USFWS, 

2003). Hybridization, which could decrease genetic variability, is also 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 

9
can 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 vegetation 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 endangered within the foreseeable future 

(USFWS, 1997). The USFWS cited the failure to implement adequate fire management 

practices and sustain suitable habitat as key factors in the continued 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 Dynamics section will cover these factors 

threatening the survival of each subpopulation 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 the Inner Coast Ranges in western and central 

Contra Costa and Alameda Counties, with occurrences additionally recorded in San 

Joaquin and Santa Clara Counties (USFWS, 1997, 2003, and 2006). The current 

distribution of the subspecies has been reduced to five separated ranges within a 

fragmented regional metapopulation, all occurring on private or public, non-Federal land, 

with little or no interchange due to habitat loss, alteration, and fragmentation (USFWS, 

2003). These ranges correspond to the designated 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 Cedar Mountain Ridge, in Alameda County 

(Sunol-Cedar Mountain population) (USFWS, 1997 and 2003). 

The Tilden-Briones population is currently threatened by habitat 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-Briones population is further at risk from 

catastrophic wildfire and from nonnative invasion (eg. Eucalyptus) into chaparral and 

10
scrub communities (USFWS, 2003). Due to partial overlap of the habitat with regional 

parklands and municipal watersheds, regional preservation and land management to the 

benefit of the Alameda whipsnake may be possible (USFWS, 2003). 

The Oakland-Las Trampas population is imperiled by the decadence of chaparral/scrub 

stands, high risk of catastrophic wildfires, and habitat loss and fragmentation from urban 

development (USFWS, 2003). 

The Hayward-Pleasanton Ridge population is most susceptible to extirpation. Similar to 

the other subpopulations, the Hayward-Pleasanton Ridge population is threatened by 

urbanization (USFWS, 2003). Unlike any of the other five areas, however, the open 

space and conservation land within this habitat 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/rural development, and land uses (eg. mining) that are at 

odds with Alameda whipsnake suitable habitat (USFWS, 2003). This population is a 

good candidate for recovery considering the location of public lands, the actions of 

private nonprofit organizations regarding wildlife corridors, 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 relatively low, although the demand for housing 

developments is increasing. Unauthorized collection may be most acute in the southern 

region of the population. The area attracts reptile enthusiasts and collectors because of its 

remote roads and diversity of native reptiles. 

The Caldecott Tunnel corridor links the Tilden-Briones and Oakland-Las Trampas 

populations, and the Niles Canyon-Sunol corridor connects the Hayward-Pleasanton 

Ridge and Sunol-Cedar Mountain 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, and revegetating the area is 

still in progress (USFWS, 2003). Future plant 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 various physical barriers that could 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 cultivation or mining (ie. gravel) and suitable 

vegetation for the Alameda whipsnake is limited (USFWS, 2003). 

Habitat Conservation Plans

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Habitat Conservation Plans are defined in Section 10 of the Endangered 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 Incidental 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 Costa County for the duration of 

30 years (Species Profile). 

1.3 REFERENCES 

Literature Cited

Species Profile: Alameda Whipsnake (=striped racer) (Masticophis lateralis 

euryxanthus). U.S. Fish and Wildlife Service (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 Silverspot 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 (USFWS). 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 (USFWS). 2005. Habitat Conservation Plans: 

Section 10 of the Endangered Species Act. Available online at : 

http://ecos.fws.gov/docs/conservation_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.access.gpo.gov/2006/pdf/06-

8367.pdf (Accessed on December 10, 2008). 

12
13
2: BAY CHECKERSPOT BUTTERFLY 

2.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 Endangered Species Act (Act). The numerous nonfederal actions that are reasonably certain to occur within the action area consist of urban 

and suburban development, infrastructure expansions, commercial and private 

construction, agriculture, research, pest (gopher) control, and activities related to climate 

change. Many of these factors are linked or act synergistically and create complex 

consequences for the BCB. For example, urban and suburban developments encourage 

the expansion of infrastructure and intensify the effects of climate change. These 

developments contribute to habitat loss and facilitate habitat fragmentation, weakening 

the strength and stability of populations. Compounded with the other non-federal actions, 

populations become even more susceptible 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 the 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, the baseline condition of the assessed butterfly’s 

habitat varies across locations and within each critical habitat unit. Details of the bay 

checkerspot butterfly’s habitat description and known locations are included in 

Attachment III. Given the large amount of habitat and extent of the action area included 

of this assessment, the discussion of environmental baseline includes a general discussion 

of factors and a few listed projects that may affect the BCB within 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. The majority of information included in the 

environmental baseline section is a summary of information on the bay checkerspot 

butterfly presented in the Recovery Plan for Serpentine Soil Species of the San Francisco 

Bay Area (USFWS, 1998), and the Designation of Critical Habitat for the Bay 

Checkerspot Butterfly (Euphydryas editha bayensis); proposed rule (USFWS, 2007). 

2.2.1 Factors affecting species environment within the action area 

A number of factors affect the species environment, defined by a habitat comprised of 

serpentine, or serpentine-like or -derived soil. This soil is formed from weathered 

ultramafic rocks, serpentinite, dunite, and peridotite, and presents harsh environments for 

14
plant 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). This native environment is primarily affected 

by destruction and degradation, and infestations of native species (accompanied by air 

pollution). Factors affecting the species include overutilization for research and private 

purposes, control of gophers, vehicular disturbance, 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 influential factors affecting the BCB 

and is caused primarily by urban and suburban 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 stepping-stone areas, small patches in between suitable habitat, and 

makes recolonization and persistence of metapopulations difficult (USFWS, 1998). Prior 

to BCB listing, two primary habitats thought to support persistent “core” populations 

were lost to housing and infrastructure 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 occur but not on serpentine soil). Extirpation was 

recorded to affect 29 of 32 probable secondary habitats, 5 of 8 known secondary habitats, 

at least 5 of 6 known marginal habitats, and over 9 other 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 County, 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 Mateo County have now been divided into 11 

smaller units (Ehrlich, 1961, 1965). Some of these units are separated by a 6- or 8-lane 

freeway, which greatly hinders trans-patch movement and promotes populations to live in 

isolation. A BCB population on San 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 significant population (Ehrlich and Murphy, 1987). 

 

15
Urban 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 number of urbanization projects potentially 

impacting the BCB. Technical assistance was required for eight projects in 1995 and 

1996, and 5 projects required informal consultations with the USFW. At the time the 

Recovery Plan for the Serpentine Soil Species (including the BCB) was released, four 

projects were proposed or currently proposed that would adversely affect serpentine 

grassland. These four projects were Cerro Plata, Metcalf 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. The project area incorporated 232 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 (HCP) (a conservation plan developed by nonFederal parties applying under section 10 of the Act for a permit for incidental taking of 

listed species) is being crafted by the site owner and consultants to revise the 

development proposal for the site (USFWS, 1998). 

Metcalf Road

The proposed project in the City of San Jose would widen and straighten a portion of 

Metcalf Road. The impacted area would include serpentine habitats and affect the 

associated serpentine plant and animal species that are threatened or rare, and would 

increase road kills of the BCB. The Federally listed species, including the California redlegged frog (Rana aurora draytonii), would also be vulnerable to the effects of the 

project. The expanded road would facilitate human access to bay checkerspot core 

habitat: the Kirby, Metcalf, and San Felipe populations. The USFWS has recommended 

that the U.S. Army Corps of Engineers consult 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 interests of the YCS Investments of San Francisco 

and the owners of the Richmond Ranch, that together wish to create a planned residential 

community not exceeding 2,450 housing units, a golf course, resort, and other 

miscellaneous developments. The extension of the 735-hectare (1,817-acre) includes 

suitable serpentine habitat for the BCB Metcalf population (City of San Jose, 1997). 

Calero Lake Estates

16
Not much information has been provided on the Calero lake Estates project. The 

available information states that the project is an incomplete housing subdivision in the 

southern Santa Teresa Hills, situated in contact with the Santa Teresa County Park. Bay 

checkerspot are known to occur in the serpentine habitat in this location and are 

vulnerable to the past and future developments (USFWS, 1998). 

 

In addition to the well-described urbanization projects above, other developments in 

serpentine areas could potentially impact the 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 County HCP, and the Court of Appeals 6th

district found that the City’s zoning did not have to be consistent with the general plan 

(Juarez et al. v. City of San Jose et al. (6th 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 influential factors affecting the 

BCB. Despite the inhospitable conditions of serpentine environments, non-natives are 

still capable of colonizing the area. Non-native grasses have been observed to choke out 

BCB host plants in the Edgewood Natural Preserve (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 pollution facilitates the spread of non-native 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 thick patches of vegetative material (thatch) 

that inhibits growth of the native plant species (Huenneke et al. 1990, p.488). Thatch 

threatens the host plants of the bay checkerspot 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 monitoring program, Stanford University has 

investigated the biology of the BCB since 1960. The research has been carried out on the 

17
Jasper 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 average, 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 environmental variability. The study indicated, 

however, that the removal increased the risk of population extinction, from a negligible 

risk to a 15 percent probability over 30 years (depending 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 handling 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 most likely affect those BCB populations that 

are small or have been reduced by natural or artificial 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 presence of gophers and BCB survival. A study 

by Singer (1972) noted that BCB larvae can survive later into 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 BCB larval host plants to stay green and 

edible longer when located on or nearby soils recently tilled by gophers (Singer, 1972, p. 

75; Murphy et al. 2004, p. 26). Another suggestion was 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 fourth instar since the larval host plants stay 

greener for longer (Huenneke et al., 1990, p. 490). 

A negative correlation exists between vehicles and BCB individuals. Bay checkerspot 

mortality results from direct vehicular strikes 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 subsequently observed (USFWS, 2007). Although only 50 

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

18
fire were implicated in their extirpation, wildfires are still considered a threat to the BCB. 

Prescribed burns, however, are regarded as potentially effective tools to combat invasion 

of non-natives and stimulate growth of species adapted to the disturbance. However, 

benefits of burn regimes on serpentine grasslands are not well documented and have been 

provided by monitoring studies made possible after wildfires. An experimental 

prescribed burn was conducted on a small segment of Coyote Ridge in 2006, but the 

benefits to the native species, including the BCB, are not yet known (USWFS, 2007). 

A limited amount of grazing is considered beneficial to BCB habitat, while over- or 

under- grazing threatens the survival 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 Francisco Bay Area is currently disputed, but any 

deviation from current conditions would most likely affect the bay checkerspot (Murphy 

and Weiss, 2002). Forecasted change scenarios impacting the BCB include wetter and 

warmer, wetter and cooler, drier and colder, and changes in the timing of rainfall. The 

BCB would likely be sensitive to weather extremes because its developmental 

requirements and host plants’ survival depends on the climate. The largest and 

potentially most viable population, the Kirby Bay population, is not well-buffered against 

changes in temperature or precipitation. 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 and 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 experienced more severe and long-lasting droughts 

in the past millennium than were ever recorded in history (Stine, 1994). The BCB high 

reproduction potential indicates the species is well-adapted to the area, as the bay region 

has been its home for a long time, but its poor resilience after recent weather extremes 

may be due to other, probably human-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 occupied the area around the San Francisco Bay, 

19
spanning from San Bruno Mountain and Twin Peaks in the west, to Contra Coast County 

in the east, and south through Santa Clara 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 Canyon and Morgan Territory areas), Alameda 

County (Oakland Hills), San Francisco County (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 Diversity 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 range 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 status of these subspecies is unknown at this 

time. Even though the BCB is patchily distributed, two large metapopulations have been 

identified. These occur in Santa Clara and San Mateo Counties (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 roughly 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 Clara core areas are located along a ridge 

immediately east of Santa Clara Valley, designated 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 each 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” population. These four core areas, comprising the 

Santa Clara County metapopulation, 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 being located on a smaller area, with smaller 

and poorer quality secondary habitats surrounding 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 satellite populations that 

generally occur on smaller or of lesser quality 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 particularly important to fields of population 

and conservation biology and ongoing studies from the 1960s have generated significant 

data. Further, satellite populations act as stepping stones for dispersal. Tulare Hill 

appears to be a stepping stone habitat for BCB dispersal across Santa Clara Valley. 

Finally, secondary populations help protect populations against complete extirpation after 

unforeseen environmental disasters: fire, extreme weather, air pollution, or climate 

20
change. While core areas may be the targets of catastrophic events, secondary 

populations may survive to recolonize the formerly inhabited areas (USFWS, 1998). 

Population Dynamics 

Since its listing in 1987, the distribution and population size of the bay checkerspot has 

changed dramatically. Since the critical habitat designation in 2001, the number of 

known occurrences has continued to decline. For example, the USFWS designated 15 

critical habitats in 2001. A revised critical habitat designation was proposed in 2007 and 

suggested redefining and reducing 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 excluded from the revised version due to developments and 

degradation from non-native invasions. Unit two (Pulgas Ridge) is a newly proposed 

area and is currently undeveloped. The unit resides within the historic range of the 

species and could potentially serve as a stepping-stone between proposed units four and 

five, the two southern most units in San Mateo County, and San Bruno Mountain. The 

proposal awaits final ruling (USFWS, 2007). 

The San Mateo County subspecies have significantly declined, and populations at San 

Bruno Mountain, Pulgas Ridge, and Jasper Ridge 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). Restoration efforts in 

February and March of 2007 reintroduced approximately 1,000 post-diapause larvae to 

the Park to maintain a viable San Mateo County population (CNDDB, 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 individuals 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, and 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; Weiss, 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 observed (WRA 2006, p. 10). The population in 

unit 15 (Tulare Hill) contained approximately 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 adults in 2004 (CH2M Hill, 2005, p. 8-2). Weiss 

21
(2007, p.1) estimated the Tulare Hill population to total 100 individuals from the 2004 

observation. In 2005, seven adults were observed, 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 the 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 publication, the plan did not specifically focus on 

the BCB, but rather on the mission blue and San 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 that would benefit both the bay checkerspot and callipe 

silverspot butterflies. The conservation actions include: (1) vegetation management (e.g.,

prescribed fire, herbicide application, mowing, and grazing); (2) replanting and 

restoration; and (3) monitoring. The plan will also substantially protect all bay 

checkerspot PCEs. A finalized amendment is expected by the USFWS in 2008 (USFWS, 

2007). 

Two other Habitat Conservation Plans, accessed online though the Fish and Wildlife 

Service webpage, have been issued on behalf of 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 for 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 dispersal in checkerspot butterfly. Science 

134: 108-109. 

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

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

Ehrlich, P.R., and D.D. Murphy. 1987. Conservation lessons from long-term studies of 

checkerspot butterflies. Conservation 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. California serpentines: Flora, vegetation, geology, soils, and 

management problems. University of California Press, Berkeley, California. 180 

pp. 

