ATTACHMENT II: 

STATUS AND LIFE HISTORY OF THE SAN FRANCISCO BAY 

LISTED SPECIES 

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TABLE OF CONTENTS 

1: ALAMEDA WHIPSNAKE........................................................................................... 5 

1.1 Species Listing Status.............................................................................................. 5 

1.2 Description............................................................................................................... 5 

1.3 Distribution and Status............................................................................................. 5 

1.4 USFWS Critical Habitat .......................................................................................... 6 

1.5 Habitat.................................................................................................................... 11 

1.6 Diet......................................................................................................................... 11 

1.7 Life History and Reproduction .............................................................................. 11 

1.8 References.............................................................................................................. 12 

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

2.1 Species Listing Status............................................................................................ 14 

2.2 Description............................................................................................................. 14 

2.3 Distribution ............................................................................................................ 14 

2.4 USFWS Critical Habitat ........................................................................................ 15 

2.5 Habitat.................................................................................................................... 15 

2.6 Diet......................................................................................................................... 16 

2.7 Life History and Reproduction .............................................................................. 16 

2.8 References.............................................................................................................. 17 

3: CALIFORNIA CLAPPER RAIL ................................................................................ 18 

3.1 Species Listing Status............................................................................................ 18 

3.2 Description............................................................................................................. 18 

3.3 Distribution ............................................................................................................ 19 

3.4 USFWS Critical Habitat ........................................................................................ 21 

3.5 Habitat.................................................................................................................... 21 

3.6 Diet......................................................................................................................... 24 

3.7 Life History and Reproduction .............................................................................. 24 

3.8 References.............................................................................................................. 28 

4. CALIFORNIA FRESHWATER SHRIMP.................................................................. 32 

4.1 Species Listing Status............................................................................................ 32 

4.2 Description and Taxonomy.................................................................................... 32 

4.3 Distribution and Status........................................................................................... 32 

4.4 USFWS Critical Habitat ........................................................................................ 34 

4.5 Habitat.................................................................................................................... 34 

4.6 Diet......................................................................................................................... 36 

4.7 Life History and Reproduction .............................................................................. 37 

4.8 References.............................................................................................................. 38 

5: CALIFORNIA TIGER SALAMANDER: CENTRAL CALIFORNIA, SANTA 

BARBARA, AND SONOMA COUNTY DISTINCT POPULATION SEGMENTS ..... 39 

5.1 Species Listing Status............................................................................................. 39 

5.2 Description and Taxonomy..................................................................................... 39 

5.3 Distribution ............................................................................................................. 40 

5.4 USFWS Critical Habitat ......................................................................................... 41 

5.5 Diet......................................................................................................................... 51 

5.6 Life History and Reproduction ............................................................................... 51 

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5.7 References............................................................................................................... 53 

6: DELTA SMELT .......................................................................................................... 55 

6.1 Species Listing Status............................................................................................ 55 

6.2 Description and Taxonomy.................................................................................... 55 

6.3 Distribution and Status........................................................................................... 55 

6.4 USFWS Critical Habitat ........................................................................................ 56 

6.5 Habitat.................................................................................................................... 57 

6.6 Activity, Movement, and Behavior........................................................................ 58 

6.7 Diet......................................................................................................................... 58 

6.8 Life History and Reproduction .............................................................................. 58 

6.9 References.............................................................................................................. 59 

7: SALT MARSH HARVEST MOUSE.......................................................................... 61 

7.1 Species Listing Status............................................................................................ 61 

7.2 Description............................................................................................................. 61 

7.3 Distribution ............................................................................................................ 61 

7.4 USFWS Critical Habitat ........................................................................................ 62 

7.5 Habitat.................................................................................................................... 62 

7.6 Diet......................................................................................................................... 62 

7.7 Life History and Reproduction .............................................................................. 63 

7.8 References.............................................................................................................. 63 

8: SAN FRANCISCO GARTER SNAKE....................................................................... 65 

8.1 Species Listing Status............................................................................................ 65 

8.2 Description............................................................................................................. 65 

8.3 Distribution ............................................................................................................ 65 

8.4 USFWS Critical Habitat ........................................................................................ 67 

8.5 Habitat.................................................................................................................... 67 

8.6 Diet......................................................................................................................... 69 

8.7 Life History and Reproduction .............................................................................. 70 

8.8 References.............................................................................................................. 70 

9: SAN JOAQUIN KIT FOX .......................................................................................... 73 

9.1 Species Listing Status............................................................................................ 73 

9.2 Description............................................................................................................. 73 

9.3 Distribution ............................................................................................................ 73 

9.4 USFWS Critical Habitat ........................................................................................ 74 

9.5 Habitat.................................................................................................................... 74 

9.6 Diet......................................................................................................................... 75 

9.7 Life History and Reproduction .............................................................................. 76 

9.8 References.............................................................................................................. 76 

10: VALLEY ELDERBERRY LONGHORN BEETLE................................................. 79 

10.1 Species Listing Status.......................................................................................... 79 

10.2 Description............................................................................................................ 79 

10.3 Distribution .......................................................................................................... 79 

10.4 USFWS Critical Habitat ...................................................................................... 81 

10.5 Habitat.................................................................................................................. 82 

10.6 Diet....................................................................................................................... 84 

10.7 Life History and Reproduction ............................................................................ 84 

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10.8 References............................................................................................................ 86 

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1: ALAMEDA WHIPSNAKE 

1.1 Species Listing Status 

The Alameda whipsnake (Masticophis lateralis euryxanthus) was listed as threatened on 

December 5, 1997 (62 FR 64306) by the U.S. Fish and Wildlife Service (USFWS) 

(USFWS, 1997 and Westphal, 1998). A recovery plan for the chaparral and scrub 

community species east of San Francisco Bay, California was approved by the USFWS 

on March 20, 2003 (USFWS, 2003 and 2005). Critical habitat was designated for this 

subspecies on October 2, 2006 (USFWS, 2005 and 2006). 

1.2 Description 

The Alameda whipsnake is one of two subspecies of the California whipsnake 

(Masticophis lateralis) (USFWS, 2003 and 2005). The other subspecies, which is more 

common, is the chaparral whipsnake (Masticophis lateralis lateralis) (USFWS, 2005). 

The Alameda whipsnake was described in 1954 from a total of six specimens collected in 

the vicinity of Berkeley, Alameda County, and near Somersville, Contra Costa County, 

and from Mount Diablo, Contra Costa County, California (USFWS, 1997). 

The Alameda whipsnake, also known as the ‘Alameda striped racer’, is a member of the 

family Colubridae which includes most of the species of snakes found in the western 

United States. It is a slender, fast-moving, diurnally active snake with a slender neck, 

broad head and large eyes (USFWS, 1997, 2003, 2005, and 2006). Adult whipsnakes 

obtain lengths of 3 to 4 feet (91 to 122 centimeters). Their dorsal side is colored “sooty” 

black or dark brown with a distinguishing yellow-orange stripe down each side. Their 

ventral side is comprised of an amber brown-colored frontal section, a cream-colored 

midsection, and a pinkish rear and tail section (USFWS, 1997 and 2005). 

1.3 Distribution and Status 

Historical Range 

The historical range of the Alameda Whipsnake is difficult to determine due to limited 

collection data. Six specimens were identified when the Alameda whipsnake was first 

described in 1954. Up until 1970, the total number of observations and specimens of the 

Alameda whipsnake amounted to 14, and two of these specimens were later identified as 

chaparral whipsnake (USFWS, 2003). These limited collections and observations 

suggest that the historical distribution extended through Berkeley Hills and around Mt. 

Diablo (USFWS, 2003). However, the Alameda whipsnake likely inhabited suitable 

chaparral and scrub habitats within Alameda, Contra Costa, and possibly western San 

Joaquin and northern Santa Clara Counties (USFWS, 2003 and 2005). 

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Current Distribution 

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, 2005, and 2006). The current distribution of the 

subspecies has been reduced to five separated ranges, all occurring on private or public, 

non-Federal, land, with little or no interchange due to habitat loss, alteration, and 

fragmentation: 

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 2005). 

The potential for gene flow between these five disjointed populations is limited to only 

two or perhaps three habitat-connecting corridors. A northern corridor connects the 

Tilden-Briones and the Oakland-Las Trampas populations, and a southern corridor links 

Hayward-Pleasanton Ridge and Sunol-Cedar Mountain populations. The remaining 

natural habitat between the populations provides land for movement, but whether the 

Alameda whipsnake can utilize these areas to promote gene flow remains unknown. For 

instance, the Oakland-Las Trampas population and the Hayward-Pleasanton Ridge 

population are divided by Interstate 580, and it has not yet been determined whether 

whipsnakes can move between these populations by traveling underneath the raised 

portions of the road (USFWS, 2003). Therefore, there may be some subpopulations 

within each population that are geographically and genetically isolated, and others that 

may contribute to gene flow within each population (USFWS, 2003). 

1.4 USFWS Critical Habitat 

Approximately 154,834 acres (ac) (62,659 hectares (ha)) of critical habitat in the counties 

of Alameda, Contra Costa, Santa Clara, and San Joaquin was designated for the Alameda 

whipsnake on October 2, 2006 (USFWS, 2005 and 2006). Critical habitat is defined in 

the Endangered Species Act (ESA) as specific areas within the geographic area that are 

occupied by a species at the time of its listing, containing physical and biological features 

necessary for the species’ conservation, and that may require special management to 

protect the listed species (USFWS, 2006). Critical habitat is not limited to the geographic 

area and may include defined areas outside the geographic area if they are determined to 

be essential for the conservation of the species (USFWS, 2006). The designation of 

critical habitat is based on habitat areas that provide essential life-cycle needs of the 

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species or areas that contain primary constituent elements (PCEs). The PCEs for the 

Alameda whipsnake include: 

1) Scrub/shrub communities with a mosaic of open and closed canopy: “Scrub/shrub 

vegetation dominated by low- to medium-stature woody shrubs with a mosaic of 

open and closed canopy, as characterized by the chamise, chamise-eastwood 

manzanita, chaparral whitethorn, and interior live oak shrub vegetation series 

occurring at elevations from sea level to approximately 3,850 feet (1,170 meters)” 

(USFWS, 2006). 

2) Woodland or annual grassland plant communities contiguous to lands containing 

PCE 1: “Woodland or annual grassland vegetation series comprised of one or 

more of the following: Blue oak, coast live oak, California bay, California 

buckeye, and California annual grassland vegetation series” (USFWS, 2006). 

3) Lands containing rock outcrops, rock debris piles (talus), and small mammal 

burrows within or adjacent to PCE 1 and/or PCE 2: “These areas are used for 

retreats (shelter), hibernacula, foraging, and dispersal, and provide additional prey 

population support functions” (USFWS, 2006). 

Six units of critical habitat comprising 154,834 ac (62,659 ha) were designated for the 

Alameda whipsnake (Table 1.1) (USFWS, 2006). 

Table 1.1: Critical habitat units for Alameda whipsnake1 by land ownership 

(excerpted from USFWS, 2006) 

Unit Federal State Local Private Total 

ac ha ac ha ac ha ac ha ac ha 

1 -- -- 15 6 8,108 3,281 25,997 10,520 34,119 13,808

2 -- -- -- -- 4,386 1,775 20,050 8,114 24,436 9,889 

3 -- -- -- -- 404 163 25,562 10,345 25,966 10,508

4 23 9 13,855 5,607 -- -- 9,348 3,783 23,225 9,399 

5A 2,492 1,008 -- -- 246 99 21,986 8,897 24,723 10,005

5B -- -- -- -- 361 146 17,854 7,225 18,214 7,371 

6 -- -- 720 291 265 107 3,166 1,281 4,151 1,680 

Total 2,515 1,018 14,590 5,904 13,768 5,572 123,962 50,166 154,834 62,659

1

Area [acre / hectare (ac / ha)] estimates reflect all land within critical habitat unit boundaries 

Unit 1: Tilden-Briones; Alameda and Contra Costa Counties

This unit is bordered approximately by State Highway 4 and the cities of Pinole, 

Hercules, and Martinez to the north; by State Highway 24 and the City of Orinda Village 

to the south; Interstate 80 and the cities of Berkeley, El Cerrito, and Richmond, to the 

west; and Interstate 680 and the City of Pleasant Hill to the east. The South end of Unit 1 

abuts Unit 6. Land ownership within the unit includes approximately 8,108 ac (3,281 ha) 

of land owned by the East Bay Regional Park District (EBRPD), 15 acres (6 ha) owned 

by the State, and 25,997 ac (10, 520 ha) of land owned privately (USFWS, 2006). 

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This unit is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently, and represents the 

northwestern portion of the subspecies’ range as well as representing one of five 

population centers (USFWS, 2006). Unit 1 “contains a complex mosaic of grassland 

with woody scrub vegetation of several types (PCE 1, PCE 2), as well as rock outcrops or 

other talus features (PCE 3) distributed throughout the unit with little habitat 

fragmentation” (USFWS, 2006). Alameda whipsnake occurrence has been documented 

uniformly throughout the unit, spanning a time period from before the species’ listing to 

after in 1986 (USFWS, 2006). In addition, this unit has been subjected to very little 

development (USFWS, 2006). 

Unit 2: Oakland-Las Trampas; Contra Costa and Alameda Counties

Unit 2 is located south of State Route 24, north of Interstate 580, east of State Route 13, 

and west of Interstate 680 and the cities of Danville, San Ramon, and Dublin. The North 

edge of Unit 2 abuts Unit 6. Land ownership includes 4,386 ac (1,775 ha) of EBRPD and 

East Bay Municipal Utilities District lands and 20,050 ac (8,114 ha) of land under private 

ownership (USFWS, 2006). 