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

 resolution of land-use conflicts involving 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 Lepidopterists’ 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 Service, 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 

23
plants; determination of threatened status 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 structure, and the population 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. Conservation strategy: the effects of 

 fragmentation on extinction. American 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 

24
3: CALIFORNIA CLAPPER RAIL 

3.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 considered because they are subject to 

consultation pursuant to Section 7 of the Endangered Species Act (Act). Numerous nonfederal actions that could affect the California 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 could 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 systems and the inland extent 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 natural 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 the 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 across locations. Given the large number of 

occupied habitats and extent of the action 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 and 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 quality dictate the maximum number of rails in 

any particular marsh and are impacted by habitat alteration. The primary causes of this 

25
loss and fragmentation include: erosion, introduction of freshwater, change in landscape, 

subsidence, lack of tidal channels, invasive species, and land management practices. 

Hunting, predation, disease, and climate extremes are additional detrimental factors 

currently affecting the CCR and its habitat. Beneficial factors include restoration and 

protection projects that have been, or are currently being completed, to reconstruct and 

enhance the salt marshes of the San Francisco Bay Area. Sections 3.2.1.1 through 3.2.1.6 

provide details on each of the major issues affecting the SFGS within the action area. 

3.2.1.1 Habitat Loss and Fragmentation 

 

Fragmentation and loss of habitat are the main factors affecting CCR populations 

(Albertson, 1996). An 84% reduction in the tidal marsh bordering San Francisco Bay has 

occurred since 1850 due to urbanization, filling, 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 vegetation 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 eliminated in Suisun Marsh due to diking and 

livestock grazing (USFWS, 1984). Since the mid 1960s, there has been little large scale 

habitat loss; however, the loss of many small habitats has resulted in significant overall 

wetland loss and degradation (Albertson, 1996). 

Physical factors that affect the marsh habitat include erosion, freshwater introduction to 

the marsh, small size, fragmentation, subsidence, and a lack of tidal 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 area (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 South Bay wastewater facilities (USFWS, 2007). The vegetation 

in this area is dominated by alkali bulrush, which does not provide suitable nesting 

habitat, and CCR populations in this area have declined (USFWS, 1984). Land 

subsidence has also reduced the available CCR nesting habitat (USFWS, 1984). In South 

Bay, the difference between the high and low tides 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” which 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 cover 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 destruction of CCR habitat has allowed 

26
the 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 nesting. Both of these plant species can be 

displaced by the non-native Spartina which invades channels and accretes sediment 

(SFEISP online). Excessive sedimentation can clog tidal sloughs which are used by the 

CCR for foraging (Goals Project, 2000). However, 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 important, all native species that depend on this 

marsh should be protected and managed appropriately (USFWS, 1984). The recovery 

plan suggests that to achieve this goal “optimal freshwater and tidal flows” should be 

maintained to simulate historic flow regimes (USFWS, 1984). In addition, the CDFG 

and the USFWS should educate “property owners and hunters in waterfowl management 

areas” including Suisun Marsh about the presence 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 species, including CCR, allowed several rail 

populations to recover in the San Francisco Bay marshes; however, the CCR never fully 

recovered (USFWS, 1984; Albertson, 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 mammalian predators of the CCR and their eggs 

include Norway rats, red foxes, and feral cats and dogs (Environmental Impact and Goals 

Project, 2000). A study published 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 (Goals 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., 

27
2006). 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 marsh displaces predators and also negatively 

affects higher order predators, 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). The population decline in several South Bay 

marshes (Greco Island, Bay Farm Island, Mowry Marsh, and Faber-Laumeister Marsh) 

after 1985 is likely due to predation by foxes and harriers (Foin et al., 1997). 

The San Francisco Bay National Wildlife Refuge (SFBNWR) implemented a predator 

management program in 1991 (USFWS, 2003), which has reduced the impact of 

predators on some populations of the CCR (Albertson, 1996 and Steiner, 1997; Steiner, 

1997). Other efforts are also underway to reduce non-native red fox 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 and eggs has also been attributed to ravens 

(Goals Project, 2000). Electric power transmission 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 perches (Foin et al., 1997). One study looking 

at predation showed that “64% of the rails killed were taken by raptors, primarily during 

the winter season” (Goals Project, 2000). Another study showed that 25% of the rail 

population in one marsh was taken by raptors during the period from April through 

November (Goals Project, 2000). The primary predator during the 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, particularly during El Niño years, have the potential 

to affect the reproductive success of CCRs. However, while not all flooding events occur 

during El Niño years (and not all El Niño years cause widespread flooding), the potential 

for flooding during these years is indeed greater (Monteverdi, 1998). Populations of 

CCR may cyclically fluctuate with rainfall patterns, as do populations of the northern 

clapper rail in New Jersey (USFWS, 1984). In a study by Schwarzbach, et al. (2006), 

28
flooding was a minor factor in reproductive success, as opposed to major factors such as 

predation or contaminants. Flooding 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, remediation, and habitat protection programs are ongoing. 

These are described in USFWS, 1984; Albertson, 1996; Goals Project, 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 historically supported the largest populations of 

CCRs. Salt marshes of the southern Bay Area included portions of San Mateo, Santa 

Clara, and Alameda Counties. Smaller populations occurred in San Francisco County 

and western Contra Costa County. Records 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 (counties all bordering the Bay). CCRs 

occurred further south of the San Francisco Bay Area in Monterey County (Elkhorn 

Slough). Reports from the 1930s and 1940s indicated populations in Humboldt County 

(Humboldt Bay) and San Luis Obispo County (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, Contra Costa, Marin, Napa, San Francisco, San 

Mateo, Santa Clara, Solano, and Sonoma counties, 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 CCRs in the north Bay 

is fragmented (USFWS, 2007). Small populations of CCRs are found throughout San 

Pablo Bay (USFWS, 2007) and 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 (Foin 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 South San Francisco Bay and 45% occurring in 

San Pablo Bay (USFWS, 1984). A breeding density of 1.6 CCR/ha in the South Bay was 

also described during this period (USFWS, 1984). A census reported in 1980 of two 

South Bay marshes supporting major CCR populations described a similar density of 

29
CCR (1.5 CCR/ha) (USFWS, 1984). This consistency 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 marshes 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 populations 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 early to mid-1980s was approximately 50% 

lower than estimates from the early 1970s (USFWS, 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 that 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 indicated that the South 

Bay population was estimated at 650 to 700 individuals (Goals Project, 2000). The 

estimated population today is about 1,200 individual 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 pages 1-3. Available online at: 

http://www.fws.gov/desfbay/Archives/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/species/t_e_spp/new_te_rpt.html 

(Accessed on September 2, 2008). 

30
California Department of Pesticide Regulation (CDPR online). Endangered Species 

Project. California Clapper Rail. Available online at: 

http://www.cdpr.ca.gov/docs/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 rail (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/science?_ob=PublicationURL&_cdi=5885&_pubT

ype=J&_acct=C000001678&_version=1&_urlVersion=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 plants, fish and wildlife. Prepared by the 

San Francisco Bay Area Wetlands Ecosystem 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 Niño and California Precipitation. Western 

Regional Technical Attachment, No 97-37, November 21, 1997. Accessed online 

at: http://tornado.sfsu.edu/geosciences/elnino/elnino.html#Not (Accessed on 

September 2, 2008). 

San Francisco Estuary Invasive Spartina Project (SFEISP online). Coastal 

Conservancy. California clapper rail (Rallus longirostris obsoletus). Available 

online at: 

http://www.southbayrestoration.org/pdf_files/CLRAhandout_final3.18.05.pdf

(Accessed on September 2, 2008). 

Save the Bay Classroom. 2005. California Clapper 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. 

31
pp 45-60. Available online at: 

http://findarticles.com/p/articles/mi_qa3793/is_200601/ai_n17186959 (Accessed 

on September 2, 2008). 

Spautz, H., J.T. McBroom, N. Nur, J.G. Evens, J. Albertson, S. Bobzien, K. Zaremba, 

and M. Herzog. 2007. California clapper rails 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 Ecological 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 for 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/Methylmercury%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/animal_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/DivisionSites/ConservationLibrary/Pubs1/sfbay_coastal.pd

f (Accessed on September 2, 2008). 

32
University of California at Berkeley (U.C. Berkeley). June 2004. Richmond Field 

Station: Western Stege Marsh Restoration. California Clapper Rail Restoration. 

Accessed online at: 

http://www.cp.berkeley.edu/RFS_Feral_Brochure_final.pdf (Accessed on 

September 2, 2008). 

33
4: CALIFORNIA FRESHWATER SHRIMP 

4.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 action are not considered because they are 

subject to consultation pursuant to Section 7 of the Endangered 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 with modifications to 

stream morphology and operate synergistically and/or cumulatively with each other in 

their effects to the CA shrimp. These activities include urban development, instream 

gravel mining, grazing, agricultural development, impoundments, and water diversions. 

These activities may simultaneously reduce the quality and availability of water, reduce 

the quality and availability of shelter, and contaminate suitable habitat. For instance, 

urban development may result in the loss of riparian vegetation. This could alter 

temperature regimes and dissolved oxygen levels in streams; increase bank erosions; and 

change the invertebrate species composition, impacting aquatic food source availability. 

The effects of urban development might then be compounded by activities that reduce 

water flow such as diversions and impoundments, which increase sediment and pollutant 

concentrations, and further decrease oxygen availability. As the CA shrimp does not 

have life history characteristics that favor quick recovery following disturbances, the CA 

shrimp is vulnerable to the cumulative effects 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 the 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 presents a general discussion of factors that may 

affect CA shrimp within the action area. This information includes both detrimental and 

potentially beneficial factors affecting the species and is presented in Section 4.2.1. 

Additional information on the current distribution and population dynamics of the CA 

shrimp is presented as part of the baseline status in Section 4.2.2. 

34
4.2.1 Factors affecting species environment within the action area 

Since the species’ listing in 1988, there continue to be numerous human-related and 

natural factors affecting the species’ habitat (USFWS, 2007). Although there have not 

been any new threats documented since the listing, some of the factors have since 

intensified (USFWS, 1998). Furthermore, the CA shrimp is most likely affected by 

multiple factors in a majority of locations, rather than just one (USFWS, 1998). These 

factors include urbanization, stream maintenance, gravel mining, agriculture, silviculture, 

impoundments, water diversions, native and introduced predators, and water pollution 

(USFWS, 1998; USFWS, 2007). Environmental extremes, compounded by human 

disturbance, also present a threat to the 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 information 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 issues affecting the CA shrimp within the action area. 

4.2.1.1 Urbanization 

On the heels of already much urban development since the CA shrimp’s listing, 

urbanization has been increasing in rural areas within the San Francisco Bay region 

(USFWS, 1998). Development outside traditional populated centers has led, and will 

lead, to a larger portion of impacted watershed 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 pollutants 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 stream 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 facilities 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). 

35
4.2.1.2 Stream Maintenance 

Stream maintenance activities that affect the 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 areas (USFWS, 1998). With such removal, CA 

shrimp habitat of undercut banks and riparian vegetation is removed, or at a minimum 

impaired, by increased water velocities and temperature fluctuations (USFWS, 1998). 

Bank protection activities result in similar consequences for CA shrimp 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 herbaceous 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 habitat though herbicide use, dredging, altering 

channel and bank configuration, and removing instream and riparian woody debris 

(USFWS, 1998). 

Direct elimination of shrimp from certain streams could occur with barriers impeding the 

movement of CA shrimp upstream (USFWS, 1998). Sills, designed to protect bridge 

footing, have scoured downstream areas and formed ledges which prevent upstream 

movement (USFWS, 1998). Barriers from culvert or grade control structures also result 

in fragmented populations, possibly restricting gene flow and increasing the likelihood of 

extirpation (USFWS, 1998). 

4.2.1.3 Water Resource Needs: Impoundments and Water Diversions 

 

Impoundments are prevalent in stream drainage 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 barriers, by eliminating upstream habitat, supporting introduced 

predators, altering hydrology and sediment transport, reducing and altering downsteam 

flows, and by ushering individuals away from the population and into diverted waterways 

(USFWS, 1998). Impoundments raise the elevation 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 production, 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). 

36
Water diversions imperil CA shrimp by directly 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 were substantial demands to appropriate water 

from many streams containing the CA shrimp (USFWS, 1998). In the Huichica Creek 

watershed, as an example, estimates of total water yield range between 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). Without instream flow 

requirements, existing pools could become dry (USFWS, 1998). Such high demands of 

groundwater are also a concern, although for the fear of saltwater intrusion and the 

corollary stress of competing with shrimp found normally in brackish water (USFWS, 

1998). 

Since 1998, the USFWS has issued 13 biological opinions under section 7 of the 

Endangered Species Act authorizing incidental 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 constructed water diversion 

(not consulted on), may have impacted the CA shrimp (USFWS, 2007). The water 

diversion channel included 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 interrupt the supply of gravel downstream 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 necessary safeguards, instream gravel 

mining activities along the historic CA shrimp habitat in Austin and Sonoma Creeks will 

prevent the reestablishment of suitable habitat conditions for the species (USFWS, 1998). 

To date, no specific studies have been conducted 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 concern 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 than the area covered in 1989 (USFWS, 

1998). Land and surface water resources in not only Napa, but also Sonoma, counties are 

being intensively developed, and threats to CA shrimp populations include loss of 

riparian vegetation, inadvertent introduction of herbicides and pesticides into creek water, 

diversion of water, and increase soil erosion (USFWS, 1998). 

37
Habitat quality for the CA shrimp is imperiled by livestock grazing 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 (USFWS, 1998). Stemple Creek watershed, as an example, 

supports approximately 30 dairy operations and grazing on 50 percent of its land 

(USFWS, 1998). Grazing activities typically occurs in the vicinity of steams and riparian 

areas where livestick are offered fresh water and palatable forage (USFWS, 1998). 

Because of the high concentration of livestock, Stemple Creek and its tributaries have lost 

much of their riparian vegetation that supported 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 zones alter invertebrate 

species composition and production in steams (USFWS, 1998). Grazed streams are 

characterized by having a high production of algae due to high insulation and increased 

nutrient input, as opposed to the limited instream primary productivity seen in streams 

with dense riparian vegetation (USFWS, 1998). 