Unit 2 is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently by the subspecies, and 

represents the central distribution of the Alameda whipsnake as well as representing one 

of five population centers (USFWS, 2006). This unit “contains a range of vegetation 

(PCE 1, PCE 2), soil types, and rocky features (PCE 3) essential to the conservation of 

the subspecies, supports viable Alameda whipsnake populations, and has minimal 

development such as roads and structures” (USFWS, 2006). Areas not included in the 

critical habitat were those with development or reduced soil and vegetation 

characteristics (USFWS, 2006). Multiple records have documented the Alameda 

whipsnake uniformly distributed within the unit as well as adjacent to the unit, and 

dispersal of snakes between Units 2 and 1 is possible by way of Unit 6 (USFWS, 2006). 

Impediments to such movement do not appear to be present (USFWS, 2006). 

Unit 3: Hayward-Pleasanton Ridge; Alameda County

Unit 3 is located immediately to the west of Interstate 680 and to the south of Interstate 

580. Land ownership includes 404 ac (163 ha) of EBRPD land and 25,562 ac (10,345 

ha) of privately owned land (USFWS, 2006). The Stonebrae Country Club project site 

was not included in the critical habitat for this unit (USFWS, 2006). 

This unit is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently by the subspecies, and 

represents the southwestern portion of the subspecies’ range as well as representing one 

of the five population centers (USFWS, 2006). “Unit 3 contains the mosaic of scrub and 

chaparral vegetation and rocky outcrops (PCE 1, PCE 3) considered essential to the 

conservation of the subspecies. The unit also includes variation in the vegetation patch 

size, an abundant edge between grassland and woodland, and a minimal amount of 

development or planned development” (USFWS, 2006). The records of Alameda 

whipsnake occurrence have been associated with areas containing Gaviota rocky sandy 

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loam, likely providing talus, and appear to coincide in aerial imagery to the species’ 

preferred scrub or chaparral vegetation (USFWS, 2006). Unit three is largely comprised 

of oak woodland communities of variable densities and statures (trees, shrubs), 

interspersed with grassland. Peripheral portions of habitat surrounding the unit were not 

included as critical habitat due to the high degree of development-related disturbance and 

fragmentation of the habitat (USFWS, 2006). 

Unit 4: Mount Diablo-Black Hills; Contra Costa and Alameda Counties

This unit encompasses Mount Diablo State Park and surrounding lands, which lies 

largely within Contra Costa County except for a small portion within Alameda County. 

Lands are owned by the Bureau of Land Management (23 ac (9 ha)), State Department of 

Parks and Recreation (13,855 ac (5,607 ha)), and private landowners (9,348 ac (3,783 

ha)) (USFWS, 2006). EBRPD lands and lands covered by the draft East Contra Costa 

County Habitat Conservation Plan and Natural Community Conservation Plan were not 

included from the critical habitat in this unit (USFWS, 2006). 

Unit 4 is designated as critical habitat for this subspecies because it contains features 

essential to the conservation of the Alameda whipsnake, is occupied currently by the 

subspecies, and represents the northeastern portion of the subspecies’ range as well as 

representing one of the five populations centers (USFWS, 2006). From 1972 to 2004, 

more than 90 observations of Alameda whipsnake have been documented throughout the 

unit, many of which are associated with dense rock outcrops (PCE 3) and chaparral, 

scrub, and oak woodland (PCE 1, PCE 2). “The pattern of woody vegetation with 

grasslands and rock outcrops forms an intricate landscape mosaic that is highly functional 

habitat for the Alameda whipsnake” (USFWS, 2006). Unit 4 likely provides some of the 

very highest quality and largest contiguous blocks of habitat within the range of the 

subspecies, indicated by the vegetation and soil characteristics, the mosaic habitat pattern, 

the abundance of Alameda whipsnake records, and the lack of surrounding development 

and relative absence of roadways. The unit also likely supports one of the species’ most 

robust populations (USFWS, 2006). 

Unit 5A: Cedar Mountain; Alameda and San Joaquin Counties

Unit 5A is located east of Lake Del Valle along Cedar Mountain Ridge and Crane Ridge 

to Corral Hollow west of Interstate 580. Land ownership within this unit includes 

approximately 2,492 ac (1,008 ha) of Department of Energy land, 246 ac (99 ha) of 

EBRPD land, and 21,986 ac (8,897 ha)) of private land (USFWS, 2006). 

Unit 5A is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently by the subspecies, and 

represents the southernmost and easternmost distribution of Alameda whipsnake as well 

as representing one of the subspecies’ five populations centers (USFWS, 2006). “The 

vegetation pattern within this unit consists of various woodland, scrub, and/or chaparral 

communities on northeast-facing slopes (PCE 1, PCE 2). Rock bearing soils are 

abundant, which are associated with multiple Alameda whipsnake records (e.g., 

Vallecitos rocky loam) and rock lands, indicated presence of PCE 3. While open, 

grassland-dominated communities are prominent on southwest-facing slopes, there is also 

9
a significant component of woodland habitat on these slopes, vegetation types known to 

support the Alameda whipsnake. These significant areas include coastal oak, chamisechaparral, mixed chaparral, blue-oak-foothill pine woodland, blue oak woodland, valley 

oak woodland, and montane hardwood. About 50 Alameda whipsnake records from 

1973 through 2002 are known in this unit. Very few structures or other land 

modifications are present in the unit, with a moderate number of light duty roads (e.g., 

paved or unpaved lightly used) (USFWS, 2006). 

Unit 5B: Alameda Creek; Alameda and Santa Clara Counties

This unit is located northeast of Calaveras Reservoir and south of the town of Sunol, 

including the areas along Wauhab Ridge in Alameda County and Oak Ridge in Santa 

Clara County. Alameda Creek is located at the west margin of the unit, with the unit 

containing the Sunol Regional Wilderness and Camp Ohlone Regional Park 

(approximately 361 ac (146 ha)). Both the Wilderness and Park are managed by the 

EBRPD, and the remaining 17,854 ac (7,225 ha) of land are in private ownership 

(USFWS, 2006). 

Unit 5B is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently by the subspecies, and 

represents the southern most distribution of Alameda whipsnake as well as representing 

one of the subspecies’ five population centers (USFWS, 2006). The vegetation in this 

unit “is a mix of blue oak—foothill pine and annual grassland with a significant amount 

of woodland patches. Coastal live oak is present in the vicinity of Lleyden Creek” 

(USFWS, 2006). Soil types in which Alameda whipsnakes are found dominate the unit, 

including coastal oak, chamise-chaparral, mixed chaparral, blue oak—foothill pine 

woodland, blue oak woodland, valley oak woodland, and montane hardwood interspersed 

with rock outcrops or talus (PCEs 1, 2, 3). This subunit contains six Alameda whipsnake 

records documented between 1972 and 2000. Very few structures or other land 

modifications are present in the unit, with a moderate number of light duty roads (e.g., 

paved or unpaved lightly used) (USFWS, 2006). Due to low development pressure from 

within or adjacent to the unit, the survey efforts for the Alameda whipsnake in unit 5B 

have not been as extensive as in the other units (USFWS, 2006). 

Unit 6: Caldecott Tunnel; Contra Costa and Alameda Counties

Unit 6 lies between Units 1 and 2, along the Alameda and Contra Costa County lines. 

Land ownership within this unit includes 265 ac (107 ha) of EBRPD land, 720 ac (291 

ha) of State land, and 3,166 ha (1,281 ha) of private lands (USFWS, 2006). 

Unit 6 is designated as critical habitat because it contains features essential to the 

conservation of the Alameda whipsnake, is occupied currently, and represents the last 

remaining habitat connecting Unit 1 and Unit 2, which are two of the five population 

centers for the subspecies. Maintaining connectivity between the units allows for 

dispersal and genetic exchange among all three units (USFWS, 2006). This “unit is 

bounded by dense urban development to the east and west. However, the vegetation and 

soil types that are known to support Alameda whipsnake are dominant throughout the 

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unit (PCEs 1, 2, 3)” (USFWS, 2006). About eight Alameda whipsnake records are 

known from the unit between 1990 and 2002 (USFWS, 2006). 

1.5 Habitat 

 

Alameda whipsnakes have been documented in several types of scrub and chaparral 

communities, including coastal sage scrub, chaparral, and northern coastal scrub. 

Telemetry data for six snakes indicated that home ranges of Alameda whipsnakes were 

centered on shrub communities, but that snakes ventured into adjacent habitats, including 

grassland, oak savanna, and oak-bay woodland. Radio locations of telemetered snakes 

were clustered in areas of scrub with an open or partially open canopy, and on south-, 

southwest-, southeast-, east-, and northeast-facing slopes. Most radio locations for five 

snakes at a study site in Tilden Regional Park, Berkeley, California, were within the 

distribution of major rock outcroppings and talus. The study also found Alameda 

whipsnakes frequently in adjacent grasslands and oak woodland/savanna habitats. Most 

grassland and woodland locations were within 50 meters (170 feet) of the scrub habitat, 

but distances of greater than 150 meters (500 feet) from scrub were also documented 

during the telemetry study. The distance that whipsnakes will move into open grassland 

is unknown; however, California whipsnakes have been observed in grassland, oak 

savanna, and along the edge of riparian vegetation at distances greater than 300 meters 

(1,000 feet) from scrub habitats, usually in areas where rock outcrops are abundant 

(USFWS, 2003). The majority of grassland use was documented during spring. The 

most common types of retreat site in both the grassland and scrub communities were 

small rodent burrows and rock crevices; however, brush piles, deep soil crevices and 

debris piles were also used (USFWS, 2003). 

1.6 Diet 

Lizards, especially the western fence lizard (Sceloporus occidentalis), appear to be the 

most important prey item of whipsnakes, although other prey items include skinks, frogs, 

snakes and birds (USFWS, 2005). Stomach contents of field-captured whipsnakes were 

exclusively lizards, including western fence lizard and western skink (Eumeces 

skiltonianus). Furthermore, prey preference tests with both adult and hatchling Alameda 

whipsnakes have shown a preference for lizard prey suggesting that this species is a 

feeding specialist (USFWS, 2003). However, other sources state that the diet of the 

Alameda whipsnake also includes invertebrates and small mammals (USFWS, 1997 and 

Westphal, 1998), and may depend on an individual’s size, sex, age, and location 

(USFWS, 2006). 

1.7 Life History and Reproduction 

Adults are characterized by having a bimodal seasonal activity pattern with a peak during 

the spring mating season and a smaller peak during late summer and early fall. Alameda 

11
whipsnakes generally enter into a hibernaculum (shelter used during the dormancy 

period) during the months of November to March, although some above-ground 

movements may occur during this time. Hibernaculum sites include rodent burrows and 

crevices between rocks (USFWS, 2003, 2005, and 2006). 

Sperm is stored by the male over winter, and copulation commences soon after 

emergence from winter hibernacula (USFWS, 2003). Courtship and mating have been 

observed from late March through mid-June. During this time males move around 

throughout their home ranges, but females appear to remain at or near their hibernacula, 

where mating occurs (USFWS, 1997, 2003, 2005, and 2006). One female was observed 

copulating with more than one male during a mating season, but the extent to which 

females mate with multiple males (polyandry) is unknown (USFWS, 2003). Females 

begin yolk deposition in mid-April, and intervals of 47, 50, and 55 days have been 

recorded between dates of first known mating and first egg laid. Average clutch size is 

7.21 (6-11, n=19), with a significant correlation between body size and clutch size 

(USFWS, 2003). The eggs are laid May through July (USFWS, 1997), and young 

whipsnakes appear after 3 months of incubation in the late summer and fall (USFWS, 

2003). California whipsnakes take 2 to 3 years to reach maturity, with adults growing to 

nearly 1.5 meter (5 feet). Captive whipsnakes may live for about 8 years (USFWS, 

2003).

1.8 References 

U.S. 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 April 17, 

2008). 

U.S. 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). 

U.S. Fish and Wildlife Service (USFWS). 2005. Species Account: Alameda Whipsnake 

(Masticophis lateralis euryxanthus). Sacramento Fish and Wildlife Office. 

Available online at: 

http://www.fws.gov/sacramento/es/animal_spp_acct/alameda_whipsnake.pdf

(Accessed on April 17, 2008). 

U.S. Fish & Wildlife Service (USFWS). 2006. Endangered and Threatened Wildlife and 

Plants; Designation of Critical Habitat for the Alameda Whipsnake; Final Rule. 

12
Available online at: http://edocket.access.gpo.gov/2006/pdf/06-8367.pdf

(Accessed on April 17, 2008). 

Westphal, M. 1998. Alameda Whipsnake: The Fastest Snake in the West. Tideline. Vol. 

18 No. 2 1-3. Available online at: 

http://www.fws.gov/desfbay/Archives/Whip/Whip.htm (Accessed on October 3, 

2007). 

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2: BAY CHECKERSPOT BUTTERFLY 

2.1 Species Listing Status 

The Bay Checkerspot Butterfly [BCB] (Euphydryas editha bayensis) was listed as 

threatened on September 18, 1987 (52 FR 35366) by the U.S. Fish and Wildlife Service 

(USFWS). Critical habitat for the BCB was designated by USFWS on April 30, 2001 (66 

FR 21449-21489) and revised designated critical habitat was proposed in 2007 (72 FR 

48177-48218). A recovery plan for the BCB was approved by the USFWS on August 30, 

1998 (USFWS, 1998). A 5-year review, which provides an updated life history for the 

BCB, was initiated by the USFWS in March of 2008 (73 FR 11945-11950). 

2.2 Description 

 The adult BCB is a medium-sized butterfly in the brush-footed butterfly family 

(Nymphalidae) with a wingspan of about 2 inches (5 cm) (USFWS 1998). The Bay 

Checkerspot Butterfly is considered an obligate with its primary larval host plant, the 

dwarf plantain (Plantago erecta). 

2.3 Distribution 

All areas currently inhabited by the BCB are island-like patches of suitable habitat 

separated by areas of unsuitable habitat and urban development (USFWS 1998). The 

BCB uses three different types of habitat: 1) primary habitat – native grasslands on large 

serpentine outcrops; 2) secondary habitat – ‘islands’ of smaller serpentine outcrops with 

native grassland; and 3) tertiary habitat – non-serpentine areas where larval food plants 

occur (all known tertiary habitat are in areas mapped geologically as Franciscan 

formation). The total area of suitable serpentine habitat in the entire historic range of the 

BCB does not exceed 5,000 ha (USFWS 1998). 

The historic range of the BCB included the area around the San Francisco Bay from Twin 

Peaks and San Bruno Mountain (west of the Bay) and Contra Costa County (east of the 

Bay) south through Santa Clara County. 

BCB populations have gone extinct in “... Contra Costa County (Franklin Canyon and 

Morgan Territory areas), Alameda County (Oakland Hills), San Francisco County (Twin 

Peaks and Mount Davidson), and San Bruno Mountain, Buri Buri Ridge (Hillsborough), 

Pulgas Ridge (sometimes referred to as ‘San Mateo’), and Redwood City (part of the site 

historically referred to as Woodside) in San Mateo County” (USFWS 1998, p. II-175 and 

II- 177). The distribution of known BCB populations is currently limited to Santa Clara 

and San Mateo Counties (66 FR 21449-21489). Because the BCB distribution is 

14
considered a metapopulation (a group of spatially distinct populations that can 

occasionally exchange dispersing individuals), individual populations may go ‘extinct’ 

and later be ‘recolonized’ from another extant population. Therefore, the exact 

distribution of the BCB varies through time, and “...any site with appropriate habitat in 

the vicinity of the historic range of the bay checkerspot should be considered potentially 

occupied by the butterfly” (USFWS 1998, p. II-177). 

 

2.4 USFWS Critical Habitat 

Critical habitat for the BCB was designated by USFWS on April 30, 2001 (66 FR 21449-

21489). A revised critical habitat ruling became effective on September 25, 2008 (73 FR 

50405-50452), with 18,293 acres (7,403 hectares) of critical habitat designated for the 

BCB (73 FR 50405-50452). 

2.5 Habitat 

All BCB habitat includes shallow, serpentine-derived (or similar)) soils that support 

larval food plants and adult nectar sources (USFWS 1998). The primary larval host plant 

for the BCB is the dwarf plantain (Plantago erecta). In many drier years, BCB larvae 

also rely on secondary host plant species [primarily purple owl’s-clover (Castilleja 

densiflora) or exserted paintbrush (Castilleja exserta)] that are used when the plantain 

dries up while the larvae are still feeding. Adults most commonly feed on the nectar of 

desertparsley (Lomatium spp.), California goldfields (Lasthenia californica) and tidy-tips 

(Layia platyglossa) (USFWS 1998). 

Topography can also influence habitat quality for BCB. South-facing slopes are warmer 

and drier than north-facing slopes, which can affect the timing of the development of the 

butterfly and its host plants. Larvae on south-facing slopes develop faster and emerge (a 

month or more) earlier than larvae on north-facing slopes and host plants on warmer 

slopes flower and senesce three to four weeks before those on cooler slopes. Either 

south- and north-facing slopes are beneficial in different years, depending on the weather 

conditions. Therefore, a serpentine habitat area having a range of slopes and exposures 

can reduce the chances of population-wide reproductive failure in years with extreme 

weather (USFWS 1998). 

‘Pre-diapause’ larvae (see below) have only limited mobility, while ‘post-diapause’ 

larvae may travel tens of meters in search of feeding, basking, and/or pupating sites. 

Adult BCBs are considered largely sedentary, however, a small fraction of a population 

may disperse up to 7.6 km from their natal site (USFWS 1998). 

15
2.6 Diet 

The primary diet for the BCB larvae are dwarf plantain plants (although they may also 

feed on purple owl’s-clover or exserted paintbrush if the dwarf plantains senesce before 

the larvae pupate). Adults feed on the nectar of a variety of plants found in association 

with serpentine grasslands [e.g., California goldfields, tidy-tips, desertparsley, scytheleaf 

(Allium falcifolium), sea muilla (muilla maritime), false babystars (Linanthus 

androsaceus), and intermediate fiddleneck (Amsinckia intermedia)] (USFWS 1998). 

2.7 Life History and Reproduction 

The BCB’s life cycle is closely tied with the biology of its host plants. “Host plants 

germinate anytime from early October to late December, and senesce from early April to 

mid May. Most of the active parts of the bay checkerspot life cycle also occur during this 

time” (USFWS 1998, p. II-183). The BCB reproduces once and dies within a single year. 

Adults emerge from pupae, feed on nectar, mate and lay eggs during a flight season that 

lasts 4 to 6 weeks from late February to early May. Males emerge up to 10 days prior to 

the emergence of females and may mate several times before dying. Females normally 

(although not always) only mate once. Adults of both sexes live on average for 10 days 

(with a maximum adult life span of over 3 weeks reported) (USFWS 1989). Females lay 

up to 5 egg masses (250 eggs/mass) typically in March and April. Eggs are deposited 

primarily near the base of dwarf plantain plants, and less commonly on purple owl’sclover and exserted paintbrush. 

Larvae hatch from eggs in roughly 10 days and grow to the 4th instar in about two weeks. 

Once reaching the 4th instar, the larvae enter into a period of dormancy (diapause) that 

lasts through the summer. The larvae spend this time under rocks or in soil cracks 

(USFWS 1998). If larvae do not enter into dormancy before the dwarf plantain plants 

senesce, they may successfully reach diapause by switching to a nearby purple owl’sclover or exserted paintbrush as a food source. 

The larvae resume activity with the start of the rainy season and the germination of dwarf 

plantain plants. The post-diapause larvae are more mobile than the pre-diapause larvae 

and may travel tens of meters in search of food and/or warm microclimates to bask or 

pupate in (USFWS 1998). Larvae pupate, with the pupae suspended few meters above 

the ground on vegetation, once they reach a weight of 300 - 500 milligrams. Adults 

emerge within 15 to 30 days depending on thermal conditions, although there is some 

evidence that a few larvae in very dry years may enter into a second diapause and 

complete their development the second spring after hatching (USFWS 1998) (see Fig. 

2.2). 

16
FIGURE 2.2: General Annual Life-History Parameters for the BCB (this is a 

generalized schematic; the timing of the life-history parameters for the BCB are 

influenced by climatic and microclimatic factors). 

2.8 References 

Federal Register 52:35366; September 18, 1987. 

http://ecos.fws.gov/docs/federal_register/fr1327.pdf 

Federal Register 66:21449; April 30, 2001. 

http://ecos.fws.gov/docs/federal_register/fr3740.pdf 

Federal Register 73 FR 50405-50452; September 26, 2008. 

http://frwebgate.access.gpo.gov/cgibin/getdoc.cgi?dbname=2008_register&docid=fr26au08-13 

United States Fish and Wildlife Service (USFWS).1998. Recovery Plan for Serpentine 

Soil Species of the San Francisco Bay Area. Portland Oregon. 330+ pp. 

http://ecos.fws.gov/docs/recovery_plans/1998/980930c.pdf. Accessed on October 

14, 2008. 

17
3: CALIFORNIA CLAPPER RAIL 

3.1 Species Listing Status 

The California clapper rail (CCR) (Rallus longirostris obsoletus) was listed with the salt 

marsh harvest mouse as endangered on October 13, 1970 (35 FR 16047) by the U.S. Fish 

and Wildlife Service (USFWS). A recovery plan for the CCR and the salt marsh harvest 

mouse was approved by the USFWS on November 16, 1984 (USFWS, 1984). 

3.2 Description 

CCRs, also known as marsh clappers or marsh hens, are described as “hen-like” in 

appearance with a short neck (USFWS, 1984 and 2007; and REFUGEnet). Their bodies 

are compact and narrow, hence the term “thin as a rail,” which allows them to move 

easily within the marsh (Environmental Impact; and REFUGEnet). They have brownishgray cheeks, a rust or cinnamon-buff colored breast, and black-and-white bars that crisscross their flanks (USFWS, 1984 and 2007; Environmental Impact; Goals Project, 2000; 

and CDFG website). Dark brown streaks mark their olive-brown back and wings and 

white undertail coverts become visible when they are agitated (USFWS, 1984 and 2007; 

and Environmental Impact). CCRs are typically darker on their dorsal side compared 

with their ventral side and their body patterning is effective camouflage in the marsh 

vegetation (USGS website and Goals Project, 2000). They have strong legs that are 

bright orange in color and long legs and toes, as well as a long, somewhat orange, slightly 

downward-curving bill (USFWS, 1984 and 2007; Environmental Impact; and Save the 

Bay). The base and sides of the bill are “pinkish to bright orange in males” and duller in 

females (USGS website). The only other difference between male and female CCRs is 

size, with the males being slightly larger than the females (USFWS, 2007). Juvenile 

CCRs have a “gray body, black flanks and sides, and indistinct light streaking” on their 

flanks and undertail coverts (USFWS, 2007). Their bill is paler and plumage darker than 

adult CCRs (USFWS, 2007). 

The CCR is one of the largest rails (USFWS, 1984 and 2007). They measure 32 to 47 cm 

(13-19 inches) in length from bill to tail and 35 to 40 cm (14-16 inches) in height 

(USFWS, 1984 and 2007; REFUGEnet; and Invasive Spartina Project). They weigh 

about 250 to 350 grams and the males are typically about 20% larger than the females 

(Goals Project, 2000; and USGS website). However, another source reported that the 

body weight of 19 female CCRs from South San Francisco Bay ranged from 300 to 400 

grams, with a mean weight of 346.1 grams (USFWS, 2003). The maximum recorded age 

for a wild clapper rail was seven and a half years old (USGS website). 

The CCR was first described as a king rail in 1874 (USFWS, 1984). In 1880, CCRs were 

reclassified as clapper rails (Rallus obsoletus), because they were found in saltwater 

18
marshes and the king rail was found in inland freshwater marshes, but also as a 

“geographically isolated species distinct from other clapper rails (Rallus longirostris)” 

(USFWS, 1984). All of the Pacific coast clapper rails were combined into one species 

(Rallus obsoletus obsoletus) in 1929 (USFWS, 1984). In 1937, 25 clapper rails were 

described as subspecies of the same species, and the CCR became Rallus longirostris 

obsoletus. A taxonomic change occurred in 1977 and now the CCR is one of 24 

subspecies of the clapper rail (USFWS, 1984). 

3.3 Distribution 

Historic Range 

CCRs were abundant in the tidal marshes of San Francisco Bay and smaller populations 

were found in coastal tidal salt marshes and brackish marshes throughout central and 

northern California, from Humbolt Bay in Humbolt County in the north to Morro Bay in 

San Luis Obispo County in the south (Environmental Impact; Save the Bay; Albertson, 

1996; and Goals Project, 2000). The former range of this subspecies also included 

Elkhorn Slough in Monterey County; however, before 1908 this slough may not have 

been suitable for CCRs because of its limited tidal access to Monterey Bay (CDFG 

website and USFWS, 1984). Historically, the largest populations of CCRs were found in 

the “salt marshes of South San Francisco Bay, including portions of San Mateo, Santa 

Clara, and Alameda counties” (USFWS, 1984). 

Dispersing juvenile CCRs were described in “residential and agricultural areas along the 

open coast and east of San Francisco Bay” in 1976 and 1979 (USFWS, 1984). In the 

mid-1980s, CCRs were found in South San Francisco Bay in remnant salt marshes 

including Bair and Greco Islands in San Mateo County, Dumbarton Point in Alameda 

County, as well as in Santa Clara County (USFWS, 1984). In San Mateo County, CCRs 

could be found as far north as San Bruno Point (USFWS, 1984). Remnant populations 

could also be found “near creek mouths in northern Alameda County, western Contra 

Costa County, and in eastern Marin County” (USFWS, 1984). Records from Richardson 

Bay in Marin County indicated that a small CCR breeding population may have existed 

there (USFWS, 1984). A breeding CCR population could also be found in northern San 

Pablo Bay “along the Petaluma River as far north as Schultz Creek and along most major 

tidal sloughs and creeks in Sonoma and Napa counties” (USFWS, 1984). They could 

also be found “north to Bull Island on the Napa River” (USFWS, 1984). A small 

breeding population also existed at Southampton Bay in Solano County (USFWS, 1984). 

At least 25 CCR were found during the 1979 breeding season on Joice and Grizzly 

Islands in Suisun Marsh (USFWS, 1984). CCRs were also found in 1979 in late April in 

Martinez in Contra Costa County which may have also indicated breeding in this area 

(USFWS, 1984). 

Current Range 

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 

19
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). 

Suisun Marsh and Carquinez Strait:

CCRs are scattered at several sites throughout Suisun Bay and Marsh indicating that 

some populations are present in some years but not in other years (Goals Project, 2000). 

CCRs have been found with some regularity since 1978 in the “shoreline marshes from 

Martinez east to Point Edith, bayshore marshes near the mouth of Goodyear Slough, the 

upper portions of Suisun and Hill sloughs, and the western reaches of Cutoff Slough and 

associated tributaries” (Goals Project, 2000). Records of CCRs in this location in the 

winter are more abundant than records during the breeding season (Goals Project, 2000). 

Persistent CCR populations have been found in “Hill Slough in the northern reaches of 

the Suisun Marsh and in the upper Napa Marsh” both of which are tidally influenced but 

not salt marsh (Foin et al., 1997). The CCR population at Hill Slough has been observed 

every year since 1992 (except for 1995) and the population at Napa Marsh was first 

recorded in 1939 (Foin et al., 1997). Although the CCR habitat is limited at Carquinez 

Strait, a small CCR population of one to three breeding pairs has persisted at this location 

(Southampton Marsh) since 1948 (Goals Project, 2000). 

North Bay:

CCRs in the North Bay are concentrated “near the mouths of the larger tributaries (e.g. 

Gallinas Creek, Novato Creek, Petaluma River, Black John Slough, Sonoma Creek, and 

Napa River)” (Goals Project, 2000). The CCR population at the Napa River was defined 

as a North Bay population center in 1979 because it supported 40% of the entire 

population (Goals Project, 2000). Studies performed in the 1990’s show that this 

population is declining but concentrations of CCRs are still found at White Slough and 

Coon Island (Goals Project, 2000). 