Poor water quality results from reduced forage cover and increased soil compaction 

(USFWS, 1998). Groundwater recharge is diminished from the compaction, as well as 

base flows during the summer and fall (USFWS, 1998). Reduced forage cover and 

compaction also result in higher peak flows following winter storms and high sedimentladen flood flows (USFWS, 1998). Runoff from manure lots contribute to raising 

nutrient levels and increase the concentration of ammonia (USFWS, 1998). Water 

samples from Americano and Stemple Creeks exceeded the Environmental Protection 

Agency’s (EPA) ammonia criteria for aquatic life protection for the years 1991-1994 

(recovery). The ammonia present is in an un-ionized form (NH3) and an ionized form 

(NH4

+

), both of which cause mortality to aquatic organisms (USFWS, 2007). The 

elevated copper concentrations in these two creeks have been linked 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). Particularly those practices that remove stream side 

vegetation, timber harvesting reduces channel stability, decreases canopy cover 

(increasing water temperature), and increasing instream debris (USFWS, 1998). Timber 

harvesting also increases peak flows, decreases base flows, and increases sediment 

transport and deposition (USFWS, 1998). Austin creek is noted as having timber 

harvesting activity near its drainage, adding to channel degradation near the confluence 

with the Russian River (USFWS, 1998). 

4.2.1.6 Predation 

It can be inferred that the CA shrimp evolved in the presence of predators due to its 

cryptic coloration and behavioral characteristics (USFWS, 1998). Some native fish that 

prey on CA shrimp include the California roach (Hesperoleucus symmetricus), threespine 

38
stickleback (Gasterostreus aculeatus), riffle sculpin (Cottus gulosus) (USFWS, 1998). It 

is suspected that the following fish generally 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, and dragonfly and damselfly nymphs (USFWS, 

1998). 

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

in the decline of native fish (USFWS, 1998). Nonnative species presence is correlated 

with the levels of human disturbance to a stream (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 (USFWS, 2007). Predation from introduced 

species can be more disruptive to a prey population than from native predators because 

the prey species have not developed mechanisms for defense or avoidance (USFWS, 

1998). Some introduced species are also tolerant of poor water quality conditions, 

increasing the predation stress on their prey items (recovery). Both the mosquitofish and 

green sunfish persist in conditions that would otherwise permit CA shrimp to live in 

isolation of natural predators (USFWS, 1998). For example, the green sunfish is capable 

of surviving water temperatures up to 97 degrees Fahrenheit, low oxygen levels down to 

3 ppm, and high alkalinities (USFWS, 1998). 

4.2.1.7 Environmental Extremes 

Environmental extremes, particularly droughts, spring flooding, and the consequences of 

climate change, threaten the persistence and stability of CA shrimp populations (USFWS, 

2007). Reduced precipitation could result in lower stream flows and thus increase the 

chance that stream segments dry out during 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 increased demand for water resources, further 

intensifying the fatal effects of stream dry-up (USFWS, 2007). 

While not mentioned explicitly in the recovery 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). 

39
4.2.1.8 Restoration Efforts 

Since 1998, the USFWS has issued 13 biological opinions under section 7 of the 

Endangered Species Act authorizing take of the 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 total of 548 linear feet combined with 5.49 acres of habitat 

restoration and/or protection in compensation 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 restoration activities for these plans have yet 

to be implemented (USFWS, 2007). Stemple Creek has received lots of restoration 

attention through activities supported by the Bay 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 date, 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 available for the Lagunitas Creek population, known 

from an eight mile reach beginning from Shafter 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 water flows and improving and/or increasing 

habitat conditions (USFWS, 2007). However, in some areas these morphological 

changes worsened and/or decreased 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 Stemple), and twelve streams in Sonoma County 

(Blucher, Jonive, Redwood, Green Valley, Salmon, 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 locations 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 canvassing of habitats for the CA shrimp that 

examines their full spatial distribution and extent (USFWS, 2007). 

40
It is unknown if shrimp populations still persist 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 (Serpa, 1996 and USFWS, 1998). A substantial 

portion of Lagunitas Creek flows through the Samuel 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 Watson 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 genetic 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 recovery plan were originally 

developed in an effort to maximize genetic diversity (USFWS, 2007). 

4.3 REFERENCES 

Literature Cited

Hedgepeth, J.W. 1968. The Atyid 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. Fish 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/animal_spp_acct/ca_freshwater_shrimp.pdf

(Accessed on April 22, 2008). 

41
5: CALIFORNIA TIGER SALAMANDER: CENTRAL CALIFORNIA DISTINCT 

POPULATION SEGMENT 

5.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects of future state, tribal, local, private, or other nonfederal entity activities on the 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 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, orchards), urban development, grazing operations, oil 

production, and contamination from runoff and spills. Many of these factors are linked or 

act synergistically and create complex consequences for the central CTS. For example, 

conversions to intensive agriculture and urban developments have resulted in the loss of 

breeding habitat from the destruction or alteration of natural vernal pools and seasonal 

ponds. If these water bodies are destroyed by deep 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-ripping, in addition to plowing and 

discing in upland habitats, can alter hydrology of the pools and ultimately destroy them. 

In contrast to destroying water bodies, some seasonal ponds are being converted into 

permanent ponds for irrigation. However, these ponds are then frequently stocked with 

fish to control mosquitoes and other problematic 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 beneficial 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 snapshot 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 large number of occupied habitats and extent of the action 

area included in this assessment, the environmental baseline includes a general discussion 

of factors that may affect central CTS within 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 presented as part of the baseline status in 

Section 5.2.2 (USFWS, 2004). 

42
5.2.1 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 habitat due to rangeland conversion for urban and 

agricultural uses. Other influential factors affecting central CTS include: disease; 

predation, competition, introduced species; contaminants; 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 neutral 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 entire range. The factors known to affect 

the larger population are still relevant to the 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 action area (USFWS, 2004). 

5.2.1.1 Rangeland Conversion and Habitat Fragmentation 

A variety of urban and agricultural land uses are implicated in the destruction, 

modification, and curtailment of central CTS 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 operation and expansion; operation of gravel 

mines and quarries; dam building and inundation of habitat by reservoirs; and other 

infrastructure activities (USFWS, 2004). Agricultural land uses are defined as including 

native habitat conversion by discing and deep-ripping; and cultivation, planting, 

irrigation, and maintenance of row crops, orchards, and vineyards (USFWS, 2004). 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 migration (USFWS, 2000). 

Urban development in central CTS habitat proceeds at an elevated rate. Between the 

years of 1980 and 1997, 2.8 million new housing units were constructed in California, 

and 220,000 units are required each year for the next 20 years to accommodate the 

growing population. Most of this development will be outside of the major metropolitan 

areas, referring to San Francisco, Los Angeles, 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 metropolitan areas, is of great threat to the 

central CTS. The housing areas and rural developments may result in extirpation of the 

CTS due to the destruction or degradation of breeding sites, upland dispersal habitat, and 

migration corridors (USFWS, 2004). 

Conversion of rangeland and vernal pool grasslands to intensive agriculture have been 

well documented in counties inhabited by the central CTS. The cumulative loss of vernal 

43
pool grasslands has been estimated at 78 percent by the later 1990s. Historically, 

approximately 2.7 million hectares (ha) of valley and coastal grasslands existed within 

the range of the central CTS. Today, virtually all valley grassland and oak savanna 

habitat has been eliminated from the Central 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/acre) at a lower cost. Other 

factors influencing rangeland conversion include a decline in farm rancher income, the 

aging of ranchers, tax implications of intergenerational 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 agriculture become scarce (USFWS, 2004). 

Changes to vernal pool or pond inundation, duration, or depth can detrimentally affect the 

reproductive success of the CTS. These changes are caused by, among others, digging of 

drainage or irrigation ditches, construction of permanent ponds or reservoirs, deepening 

or berming of seasonal wetlands, and redirection or runoff from developments (USFWS, 

2000). The repercussions of these activities on the reproductive success of the CTS 

include: (1) prematurely drying wetlands and desiccating CTS larvae; (2) extending the 

inundation period and facilitation invasion of non-native predators; (3) creating 

conditions that foster the hybridization with the non-native tiger salamander; and (4) 

increasing vulnerability to disease from isolation and fragmentation. Wetland habitats 

are utilized for reproduction; thus destructive activities such as filling, discing, or 

excavating, are injurious or lethal to the eggs, larvae, or breeding adults. Earthmoving 

operations and cultivation in upland habitat also threaten the 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 habitat. Indirect impacts to the CTS include 

increased predation from over-exposure, high temperatures, low humidity, and 

diminished food sources. Earth moving operations may further disturb California ground 

squirrel burrows and crevices, protected habitat utilized by the CTS, and may render 

upland locations untenable or unavailable (USFWS, 2004). 

Fragmentation 

The widespread conversion of land to residential and agricultural uses has led to the 

fragmentation and isolation of habitat throughout the range of the central CTS. Humancaused fragmentation places the CTS at particular risk to local extinctions because its 

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

“A metapopulation is a group of spatially 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 individual populations may be extirpated from a 

local area and later be recolonized from another population that is still extant” 

(FR, 72:48177, p.6). 

44
A reduction in CTS dispersal greatly inhibits the dynamics of a metapopulation and 

reduces the abilities of the CTS to persist over time. Of all factors associated with 

urbanization and land conversion, roads accelerate fragmentation by increasing mortality 

and preventing recolonization of sites that 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). While no information suggests disease is 

prolific in existing populations in California, several pathogenic (disease-causing) agents 

have been linked to deaths of closely-related 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 the genetic material 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 are 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 artificial 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, including tiger salamanders (USFWS, 2004). 

Non-native species of bullfrogs and tiger salamanders are potential carriers of these 

diseases (USFWS, 2004). 

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

contaminated with silt were susceptible 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 agricultural or urban runoff may also 

increase susceptibility to disease (USFWS, 2000). High levels of nitrogen have been 

associated with bacterial blooms and increased silt has been associated with fungal 

infections (USFWS, 2000). 

5.2.1.3 Predation, Competition, and Hybridization 

45
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 crayfish 

also prey on CTS (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 subjected to the cumulative 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). Bullfrogs are known to prey on CTS larvae and studies have shown that the 

number of CTS decreases as bullfrog numbers increase (USFWS, 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 metamorphosis 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 intentional establishment of bullfrogs in central CTS 

suitable habitat is significant (USFWS, 2004). 

Western mosquito fish, which are used to control 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 mosquito 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 metamorphosis 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 largemouth bass, bluegill, catfish, and fathead 

minnows may also either be directly responsible for or have the potential to cause the 

decline of the CTS (USFWS, 2003). In eastern 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 supported populations of CTS. These non-native fish may affect 

the prey base of the CTS or prey on larval CTS, either of which is capable of reducing or 

46
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 

Hybridization is a serious threat in the Central 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 extent of interbreeding, though, was found to 

depend on habitat quality. Pure central CTS were found to be most prevalent in natural 

habitats, rather than artificial or disturbed ones. According to the study, vernal pools 

contained a larger percentage of pure CTS larvae. The authors suggest that more hybrids 

are found in artificial ponds because of the lack 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 indicated that salamanders from oil-contaminated 

natural ponds metamorphosed earlier at smaller 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. 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). Researchers evaluated concentrations at 

levels commensurate to those measured in service stations and other 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 rather than in artificial light (USFWS, 2000). 

47
Sedimentation from road construction, maintenance, and runoff is a second type of 

contaminant threatening the CTS. Breeding 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 affects aquatic and emergent vegetation and may 

asphyxiate CTS eggs. Excessive sedimentation 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 contaminants in runoff is of concern and will 

likely increase in both roadside ditches and the rest of CTS suitable 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 rodenticides used to control 

these two species, the CTS may potentially be at risk from indirect exposure to them 

inside the burrows or concentrated in breeding ponds (USFWS, 2003). Some of these 

rodenticides used in central CTS habitat include chlorophacinone, diphacinone, and 

strychnine (USFWS, 2003). Fumigants are other pesticides used for rodent control, such 

as aluminum phosphide, carbon monoxide, and methyl bromide, which are injected into 

burrows by using a cartridge or by pumping (USFWS, 2003). These fumigants can be 

both directly and indirectly lethal to the CTS, although the effects of these poisons on 

CTS have not been assessed (USFWS, 2003). Besides the use of rodenticides, control of 

rodents by means of eliminating burrows results is a loss of tenable 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 affect the CTS, grazing can, in moderation, 

have a neutral to positive impact on the CTS. Grazing maintains shorter vegetation and 

promotes the persistence of ground squirrel burrowing, which creates habitat essential for 

the CTS. In some cases rangelands present the only undeveloped habitat in the County, 

and thus provided the only opportunity for the salamanders to maintain sustainable 

populations (USFWS, 2000). Rangelands not only provide natural vernal pools, but 

artificial stock ponds which 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 still compatible with CTS as long as burrowing rodents are 

not completely eradicated (USFWS, 2004). 

 

Road-Crossing Mortality

It is well documented that numerous CTS are killed by vehicular traffic while crossing 

roads (USFWS, 2003). In one study, there were 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. Estimations of CTS mortality from vehicular 

strikes range from 25 to 72 percent. Mortality may be increased by the presence of curbs 

and berms, which allow salamanders to climb onto the road but can restrict their 

48
movement off of the road (USFWS, 2003). Vehicle usage in California 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 relatively 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 historic 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 southern 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 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). 

Although the CTS has been eliminated from much 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, even 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 distribution pattern of CTS inhabited areas was 

caused by a combination of extreme anthropogenic changes in and around the Central 

Valley and the restrictive breeding requirements of the species. Geographic Information 

Systems (GIS) indicate that there are approximately 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 residential, 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). 

49
5.3 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. Petranka. 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/cgi/content/abstract/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. Federal Register 65 

(184):57242-57264. Available online at 

http://ecos.fws.gov/speciesProfile/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. Available 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 threatened 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 (USFWS). 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). 

50
6: CALIFORNIA TIGER SALAMANDER: SANTA BARBARA COUNTY 

DISTINCT POPULATION SEGMENT 

6.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects of future state, tribal, local, private, or other nonfederal entity activities on the 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 require 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), urban development, grazing operations, oil 

production, and contamination from runoff and spills. Many of these factors are linked or 

act synergistically and create complex consequences for the SB CTS. For example, 

conversions to intensive agriculture and urban developments have resulted in the loss of 

breeding habitat from the destruction or alteration of natural vernal pools and seasonal 

ponds. If these water bodies are destroyed by deep 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-ripping, in addition to plowing and 

discing in upland habitats, can alter hydrology of the pools and ultimately destroy them. 

In contrast to destroying water bodies, some seasonal ponds are being converted into 

permanent ponds for irrigation. However, these ponds are then frequently stocked with 

fish to control mosquitoes and other problematic insects, and can limit SB CTS 

populating the water edges. Both destruction and reduced suitability of breeding habitat, 

compounded with increased urbanization, fragments 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 snapshot of the SB CTS’s status at this time. 