Central Bay:

The areas of the Central Bay that support CCRs include Corte Madera and Muzzi 

marshes, the San Leandro Area (Arrowhead and Elsie Romer marshes), and inner 

20
Richmond Harbor (Goals Project, 2000). Muzzi Marsh is a restored marsh (Goals 

Project, 2000; Foin et al., 1997). Other sites in the Central Bay include Richardson Bay 

and Creekside Marsh in Marin County (Goals Project, 2000). 

South Bay:

The CCR populations in the South Bay have remained stable on the western side of the 

Bay; however, the East Bay population (Ideal, Dumbarton, and Mowry marshes) has 

decreased considerably (Goals Project, 2000). This population seems to be making a 

recovery with over 330 individuals in 1997-1998 (Goals Project, 2000). This increase 

was likely due to predator management in this area (Goals Project, 2000). The largest 

populations of CCRs are currently found in Dumbarton and Mowry marshes in the East 

Bay, and in Palo Alto and Greco marshes in the West Bay (Goals Project, 2000). CCR 

populations seem equally divided between the east and west sides of the South Bay 

(Goals Project, 2000). The marshes in South San Francisco Bay still support the largest 

number of rails in California (CDPR online). 

3.4 USFWS Critical Habitat 

No critical habitat has been designated for the CCR (USFWS, 1984). 

3.5 Habitat 

 

CCRs require tidal marsh habitat because it provides protection from predators and also 

contains the types and concentration of invertebrate species on which they feed (Foin et 

al., 1997). CCRs use second and third order marsh channels to move within the marsh, 

feed, and also as escape routes to move to higher ground during high tides (Foin et al, 

1997). Marshes typically have three zones: a low marsh that receives maximum 

submergence comprised of cordgrass (Spartina foliosa) or tules (Scirpus spp.); a middle 

marsh zone comprised of pickleweed (Salcornia virginica), alkali bulrush (Scirpus 

robustus), or cattails (Typha spp.); and a high marsh dominated by “peripheral 

halophytes, which receives infrequent to no tidal coverage” (USFWS, 1984). Salt 

tolerant plants (halophytes) include gum-plant (Grindelia spp.), salt grass (Distichlis 

spicata), jaumea (Jaumea carnosa), and alkali heath (Frankenia grandifolia) (USFWS, 

1984). Within the salt marsh CCRs prefer low marsh habitat (below mean higher-high 

water) which corresponds with tall marsh vegetation, especially cordgrass (Foin et al, 

1997). CCRs prefer emergent wetland areas dominated by dense native cordgrass and 

pickleweed, as well as brackish areas dominated by these two species in addition to 

bulrush (Berkeley, 2004; and Harvey, 1999). CCRs also use the ecotone (a transition 

zone between two ecosystems) between the wetland and the upland areas (Harvey, 1999). 

High quality CCR habitat should include “direct tidal circulation sufficient to allow the 

full tidal cycle; a predominant pickleweed marsh with cordgrass, gumplant, and other 

high marsh plants; abundant, dense high marsh cover; and an intricate network of tidal 

sloughs” (Goals Project, 2000). “The wetland border within 15 m (49.2 ft) of open, 

21
tidally influenced, salt or brackish water seems optimum for food and nest sites” and “at 

least 2 hectares (5 acres) of contiguous habitat, of the appropriate plant species, must be 

present to support a rail population” (Lewis and Garrison, 1983). The two largest areas 

of contiguous habitat are in the San Francisco Bay National Wildlife Refuge (SFBNWR) 

and San Pablo Bay (Foin et al, 1997). 

CCRs are found year-round in coastal salt and brackish marshes and tidal sloughs in San 

Francisco and Suisun Bay and are rarely seen in non-tidal (diked) marshes (USFWS, 

2007; CDPR website, and Environmental Impact). Some non-tidal marshes have been 

used by breeding pairs but it is thought that nearby tidal marshes that support other 

breeding pairs contribute to the use of non-tidal marshes (Goals Project, 2000). CCRs 

can also be found in the brackish marshes associated with the “major sloughs and rivers 

of San Pablo Bay and Suisun Marsh, and along Coyote Creek in south San Francisco 

Bay” (USFWS, 2007). 

In the south and central San Francisco Bay areas and along San Pablo Bay, CCRs live in 

salt marshes dominated by pickleweed (Salicornia virginica) and Pacific cordgrass 

(Spartina foliosa), whereas the CCR in the North Bay (Petaluma Marsh, Napa-Sonoma 

marshes, and Suisun Marsh) can be found in tidal brackish marshes with varying 

vegetation (Invasive Species Project and USFWS, 2007). Another source states that 

“along the larger creeks in the South Bay, in some areas of Napa Marsh, Petaluma River, 

and Sonoma Creek in San Pablo Bay, and in Suisun Bay” the CCR can be found in 

“brackish wetlands consisting of bulrush” (Goals Project, 2000). Bulrush in these areas 

is used for building their nests and cover (Goals Project, 2000). In the North Bay, CCR 

habitat is found in the “saline and marginally brackish tidal marshland with small 

channels that extend through or into patches of tall monocot vegetation” which is used as 

nesting material (Goals Project, 2000). The vegetation must be at least 50 cm tall at 

elevations near Mean High Water to allow the nest to be hidden but still high enough to 

not become inundated by maximum high tides (Goals Project, 2000). The vegetation 

used can be shorter if the elevation of the marsh is higher (Goals Project, 2000). CCRs 

typically use the tallest vegetation available for cover which is usually S. foliosa (Foin et 

al, 1997). CCRs use Scirpus “for cover in several brackish marshes, including the Napa 

River” (Foin et al, 1997). 

Pickleweed has become more abundant in Suisun Marsh and will continue to do so as the 

salinity in this area increases (USFWS, 1984). The salinity in the Suisun and San Pablo 

marshes has increased because “nearly 50% of the historic median freshwater flow of the 

Central Valley no longer reaches those bays because of diversions for agricultural, as 

well as municipal and industrial uses” (USFWS, 1984). 

The “most heavily used portions of San Francisco Bay salt marshes are the lower, 

cordgrass-dominated areas” (USFWS, 1984). Calling pairs and the majority of the nests 

in 1980 were found in areas of cordgrass in South San Francisco Bay marshes (USFWS, 

1984). In addition, in 1972, the highest densities of rails in the summer were found in 

areas dominated by cordgrass (USFWS, 1984). It is thought that cordgrass may be 

preferred because it seems to allow CCR nests to float (USFWS, 1984). It also occurs 

22
“along tidal sloughs and at the marsh edge, where rails prefer to forage” (Goals Project, 

2000). Cordgrass habitat may also be preferred because it is farther from the drier 

uplands where predation is more likely and it seems to provide better protection for the 

CCR adults and young because it is denser and more uniform than the vegetation in the 

upper marsh areas (USFWS, 1984). Rails may be more dependent on upper marsh 

vegetation in the winter especially during high tides (USFWS, 1984). 

Both low and high marsh areas must be available to sustain a successful CCR population 

(Albertson, 1996). CCRs forage in shallow water, mudflats, and small tidal sloughs 

within the marsh during low tide (USFWS, 1984 and Harvey, 1999). Clapper rails are 

not expected to forage in mudflats that are more than 15 m (49.2 ft) from vegetative 

cover (Lewis and Garrison, 1983). Optimal habitat is defined as having at least 50% of 

the shoreline of persistent emergent wetland bordered by tidal flats and exposed channels 

(Lewis and Garrison, 1983). Food is abundant in these channels because of the constant 

supply of nutrients entering the channel during each tide cycle (Albertson, 1996). The 

number of tidal channels affects the number of rails that can be supported by a marsh 

with the number of rails increasing as the number of channels increases (Albertson, 1996 

and Goals Project, 2000). These channels also provide a safe haven from predators 

because they are too narrow to allow the predators to hunt effectively (Albertson, 1996). 

CCRs are preyed on most often during high tide when they cannot hide within the tidal 

channels (Albertson, 1996). Predation is highest in the winter when high tides are 

common (Albertson, 1996). Low marsh areas, including tidal sloughs, have little 

vegetation and are used for foraging, whereas higher marsh areas complete with dense 

vegetation are used for nesting and cover during periods of high water (Albertson, 1996; 

Harvey, 1999; and Goals Project, 2000). In the late 1970’s, one site within Suisun 

Marsh, characterized by a well-developed high marsh plant community, supported the 

greatest number of clapper rails (USFWS, 1984). 

Populations of CCR are “most dense where patches of habitat are at least 100 hectares in 

size” (Goals Project, 2000). Less than 15 of these patches are found within the northern 

estuary and one third of these patches “adjoin the mouths of major tributaries 

downstream from Carquinez Straits” (Goals Project, 2000). Generally, CCR density 

decreases upstream “toward the headward extent of the major tributaries of the estuary” 

(Goals Project, 2000). Marsh habitat areas provide “food resources, cover from 

predators, breeding and nesting habitat, and refuge areas at high tides” (Goals Project, 

2000). 

During the winter, CCR can be found in medium-height Spartina in areas with fewer 

tidal streams and ditches compared to the nesting habitat (Lewis and Garrison, 1983). 

Rails can also be found during high fall and winter tides in “large racks of floating, dead 

cordgrass, usually deposited along the marsh side of creek levees” (Lewis and Garrison, 

1983). 

23
3.6 Diet 

CCRs are generalist and opportunistic feeders that forage for food in tidal sloughs and 

channels (CDPR website; USGS website; Garrison, 2000; and Berkeley, 2004). During 

low tide, the soft mud in these areas is exposed and the CCRs use their long bill to probe 

for invertebrates and seeds (CDPR website). CCRs consume worms, mussels, snails, 

clams, crabs, insects, and spiders (Save the Bay and Berkeley, 2004). Amphipods have 

also been found in the esophagus of CCRs (USFWS, 1984). Although CCRs typically 

consume invertebrates, they have also been known to occasionally consume small birds 

and mammals, including the salt marsh harvest mouse, which is also an endangered 

species (Save the Bay and Harvey, 1999). Dead fish may also be scavenged (Harvey, 

1999). 

A study examining the stomach contents of 18 CCRs in South San Francisco Bay showed 

that 85.5% of the contents were animal matter, indicating that these animals are primarily 

carnivores (USFWS, 1984). The stomach contents included the non-native horse mussel 

(Modiolus demissus), wolf spiders (Lycosidae spp.), little macoma clams (Macoma 

balthica), yellow shore crabs (Hemigrapsus oregonensis), and nassa snails (Ilyanassa 

obsoletus) (USFWS, 1984 and USFWS, 2003). Worms, insects, and carrion accounted 

for about 1% of the diet in these CCRs (USFWS, 2003). The CCR diet may contain up to 

15% plant material but it is believed that this represents a maximum value (USFWS, 

2003). This belief is due to the fact that the CCRs were collected in February when 

animal prey items would be least abundant (USFWS, 2003). 

Rails have been observed consuming the striped shore crab (Pachygrapsus crassipes) in 

Elkhorn Slough in Monterey County (USFWS, 1984). The diet of the CCR in San Pablo 

and Suisun Marsh has not yet been investigated; however, in Suisun Marsh which is 

brackish, CCRs may consume saltwater invertebrates including mussels and crustaceans 

as well as freshwater prey including crayfish (Pasifastacus leniusculus) and the Asiatic 

clam (Corbicula spp.) (USFWS, 1984). Salt glands allow the CCR to drink either fresh 

or salt water (Harvey, 1999). 

Non-native horse mussels, although a favorite prey item of the CCR, are capable of 

injuring or killing CCRs by closing on their bills or feet if they step on or probe the 

mussel (USFWS, 1984). Invertebrate prey items preferred by the CCR can be negatively 

affected by pollution, sedimentation, and fluctuations in freshwater (USFWS, 1984). 

Low numbers of CCR have been associated with low numbers of invertebrate prey items 

(USFWS, 1984). 

3.7 Life History and Reproduction 

CCRs display year-long circadian activity and are most vocal nocturnally and 

crepuscularly (Harvey, 1999). They forage in the early morning and late evening and 

24
“roost at high tide during the day” (USFWS, 2007). Night-time CCR activities are 

expected to be minor (USGS-WERC website). CCRs are seen most often during very 

low or very high tides, either flapping awkwardly into the vegetation to escape the high 

tide, or crossing the sloughs (Save the Bay). They typically spend “most of their time 

hidden in thick marsh vegetation” (Garrison, 2000). 

The CCR blends in well with its surroundings and is hard to see in dense vegetation; 

however, its “unmistakable, clattering call often gives it away” (USFWS, 2007 and 

REFUGEnet). CCRs often freeze when they are spotted and flushed; however, they may 

also hide “in small sloughs or under overhangs” or run quickly through the vegetation or 

along sloughs, “hunched over with their necks outstretched and plumage compacted” 

(USFWS, 1984 and 2007). CCRs prefer to walk or run and generally walk upright 

(USFWS, 2007). They have been “compared to chickens in size, shape, and 

maneuverability” as these birds are not particularly graceful when swimming or flying 

(Save the Bay). If they have been discovered they will sometimes fly a short distance 

and then land (USFWS, 2007). They are good swimmers but only swim when crossing 

sloughs or escaping an immediate threat at high tide (USFWS, 2007). 

CCRs make a number of calls including a “he-e-eh-heh-heh-heh” and a “chack-chackchack” (REFUGEnet). They also make a “harsh, clattering” kek-kek-kek-kek or cha-chacha call and will respond with a “clappering” call when alarmed (Invasive Spartina 

Project and Save the Bay). CCR calls are loud and typically have 20 to 25 notes that 

lower in pitch and increase in tempo (REFUGEnet). Female CCRs occasionally make a 

purring call (REFUGEnet). Rails use calls to contact each other, advertise their breeding 

status, and defend their territories (Albertson, 1996). CCRs will “fiercely defend 

overlapping, year-round territories” (Goals Project, 2000). Most CCRs show “strong site 

tenacity, with very little movement between seasons” (Goals Project, 2000). Home range 

size differs by individual and “significant within-season differences are apparent among 

marshes, particularly in core-use areas” which are “defined as the highly defended 

portion of the territory” which also contains the nest site (Goals Project, 2000). Predation 

pressure, habitat quality, as well as size and orientation of the marsh are likely factors 

that affect the CCR’s home range size (Goals Project, 2000). 

CCRs are considered to be non-migratory; however their movements between marshes 

are unknown (USFWS, 1984 and Goals Project, 2000). It is known that juveniles 

disperse widely from the breeding habitat and that adults disperse during the fall and 

early winter after breeding (USFWS, 1984). Several older records suggest that “there is a 

fairly regular fall dispersal period from August through November” although this may 

only occur in some years (Goals Project, 2000). A study looking at dispersal showed that 

many birds did not leave the marsh where they were banded, although three of 54 birds 

moved one km and one bird moved 10 km (Goals Project, 2000). Another study showed 

that one individual moved 3 km and established a breeding territory; however, CCRs 

typically disperse between one and three km (Goals Project, 2000). 

The CCR breeding season begins in February, with nesting starting in mid-March and 

extending into August (USFWS, 2007). “Clapper rails tend to concentrate along tidal 

25
creeks of marshes during the breeding season” and it appears that these concentration 

areas are ancestral nesting grounds with a long history of use (Lewis and Garrison, 1983). 

High densities of breeding pairs are typically centered around second and third order tidal 

channels in the high marsh in pickleweed dominated habitat (Foin et al., 1997). Males 

initiate courtship and this activity includes “the male approaching the female with an 

uplifted tail, pointing his bill to the ground and swinging it from side to side” (Goals 

Project, 2000). The male also sometimes feeds the female during courtship (Goals 

Project, 2000). 

Rails typically nest in lower marsh zones where cordgrass is abundant (Harvey, 1999). 

They “lay their eggs on the ground in a shallow nest of dead marsh grasses” (Save the 

Bay). The male clapper rail typically builds the nest which has been described as domed; 

however, other sources have described the nest as basket or funnel shaped with an inside 

diameter of about 14.2 cm (5.6 inches), an inside depth of 5.3 cm (2.1 inches), and an 

outside diameter of 23.6 cm (9.3 inches) (Garrison, 2000; Goals Project, 2000; USGS 

website; and Lewis and Garrison, 1983). CCR nests typically have a canopy over the 

nest constructed using vegetation including: “cordgrass, pickleweed, gum-plant, salt 

grass, and drift materials” (USFWS, 1984). CCR nests in the South Bay are typically 

found in gumplant bushes, pickleweed, cordgrass, saltgrass, and wrack (Goals Project, 

2000). In the North Bay, CCR nests are found in alkali bulrush, pickleweed, or gumplant 

(Goals Project, 2000). It is thought that pickleweed is used more frequently in the 

“summers with disruptive high tides of +6.7 feet or more” whereas; gum-plants and drift 

materials are used early in the summer before the cordgrass is long enough to provide 

sufficient cover (USFWS, 1984). The differences in nesting material may also be due to 

“rainfall-induced fluctuations in the biomass of cordgrass and its availability as nesting 

habitat” (USFWS, 1984). Dried cordgrass stems seem to be the preferred material for the 

nest platform; however, dead drift vegetation may also be used (USFWS, 1984; and 

Harvey, 1999). CCRs also build “brood” nests which function as “high tide refuges for 

young rails” (USFWS, 1984). These nests typically consist of “a platform of stems 

without a canopy” (USFWS, 1984). 

CCR nests are typically constructed near (usually within 10 m) of tidal sloughs because 

these areas provide the CCR “with a protected route for movement within the marsh as 

well as easily accessible foraging habitat and a nearby avenue of escape, particularly for 

vulnerable flightless young” (USFWS, 1984). Nests are often located “less than two 

meters from first-order channels and at least 100 meters upstream from the marshland 

shoreline” (Goals Project, 2000). Nests are also constructed above mean high higher 

water (Goals Project, 2000). One source reported that all CCR nests they observed were 

“constructed entirely above mean high water, with rims of the nests closely 

corresponding to the maximum elevation of tides during the breeding season” 

(Schwarzbach et al., 2006). Most clapper rail nests are “about 20 to 35 cm (7.9 to 13.8 

inches) above the ground and 10 to 50 m (32.8 to 164.0 ft) from other nests” (Lewis and 

Garrison, 1983). Nests were also about 7 m (23 ft) from a variation in cordgrass height 

and density, with a “correlation between the density of nests and the amount of edge 

between tall and medium-height smooth cordgrass (20-46 cm or 8-18 inches) (Lewis and 

Garrison, 1983). 

26
CCRs lay their eggs March through July (Goals Project, 2000). Clutches range from five 

to 14 eggs, with the average around seven eggs per clutch (USFWS, 1984 and 2007; and 

Goals Project, 2000). The eggs are about 45 mm long and “light tan or buff-colored with 

cinnamon-brown or dark lavender spotting concentrated at the broader end” (USFWS, 

1984). Both males and females are involved in incubation of the eggs, which lasts from 

23 to 29 days, and rearing of the young (USFWS, 1984 and 2007; and Goals Project, 

2000). This behavior suggests that this subspecies may be monogamous (Birds of North 

America website; Goals Project, 2000; and Lewis and Garrison, 1983). The nestlings are 

precocial and able to leave the nest soon after they hatch; however, their parents usually 

continue to care for or accompany them for the first eight weeks (CDPR website; 

Berkeley, 2004; and Goals Project, 2000). The young are chased by their parents from 

the parents’ territory once there are able to feed on their own, usually after 35 to 42 days 

(Lewis and Garrison, 1983). Juveniles fledge at ten weeks and can breed during the 

spring after they hatch (Goals Project, 2000 and Lewis and Garrison, 1983). 

The breeding season ends at the end of August “when eggs laid during renesting attempts 

have hatched and the young are mobile” (USFWS, 2007 and USFWS, 2003). There are 

two peaks in nesting activity; in late April to early May and late June to early July 

(USFWS, 1984 and USFWS, 2003). It has been hypothesized that the second peak is due 

to “late nesters” or “second attempts after initial nesting failures” (USFWS, 1984). 

Clapper rails can “re-nest up to five times if their first attempts fail” (Garrison, 2000 and 

Birds of North America website). Nest failures are most often caused by predation of the 

eggs and chicks by the Norway rat (Rattus norvegicus) or inundation of the nest during 

high tide (USFWS, 1984). Nests that had been abandoned or disrupted were usually 

preyed on by rats and nests composed of cordgrass and gum-plant were disrupted by tides 

greater than +6.7 feet (USFWS, 1984). Heavy spring storms in combination with high 

tides can “destroy up to half of the clapper rails nests found in the marsh” (Garrison, 

2000). In 1980, there was 38% hatching success for 31 CCR nests; however, “28 of 50 

nests successfully hatched the majority of their eggs (56% nest success)” (USFWS, 

1984). The fledging success of CCR is difficult to determine and unknown at this time 

(USFWS, 1984). 

A study of CCR hatching success in six marshes in San Francisco Bay over four breeding 

seasons (1991, 1992, 1998, and 1999) determined that egg predation and contamination 

are the “major factors limiting the reproductive success of California clapper rails in both 

the northern and southern reaches of the bay” (USFWS, 2003 and Schwarzbach, 2006). 

This study was conducted in two marshes (Corte Madera and Wildcat) in the North Bay 

(north of the Golden Gate Bridge) and four marshes (Greco Island, Mowry, Laumeister, 

and Faber) in the South Bay (south of the San Mateo Bridge) (Schwarzbach, 2006). The 

results of this study showed that CCR productivity was lower than their natural potential 

(Schwarzbach, 2006). Egg hatchability was depressed in all six of these marshes below 

their normal hatchability rate of greater than 90% (Schwarzbach et al., 2006). Only 69% 

of the CCR eggs that could be assessed for viability were viable (Schwarzbach, 2006). 

Thirty-one percent of the eggs were therefore nonviable (Schwarzbach et al., 2006). 

Hatchability for the North and South bays were 65% and 70%, respectively 

27
(Schwarzbach, 2006). “Only 45% of the nests successfully hatched at least one egg” 

(Schwarzbach, 2006). The mean clutch sizes for the North and South bays were 6.7 and 

6.9, respectively; however, CCRs only produced 1.9 and 2.5 young per nesting attempt 

(Schwarzbach, 2006). Predation was a major factor affecting nest success because it 

reduced productivity by a third (Schwarzbach, 2006). In 1992, in marshes in the South 

Bay, 90% of the eggs lost to predation were lost to rodents and the Norway rat in 

particular (Schwarzbach, 2006). Flooding was not a major factor and only reduced the 

number of eggs available to hatch by 2.3% in this study although it was acknowledged 

that flooding may vary by marsh and year (Schwarzbach, 2006). Tides in San Francisco 

Bay that were greater than two meters were “particularly detrimental to California 

clapper rail nests located in Grindelia humilis bushes, with eggs being lost from all such 

nests” (Schwarzbach et al., 2006) 

3.8 References 

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 November 16, 2007). 

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

Available online at: 

http://www.dfg.ca.gov/habcon/cgi-bin/read_one.asp?specy=birds&idNum=45

(Accessed on November 16, 2007). 

California Department of Pesticide Regulation. Endangered Species Project. California 

Clapper Rail. Available online at: 

http://www.cdpr.ca.gov/docs/endspec/espdfs/ccrbio.pdf (Accessed on November 

16, 2007) 

Drennan, J. 2007. California Clapper Rail Surveys for the Off-Bridge Storm Water 

Project. Garcia and Associates. Available online at: 

http://www.biomitigation.org/reports/files/clapper_rail_memo_June_2007_0_184

0.pdf (Accessed on November 16, 2007). 

Eddleman, W.R, and C.J. Conway. 1998. Clapper Rail (Rallus longirostris). The Birds of 

North America Online (A. Poole, Ed.). Ithaca: Cornell Lab of Ornithology; 

Retrieved from the Birds of North America Online. Available online at: 

http://bna.birds.cornell.edu/bna/species/340 (Accessed on November 16, 2007). 

Environmental Impact on Endangered Animals – California Clapper Rail (Rallus 

longirostris obsoletus). Available online at: 

http://library.thinkquest.org/2878/ca_clapper_rail.html (Accessed on November 

16, 2007). 

28
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 November 

16, 2007).

Garrison, B. 2000. Clapper Rails. Outdoor California. Available online at: 

http://www.californiawildlifefoundation.org/articles/C_Rails_MarchApril2000.pd 

f (Accessed on November 16, 2007).

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 November 27, 

2007). 

Harvey, T. 1999. B144-Clapper Rail (Rallus longirostris). 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: 

www.nrm.dfg.ca.gov/FileHandler.ashx?DocumentVersionID=1754 (Accessed on 

November 16, 2007). 

REFUGEnet. Critter corner: California Clapper Rail. Available online at: 

http://www.refugenet.org/critter/ccrail.html

http://www.refugenet.org/critter/ccrVital.html

http://www.refugenet.org/critter/ccrFacts.html

http://www.refugenet.org/critter/ccrRefuge.html (Accessed on November 16, 

2007). 

San Francisco Estuary Invasive Spartina Project. Coastal Conservancy. California 

clapper rail (Rallus longirostris obsoletus). Available online at: 

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

(Accessed on November 16, 2007) 

Save the Bay Classroom. 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 November 16, 2007). 

29
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: November 16, 2007). 

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. 

pp 45-60. Available online at: 

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

on November 16, 2007). 

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 

November 27, 2007). 

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 November 

26, 2007). 

U.S. Geological Survey (USGS). Biological and Ecotoxicological Characteristics of 

Terrestrial Vertebrate Species Residing in Estuaries: Clapper Rail. Available 

online at: http://www.pwrc.usgs.gov/bioeco/clapper.htm (Accessed on November 

16, 2007). 

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/dioxin/rails/planB.html (Accessed on November 16, 

2007). 

Lewis, J.C. and R.L. Garrison. 1983. Habitat suitability index models: clapper rail. U.S. 

Department of the Interior Fish and Wildlife Service. FWS/OBS-82/10.51. 15 pp. 

Available online at: http://www.nwrc.usgs.gov/wdb/pub/hsi/hsi-051.pdf

(Accessed on November 16, 2007). 

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 November 16, 2007). 

U.S. Fish and Wildlife Service (USFWS). 1984. Salt Marsh Harvest Mouse and 

30
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 November 16, 2007). 

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 November 16, 2007). 

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 November 16, 2007). 

University of California at 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 

November 16, 2007). 

31
4. CALIFORNIA FRESHWATER SHRIMP 

4.1 Species Listing Status 

The California freshwater shrimp (Syncaris pacifica) was listed as endangered on 

October 31, 1988 (53 FR 43884) by the U.S. Fish and Wildlife Service (USFWS) 

(USFWS, 1988). A recovery plan for this species was approved by the USFWS on July 

31, 1998 (USFWS, 1998). A 5-year review for this species was finalized in December of 

2007 (USFWS, 2007). 

4.2 Description and Taxonomy 

The California freshwater shrimp (CA shrimp) is a decapod or 10-legged crustacean of 

the family Atyidae. Adult CA Shrimp are generally less than 50 millimeters (2.17 

inches) in postorbital length (from eye orbit to tip of tail) (USFWS, 1988 and 1998). 

Females are generally larger and deeper bodied than males (USFWS, 1998 and 2007). 

Females range between 32 to 45 millimeters (1.3 to 1.8 inches) in length, whereas males 

range in length from 29 to 39 millimeters (1.2 to 1.5 inches) (USFWS, 1998). 

S. pacifica was first described as Miersia pacifica in 1895 (USFWS, 1988). In 1990, a 

new genus, Syncaris, was described for the California atyids based on notable differences 

in the chelae (pinchers) and rostrum (horn-shaped structure between the eyes). S. 

pacifica can be distinguished from Palaemonias, the only other atyid genus in the United 

States, by its well-developed stalked eyes. Palaemonias are blind and dwell in caves in 

the eastern United States. S. pacifica is the only surviving species in the genus Syncaris

(USFWS, 1988 and 1998). 