However, the baseline condition of each assessed SB CTS species and habitat varies 

across locations. Given the large number of occupied habitats and extent of the action 

area included in this assessment, the environmental baseline includes a general discussion 

of factors that may affect SB CTS within the 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. 

51
6.2.1 Factors affecting species continued existence within the action area 

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

curtailment of suitable habitat due to rangeland conversion for urban and agricultural 

uses, with road construction, intensive agriculture, and urbanization constituting the 

major three uses. Other influential factors affecting SB CTS include contaminants; pest 

control; grazing practices and water drawdown; predation 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 issues 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 uses are implicated in the destruction, 

modification, and curtailment of SB CTS habitat. The USFWS (2004a) 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 

operation and expansion; operation of gravel mines and quarries; dam building and 

inundation of habitat by reservoirs; and other infrastructure activities. Agricultural land 

uses are defined as including native habitat 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 migration (USFWS, 2000). 

All known locations of the SB CTS are affected by railroads, highways, or other roads 

causing extensive habitat fragmentation. SB CTS require large tracts of unobstructed 

landscape for dispersal and migration. Larger roads, highways, and railroads act as 

permanent physical barriers and can prevent genetic interchange and movement to and 

from breeding and aestivation sites. The temporary construction of road and rail is also 

detrimental to the SB CTS. Slow-moving 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, the salamanders are at risk for being run over 

on their first dispersal runs to the pond. Studies indicate that up to 9 to 12 SB CTS are 

killed as they try to cross roads during migrations between breeding and upland sites 

(USFWS, 2000). Soil compaction and alteration, 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 the road difficult for the SB CTS. A study 

52
on road distances to wetlands indicated that the number of amphibian 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 curbs 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 from 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, digging of drainage or irrigation ditches, 

construction of permanent ponds or reservoirs, deepening or berming of seasonal 

wetlands, and redirection or runoff from developments (USFWS, 2000). The 

repercussions of these activities on the reproductive success of the SB CTS include: (1) 

prematurely drying wetlands and desiccating SB CTS larvae; (2) extending the 

inundation period and facilitation invasion of non-native predators; (3) creating 

conditions that foster the hybridization between the non-native tiger salamander; and (4) 

increasing vulnerability to disease from isolation and fragmentation. Wetland habitats 

are utilized for reproduction; thus destructive activities such as filling, discing, or 

excavating, are injurious or lethal 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 upland habitat. Indirect impacts to the SB CTS 

include increased predation from over exposure, high temperatures, low humidity, and 

diminished food sources. Earth moving operations may further disturb California ground 

squirrel burrows and crevices, protection utilized by the SB CTS, and may render upland 

locations untenable or unavailable (USFWS, 2004 a). 

Urbanization and rural residential 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 decline in farm rancher income, the aging of 

ranchers, tax implications of intergenerational transfers of ranches, and the difficulty of 

beginning a ranching operation (e.g., cost and knowledge) (USFWS, 2004 a). 

Fragmentation 

53
The primary factors causing SB CTS fragmentation are discussed above: road 

construction, urbanization, and intensive agriculture. 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 spatially 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 individual populations may be extirpated from a 

local area and later be recolonized from another population that is still extant” 

(FR, 72:48177, p.6). 

A reduction in SB CTS dispersal greatly inhibits 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 mortality and preventing recolonization of sites 

that would otherwise be only temporarily 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 habitats 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 indicated that salamanders from oil-contaminated 

natural ponds metamorphosed earlier at smaller 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 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 rather than in artificial light (USFWS, 2000). 

Sedimentation from road construction, maintenance, and runoff is a second type of 

contamination threatening the SB CTS. Breeding 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 affects aquatic and emergent vegetation and 

may asphyxiate SB CTS eggs. Excessive sedimentation ultimately fills pools otherwise 

54
usable by the SB CTS. Sedimentation may also impair the SB CTS from detecting food 

items (USFWS, 2000). 

 

6.2.1.3 Pest control 

Pesticides and rodenticides are heavily used in the agricultural 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 reducing 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 reported that other insecticides besides 

methoprene have adversely impacted growth rates in gray treefrog (Rana clamitans) 

tadpoles and increased mortality rates in southern leopard frogs (R. sphenocephala) 

(USFWS, 2000). Temephos was identified by the USFWS as an example of these 

additional insecticides (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 unknown (USFWS, 2000). 

CTS are also negatively affected by rodenticides because they are smaller than the target 

species (USFWS, 2007). Ground squirrel populations were controlled in Santa Barbara 

County using compound 1080 (sodium fluoroacetate) until about 1990 (USFWS, 2000). 

This chemical is highly toxic to non-target species, including fish, 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 preferred method to control ground squirrels where 

children, pets, or poultry might be present, although grains poisoned with strychnine are 

also used (USFWS, 2003). The rodenticide, zinc phosphide, can indirectly 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 toxic to CTS (USFWS, 2003). 

Several gasses also used to control rodents, identified as aluminum phosphide, carbon 

monoxide, and methyl bromide, are introduced into the small mammal burrows where 

CTS may live (USFWS, 2003). 

Another threat to CTS includes habitat loss due to elimination of small mammal burrows. 

Small mammal control programs have a profound 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 use collapsed burrows (USFWS, 2000 and 2003). 

55
6.2.1.4 Grazing and Water drawdown 

As opposed to many factors that negatively 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 squirrel burrowing, which creates 

habitat essential for the SB CTS. As of the Federal Register final rule (2000), grazing 

land in Santa Barbara County offered the only large amounts of suitable habitat for the 

SB CTS. Because rangelands presented the only undeveloped habitat in the County, they 

provided the only opportunity for the salamanders to maintain sustainable populations 

(USFWS, 2000). Rangelands not only provide natural vernal pools, but artificial stock 

ponds, which have likely saved many populations from extirpation (USFWS, 2004 a). 

Although trampling from cattle may impact water 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 eradicated (USFWS, 2004 a). 

Water drawdown affects many of the ponds in Northern Santa Barbara County from 

agricultural practices such as irrigation and frost 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. Water drawdown also puts the pond at risk of 

prematurely drying in the spring or summer, thus desiccating the un-metamorphosed 

larvae (USFWS, 2000). 

6.2.1.5 Predation, Competition, and Hybridization 

At least four of the six SB CTS metapopulations 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 crayfish also prey on CTS (USFWS, 2003). 

Predation of CTS by sticklebacks, fish which 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 subjected to the cumulative 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, 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). Louisiana 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 numbers increase (USFWS, 2000). A study observing the effect of 

56
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 tadpoles (USFWS, 

2000). 

Western mosquito fish, which are used to control 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 mosquito 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 metamorphosis 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 largemouth bass, bluegill, catfish, and fathead 

minnows may also either be directly responsible 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-native fish species and CTS suitable habitat has 

supported non-native fish populations for a number 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 have been brought to California and used for 

fishing bait (USFWS, 2004 a). Whether by bait-bucket release 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). This 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 (USFWS, 2000). The non-native species 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 

57
and CTS breed were originally thought to be poorly-adapted to survive or be sterile past 

the first few generations (USFWS, 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 natural 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 existing natural vernal pools (USFWS, 2004 a). 

6.2.1.6 Disease 

The direct effect of disease on the SB CTS 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 portion 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 animal feces (USFWS, 2000). In 

one study, this bacterium was found to increase with increasing nitrogen levels from 

atmospheric deposition as the study lake in Utah (Desolation Lake) dried out (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 the genetic material 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 are of particular concern because these 

viruses can be spread on fishing gear, artificial stocking of ponds for fishing, and water 

birds (USFWS, 2003). Outbreaks of ranavirus in tiger salamanders have been associated 

with altered habitats and artificial 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 susceptible 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 agricultural 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 grasslands and are at risk of receiving 

runoff that has both high nitrogen and high silt 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 

58
bacterial blooms and increased silt has been associated with fungal infections (USFWS, 

2000). 

6.2.2 Baseline Status 

The CTS is found only in California. The historic 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 southern 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 these 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 metapopulations are listed by region as follows, 

with the critical habitat unit identified in parentheses: (1) West Orcutt (Western Santa 

Maria/Orcutt); (2) Bradley-Dominion (Eastern Santa Maria); (3) North Los Alamos 

(Western Los Alamos/Careaga); (4) East Los Alamos (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 continued existence are used as a representation 

of the metapopulation’s current baseline status. 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 have 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 natural ponds (vernal pools) (USFWS, 2004b). The 

greatest threat to this metapopulation is human population growth coupled with 

residential and commercial development (USFWS, 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 total area identified containing SB CTS PCEs, as 

well as containing four known breeding ponds (natural vernal pools) (USFWS, 2004b). 

This unit faces increased development pressure 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). The 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 extensive, dense coast live oak woodland, in 

addition to coastal sage scrub and grasslands on the others (USFWS, 2004b). This unit 

requires special management to preserve habitat 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 breeding 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 conservation strategy created by landowners to 

enhance or create SB CTS aquatic habitat (USFWS, 2004b). Even without these 

breeding ponds, this site provides essential upland habitat and acreage needed to foster a 

self-sustaining population (USFWS, 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 chaparral (USFWS, 2004b). This metapopulation 

is the least threatened of the six, and one landowner expressed 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 agricultural grading, conversion to row crops, and 

livestock facilities in the west (USFWS, 2000). The eastern part, and population of SB 

CTS, is affected by alterations to breeding 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 contamination from toxic water bodies, potentially causing 

developmental deformities or death (USFWS, 2000). 

60
6.3 REFERENCES 

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

 status review of the California 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/nongame/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/speciesProfile/SpeciesReport.do?spcode=I021. (Accessed on 

October 16, 2008). 

Harp, Elizabeth M, and James W. Petranka. 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/cgi/content/abstract/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. Federal Register 65 

(184):57242-57264. Available online at 

http://ecos.fws.gov/speciesProfile/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 (USFWS). 2003. Endangered and threatened 

wildlife and plants: determination of endangered status for the Sonoma County 

distinct population segment of the California tiger salamander. 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). 2004a. Endangered and threatened 

61
wildlife and plants: determination of threatened 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; Designation 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 (USFWS). 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). 

62
7: CALIFORNIA TIGER SALAMANDER: SONOMA COUNTY DISTINCT 

POPULATION SEGMENT 

7.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects of future state, tribal, local, private, or other nonfederal entity activities on the Sonoma County distinct population 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 related to the proposed 

action are not considered because they require 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 urban development, intensive agriculture 

(e.g., vineyards), grazing operations, oil production, contamination from runoff and 

spills, and non-native species introductions. Many of these factors are linked or act 

synergistically and create complex consequences for the STS. For example, conversions 

to intensive agriculture and urban developments have resulted in a reduction in the sizes 

and connectivity between patches of suitable and occupied habitat on the Santa Rosa 

Plain. The extent of this habitat reduction 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, fragments 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 snapshot of the STS’s status at this time. 

However, the baseline condition of each assessed STS species and habitat varies across 

locations. Given the large number of occupied habitats and extent of the action area 

included in this assessment, the environmental baseline includes a general discussion of 

factors that may affect STS within 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 

63
STS’s continued existence is primarily affected by continued destruction, degradation, 

and fragmentation of suitable habitat. Secondary threats to the DPS include predation 

and competition from introduced exotic species; possible commercialization with nonnative salamanders; various chemical contaminants; road-crossing mortality; rodent 

control operations; and a small remaining population. Livestock grazing is another factor 

affecting STSs, although it can in moderation be a positive rather than negative 

influential factor (USFWS, 2002; USFWS, 2003; USFWS, 2004). Some of these factors 

are known to affect the California Tiger Salamander population in Sonoma County 

(STS), while others are known to generally affect the California Tiger Salamander (CTS) 

population throughout its entire range. The factors known to affect the larger population 

are still relevant to the STS, but are referred to as CTS. Sections 7.2.1.1-7.2.1.4 provide 

details on the major issues affecting STS environment within the action area. 

7.2.1.1 Habitat Destruction, Degradation, and Fragmentation 

As of 2003 when the Sonoma County DPS was listed as endangered, there were eight 

remaining known breeding sites on the Santa Rosa Plain. These subpopulations are 

threatened by construction of high-density housing, office buildings, roads, and other 

developments. A study conducted in 1990 found that 25 percent of a study area of 

11,300-hectares (ha) was being used for subdivisions, “ranchettes”, golf courses, and 

commercial buildings. Seventeen percent of the study area had been converted for 

agricultural uses. Since 1990, land conversion to urban sites and intensive agriculture 

continue, particularly to vineyard operations. Other relatively minor land conversions to 

roads, storm drains, and road curbs have the potential to adversely impact the STS by 

fragmenting habitat or impeding migration. Of the eight known 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 and residential development (USFWS, 2003). 

Urban Development

The Santa Rosa County is rapidly urbanizing. Since 1980, the city of Santa Rosa has 

increased 53% in population size. Between 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 residential development between 

2001 and 2003. Six of the eight known remaining breeding sites are located around the 

former Air Center, in Southwest Santa Rosa. This area contains one of the largest blocks 

of undeveloped lands within the city limits. In the mid-1980s, the airport closed and the 

property was sold to the City. The Southwest Area Plan proposes to development the 

majority of this area and places STS breeding grounds in peril (USFWS, 2003). 

Roads and Highways

Roads and highways act as physical barriers that inhibit successful migration of the STS. 

The CTS needs large tracts of barrier-free landscape and roads present an obstacle in the 

way of moving to new breeding habitat, or returning to aestivation sites. In worst case 

scenarios, roads can completely isolate a breeding site or larger portions of a 

metapopulation and render them untenable for the species (USFWS, 2003). 

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

on road distances to wetlands indicated that the number of amphibian 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 fragmentation, 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 traffic by about four fold due to its recent support of heavy 

commuter traffic. The combination of roads 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 the 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 impacted 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 which do not allow surveying and the presence 

of STS there are unknown. Furthermore, the 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 fragmentation are discussed above: road construction, 

urbanization, and intensive agriculture. Human-caused fragmentation places the STS at 

particular risk to local extinctions because its metapopulation structure is distributed 

across the landscape (USFWS, 2000). 

“A metapopulation is a group of spatially 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 individual populations may be extirpated from a 

local area and later be recolonized from another population that is still extant” 

(USFWS, 2007 a). 

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

reduces the abilities of the CTS to persist over time. Of the three factors, roads accelerate 

fragmentation by increasing mortality and preventing recolonization of sites that would 

otherwise be only temporarily extirpated (USFWS, 2000). 

7.2.1.2 Disease

65
The 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, viruses, 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 the genetic material 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 are 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 artificial 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, including tiger salamanders (USFWS, 2004). 

Non-native species of bullfrogs and tiger salamanders are potential carriers of these 

diseases (USFWS, 2004). 