4.3 Distribution and Status 

Historical Range: 

The historic distribution of the shrimp is unknown, but it probably extended across the 

low elevation, perennial freshwater streams in Marin, Sonoma, and Napa counties in 

California (USFWS, 1998 and 2007). The CA shrimp was known to occupy only areas 

within restricted portions of 12 streams in the three counties listed above when the 

species was listed in 1988 (USFWS, 1988). A study published in 1985 reported that the 

species inhabited eleven streams in the Russian River, San Francisco Bay, and other 

coastal drainages (USFWS, 1988). These streams were East Austin, Salmon, Lagunitas, 

Big Austin, Sonoma, Huichica, Green Valley, Jonive, Walker, Yulupa, and Blucher 

(USFWS, 1988). CA shrimp were also found in the Napa River near Calistoga (USFWS, 

1988). This finding increased the total number of streams in the area known to contain 

CA shrimp to 12 (USFWS, 1988). Since the species was listed, the CA shrimp has been 

rediscovered in Stemple Creek, and new populations have been found in Keys, Redwood, 

and Garnett Creeks (USFWS, 1998). A total of eleven separate stream systems (sixteen 

streams) are inhabited in the three counties mentioned above (Marin, Sonoma, and Napa) 

(Serpa, 1996 and USFWS, 2007). Another CA shrimp population was found in a new 

32
location on Austin Creek, upstream of its confluence with East Austin Creek (USFWS, 

1998). With the exception of Stemple Creek, CA shrimp at these locales are adjacent to 

previously known populations. As evidenced by the recent discovery of CA shrimp 

within Keys, Garnett, and Redwood Creeks, unsampled and inadequately sampled 

streams within Marin, Sonoma, and Napa Counties could contain additional populations 

(USFWS, 1998). 

Current Range: 

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 these species in 

the additional streams is a result of recent independent surveys. It should be noted, these 

findings do not represent an attempt at a systematic canvassing of habitats for the CA 

shrimp to examine their full spatial distribution and extent (USFWS, 2007). 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. A small segment of Salmon 

Creek flows through the Watson School historic site, managed by the Sonoma County 

Department of Parks and Recreation. On East Austin Creek, the Austin Creek State 

Recreation Area lies immediately upstream of shrimp populations (USFWS, 1998). 

Distribution: 

Based on existing information, the distribution of shrimp within streams is quite 

restricted and without continuity, primarily because unsuitable habitat is often 

interspersed between suitable habitat (USFWS, 1998). Furthermore, because access is 

not available to survey all potential habitats, the actual extent of distribution may extend 

beyond the reported locations (USFWS, 1998). Distribution of shrimp populations 

within streams is not expected to be static because of habitat changes by natural or human 

made forces. For example, recent long-term drought conditions in California may have 

resulted in more discontinuous shrimp populations in Huichica Creek (USFWS, 1998). 

Gradual removal of unnatural barriers to shrimp dispersal and restoration of natural 

habitat conditions in Austin Creek are expected to expand the distribution of shrimp 

beyond its existing occurrence (USFWS, 1998). Distribution of age classes varies within 

33
streams; streams sampled in the fall have contained proportionally higher numbers of 

juveniles than adults (USFWS, 1998). 

In instances where shrimp are present (historically or currently) in two connecting 

watercourses, the smaller tributaries generally support more abundant numbers of shrimp 

than the larger, receiving streams (USFWS, 1998). An exception to this pattern, Yulupa 

Creek (tributary to Sonoma Creek) contained fewer shrimp than Sonoma Creek (USFWS, 

1998). However, Yulupa Creek has less suitable habitat than Sonoma Creek due to 

relatively high channel gradient and the absence of overhanging vegetation and undercut 

banks (USFWS, 1998). Populations on Salmon and Lagunitas Creeks were rated “good” 

to “excellent” due to the relatively high numbers of sampled shrimp over a relatively long 

distance. Populations on Stemple, Green Valley, Austin, Walker, and Yulupa Creeks and 

Napa River were rated “extremely poor” to “fair poor” due to limited distribution and low 

numbers of sampled shrimp. No ratings are available for Atascadero Creek, Redwood 

Creek, Olema Creek, and Laguna de Santa Rosa due to insufficient information (USFWS, 

1998). These ratings are based on a qualitative, relative index of health (USFWS, 1998). 

The index assumes equivalent abundance estimates and lengths of distribution on 

separate streams afforded somewhat similar levels of protection from disturbance 

(USFWS, 1998). 

4.4 USFWS Critical Habitat 

No critical habitat for the CFS has been designated by the USFWS to date. 

4.5 Habitat 

 

The CA shrimp is endemic to perennial streams in Marin, Napa, and Sonoma Counties, 

California (USFWS, 1998). This species is adapted to freshwater environments and 

cannot tolerate salt or brackish water and does not occur in the intertidal reaches or 

estuarine areas of any of the streams in which it is found (USFWS, 1988 and 1998). 

Although laboratory studies indicate that the shrimp can tolerate brackish water 

conditions, at least for short periods of time, all records of CA shrimp are from 

freshwater reaches in streams (USFWS, 1998). 

The shrimp is found in low elevation (less than 116 meters, 380 feet), low gradient 

(generally less than 1 percent) perennial freshwater streams or intermittent streams with 

perennial pools where banks are structurally diverse with undercut banks, exposed roots, 

overhanging woody debris, or overhanging vegetation (USFWS, 1998). The species, a 

true freshwater shrimp, inhabits quiet portions of tree-lined streams with underwater 

vegetation and exposed tree roots in free-flowing, permanent streams (USFWS, 1988). 

The species is found within stream pools, in areas away from the main current, where 

there are often undercut banks, exposed root systems, and vegetation hanging into the 

water (Serpa, 1996). 

34
Excellent habitat conditions for the shrimp include streams 30 to 90 centimeters (12 to 36 

inches) in depth with exposed live roots (e.g., alder and willow trees) (USFWS, 1998 and 

2007). They are usually found along completely submerged undercut banks (horizontal 

depth greater than 15 centimeters, 6 inches) with overhanging stream vegetation and 

vines (e.g., blackberry) (USFWS, 1998 and 2007). Filamentous blackberry roots sprout 

from stems wherever they extend beneath the surface, and form an ideal refuge most of 

the year (Serpa, 1996). Dense beard-like willow roots, often extending more than a foot 

out into the water, are more dependable for habitat by remaining submersed in water. 

Alders provide both short filamentous roots, and the coarser hard roots that support the 

stream banks. As the bank soils partially erode from the force of the current, a network 

of the rigid roots is exposed. Overhanging the undercut banks, these roots reduce the 

erosive power of the water, and protect the banks from further damage (Serpa, 1996). 

The roots also form a useful highway system for the shrimp. During the heavy flows of 

water accompanying storms, the shrimp abandon the softer vegetation and travel close to 

these sturdy roots, or even move within the undercut banks for protection (Serpa, 1996). 

With the exception of Yulupa Creek, shrimp have not been found in stream reaches with 

boulder and bedrock bottoms. In fact, high velocities and turbulent flows in these 

streams may hinder upstream movement of shrimp (USFWS, 1998). 

Some of the shrimp streams are completely enclosed with streamside vegetation, while 

others have just a few scattered trees along the banks. In the latter case, dark, shaded 

water is necessary to help protect the CA shrimp from visual predators (Serpa, 1996). 

Typically only the sides of the pools are utilized. Shrimp avoid the pool bottoms, and are 

only found there after being disturbed, or when populations are especially high (Serpa, 

1996). Undisturbed shrimp move slowly and are virtually invisible on submerged leaf 

and twig substrates, and among the fine, exposed, live roots of vegetation along undercut 

stream banks (USFWS, 1998 and 2007). 

Precipitation falls mainly between the months of October and March in the CA shrimp 

range with annual precipitation ranging from 71 centimeters (28 inches) in the town of 

Sonoma, Sonoma County, to 104 centimeters (41 inches) in the town of Graton, Sonoma 

County (USFWS, 1998). Consequently, stream flows are markedly different throughout 

the year with flash flood flows in the winter to minimal or zero flows in the summer and 

fall months (USFWS, 1998). As a result, habitat preferences change during late-spring 

and summer months (USFWS, 1998). During the winter, the CA shrimp is found beneath 

undercut banks with exposed fine root systems or dense, overhanging vegetation 

(USFWS, 1998 and 2007). These microhabitats may provide shelter from high water 

velocity as well as some protection from high suspended sediment concentrations 

typically associated with high stream flows (USFWS, 1998 and 2007). However, in the 

summer shrimp were rarely found beneath undercut banks (USFWS, 1998). Submerged 

leafy branches were the preferred summer habitat. In Lagunitas Creek, Marin County, 

the shrimp was found in a wide variety of trailing, submerged vegetation (USFWS, 

1998). Populations of shrimp were proportionately correlated with the quality of summer 

habitat provided by trailing terrestrial vegetation (USFWS, 1998). The highest 

concentrations of shrimp were in reaches with adjacent vegetation consisting of stinging 

nettles (Urtica sp), grasses, vine maple and mint (USFWS, 1998). However, in the late 

35
summer and fall some shrimp streams are reduced to isolated pools (Serpa, 1996). As 

temperatures rise and oxygen diminishes, trapped fish begin to die (Serpa, 1996). 

However, these conditions are still conducive to CA shrimp persistence and can be still 

considered good habitat. As long as some water remains in the pools, the species can 

survive (Serpa, 1996). Isolated pools with minimal cover and opaque waters may allow 

the shrimp to escape predation and persist despite the lack of cover (USFWS, 1998). 

 

The CA shrimp has evolved to survive a broad range of stream and water temperature 

conditions characteristic of small, perennial coastal streams (USFWS, 1998 and 2007). 

However, no data are available for defining the optimum temperature and stream flow 

regime for the shrimp or the minimum and maximum limits it can tolerate. The shrimp 

appears to be able to tolerate warm water temperatures (greater than 23 degrees Celsius, 

73 degrees Fahrenheit) and no-flow conditions (USFWS, 1998). One study that collected 

both shrimp and water quality information found shrimp in Salmon, Jonive, Blucher, 

Lagunitas, and Yulupa Creeks between temperatures of 7 and 16 degrees Celsius (45 to 

61 degrees Fahrenheit), dissolved oxygen levels of 3.3 to 12.3 parts per million, and pH 

ranges from 5.85 to 9.1. However, the study period did not sample during the summer 

months when water quality conditions for aquatic organisms are generally the most 

stressful (USFWS, 1998). The toxicity of ammonia is of particular concern for the 

shrimp, because many streams drain land uses such as grazing and dairy operations, 

which are sources of nitrogenous waters (USFWS, 1998). 

4.6 Diet 

California freshwater shrimp are detritus feeders, feeding on the small, diverse particles 

brought downstream to their pools by the current. As the water slows, the particles are 

filtered out by exposed roots and other vegetation. The shrimp simply brush up the 

detritus which may be colonized by algae, bacteria, fungi, and microscopic animals with 

tufts at the ends of their small claws, and lift the collected particles to their mouths 

(Serpa, 1996). Larger pieces of detritus are picked up or manipulated with the claws 

(Serpa, 1996). The food sources may range from fecal material produced by shredders (a 

functional group that feeds on coarse particulate organic matter), organic fines produced 

by physical abrasion and microbial maceration, senescent periphytic (organisms attached 

to underwater surfaces) algae, planktonic (free-floating) algae, aquatic macrophyte (large 

plants) fragments, zooplankton (microscopic animals), particles formed by the 

flocculation (small loose clusters) of dissolved organic matter, and aufwuchs (a matrix of 

bacteria, extracellular materials, fungi, algae, and protozoa) (USFWS, 1998). 

Much of this material is picked up indiscriminately, and contains indigestible material 

along with the more edible items. Although shrimp usually walk slowly about the roots 

as they feed, these crustaceans will undertake short swims to obtain particular particles 

(Serpa, 1996). 

Presumably, shrimp diets change with food availability and age (USFWS, 1998). Shrimp 

observed on pool bottoms, submerged twigs and vegetation seemed to feed on fine 

particulate matter (USFWS, 1998). However, much of the material ingested is probably 

indigestible cellulose (USFWS, 1998). Shrimp maintained in aquaria scavenge dead fish 

36
and shrimp (USFWS, 1998). Shrimp may use visual, tactile, or chemical cues in foraging 

activities (USFWS, 1998). 

4.7 Life History and Reproduction 

The reproductive ecology of the California freshwater shrimp has not been formally 

described (USFWS, 1998). However, it is known that they breed once a year in the fall, 

typically September (Serpa, 1996; USFWS, 1998 and 2007). Based upon the 

reproductive physiology and behavior of other marine and freshwater shrimps, the male 

probably transfers and fixes the sperm sac to the female shrimp immediately after her last 

molt, before autumn. It is typical for aquatic crustaceans to copulate during the female’s 

molt just prior to the time of year she becomes egg bearing. The timing of the mating 

was deduced from the presence of ovigerous (egg bearing) females starting in September 

(USFWS, 1998). One researcher noted that by November, most adult females in 

Huichica Creek are bearing eggs (USFWS, 1998). 

Adult females produce relatively few eggs, generally, 50 to 120 (USFWS, 1998 and 

2007). Average egg dimensions for shrimp from Salmon Creek are 1.3 by 0.9 millimeter 

(0.05 by 0.04 inch) (USFWS, 1998). Although not documented, fecundity and egg size 

may vary based on the size of the female. In studies of other freshwater atyid shrimps, 

fecundity and egg size increased as the size of the female increased (USFWS, 1998). The 

eggs adhere to the pleopods (swimming legs on the abdomen) where they are protected 

and cared for during the winter incubation (Serpa, 1996; USFWS, 1998 and 2007). 

While she carries the eggs on her body for 8 to 9 months, slow overwintering 

development of the eggs occurs (USFWS, 1988). During this period, many larvae die 

due to adult female death and genetic or embryonic developmental problems. As a result, 

the number of embryos emerging from eggs during May is reduced from those formed, 

typically by 50 percent (USFWS, 1988). However, one researcher determined that the 

winter (December-March) incubation period was advantageous because the larvae are 

released during the favorable part of the hydrologic cycle in California, following winter 

and spring high flows (USFWS, 1998). This adaptation ensures that the juveniles do not 

have to face the heavy stream flows of the rainy season (Serpa, 1996). 