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

contaminated with silt were susceptible 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 bacterial blooms and increased silt has been 

associated with fungal infections (USFWS, 2000). 

7.2.1.3 Predation, Competition, and Hybridization 

All of the known STS metapopulations are potentially affected by native and non-native 

species predation and competition (USFWS, 2003). 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 crayfish also prey on CTS (USFWS, 2003). 

Predation of CTS by sticklebacks, fish which 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 restricted (USFWS, 2003). 

66
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 subjected to the cumulative 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 responsible for the elimination 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, either 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 number of CTS decreases as bullfrog numbers 

increase (USFWS, 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 metamorphosis 

when they were raised with bullfrog tadpoles (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 control 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 mosquito 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 control 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 molting hormones as insects. The use of 

67
methropene may decrease the availability of prey of aquatic invertebrates and thus may 

indirectly affect the STS (USFWS, 2003). 

Other species of non-native fish, including largemouth bass, bluegill, catfish, and fathead 

minnows may also either be directly responsible 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 have been brought to California and used for 

fishing bait (USFWS, 2004). This is still legal in California 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 disturbed ones (USFWS, 2004). 

It seems that hybrids are less likely to be found in vernal pools making 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 hybridization 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). STS 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 indicated that salamanders from oil-contaminated 

natural ponds metamorphosed earlier at smaller 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. 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), 

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

levels commensurate to those measured in service stations and other 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 rather than in artificial light (USFWS, 2000). 

Sedimentation from road construction, maintenance, and runoff is a second type of 

contaminant threatening the CTS. Breeding 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 affects aquatic and emergent vegetation and may 

asphyxiate CTS eggs. Excessive sedimentation ultimately fills pools otherwise usable by 

the STS. Sedimentation may also impair the CTS from detecting food items (USFWS, 

2000). Many STS breeding populations inhabit roadside ditches in place of pools or 

ponds because these ditches are the last remaining habitats available (USFWS, 2003). 

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

increase in both roadside ditches and the 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 rodenticides used to control 

these two species, the CTS may potentially be at risk from indirect exposure to them 

inside the burrows or concentrated in breeding ponds (USFWS, 2003). Some of these 

rodenticides used in Sonoma County include chlorophacinone, diphacinone, and 

strychnine (USFWS, 2003). Fumigants are other pesticides used for rodent control, such 

as aluminum phosphide, carbon monoxide, and methyl bromide, which are injected into 

burrows by using a cartridge or by pumping (USFWS, 2003). These fumigants can be 

both directly and indirectly lethal to the CTS, although the effects of these poisons on 

CTS have not been assessed (USFWS, 2003). Besides the use of rodenticides, control of 

rodents by means of eliminating burrows results is a loss of tenable 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 rodent control due to 

the landscaping concerns of developed areas (USFWS, 2003). Cattle owners also destroy 

ground squirrel burrows, and, thus, eliminate CTS habitat because the burrows put cattle 

at risk of breaking their legs (USFWS, 2003). 

Road-Crossing Mortality

Although no ‘systematic’ studies of road-crossing mortality of CTS in Sonoma County 

have been conducted, CTS killed by vehicular traffic have been documented both in 

Sonoma County and in other portions of the species ranges. In addition to the road kills 

mentioned previously, in one study there were 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. Estimations of CTS mortality from vehicular 

strikes range from 25 to 72 percent. Mortality may be increased by the presence of curbs 

69
and berms, which allow salamanders to climb onto the road but can restrict their 

movement off of the road (USFWS, 2003). 

Livestock Grazing

As opposed to many factors that negatively affect the CTS, grazing can, in moderation, 

have a neutral to positive impact on the CTS. Grazing maintains shorter vegetation and 

promotes the persistence of ground squirrel burrowing, which creates habitats essential 

for the CTS. Rangelands not only provide natural vernal pools, but artificial stock ponds, 

which 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 

still compatible with CTS as long as burrowing rodents are not completely eradicated 

(USFWS, 2004). 

7.2.2 Baseline Status 

The CTS is found only in California. The historic 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 southern 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 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). 

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

Plain are uncertain due to limited information 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 elevation, seasonally filled breeding ponds and small 

rodent burrows, the ecology of the taxon, the general trend of urban development, and 

other adverse factors affecting the species. The closest CTS populations to Sonoma 

County are located in Contra Costa, Yolo, and Solano Counties, which are separated from 

the Sonoma County population by the Coast Range, Napa River, and the Carquinez 

Straits, and distance of about 72 km (USFWS, 2003). 

Population Dynamics 

Currently, the Sonoma County CTS and the Santa Barbara CTS are considered the most 

vulnerable populations of California tiger salamanders. Urban development causing 

habitat loss continues to be the primary factor affecting their continued existences, and 

both populations are particularly vulnerable to the risks associated with 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 future environmental changes, 

thus reducing overall fitness. Small populations are also threatened by the deterioration 

of environmental quality (USFWS, 2003) 

70
 

Although the total number of individual CTS in Sonoma County is unknown, the STS 

population is scattered in isolated breeding sites 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 around the City of Santa 

Rosa. Other sightings of STS had been documented in locations south of the Cotati area 

in roadside ditches and low quality pools, although these locations were not considered 

viable breeding sites. The eight viable breeding sites were defined as follows: (1) Hall 

Road Preserve; (2) Federal Emergency Management 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 preserved 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 population 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 productive STS breeding sites, and the Broadmore 

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

encroaches on the site from the north and east sides, and a new road and housing 

development on the west partially blocks the migration route to breeding pools at the Air 

Center. This construction, as of 2003, was only 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-owned preserve, salamanders were not found at 

this breeding habitat until the 2001/2002 rainy season. The presence of Todd Road along 

the southern boundary of the preserve threatens 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 rendering the breeding area isolated from the 

remaining seven (USFWS, 2003). 

5) Southwest Air Center

71
This breeding site also consists of one pond on private land. The City of Santa Rosa has 

issued permits for development that will likely extirpate the population from this site. 

The destruction of the breeding area will further isolate this population and all STS 

populations, although individuals may still utilize the breeding areas in the 

FEMA/Broadmore Preserve (USFWS, 2003). 

6) North Air Center

This breeding site consists of one pond on private land. Migration 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 temporarily 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; however, no protection exists to prevent breeding 

sites and upland habitat from being developed. The City of Santa Rosa approved 

residential development along Wright and Ludwig Avenues, which will concomitantly 

destroy habitat and increase vehicular traffic (USFWS, 2003). 

8) South Ludwig

The condition or existence of this population 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 breeding sites and upland habitat from being 

developed. Threats from increased traffic on Ludwig Avenue threaten this population 

(USFWS, 2003). 

Not long after the STS was listed as endangered, six additional breeding sites were 

recognized: (1) Gobbi; (2) Duer Road; (3) Haroutunian; (4) Alton Lane; (5) Southwest 

Community Park; (6) Yuba Drive. All breeding locations with the exception of 

Haroutunian and Alton Lane are 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 development 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 component 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). 

72
7.3 References

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

Office. United States Fish and Wildlife 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/servlet/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. Federal Register 65 

(184):57242-57264. Available online at 

http://ecos.fws.gov/speciesProfile/SpeciesReport.do?spcode=D01T (Accessed 

January 25, 2009). 

United States Fish and Wildlife Service (USFWS). 2002. Endangered and threatened 

wildlife and plants; listing the Sonoma County distinct population segment of the 

California tiger salamander as endangered. 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 (USFWS). 2003. Endangered and threatened 

wildlife and plants: determination of endangered status for the Sonoma County 

distinct population segment of the California tiger salamander. 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 threatened 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 (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 (USFWS). 2007 a. Endangered and threatened 

73
wildlife and plants; designation of critical habitat for the bay checkerspot butterfly 

(Euphydras editha bayensis); proposed rule. Accessed online at 

http://ecos.fws.gov/speciesProfile/SpeciesReport.do?spcode=I021. (Accessed on 

October 16, 2008). 

United States Fish and Wildlife Service (USFWS). 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). 

74
8: DELTA SMELT 

8.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 (Act). The non-federal actions that are 

reasonably certain to occur within the action area consist of urbanization, toxic substance 

contamination of Sacramento-San Joaquin Delta water, and water resource developments 

for agriculture and municipal demands. The 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 developments increase in number, the volume 

of outflow in the Delta incrementally diminishes and causes complex consequences for 

the delta smelt. Coupled with seasonal fluctuations in precipitation, these water 

diversions act synergistically to hinder sufficient food resources, influence natural flow 

patterns, physically entrain individuals in pumping facilities, change non-native species 

abundance, and alter concentrations 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 snapshot 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 number 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 smelt 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 presented as part of the baseline status in 

Section 8.2.2. 

8.2.1 Factors affecting species environment within the action area 

The delta smelt is highly vulnerable to extinction because of its short life span, present 

small population size, and restricted distribution (USFWS, 1993). According to the 

USFWS Sacramento-San Joaquin Delta Native Fishes Recovery Plan (USFWS, 1996), 

delta smelt decline has multiple and synergistic causes (USFWS, 1996). The Plan listed 

75
the following causes in order of relative importance to the species decline: (1) Reduction 

of outflows; (2) Entrainment losses to water 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 rearing areas in upstream locations, the Delta, and Suisun Bay 

and Marsh (USFWS, 1996). While the trend of building large-scale water projects 

upstream that deplete Delta inflows has subsided, huge demands on already dwindling 

water resources will continue as the population 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 weak stock-recruitment relationship (ie., little 

evidence of the effect of parent population size on subsequent recruitment), which 

indicates that environmental or habitat factors 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 downstream to shallow water areas around Suisun 

Bay (USFWS, 1996). Production of zooplankton and phytoplankton are promoted by the 

well-mixed shallow water and offer rich feeding grounds for the delta smelt (USFWS, 

1996). Both a reduction and an increase in the 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 and diversions are determined to be the 

primary cause of delta smelt decline, particularly 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 phytoplankton is lower due to 

lack of sunlight penetration (USFWS, 1996). Inadequate food resources in these habitats 

result in threats of poor nutrition and starvation for the delta smelt (USFWS, 1996). 

While no statistical relationship has been found between outflow rate and abundances of 

delta smelt, Kimmerer (2002) has shown a change in abundance as it relates to historical 

flow (USFWS, 2004a). Moyle and 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 declines 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 (USFWS, 1996). Years of high delta smelt 

abundance were strongly correlated with springtime location and duration of the 2 parts 

per thousand (ppt) bottom isohaline (X2) demarcation (USFWS, 2004a). This correlation 

76
is supported by the higher captures of delta smelt below 2 ppt and in shallow habitats 

(when waters of 2 ppt are near shallow habitats). The link between preferred habitat and 

fall abundance of the delta smelt also supports the notion that suitable habitat (eg. 

available nursery habitat) may limit population abundance (USFWS, 2004a). 

High outflows also change the Delta hydrology, although the resulting consequences to 

the delta smelt are less severe than those resulting from reduced outflows (USFWS, 

1996). High outflows may flush delta smelt and its spawn out of the system, along with 

its food source, zooplankton (USFWS, 1996). These depleted populations of 

invertebrates reduced the native fish populations 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. Especially 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 islands (USFWS, 1996, 2004a). Efforts are made to salvage the 

detained fish and truck them back to the Delta, but only those fish longer than 20 mm are 

rescued (USFWS, 2004a). Unfortunately, effectiveness 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 their 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 from entrainment (USFWS, 2004a). Studies 

have quantified the losses of entrained larvae and juvenile delta smelt and have estimated 

numbers to be around several million (USFWS, 2004a). More studies are being 

conducted, as the season, location, and size of the diversion are all major factors 

influencing entrainment (USFWS, 2004a). The 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 conditions (USFWS, 2004a). They have estimated the loss of 

juvenile smelts to the CVP and SWP operations 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 conditions within the Delta have been removed 

77
since the 1970s due to water exports: delta smelt were more abundant in the delta and less 

abundant in Suisun Marsh in pre-decline period, and delta smelt are now less abundant in 

the Delta and more abundant in Suisun Marsh1

 (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 operating 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, increasing central delta flows toward the state and federal 

export facilities (USFWS, 2004a). These barriers are currently being 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 California, six new projects are proposed that would 

greatly increase the amount of water diverged and would likely result in lower Delta 

outflows and increased entrainment (USFWS, 2004a). 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 Expansion; (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 agencies, 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 Increase1 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 ft3

/s, 

to 8,500 ft3/s, eventually 

reaching 10,300 ft3/s. 

State Water Projects (SWP) 

Banks pumping plant 

 

1 This “decline” period refers to the years of 1982-1983 when the delta smelt population took a precipitous 

decline, and populations numbers stayed consistently low though the years 1984-1992 (USFWS, 1995, 

2004a, 2004b). 

78
Reclamation and CDWR Construction of a 400 ft3

/s 

intertie connecting their 

aqueducts, increasing 

pumping ability from 4,200 

to 4,600 ft3/s. 

Increased pumping at Tracy 

Pumping Plant. 

CALFED2 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 ft3/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). While a study by Kimmer (2002) demonstrated 

that the delta smelt declined in abundance 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 plankton 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 graze on (USFWS, 2004a). Thus, the growth of 

this diatom may also be implicated in zooplankton 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 with 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 items 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). 

79
8.2.1.4 Disease, Predation, and Competition 

Disease 

The bacterium Mycobacterium ssp. and its correlated disease, mycobacteriosis, has been 

identified as potentially impacting the delta smelt (USFWS, 2004a). In a study by 

Antonio et. al. (2000), presence and infections from 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 water 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 population, with infections breaking out under 

intensive culture conditions (USFWS, 2004a). The relevance and threat to wild delta 

smelt populations remain unknown at this 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 after an accidental introduction in 1975, and 

estimates of silverside population abundance are inversely correlated with that of the 

delta smelt (USFWS, 2004a). Further, shallow 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 planktivore 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 that have seen population 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 result in loss of valuable gametes of 

felta smelt and hinder the population from 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 viable offspring (USFWS, 2004a). According to 

Swanson et al. (2000), temperature, salinity, and flow tolerances of the delta smelt place 

it at a disadvantage to the wakasagi against suboptimal conditions (USFWS, 2004a). 

 

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8.2.2 Baseline Status 

The delta smelt currently occupies its historic 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 are relatively cool, usually less than 20-22 

degrees Celsius in the summer (68-72 degrees Fahrenheit) (USFWS, 1996 and 2004b). A 

substantial population size is necessary to compensate for a life history that is at a 

disadvantage in current Delta conditions: pelagic life style, short life span, spawning 

habits, weak swimming ability compared with other Delta fishes, and relatively low 

fecundity (USFWS, 2004a). 