The young shrimp are released as miniature adults in late Spring, after the rainy season is 

almost over, and the streams are carrying much less water (Serpa, 1996). Young are 

released in May or early June and are approximately 6 millimeters (0.24 inch) in length 

(USFWS, 1998). Newly hatched young (postlarvae) grow rapidly and reach 19 

millimeters (0.75 inch) in length by early autumn (USFWS, 1988 and 1998). Growth 

slows through the fall, winter, and early spring, and then increases through the second 

summer (USFWS, 1998). By the end of their second summer of growth, a size difference 

between males and females is apparent and shrimp reach sexual maturity (USFWS, 1998 

and 2007). No information is available on the percentage of larvae that reach 

reproductive maturity (USFWS, 1998). Although a few shrimp have been known to 

survive three years, the CA shrimp may live longer than 3 years (Serpa, 1996 and 

USFWS, 1998). 

37
4.8 References 

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 & Wildlife Service. 1988. Endangered and Threatened Wildlife and Plants; 

Determination of Endangered Status for the California Freshwater Shrimp. Available 

online at: http://ecos.fws.gov/docs/federal_register/fr1497.pdf (Accessed on April 22, 

2008). 

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). 

38
5: CALIFORNIA TIGER SALAMANDER: CENTRAL CALIFORNIA, SANTA 

BARBARA COUNTY, AND SONOMA COUNTY DISTINCT POPULATION 

SEGMENTS 

5.1 Species Listing Status 

There are currently three Distinct Population Segments [DPS] of the California tiger 

salamander [CTS] (Ambystoma californiense): the Central California DPS, the Santa 

Barbara County DPS, and the Sonoma County DPS. 

Santa Barbara County DPS: 

The Santa Barbara population was the first CTS DPS to be listed; it was listed on 

September 21, 2000, and was determined to be endangered (USFWS, 2000). On August 

4, 2004, the CTS was listed as threatened throughout its range (including all current 

DPSs), thereby downlisting the Santa Barbara County DPS from endangered to 

threatened (USFWS, 2004 a). On August 19, 2005, the downgrading of the Santa 

Barbara County DPS was vacated. As a result, the endangered species status for the 

Santa Barbara County DPS was reinstated (USFWS, 2007). 

Sonoma County DPS: 

The Sonoma County DPS of the CTS was listed as endangered on March 19, 2003 

(USFWS 2003 a). On August 4, 2004, the CTS was listed as threatened throughout its 

range (including all current DPSs), thereby downlisting the Sonoma County DPS from 

endangered to threatened (USFWS, 2004 a). On August 19, 2005, the downgrading of 

the Sonoma County DPS was vacated. As a result, the endangered species status for the 

Sonoma County DPS was reinstated (USFWS, 2007). A proposed rule was published to 

designate critical habitat for the Sonoma County DPS on August 18, 2009; however, it 

has not been finalized (74 FR 41662 41673). 

Central California DPS: 

The Central California DPS of the CTS was listed as threatened on August 4, 2004 

(USFWS, 2004 a).

5.2 Description and Taxonomy 

The CTS is a large, stocky, terrestrial salamander (USFWS, 2007). The average adult 

CTS is 190 mm (7.5 inches) in length with some adults reaching a total length of 208 mm 

(8.2 inches) (Hurt, 2000 and USFWS, 2003 a). Male CTS average about 203 mm (8 

inches), and females average about 173 mm (6.8 inches) (USFWS, 2003 a). The average 

snout-vent length for both sexes is about 91 mm (3.6 inches) (USFWS, 2003 a). The 

average weight for the CTS is 50 g (www.saczoo.com). CTS larvae range from 11.5 to 

14.2 mm (0.45 to 0.55 inches) in length (USFWS, 2003 a). 

39
The CTS was first described as A. californiense in 1853, based on specimens collected in 

Monterey, California (USFWS, 2003 a). Some considered the CTS to be a distinct 

species, whereas others considered the CTS a subspecies (A. t. californiense) of the more 

widely spread tiger salamander (A. tigrinum) (USFWS, 2004a). The CTS is now 

considered to be a separate species, A. californiense, because of its geographic isolation 

from A. tigrinum, differences in coloration between the two species, and the findings of 

recent genetic comparison studies (USFWS, 2003 a). These two species, A. tigrinum and 

A. californiese will hybridize if A. tigrinum are introduced into the habitat of A. 

californiese (USFWS, 2003 a). However, the range of the CTS does not naturally 

overlap with any other species of tiger salamander (USFWS, 2003 a). 

5.3 Distribution 

The CTS is found only in California and requires seasonal ponds, vernal pools, or vernal 

pool complexes in association with annual grasslands, oak savannah, or coastal scrub 

plant communities. CTS spend most of their life-cycle estivating underground (primarily 

in abandoned mammal burrows) in valley oak woodland or grassland habitat (from sea 

level to about 1,500 ft). 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). Approximately 9.1 million acres of 

valley and coastal grassland comprised the historic range of the Central California CTS 

(USFWS, 2004a). CTS have been historically documented in 27 counties but are no 

longer found in three of these counties (USFWS, 2005c). 

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, 2004a). 

In the coastal region, populations of CTS are scattered from Sonoma County in the 

northern San Francisco Bay Area to Santa Barbara County, and in the Central Valley and 

Sierra Nevada foothills from Yolo to Kern County (USFWS, 2007). 

The USFWS admits that they do not have a good understanding of the historic 

distribution of the CTS and that what is reported above is based on the estimated current 

distribution, habitat availability, and the assumption that the available habitat is populated 

(USFWS, 2004 a). 

Mitochondrial DNA studies identify 6 populations of CTS which are found in Sonoma 

County (the Sonoma County DPS), Santa Barbara County (the Santa Barbara County 

DPS), and the remaining populations represent the Central California DPS found in the 

Bay Area, Central Valley, southern San Joaquin Valley, and the Central Coast Range. 

40
Santa Barbara County CTS have gene sequences that are not found in any other CTS 

populations, indicating that Santa Barbara County CTS may have been separated from 

the other CTS populations for 1 to 1.5 million years (USFWS, 2000). 

Sonoma County DPS: 

The Sonoma County CTS are primarily found on the Santa Rosa Plain in Sonoma 

County. The breeding sites of Sonoma County CTS are limited to areas with HuichicaWright-Zamora and Clear Lake-Reyes soils series/associations as defined by the USDA 

(USDA 1972, 1990 and USFWS, 2002). The Huichica-Wright-Zamora association is 

limited to the Santa Rosa Plain and the vicinity of the town of Sonoma. The Clear LakeReyes association is found from the Cotati region south and east of the city of Petaluma 

to the northern part of the San Francisco Bay. 

Central California DPS: 

The Central California DPS of CTS occupies the Bay Area (central and southern 

Alameda, Santa Clara, western Stanislaus, western Merced, and the majority of San 

Benito Counties), Central Valley (Yolo, Sacramento, Solano, eastern Contra Costa, 

northeast Alameda, San Joaquin, Stanislaus, Merced, and northwestern Madera 

Counties), southern San Joaquin Valley (portions of Madera, central Fresno, and northern 

Tulare and Kings Counties), and the Central Coast Range (southern Santa Cruz, 

Monterey, northern San Luis Obispo, and portions of western San Benito, Fresno, and 

Kern Counties). 

Santa Barbara DPS: 

The Santa Barbara County CTS population is the only population west of the outer Coast 

Ranges, and is the southernmost population of this species (USFWS, 2000). 

The CTS in Santa Barbara County are found in six metapopulations: 1) southwestern 

Santa Maria Valley (West Orcutt); 2) southeastern Santa Maria Valley (BradleyDominion); 3) west Solomon Hills/north Los Alamos Valley (North Los Alamos); 4) east 

Los Alamos Valley (East Los Alamos); 5) Purisima Hills; and 6) Santa Rita Valley 

(USFWS, 2000). Historical evidence suggests that CTS were found San Luis Obispo 

County; however, no CTS have been found in that county in recent survey events 

(USFWS, 2000). If any CTS were found in San Luis Obispo County, they would likely 

be part of the Santa Barbara County DPS (USFWS, 2000). 

5.4 USFWS Critical Habitat 

Critical habitat is defined in the ESA as specific areas within the geographic area 

occupied by a species at the time it is listed, containing physical and biological features 

necessary for the conservation of the species, and that may require special management to 

protect the listed species. The designation of critical habitat is based on habitat areas that 

provide essential life-cycle needs of the species or areas that contain primary constituent 

elements (PCEs). PCEs include, but are not limited to, space for individual and 

population growth and for normal behavior; food, water, air, light, minerals, or other 

nutritional or physiological requirements; cover or shelter; sites for breeding, 

41
reproduction, rearing (or development) of offspring; and habitats that are protected from 

disturbance or are representative of the historic geographical and ecological distributions 

of the species (USFWS, 2004 b). 

5.4.1 Sonoma County DPS: 

On December 14, 2005, the USFWS determined that the designation of critical habitat for 

the Sonoma County DPS of the CTS would have a negative impact on the completion 

and implementation of the Santa Rosa Plain Conservation Strategy (USFWS, 2007). As 

a result, no critical habitat was designated for the Sonoma County DPS (USFWS, 2007). 

5.4.2 Central California DPS: 

Critical habitat was designated in the Federal Register (70 FR 49380) on August 23, 

2005, for 199,109 acres of critical habitat in 19 counties for the central population of the 

CTS (USFWS, 2005 a). Thirty one units were designated in four regions: (1) the Central 

Valley Region; (2) the Southern San Joaquin Valley Region; (3) the East Bay Region 

(including Santa Clara Valley area); and (4) the Central Coast Region (USFWS, 2005 a). 

The designated critical habitat areas for the central CTS have the following PCEs: 

1. Aquatic Habitat: standing freshwater bodies including: natural and man-made 

(stock) ponds, vernal pools, and other ephemeral or permanent water bodies that 

become filled with water during winter rains and maintain this water for a 

minimum of 12 weeks (USFWS, 2005 a) 

2. Upland (non-breeding season) habitat: accessible (barrier-free) uplands near the 

breeding ponds that contain small mammal burrows or other underground habitat. 

3. Dispersal habitat: upland areas located between breeding areas and areas 

containing small mammal burrows that allow for the dispersal of the central CTS 

between sites (USFWS, 2005 a). 

Central CTS Critical Habitat Units: 

Thirty-two units were designated as critical habitat for the Central population of the CTS 

in four geographic regions (USFWS, 2005a). The units are described below. 

Central Valley Region:

The Central Valley Region is found from northern Yolo County south and southeast to 

the northern half of Madera County, and includes eastern Solano and Contra Costa 

counties (USFWS, 2005 a). This region is 4.9 million acres (USFWS, 2005 a). The 

USFWS designated 12 critical habitat units in this region that total 97,045 acres 

(USFWS, 2005 a). The selected critical habitat units represent the varying habitats 

available to the CTS in this region (USFWS, 2005 a). 

1. Dunnigan Creek Unit, Yolo County:

Unit 1 includes 2,730 acres and is the only unit in Yolo County (USFWS, 2005 a). 

This unit is crucial because it represents the northernmost portion of the CTS 

range and the northernmost portion of the Solano-Colusa vernal pool region 

(USFWS, 2005 a). This region is bounded on the east by Interstate 5, to the south 

42
by Bird Creek, and to the north and west by Buckeye Creek (USFWS, 2005 a). 

The land in this unit is privately owned (USFWS, 2005 a). 

2. Jepson Prairie Unit, Solano County:

This unit includes 5,699 acres and represents the northwestern portion of the 

CTS’s range and the southern end of the Solano-Colusa vernal pool region in 

Solano County (USFWS, 2005 a). This unit is located south of Dixon, west of 

State Route 113, north of Creed Road, and east of Travis Air Force Base 

(USFWS, 2005 a). The land comprising this unit is predominantly privately 

owned but also includes some land that is owned by the California Department of 

Fish and Game (USFWS, 2005 a). 

3. Southeastern Sacramento Unit, Sacramento County:

This unit includes 9,966 acres and is the only unit in Sacramento County 

(USFWS, 2005 a). It represents the northern-central part of the range of the CTS, 

the southern part of the Southeastern Sacramento Valley vernal pool region, and 

one of only a few areas occupied by this species in the Sacramento Valley 

(USFWS, 2005 a). This unit is bounded to the south by the Sacramento and San 

Joaquin County border, to the north by Laguna Creek, to the east by the 

Sacramento and Amador County border, and to the west by the Alta Mesa Road 

(USFWS, 2005 a). The land comprising this unit is privately owned (USFWS, 

2005 a). 

4. Northeastern San Joaquin Unit, and Amador Counties:

This unit includes 9,603 acres and is the only unit in San Joaquin and Amador 

counties (USFWS, 2005 a). This unit is located in an area south of the San 

Joaquin and Sacramento county line, east of Day Creek Road, north of Liberty 

Road, and west of Comanche and Jackson Valley Roads. The land comprising 

this unit is privately owned (USFWS, 2005 a). 

5. Indian Creek Unit, Calaveras County:

This unit includes 3,128 acres and represents the northeastern part of the CTS 

range (USFWS, 2005 a). This unit is bordered to the south and east by State 

Route 26, to the west by Warren Road, and to the north by State Route 12 

(USFWS, 2005 a). The land in this unit is privately owned (USFWS, 2005 a). 

6. Rock Creek Unit, Calaveras, San Joaquin, and Stanislaus Counties:

This unit includes 23,491 acres and represents the northern end of the Southern 

Sierra Foothills vernal pool region and a part of the east-central portion of the San 

Joaquin Valley (USFWS, 2005 a). This unit is located west of San Joaquin 

County Road J6, north of Sonora Road, east of Stanislaus County Road J12, and 

south of the Calaveras River (USFWS, 2005 a). The land in this unit is privately 

owned (USFWS, 2005 a). 