Population Dynamics

The Summer Tow Net Survey data show an almost complete disappearance of juvenile 

delta smelt in the south delta sampling stations by the mid-1970s (USFWS, 2004a). 

Additional studies have shown that the population 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 running 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 continuing 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 and temperature regimes that favor the smelt 

(USFWS, 2004a). Thus, the USFWS has concluded 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 individuals between 1 million and 12 million 

(USFWS, 2004a). The USGWS and others have identified flawed methods with this 

estimation, specifically in the reinterpretation of the Fall Midwater Trawl (FMWT) index 

(USFWS, 2004a). The USFWS acknowledges 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 which are likely to demonstrate different 

abundances and distributional patterns in different parts of their range are unlikely to be 

estimated with any useful degree of accuracy (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 the probability of extinction of delta smelt (USFWS, 2004a). 

They estimated that if the sub-adult population 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 

81
estimating extinction probability would result in a severe underestimate (USFWS, 

2004a). Bennett (2003) provided another type of analysis (USFWS, 2004a). He 

evaluated the likelihood of delta smelt populations falling below an “effective population 

size” (ie. a Fall Midwater Trawl index of less 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, Joeseph J Cech Jr., Randy C. Mager, Sergei 

Dorshov, and Ronald P. Hedrick. 2000. Prevalence of Mycobacterium in Wild 

and Captive Delta Smelt. California 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 flow 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 Division, 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 and Wildlife Service, Portland, Oregon. 

Available online at: http://ecos.fws.gov/docs/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). 

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

the Issuance of Section 10 and 404 Permits 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, California. 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 Central Valley Project and the State Water 

Project on the Threatened Delta Smelt, Delta 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 Five Year Status Review of the Delta 

Smelt. 3 pp. 

83
9: SALT MARSH HARVEST MOUSE 

9.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 considered because they are subject to 

consultation pursuant to Section 7 of the Endangered Species Act (Act). Numerous nonfederal actions that could affect the SMHM 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. Many of these activities are linked and create complex consequences for the 

listed species in the action area. These factors 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 developments exacerbate the inland extent of tides by 

reducing SMHM escape cover from predators. Moreover, predatory impacts are 

intensified as urbanization displaces predators 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 the status of the species, its habitat, and ecosystem, within 

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

time. Details of the SMHM’s habitat description and known locations are included in 

Attachment III. However, the baseline condition of each assessed SMHM species and 

habitat varies across locations. Given the large number of occupied habitats and extent of 

the action area included in this assessment, the 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 affecting 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 environment within the action area 

In the US Fish and Wildlife Service (USFWS) Recovery Plan (1984), SMHM decline is 

attributed to five primary factors: 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 

84
most significantly to SMHM decline. These factors all relate to habitat alteration and are 

discussed together in Section 9.2.1.1. Predatory impacts also affect the SMHM and its 

environment. Predators include cats, non-native 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 the 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 tidal marsh bordering San Francisco Bay has 

occurred since 1850, with the greatest degree of destruction occurring in the southern Bay 

region (USFWS, 1984). This destruction is attributed to urbanization, and the filling and 

diking of wetland areas (USFWS, 2007a). Diked wetlands only 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 more 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 (South San Francisco Bay) has caused salt 

water vegetation to be degraded and converted to freshwater and brackish water 

vegetation. The South Bay wastewater facilities in the Alviso and Sunnyvale areas are 

responsible for the freshwater input into about 600 acres of previous 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 marsh 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 from 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 establishing in the salt 

marshes and mud flats in the San Francisco Estuary and threaten the physical and 

biological ecology of the estuary (SFEISP website). Three of these species, “S. 

85
densiflora, S. patens and S. alterniflora-hybrids can all displace native pickleweed 

(Salicornia spp.), which provides critical habitat for the salt marsh harvest mouse” 

(SFEISP website). Non-native Spartina populations 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 especially in South San 

Francisco Bay, have eliminated the peripheral halophyte zone which is important to the 

SMHM (USFWS, 1984). The upper peripheral halophyte zone of most marshes has been 

filled in, covered over, or converted to salt ponds. Certain marshes are completely 

submerged during high tides, leaving insufficient 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 subsidence 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 subspecies of SMHM is also endangered due 

to commercial and residential development around San Francisco Bay which has caused a 

decrease in the available pickleweed habitat (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, egrets, herons, clapper 

rails, and other raptors, the SMHM also has non-native predators such as cats (house and 

feral), dogs (feral) and red foxes (USFWS, 1984; Shellhammer, 1998; CDFG, 2000; 

Rendon, 1999; CDPR online; Goals Project, 2000; and eNature, 2007). Other predators 

may include gulls, weasels, and other mammals (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 the SMHM (Goals Project, 2000). Predator 

control, usually for red foxes, has been implemented in several marshes containing 

California clapper rails and SMHM; however, predator control is not typically found in 

marshes that may only contain SMHM (Goals Project, 2000). Non-native predators have 

gained access to the SMHM habitat because most remaining marshes share an upper side 

with a leveed salt pond, business park, or subdivision (Shellhammer, 1998). The amount 

of upland buffer necessary to protect the SMHM from predators (especially cats) is 

currently unknown (Goals Project, 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 interactions between rodent species within the diked marshes; 

however, one study in 1988 showed that SMHM were seasonally displaced from 

“optimal habitat by California voles” (Goals Project, 2000). In addition, little is known 

about the interaction between SMHM and non-native rats. The non-native Norway and 

roof rats are considered potential predators of the SMHM and are known to occur with 

86
the SMHM in several marshes (Goals Project, 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 SMHM (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 potential habitat; (2) create new habitat; (3) 

restore upper portions of marshes; (4) conduct additional biological research; and (5) 

continue ongoing management. The Plan documented several recovery actions by the 

USFWS and the California Department of Fish 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 Marsh, and other smaller marshes and bays along 

the San Francisco Bay coast. 

Conservation plans have continued to be implemented in the 24 years since the Recovery 

Plan was publicly released. One Habitat Conservation 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 diked and salt water-degraded marshes, acquisitions of private 

property for wetland restoration, the South Bay Restoration Project involving the Cargill 

Company, and conversions of agricultural land to marsh habitat. These conservation 

actions are described in Winton, 2001; 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 (USFWS, 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 their distribution (USFWS, 1984 and 2007a). 

Populations of SMHM occur in the diked marshes near Collinsville and in both diked and 

tidal marshes along the Contra Costa County coast (USFWS, 1984). The 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 

87
the presence of SMHM (USFWS, 1984). However, 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 the 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) (USFWS, 1984). In 1980, SMHM populations in 

several of the larger marshes around the Bay, including Petaluma Marsh, Corte Madera 

Ecological Reserve, Benecia State Park (Southampton Bay), areas west of Pittsburg, 

Belmont, New Chicago Marsh near Alviso, along Mowry Slough, and along the Alameda 

Flood Control Channel were either extremely 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 Bay National Wildlife 

Refuge headquarters in Newark, near the mouth of Old Alameda-Mt. Eden Creek, and the 

Collinsville marshes (USFWS, 1984). In the mid-1980s, there appeared to be a few 

thousand animals at the peak of their numbers each summer, distributed around the Bay 

in small, disjunct populations, often in marginal vegetation and almost always in marshes 

without an upper edge of upland vegetation (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 deteriorating due to the decreasing salinity and 

corresponding vegetation changes (Goals Project, 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 New 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 California Department of Fish and Game 

(CDFG), in cooperation with the California Interagency Wildlife Task Group. 

Database version 8.1. Available online at: 

http://www.dfg.ca.gov/biogeodata/cwhr/lha/lha_M114.pdf and 

http://sibr.com/mammals/M114.html (Accessed on September 9, 2008).

88
Buffa, J. 2007. U.S. Fish and Wildlife Service – 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 (CDFG). 2000. The Status of Rare, Threatened, 

and Endangered Animals and Plants of California 2000. Available online at 

http://www.dfg.ca.gov/wildlife/species/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/show_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 plants, fish and wildlife. Prepared by the 

San Francisco Bay Area Wetlands Ecosystem 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/servlet/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 – Lingering 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/species/rodent/reitravi.htm#IUCN (Accessed on 

September 9, 2008). 

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

89
December 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 online). Coastal Conservancy. 

Salt Marsh Harvest Mouse (Reithrodontomys raviventris). Available online at: 

http://www.southbayrestoration.org/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/Departments/Parks+and+Recreation/Parks/Baylands/Natu

re+and+Preservation/SaltMarshHarvestMouse.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/DivisionSites/ConservationLibrary/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 Salt Ponds to Wetlands for Wildlife at 

Don Edwards San Francisco Bay National Wildlife 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/animal_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 

90
Mouse (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 Islands National Wildlife Refuges – Refuges 

in the North Bay. Tideline. Vol 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. Bay Nature. Special Section, OctoberDecember 2004. Available online at: 

http://www.baynature.com/2004octdec/v04n04s_voices.html (Accessed on 

September 9, 2008). 

91
10: SAN FRANCISCO GARTER SNAKE 

10.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 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 (Act). The 

numerous non-federal actions that are reasonably certain to occur within the action area 

consist of expansion of utility matrices, residential and commercial developments, 

recreational facilities, land management, agriculture, dredging, channelization, flood 

control, and overutilization. Many of these factors are linked or act synergistically and 

create complex consequences for the SFGS. For example, roads often impede dispersal 

and movement of species. Highways with heavy 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 the water quality from chemical 

run-off and thus affect the recruitment 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 snapshot of the SFGS status at this time. 

However, the baseline condition of each assessed SFGS 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 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 environmental baseline section is a summary of 

information presented in the 5-Year Review: Summary and Evaluation of the San 

Francisco Garter Snake (USFWS, 2006b). 

10.2.1 Factors affecting species environment within the action area 

SFGS are primarily affected by habitat loss and 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 degradation continues to be the primary cause 

today. Other influential factors include overutilization, disease, predation, and invasive 

92
species. Additional anthropogenic and natural factors 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 lower 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 expansion of infrastructure, management practices, 

and fluctuating water levels. The expansion of infrastructure causes habitat 

fragmentation by increasing residential and commercial developments such as new roads, 

utility matrices, and recreational activities and facilities. Management practices, such as 

seral succession, use of perch ponds (e.g., shallow man-made ponds for irrigation often 

used in San Mateo County), decreased use of stock ponds, and practice of dredging 

waterways may result in SFGS habitat loss and degradation. In addition, fluctuating 

water levels in reservoirs, channelization and flood control, and saline inundation events 

can also affect habitat 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 development as well as intense agriculture 

operations (San Mateo County Department of Agriculture, 2004). Table 10.1 shows a 

number of proposed urbanization projects within San Mateo County that potentially 

threaten known populations of the SFGS. These five projects are currently undergoing 

consultation with the USFWS (USFWS 1996b). Other urbanization projects 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 within 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 

93
Pilarcitos 

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 projects 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 project affected 0.38 acres of wetlands that 

provided foraging and dispersal area for the SFGS due to substation expansion. The 

construction also temporarily affected 7.55 acres 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 temporary disturbance, but it indicates the 

continuing threat of habitat destruction for the SFGS (USFWS, 2006a). The expansion of 

a Bay Area Regional Transportation (BART) station at the San Francisco International 

Airport (SFO) bisected a West of Bayshore SFGS population (USFWS,1996b; California 

Department of Fish and Game, 2005). The BART expansion project required the 

realignment of a creek and Cupid’s Row Canal, and human activity during the 

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

construction caused the take of SFGS individuals, 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 restoration activities at West of Bayshore 

(USFWS, 1996b). However, both mitigation efforts were never fully realized (McGinnis, 

pers.comm. 2006), and no further information on the efforts is available (USFWS, 

2006b). 

The increased growth in human population has increased the demand for recreational 

opportunities and supported the growth of golf courses. Recreational activities, such as 

running and jogging, are not threats 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 private and protected public land. 

Chemical and pesticide use at golf courses contaminates nearby lakes and streams that 

are not usually associated with urban development. These waterways are important 

aquatic habitats and movement corridors for the SFGS and its primary anuran prey base. 

Chemical applications may potentially contribute 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 County resulted in the mortality of the 

California Red-Legged Frogs (Rana aurora draytonii) and their larvae (USFWS, 2002a). 

Similar events causing direct mortality of the SFGS are a possibility. 

Management Practices 

Changes in management practices have encouraged 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 process 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 rodent 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 potentially inhibits rodent burrowing (D. Hankins, in 

litt. 2006). The absence of domestic grazing, which results in thick brush canopies, 

renders grassland habitat unsuitable for the SFGS. Seral conditions in aquatic habitats 

also threaten the SFGS and its amphibian prey. 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 contribute to the loss of suitable SFGS 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 

95
been plowed, but not from fields that had been grazed or burned (Conant et. al., 1945). 

More recent studies have found garter snake numbers to be lower than average in suitable 

wildlife habitats surrounded by plowed agricultural areas (Keller and Heske, 2000). 

Scientists attribute these low numbers primarily to plowing activities and speculate that 

heavy machinery increases soil compaction, reduces overall soil tilth (physical condition 

of the soil in relation to its fitness for growth), 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 decreasing. 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 used for irrigation, water levels fluctuate 

between growing seasons. Rapid draw-down for summer crops, a high utilization period, 

removes much of the water and renders the ponds unsuitable for the SFGS and amphibian 

prey species (McGinnis, 1984; McGinnis, 1987; San Mateo County Department of 

Agriculture, 2004). Perch ponds further affect the SFGS because the water is acquired 

from nearby waterways. Extracting water from these creeks and streams results in 

unreliable water levels, potentially extirpating the SFGS and its prey species (McGinnis, 

1984). 

Shallow ponds are important habitats for SFGS 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 masses may become exposed to predation and 

dry out when water levels drop. In areas where their prey species are unable to survive, 

SFGSs will likely disperse and potentially be subject to predation. Rapid draw down also 

increases the potential for bullfrogs to establish 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 the feeding opportunities 

of the SFGS (P. Keel, pers. comm. 2006). Bullfrogs pose a direct threat to the SFGS 

because they consume juvenile individuals, although the SFGS may also feed on juvenile 

bullfrogs. While the predatory threat 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 (Freel and Giorni, 1994). 

Degradation of riparian habitats, stream channelization, and increased levels of salinity in 

freshwater habitats also threaten the SFGS (USFWS, 1985; Larsen, 1994). Alterations in 

stream and riparian habitats reduce the connectivity between sites, limit these habitats 

from functioning as movement areas, and reduce the complexity of streams serving as 

migration corridors (USFWS, 1985). Both the SFGS and its amphibian prey are 

negatively affected by these alterations (California Department of Fish and Game, 2005). 

Salinity in freshwater is detrimental to anurans, as concentrations over 7.0 ppt are lethal 

to Pacific tree frogs and their larvae (Larson, 1994). Increased salinity has been 

documented in a number of areas used as habitat by the SFGS, and the presence of salinetolerant plants indicates degradation in freshwater quality (S. O’Brien, pers. comm. 

96
2006). Places affected by salinization 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 recreational, scientific, commercial, and 

educational purposes has decreased in recent years, it is still considered a threat to the 

species according to employees with the California State Parks (J. Kerbavaz, pers. comm. 

2006; P. Keel, pers. comm. 2006). During the 1970s and 1980s, illegal take was a 

primary threat occurring at SFGS 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 and 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 rarity, 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 SFGS take enforcement (P. Keel, pers. comm. 

2006). 

10.2.1.3 Disease and Predation 

 

Disease, parasites, and predation all negatively affect the SFGS. Of the three, disease 

caused by the chytrid fungus is the most threatening. The chytrid fungus 

(Batrachochytrium dendrobatridus), a lethal parasite, poses an indirect threat to the 

SFGS by drastically affecting its anuran prey base. The fungus has caused an epidemic 

that has seen prolific growth throughout the 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 warming, inhabit locations 

where humidity is high and daily temperature extremes are minimized (P. Johnson in litt., 

2006). A chytrid fungus pandemic can spread rapidly and is capable of wiping out entire 

amphibian populations on the Peninsula. Combined 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 known to affect the SFGS include tapeworms, 

flagellate protists, and nemotode worms (Larson, 1994). Several juvenile mortalities in 

the West of Bayshore are attributed to these three types of parasites. Parasitic tapeworms 

and thorny-headed worms may use mosquito fish as hosts in the northern Bay area. 

97
Various 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 bullfrogs 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 predators 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 predators 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 population 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 California red-legged frog and the Pacific tree frog, two significant 

food sources of the SFGS (Lawler et al., 1999; USFWS, 2002b). Bullfrogs may also 

compete with the California red-legged 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 preclude competition. Some scientists argue that 

the cooler annual climate on the Peninsula limits reproduction and prevent bullfrogs from 

out-competing native frogs that are better adapted to the cooler temperatures (Barry, 

1994; P. Keel, pers.comm. 2006). 

10.2.1.4 Other natural and anthropogenic factors affecting existence 

Invasive species, such as the bullfrog (discussed in the preceding paragraph), threaten the 

continued existence of the SFGS. Other invasive 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 California 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 and 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 level 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 

98
mortality from vehicular strikes. 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 and 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 pollutants and are adversely affected by roads in 

proximity to wetlands. Storm water runoff contaminates aquatic habitats and reduces 

recruitment of anuran individuals, potentially contributing to the decline of the SFGS. 

Hybridization and interspecific competition have been suggested as possible low level 

threats to the SFGS. A broader range of color variation in western populations lends 

support to the idea of hybridization (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 County, SFGSs are mainly found in the coastal 

areas, in addition to other small inhabited locations (USFWS, 2005). A population in San 

Bruno Mountain once represented the most northeastern extension of the range, although 

today it may be extirpated. The San Bruno Mountain population may have been moved 

to that area for conservation purposes by amateur herpetologists. The species from the 

Half Moon Bay region may have had a similar origin from attempted conservation, 

although no exact records are available for confirmation (Barry, 1994). Regardless, the 

species remain extant at Half Moon Bay (McGinnis, 1988). 

The current distribution is not precisely known 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 and 2007). The historic distribution of the 

SFGS extends just north of the San Francisco-San Mateo County line near Merced Lake 

south to Waddell Creek located within the Big Basin Redwoods State Park. The 

population at Waddell Creek is questionable because 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 certain locales, and field studies in these areas 

are restricted due to private property (California Natural Diversity Data Base, 2006). The 

99
historic distribution extends along the western coast of the peninsula south to Ano Nuevo 

State Reserve (ANSR). On the eastern edge of their range, the SFGS 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 throughout 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 practices of disking and planting cycles increases 

the fragmentation of suitable habitat (Barry, 1994). Sightings of the SFGS have occurred 

in the Upper Crystal Springs Reservoir and Mud Dam in 1998 (San Francisco Planning 

Department, 2001). Others sightings have been recorded from “San Andreas Reservoir 

and in a sag pond between San Andreas and Crystal Springs” (San Francisco Planning 

Department, 2001). Currently, wild SFGS populations 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 San Francisco Peninsula (Kaplan, 2002 and 

Goals Project, 2000). The total SFGS population is believed to be around 1500 snakes 

over one year old (Kaplan, 2002 and Goals Project, 2000). All young under one year old 

are not included in population counts because the population increases when the young 

are born and returns to around 1500 the following spring due to insufficient resources 

(Kaplan, 2002). It is thought that 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 populations 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 Springs Reservoirs), 4) Pescadero Marsh 

Natural Preserve, 5) Ano Nuevo State Reserve (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 population trends. Alternatively, these trends 

are inferred from current habitat dynamics and conditions. 

West of Bayshore

Sufficient population data exists to reveal a trend for the West of Bayshore habitat, near 

the SFO. At one time, this area was considered to hold the largest SFGS population, and 

between 1983 and 1985, 695 individuals were captured (USFWS, 1985; Natureserve in 

litt., 2006; Larsen, 1994). Based on another study completed in the mid-1990s, only 179 

individuals were captured (Larsen, 1994). Although drawing comparisons between the 

studies is difficult due to different methods and sampling techniques, both studies 

indicate that the population has declined. A third trapping occurred in 1997 before the 

construction of the Bay Area Regional Transport (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 limited region of the West of Bayshore habitat, 

100
the 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 population are expected due to ongoing construction 

and habitat degradation. The reduction in the open water component of the canal system 

in recent years has led to a decrease in suitable habitat for an amphibian prey base. Both 

increases in vegetation and siltation reduce the quantity and quality 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 Salada is also thought to have declined. This population 

trend can be attributed to two influxes of salt water into the snake’s habitat in the 1980s 

(Steiner and Hafernik, 1992). No salination events have occurred since a protective levee 

was built, and it has been suggested that the snakes never historically occupied the site 

(Barry, 1994). Other detrimental activities include off-road vehicle use and illegal trash 

dumping at the Mori Point area (Steiner and 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 Service, pers. comm. 2006), although no 

information on these actions has been provided (USFWS, 2006b). Further relief has 

come from a partnership between the National Park Service and the USFWS via an 

agreement to construct two ponds for amphibian 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 greater Laguna Salada area. Although the SFGS 

historically occupied Laguna Salda at Mori Point, the species is not thought to currently 

exist in this area (McGinnis, 1990; McGinnis, pers. comm. 2006). The extirpation of the 

SFGS occurred after ponds in the area were filled and agricultural disking practices were 

implemented in 1990 along Calera Creek. Prior to these landscape changes, high 

occurrences of SFGS individuals were reported in Calera Creek Channel (McGinnis, 

1990; McGinnis, pers. comm. 2006). Following these changes, no sightings have been 

reported at Calera Creek based on informal walk-through surveys (MsGinnis, pers. 

comm.; K. Swaim, pers. comm. 2006). Observations from 1978 and 1990 indicate that 

there may have been SFGS movement between the Calera Creek corridor and Mori Point, 

based on SFGS sightings along a ridgeline separating 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 species (S. Larsen, pers. comm. 2006; H. 

McQuillen, pers. comm. 2006). 

San Francisco State Fish and Game Refuge

101
This 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 the SFGS because of the restricted access 

designated near the reservoirs (J. Naras pers. comm. 2006). Large quantities and high 

densities of individuals have been observed (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 refuge increase human presence and possible 

disturbances to the SFGS. One SFGS individual was run over by a bicycle 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 plan 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 thought to be declining, despite recent 

improvements in certain habitat conditions (USFWS, 2006b). This population has been 

deemed genetically significant 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 group) than any other population (Larsen, 

pers.comm. 2006). Pescadero Marsh has regular 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 information on those actions is provided 

(USFWS, 2006b). The SFGS now inhabits eastern portions of the marsh and a few 

artificial ponds that are adjacent to originally 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 limit 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 needed to evaluate the effectiveness of the 

project; however, it is anticipated to help the population (A. Willy, pers.comm. 2006). 

Ano Nuevo State Reserve (ANSR)

There have been sightings of the SFGS at the ANSF since 1975. In 1987, 13 SFGS 

individuals were trapped around the headquarters’ pond (Barry, 1978; McGinnis et al., 

1987). In 1988, a more comprehensive survey 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 large numbers, in part, to the 

available wetlands and suitable upland foraging sites for amphibian prey. Between 2004 

and 2005, the California State Parks and the USFWS performed two burns on 45 acres of 

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

102
surveys 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, additional information is needed to access the 

effectiveness of burn disturbance in improving 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 future. The California State Parks is currently 

discussing acquisition of the land, which would 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 private property discussed in the Recovery Plan for the SFGS 

(USFWS, 1985). Little is known about the population 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 (Biosearch Associates, 2003). The final monitoring report in 2005 

demonstrated that the recovery plan had succeeded in providing suitable habitat for the 

SFGS as well as its amphibian prey (Biosearch Associates, 2005). In 1994, Cascade 

Ranch was designated as a “high quality” SFGS habitat due to the presence of ANSR 

breeding ponds nearby. However, the presence 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

103
Goals 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 Ecosystem 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. Melissa Kaplan’s Herp Care Collection.Last 

 updated April 19, 2007. Available online at: http://www.anapsid.org/garters.html 

 (Accessed on October 16, 2007). 

104
Myers, 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 

105
 San Francisco Planning Department. 2001. Peninsula Watershed Management Plan – 

 Final Environmental Impact Report (EIR). 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 section 7 consultation for Pacific Gas and 

 Electric’s Jefferson-Martin 230kV Transmission 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 construction of a clean-up and restoration and 

 development of a bicycle and pedestrian trail in Oak Avenue Park along Pilarcitos 

 Creek, City of Half Moon Bay, San Mateo County, California. Service file # 1-1-06- 

106
 0197. 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/animal_spp_acct/sf_garter_snake.pdf (Accessed on 

 October 16, 2007). 

Personal Communication

107
In Litt. References 

108
109
11: SAN JOAQUIN KIT FOX 

11.1 CUMULATIVE EFFECTS 

Cumulative effects include the effects 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 considered because they require additional 

consultation under Section 7 of the Endangered Species Act (Act). The numerous nonfederal actions that are reasonably certain to occur within the action area consist of 

industrial and petroleum field development, agriculture, surface mining, and urbanization 

projects related to infrastructure, irrigation canals, wind farms, power lines, and 

aqueducts. Many of these factors are linked or act synergistically and create complex 

consequences for the SJKF. More specifically, these habitat modifications compress and 

fragment the species’ range. Combined with 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 snapshot of the SJKF status at this time. 

However, the baseline condition of the assessed SJKF’s habitat varies across locations. 

Given the large number 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 the SJKF within the action area. This information is presented in Section 11.2.1. 

Additional information on the current distribution and population dynamics 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 section 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 environment within the action area 

The San Joaquin kit fox was listed as “endangered” by the U.S. Fish and Wildlife Service 

(USFWS) in 1971. More than 90% of its native habitat in the San Joaquin Valley has 

become fragmented or destroyed as a result 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 

110
declines through displacement, reduction in prey abundance, and direct 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-native invasion, predation, and competition; and (2) disease and 

climatic extremes. A detailed discussion of these 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 primarily by industrial, agricultural, and urban 

developments that readily reduce the size and quality of available 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 intensity 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 networks, non-petroleum industrial 

projects, power lines, and wind farms. While these actions are detrimental to suitable 

habitat, the SJKF may still utilize 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 levees (Jones and Stokes, 1981; Hansen, 1988), 

abutting highways (ESA Planning and Environmental 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, pers. 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, demonstrate 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 grading of roads, well pads, tank 

settings, pipelines, and settling ponds. Habitat is degraded from noise, ground vibrations, 

venting of toxic and noxious gases, and the release of petroleum 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 adequate 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 were reported between populations living on 

developed or undeveloped areas of the reserve (Berry et al., 1987a). Likewise, a 

111
correlation between population size and habitat disturbance for SJKF populations in Kern 

County is unclear. Nonetheless, 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 Santa Clara Valley (T. Rado, pers.comm.). Red 

foxes are also implicated in declines in the northwestern portion of their range (USFWS, 

1998). Red foxes may potentially limit opportunities for the SJKF through competition 

or predation. Competition arises from the foxes 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 expansion 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 their effects are nonetheless mentioned as 

adversely affecting the species. For example, coyote injuries are listed as the primary 

factor in the majority of SJKF mortalities (White et al., 2000). Coyotes will 

“aggressively dominate encounters with red foxes and will pursue and kill” red, gray 

(Sargent and Allen, 1989), and kit foxes. However, a coyote control program at the 

Naval Petroleum Reserves in California reported no increase in survivorship among the 

SJKF, nor was there a decrease in coyote-induced mortality (Cypher and Scrivner, 1992; 

Scrivner and Harris, 1986; Scrivner, 1987). Incidentally, the coyote may simultaneously 

benefit the SJKF by reducing the competition and predation by the non-native red fox. 

The gray fox is a native species which may 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 implicated in SJFK mortality (USFWS, 1983). At 

Camp Roberts, rabies caused a 6.3 percent decline 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 significant threat is posed by stochastic 

environmental events, particularly drought and flooding. Drought affects the 

reproductive success of the SJKF by affecting the availability of prey (White and Ralls, 

1993; Spiegel et al. in press). There is a concern of local extinctions in certain isolated 

areas. Excessive rainfall also adversely affects prey populations. The above-average 

rainfall in 1994-1995 caused a “rapid and severe” decline of small mammal populations. 

Fewer pupping dens were found in the Elk Hills region in 1995, and the proportion of 

pup rears was relatively small (B.L. Cypher pers. comm., L.K. Spiegel pers. comm.). 

112
11.2.2 Baseline Status 

Though the SJKF has been listed for over 30 years, the status throughout most of its 

range is poorly known, in part due to limited access on private properties. Despite the 

lack of a comprehensive survey, research projects, incidental sightings, 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, Tehachapi Mountains (from southern Kern County 

north to Contra Costa, Alameda, and San Joaquin 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, Kings, Fresno, Madera, and Merced Counties. 

Kit foxes occur westward into the interior coastal ranges in Monterey, 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 San Luis Obispo County. Kit foxes are also 

known to live within the city limits of the city of Bakersfield in Kern County (USFWS, 

1998). 

“The largest extant populations of kit foxes 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 populations of Elk Hills and the City of 

Bakersfield, Kern County, Carrizo Plain Natural 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, Merced County, North Grasslands and Kesterson 

National Wildlife Refuge area on the Valley floor, Merced County, and in the Los 

Vaqueros watershed, Contra Costa County in the early 1990s. Smaller populations and 

isolated sightings of kit foxes are also known from other parts of the San Joaquin Valley 

floor, including Madera County and eastern Stanislaus County” (USFWS, 1998, p.124) 

Population Dynamics 

The SJKF is known for its instability in population size. It is not uncommon for the 

SJKF population to fluctuate fivefold 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 and vegetative biomass, leading to associated fluctuations 

in leporids (rabbits and hares) and rodents. Ultimately, these density independent 

variables lead to fluctuations in kit fox reproductive rates. Both extended episodes of 

drought or rainfall can contribute to low reproduction and population crashes (White et 

al. 2000). 

The San Joaquin kit fox is found within three or four core populations, and approximately 

nine satellite populations that vary in size and degree of isolation (White et al. 2000). 

113
These core populations are thought to “anchor 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 inhabited by kit foxes (e.g., Elk Hills, 

Buena Vista Hill, and the Buena Vista Valley, 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 environmental conditions, as 

manifested in their unsynchronized population dynamics (B.L. Cypher, pers. comm.). 

Population viability studies suggest that extinction probabilities increase dramatically if 

either the Carrizo Plain or western Kern County population is extirpated. The 

combination of these three populations is advantageous compared to other groupings, 

because they are all more or less interconnected 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 Region at Camp Roberts and Fort Hunter 

Liggett. This population has natural connections 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 owner incentive programs have been initiated to reduce the 

degree of isolation between populations and promote conservation of SJKF populations 

on agricultural lands. These initiatives should ensure that farmers are not penalized, 

farming is not disrupted, and habitats are protected 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 the larger populations “along 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 SJKF 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 Joaquin kit fox at Camp Roberts, California, 

1981. Unpubl. Rep., U.S. Department of Army, 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. 

114
1987. Sources and rates of mortality 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 control to protect endangered San Joaquin 

kit foxes at the Naval Petroleum Reserves, California. Pp. 42-47, in Proceedings 

of the 15th 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, Alameda County, California. Unpubl. Rep., 

California Department of Fish and Game, Sacramento, 34 pp. 

Hansen, R.B. 1988. Porterville urban area boundry biotic survey. Unpubl. Rep., Hansen’s 

Biological Consulting, Visalia, CA, 219 pp. 

Jones and Stokes Associates, Inc. 1977. Ground squirrel control, Fort Ord Complex, Fort 

Ord, California. U.S. Department Army, HQ 7th Infantry Division, Fort Ord, 

Sacramento, CA, Final Environmental impact 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. Golightly, 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 distribution and abundance in 1975. California 

Department of Fish and Game, Sacramento, Wildlife Management Branch, 

Admin. Rep. No. 75-3, 28 pp. 

115
O’Farrell, T.P., and P.M. McCue. 1981. Inventory of San Joaquin kit fox on USBLM 

lands in the western San Joaquin Valley—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 endangered giant kangaroo rat, 

Dipodomus ingens, on the Naval Petroleum Reserves, Kern County, California. 

Rep. No. EGG 10282-2173, Santa Barbara 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 Energy Measurements, Goleta, CA, 74 

pp. + Appendices. 

Orloff, S.G., F. Hall, and L. Spiegel. 1986. Distribution and habitat requirements of the 

San Joaquin kit fox in the northern extreme of their range. Trans. West. Sect. 

Wildl. Soc. 22:60-70. 

Ralls, K., and P.J. White. 1995. predation on endangered 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. Harris. 1986. Summary and evaluation 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. Dao. In press. Reproduction of San Joaquin kit 

fox (Vulpes macrotis mutica) in undeveloped and oil developed habitats of kern 

County, California. In, Studies of San Joaquin kit fox in undeveloped and oil 

developed areas. California Energy 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. Rep. No. EGG 10617-2157, EG&G Energy 

Measurements, Goleta, CA, 19 pp. 

Swick, C.D. 1973. Setermination of San Joaquin kit fox range in Contra Costa, Alameda, 

San Joaquin, and Tulare Counties, 1973. California Department of Fish and 

Game, Sacramento, Spec. Wildl. Invest., Unpubl. Rep., 15 pp. 

116
U.S. Fish and Wildlife Service (USFWS). 1998. Recovery plan for upland species for the 

San Joaquin Valley, California. Region 1, Portland, OR. 319 pp. 

U.S. Fish and Wildlife Service (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 availability. 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 population of kit foxes. The Southwestern 

Naturalist 45(2): 204-211. 

Personal Communication 

Cypher, B.L., Program Manager, Enterprise Advisory 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 Research Biologist, Camp Roberts Endangered 

Species Study Group, San Luis Obispo, CA. 

 

117
12: VALLEY ELDERBERRY LONGHORN BEETLE 

11.2 CUMULATIVE EFFECTS 

Cumulative effects include the effects of future state, tribal, local, private, or other nonfederal entity activities on the valley elderberry longhorn beetle (VELB) (Desmocerus 

californicus dimorphus) that are reasonably certain to occur in the action area. Future 

federal actions unrelated to the proposed action are not considered because they are 

subject to consultation pursuant to Section 7 of the Endangered 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 effects on listed species or their habitat in the 

action area. For example, maintenance 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 further 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 the 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 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 includes 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 distribution and population dynamics of the VELB 

is presented as part of the baseline status in Section 12.2.2. Tables 12.1, 12.2, and 12.3, 

present restoration and preservation 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 section 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 environment 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 species. When the species was first listed by 

118
the United States Fish and Wildlife Service (USFWS), 90% of the riparian habitats that 

once occupied the Central Valley 150 years 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 within the species range, 

although for mitigation purposes, adjoining habitat conservation plans for each action are 

also underway. These plans are in conjunction with former and ongoing riparian 

restoration and conservation activities. Projects 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, State 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 contributing to VELB decline. In particular, the 

removal of riparian habitat, and as a consequence the removal of the elderberry host plant 

(Sambucus spp.), has been the primary factor since the species was first listed as 

“Threatened” in 1980. The overall loss continues to this day (USFWS, 1984 and 2007a). 

This reduction in habitat is linked to urban development, flood controls, levees and 

canals, agriculture, and park management. These factors have the potential to remove, 

degrade or fragment VELB habitat. The species is particularly sensitive to these adverse 

factors because of its high habitat 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 historically been a major threat to the VELB. Between 1900 and 

1990, there was a 96% loss of riparian habitat 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 remaining 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 south, 65% loss in the middle, and 35% loss in 

the northern Central Valley (Geographic Information Center, 2003). Quantifying the 

actual loss of elderberry is difficult, however. It is uncertain how much of the riparian 

habitat contained elderberry, or even if it was occupied by the VELB (USFWS, 2006). 

The VELB “is in long-term decline due to human activities that have resulted in 

widespread alteration and fragmentation of riparian habitats, and to a lesser extent, 

upland habitats, which support the beetle” (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 riparian loss has slowed 

significantly due to the decreasing number of existing riparian 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, oak woodland, and mixed chaparral-woodland. 

119
Since 1980, the USFWS has allowed an estimated incidental take of 10,000 to 20,000 

acres of beetle habitat, for the purposes 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 elderberry 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 1980s 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 (USFWS, 2006). Non-Federal parties 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 canals for the purposes of flood control and 

agriculture could result in a loss of habitat for the VELB (Talley et al. 2006). 

Historically, artificial levees, river channelization, dam construction, water diversion, and 

heavy groundwater pumping have all been attributed to the destruction of VELB habitat 

(USFWS, 1984). Flood control levees constructed 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 restoration projects, the potential benefits to the beetle are 

undermined. However, land owner incentive programs, discussed later, offer a means to 

mitigate the threat to the VELB caused by levee 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 impacts these predators have on the beetle 

(USFWS, 2006). The Argentine ant is an aggressive competitor and appears to be the 

main predator of the VELB (Huxel, 2000). The ant displaces native 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 time period increased by a factor 

of 3 (Huxel, 2000; Holyoak and Talley, 2001). According to Huxel (2000), there was a 

negative correlation between the 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 prey 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). 

120
Insectivorous birds, insectivorous lizards and the European earwig are 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 scavenger 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 urban areas, and like the Argentine ant, 

also in riparian and irrigation areas because of the availability 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 species 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-woody 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 the VELB and the black locust. However, 

this positive association was thought to be temporary as elderberry would soon be 

crowded out (Talley et al., 2006). 

Other issues attributed to VELB habitat decline include grazing 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 the California Department of Fish and Game 

(CDFG) biologists, cattle “readily” forage on new elderberry growth (USFWS, 1984). 

Additionally, rodents may damage new saplings, and voles have reportedly girdled 

elderberry shrubs at two different 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 occur in the few natural woodlands remaining, 

further reducing suitable habitat (USFWS, 1980). 

12.2.1.3 Habitat Protection and Restoration 

The number of riparian restoration projects and protective actions 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 existing riparian habitats, the enhancement or 

restoration of riparian habitats plus the planting of elderberry shrubs, or the enhancement 

or restoration of riparian habitats without the planting of elderberry. Table 8.1 provides a 

summary of projects in which riparian habitat 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 protected approximately 50,000 acres of existing land. Table 8.2 

provides a summary of projects in which riparian habitat was restored and elderberry 

121
were plated in the Central Valley (excerpted from Talley et al. 2006). Seven agencies are 

responsible for 19 projects which have or are restoring 5,193 acres of habitat and planting 

130,345 elderberry saplings. Table 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 Much 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 

122
Fine 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 # EB1

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 TNC 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 Sacramento 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 Sacramento 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 

123
Mining 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 riparian habitat was restored yet no 

elderberry were planted in the Central 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 

124
Thomas 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 habitat from year-to-year. The colonization of 

the beetle may be difficult to overcome because of a barrier or dispersal limitation. The 

site should also be ecologically suitable for elderberry species over the long term 

(USFWS, 2006). For example, although some restoration projects do not plan on directly 

introducing elderberry, the projects may still 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 rate than if it had been directly planted (River 

Partners, 2003, River Partners 2004b). Factors such as the distance from known beetle 

locations, suitability of the habitat for elderberry 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 developed 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 their property for the benefit of 

endangered species through issuance of Section 10 permits, without incurring additional 

regulatory restrictions (EDF, 2008; USFWS, 2006). The landowner opines to return the 

property to its “baseline condition”, the mutually 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 agreement 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 and 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 Valley (Barr, 1991). Records primarily based 

125
on exit holes indicate that there are roughly 190 locations in the Central Valley where the 

beetle is known to occur (California 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 representative 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 locations. 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 elderberries 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-riparian scrub area to 7-11.2% of shrubs in 

riparian reaches of Putah Creek and the American 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 holes 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 affect the accuracy of population estimates. 

The two main types of survey error include overestimates 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 beetle 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 holes 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 beetle’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 studies observed the VELB at roughly 20% of 

the sites and on approximately 25% of the elderberries examined. Although the 

126
proportions of occupancy between the two studies 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 elderberry 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 variation 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 compensated for by restored habitats (Talley et 

al. 2006). Compared to the historic extent of habitat reduction, the total area of restored 

and enhanced habitats still remains quite small. Restoration and mitigation efforts are 

valuable, however, with the hope that proactive efforts will provide habitat for persistent 

and sustainable metapopulations. Mitigation efforts to replace elderberry shrubs more 

than compensate for the number of elderberry lost to development, but the quality, size, 

and persistence of these shrubs 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 significant, unquantified number of elderberries 

may be planted in upland, non-riparian, areas which are not preferred habitats for the 

VELB. Incidentally, even with an overall net population loss, there is not a strong trend 

toward decline or recovery (Talley et al. 2006). 

12.3 REFERENCES 

Literature Cited

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beetle, Desmocerus californicus dimorphus. U.S. Fish and Wildlife Service, 

Sacramento, California. 134 pp. Available online at: 

http://www.fws.gov/sacramento/es/documents/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 

127
Fragmentation and population persistence of the threatened valley elderberry 

longhorn beetle in central California. Biological Conservation 100:103-113. 

Environmental Defense Fund (EDF). 2008. Providing a safe harbor for endangered 

species on private land. Environmental 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 woodlands. Oecologia (Berlin) 116:252-258. 

Huxel, G. R. 2000. The effect of the Argentine 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 Annual 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 populations of the valley 

elderberry longhorn beetle along the Sacramento River. USDA Forest Service 

General Technical Report PSW 110:242-247. 

LSA Associates, Inc. 2004. Valley Elderberry Longhorn Beetle. Solano HCP/NCCP. 

Solano County Water Agency. Species Descriptions. Available online at: 

http://www.scwa2.com/hcp/Final%20Draft%202.0/Appendices/APPX%20BSpecies%20Descriptions/Valley%20Elderberry%20Longhorn%20Beetle.pdf

(Accessed on July 24, 2008). 

River Partners. 2003. River Partners 2003 Annual Report. River Partners, Chico, 

California. 16 pp. 

River Partners. 2004a. Survey of planted elderberry on Sacramento River National 

Wildlife Refuge riparian restoration sites for use by valley elderberry longhorn 

beetles, Tehama, Butte and Glenn County, California. Report prepared for: U.S. 

Fish and Wildlife Service. Helen Swagerty and Scott Chamberlain, authors. River 

Partners, Chico, Claifornia. 

River Partners. 2004b. Riparian habitat restoration, Sacramento River Wildlife Area, 

Mouton Weir Unit. Colusa County, California. Final Report. Michelle Cederborg, 

author. River Partner, Chico California. 

River Partners. 2004c. Riparian habitat restoration, Sacramento River Wildlife Area, Pine 

Creek Unit. Glenn and Butte County, California. Final report. Helen Swagerty 

and Michelle Cederborg, authors. River Partners, Chico California. 

128
River Partners. 2004d. Riparian habitat restoration, Upper Butte Basin Wildlife Area, 

Fields 229 and 232 of the Howard Slough Unit. Glenn County, California. Final 

report. Helen Swagerty, author. 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. Murphy, and A. Ballard. In press. Rethinking 

a rare-species conservation strategy in an urbanizing landscape. The case of the 

valley elderberry longhorn beetle. 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/documents/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 Critical 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 Wildlife Service, Portland, Oregon. 62 pp. 

Available online at: 

http://www.fws.gov/sacramento/es/recovery_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 Sacramento 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/documents/velb_coe_prog_text.htm (Accessed 

on July 24, 2008). 

U.S. Fish and Wildlife Service (USFWS). 2006. 5-Year Review: Summary and 

Evaluation for the Valley Elderberry Longhorn Beetle (Desmocerus californicus 

dimorphus). U.S. Fish and Wildlife Service, 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). 

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