43
7. Rodden Lake Unit, Stanislaus County:

This unit includes 562 acres in the northern end of the Southern Sierra Foothill 

vernal pool region in the eastern San Joaquin Valley (USFWS, 2005 a). This unit 

is the only unit near the Stanislaus River (USFWS, 2005 a). It is bordered to the 

east by Horseshoe Road, to the north by Frankenheimer Road, to the west by 

Twenty Eight Mile Road, and to the south by the Stanislaus River (USFWS, 2005 

a). The land in this unit is privately owned (USFWS, 2005 a). 

8. La Grange Ridge Unit, Stanislaus and Merced Counties:

This unit includes 4,013 acres in the northeastern area of the Southern Sierra 

Foothills vernal pool region (USFWS, 2005 a). It represents the east central part 

of the CTS distribution within the Central Valley and is bounded to the east by the 

Cardoza Ridge, to the west by Los Cerritos Road, to the north by State Route 132 

and to the south by Fields Road (USFWS, 2005 a). The land in this unit is 

privately owned (USFWS, 2005 a). 

9. Fahrens Creek Unit, Merced County:

This unit includes 17,799 acres and represents the South Sierra Foothills vernal 

pool region in Merced County, the central part of the CTS distribution in the 

eastern San Joaquin Valley, and the south-eastern part of the CTS distribution in 

the Central Valley region (USFWS, 2005 a). This unit is located northeast of 

Merced, east of the Merced and Mariposa county line, north of Bear Creek, and 

south of the Merced River (USFWS, 2005 a). The land in this unit is privately 

owned (USFWS, 2005 a). 

10. Miles Creek Unit, Merced County:

This unit includes 10,585 acres and is the only other unit in the Southern Sierra 

Foothills vernal pool region in Merced County (USFWS, 2005 a). This unit 

represents the central part of the CTS distribution in the eastern San Joaquin 

Valley and the south-eastern part of the CTS distribution in the Central Valley 

region (USFWS, 2005 a). This unit is located to the “east of Owens Lake in 

Mariposa County, west of Cunningham Road in Merced County, south of South 

Bear Creek Road in Merced County, and north of Childs Avenue (USFWS, 2005 

a). The land in this unit is privately owned (USFWS, 2005 a). 

11. Rabbit Hill Unit, Madera County:

This unit includes 8,291 acres and “represents the Sierra Foothills vernal pool 

region in Madera County and is the southernmost unit within the Central Valley 

Geographic Region” (USFWS, 2005 a). This unit is “located west of Hensley 

Lake, south of Knowles Junction, west of the Daulton Mine, and north of the 

Fresno River (USFWS, 2005 a). The land in this unit is privately owned 

(USFWS, 2005 a). 

 

12. Doolan Canyon Unit, Alameda County:

This unit includes 1,178 acres and represents the Livermore vernal pool region 

and the western part of the Central Valley region (USFWS, 2005 a). This unit is 

44
bounded to the north by the Contra Costa County line, near Collier Canyon Road 

on the east and the south, and the City of Dublin to the west (USFWS, 2005 a). 

The land in this unit is privately owned (USFWS, 2005 a). 

Southern San Joaquin Region:

This region contains about 1.4 million acres and is found from the southern half of 

Madera County south to northeastern Kings County and northwestern Tulare County 

(USFWS, 2005 a). Four critical habitat units totaling about 20,293 acres were designated 

in this region (USFWS, 2005 a). These critical habitat units represent the San Joaquin 

Valley and Southern Sierra Foothills vernal pool regions in the southern San Joaquin 

Valley (USFWS, 2005 a). 

Millerton Unit, Madera County:

1. This unit is comprised of two subunits and includes a total of 6,811 acres 

(USFWS, 2005 a). Subunit 1 a includes 3,808 acres and Subunit 1 b includes 

3,003 acres (USFWS, 2005 a). This unit represents the Southern Sierra Foothills 

vernal pool region, one of two different vernal pool regions in the Southern San 

Joaquin region, and the southeastern part of the CTS range in the San Joaquin 

Valley (USFWS, 2005 a). This unit is the only critical habitat unit in this vernal 

pool region in Madera County (USFWS, 2005 a). It is located “west of State 

Highway 41 and generally north of the San Joaquin River” (USFWS, 2005 a). 

The unit is bounded to the east by the western side of Millerton Lake, and to the 

north by the by O’Neal Road, south of Berry Hill (USFWS, 2005 a). The land in 

this unit is privately owned (USFWS, 2005 a). 

2. Northeastern Fresno, Fresno County:

This unit includes 4,961 acres and represents the Southern Sierra Foothills vernal 

pool region within Fresno County, the northern end of the Southern San Joaquin 

region, and the southern part of the CTS range in the San Joaquin Valley 

(USFWS, 2005 a). This unit is located “northeast of Fresno, southwest of 

Millerton Lake, east of Friant Road, and generally west of Academy” (USFWS, 

2005 a). The land in this unit is privately owned (USFWS, 2005 a). 

3. Hills Valley Unit, Fresno and Tulare Counties:

This unit includes 4,181 acres and two subunits (USFWS, 2005 a). Subunit 3 a 

includes 1,626 acres and subunit 3 b includes 2,553 acres (USFWS, 2005 a). This 

unit represents the foothills of northwest Tulare County, the Southern Sierra 

Foothills vernal pool region, and the southeastern part of the CTS range within the 

San Joaquin Valley (USFWS, 2005 a). This unit is located south of State 

Highway 180, west of George Smith and San Creek Roads, north of Curtis 

Mountain, and east of Cove Road (USFWS, 2005 a). The land comprising this 

unit is privately owned (USFWS, 2005 a). 

4. Cottonwood Creek Unit, Tulare County:

This unit includes 4,342 acres and represents a significant area at the very 

southernmost portion of the range of the Central population of the CTS (USFWS, 

45
2005 a). “Unit 5 represents a low-elevation vernal pool complex within the San 

Joaquin Valley vernal pool region” (USFWS, 2005 a). This unit is bounded to the 

north by County Road J36, to the east by Dinuba Road, to the south by Avenue 

352, and to the west by County Road 112 (USFWS, 2005 a). The land 

comprising this unit is privately owned (USFWS, 2005 a). 

East Bay Region:

This geographic region is located in Alameda County, south to Santa Benito and Santa 

Clara counties, and west to the eastern portions of San Joaquin and Merced counties 

(USFWS, 2005 a). This region includes 2.4 million acres with 24,045 acres of critical 

habitat designated into 14 critical habitat units (USFWS, 2005 a). These 14 critical 

habitat units occur in the Livermore, Central Coast, and San Joaquin vernal pool regions 

(USFWS, 2005 a). Some of these critical habitat units are pristine (USFWS, 2005 a). It 

is thought that the CTS in the East Bay Region does not occur west of Interstate Highway 

680, south of Interstate Highway 580, or north of State Highway 4 in Contra Costa or 

Alameda counties (USFWS, 2004 a). 

1. Alameda Creek Unit, Santa Clara County:

This unit includes 619 acres and represents the north-central part of the Bay Area 

region and the northwestern Livermore vernal pool region (USFWS, 2005 a). 

This unit is bounded to the south by the Calaveras Reservoir, to the west by Sugar 

Butte, to the east by Fremont, and to the north of Livermore. The land in this unit 

is a mixture of county parks and private land (USFWS, 2005 a). 

2. Poverty Ridge Unit, Santa Clara County:

This unit includes 2,814 acres and represents the north-central part of the Bay 

Area region and the southern end of the Livermore vernal pool region (USFWS, 

2005 a). This unit is bounded to the east by Alum Rock, to the north by the 

Alameda and Contra Costa counties line, to the east by Kincaid Road, and to the 

south by Master Hill (USFWS, 2005 a). The land in this unit is privately owned 

(USFWS, 2005 a). 

3. Smith Creek Unit, Santa Clara County:

This unit includes 7,976 acres and represents the north-central portion of the 

range of the CTS within the Bay Area region, and the northern range of the 

Central Coast vernal pool region (USFWS, 2005 a). This unit is bounded to the 

east by Sugarloaf Mountain, to the north by Packard Ridge, to the west by 

Masters Hill, and to the south by Panochita Hill (USFWS, 2005 a). This unit is 

comprised of county, private, and University of California owned land (USFWS, 

2005 a). 

4. San Felipe Creek Unit, Santa Clara County:

This unit includes 9,080 acres and represents the center of the Bay Area region 

and the north-central portion of the Central Coast vernal pool region (USFWS, 

2005 a). This unit is bounded on the east by Silver Creek, on the north by 

Panochita Hill, on the west by Bollinger Mountain, and on the south by Morgan 

46
Hill (USFWS, 2005 a). The land in this unit is privately owned (USFWS, 2005 

a). 

5. Laurel Hill Unit, Santa Clara County:

This unit includes 2,535 acres and represents the northwestern part of the CTS in 

the Bay Area region and the northwestern area of the Central Coast vernal pool 

region on the western side of the Santa Clara Valley (USFWS, 2005 a). Unit 8 is 

bounded to the west by Morgan Hill, to the north by San Jose, to the east by the 

Santa Cruz Mountains, and to the south by Croy Ridge (USFWS, 2005 a). The 

land in this unit is privately owned (USFWS, 2005 a). 

6. Cebata Flat Unit, Santa Clara County:

This unit includes 2,934 acres and represents the center of the Bay Area region 

and the central part of the Central Coast vernal pool region (USFWS, 2005 a). 

This unit is bounded to the east by Gilroy, to the north by Henry Coe State Park, 

to the west by Lake Mountain, and to the south by Canada Road (USFWS, 2005 

a). The land in this unit is privately owned (USFWS, 2005 a). 

7. Lions Peak Unit, Santa Clara County:

This unit includes 892 acres and is divided into two subunits (USFWS, 2005 a). 

Subunit 10 a includes 194 acres and subunit 10 b includes 698 acres (USFWS, 

2005 a). This unit represents the second unit on the west side of the Santa Clara 

Valley in the center of the Bay Area region and the center of the Central Coast 

vernal pool region (USFWS, 2005 a). This unit is bounded to the west by State 

Highway 101, to the north by Morgan Hill, to the south by Hecker Pass, and to 

the east by Uvas Reservoir (USFWS, 2005 a). The land in this unit is privately 

owned (USFWS, 2005 a). 

8. Braen Canyon Unit, Santa Clara County:

This unit includes 6,991 acres and represents the eastern central part of the CTS 

range within the Bay Area region and the central part of the Central Coast vernal 

pool region (USFWS, 2005 a). Unit 11 is located in southern Santa Clara County 

and is bounded to the east by Gilroy, to the north by Kelly Lake, to the west by 

Pacheco Lake, and to the south by Jamison Road (USFWS, 2005 a). The land in 

this unit is privately owned (USFWS, 2005 a). 

9. San Felipe Unit, Santa Clara and San Benito Counties:

This unit includes 6,642 acres and represents a part of the center of the CTS range 

in the Bay Area region and the southernmost part of Santa Clara County, northern 

San Benito County, and the center of the Central Coast vernal pool region 

(USFWS, 2005 a). Unit 12 is bounded to the east by Camadero, to the north by 

Kickham Peak, to the west by San Joaquin Peak, and to the south by Dunneville 

(USFWS, 2005 a). The land in this unit is privately owned (USFWS, 2005 a). 

47
10. Los Banos Unit, Merced County:

This unit includes 2,409 acres and represents a part of the southeastern range of 

the CTS in the Bay Area region and the San Joaquin Valley vernal pool region 

(USFWS, 2005 a). Unit 13 is bounded to the west by Los Banos Reservoir, to the 

south of Bullard Mountain, to the east of Cathedral Peak, and to the north by San 

Luis Reservoir State Recreation Area (USFWS, 2005 a). The land in this unit is 

privately owned (USFWS, 2005 a). 

11. Landgon Unit, Merced County:

This unit includes 2,212 acres and represents the easternmost range of the CTS in 

the Bay Area region and is the only other unit in the San Joaquin Valley vernal 

pool region (USFWS, 2005 a). Unit 14 is bounded to the east by Sweeny Hill, to 

the north by Gasten Bide Road, and to the south by Ortigalita Peak (USFWS, 

2005 a). The land in this unit is privately owned (USFWS, 2005 a). 

12. Ana Creek Unit, San Benito County:

Unit 15 includes 3,165 acres and consists of two subunits (USFWS, 2005 a). 

Subunit 15 a includes 2,722 acres and subunit 15 b includes 194 acres (USFWS, 

2005 a). This unit represents the southwestern part of the CTS range in the Bay 

Area region and southern Central vernal pool region (USFWS, 2005 a). Unit 15 

is bounded to the east by Hollister, to the south by Tres Pinos, to the west by Cibo 

Peak, and to the north by Coyote Peak (USFWS, 2005 a). The land in this unit is 

privately owned (USFWS, 2005 a). 

13. Bitterwater Unit, San Benito County:

This unit includes 16,952 acres and represents the southernmost range of the CTS 

in the Bay Area region and the southern end of the Central Coast vernal pool 

region (USFWS, 2005 a). This unit is bounded to the north by Pinnacles, to the 

west by Hernandez Reservoir, to the south by Lonoak, and to the east by Murphy 

Flat (USFWS, 2005 a). The land in this unit is privately owned (USFWS, 2005 

a). 

14. Gloria Valley Unit, Monterey and San Benito Counties:

This unit includes 3,881 acres and represents the northeastern part of the CTS’s 

range in the Bay Area region and the western area of the Central Coast vernal 

pool region (USFWS, 2005 a). Unit 17 is bordered to the south by Soledad, to the 

west by Pinnacles National Monument, to the north by Tres Pinos, and to the east 

by Gonzales (USFWS, 2005 a). The land in this unit is privately owned 

(USFWS, 2005 a). 

Central Coast Region:

The Central Coast Region is found from Monterey County to northeastern San Luis 

Obispo County (USFWS, 2005 a). This region is 3.6 million acres and includes two 

critical habitat units consisting of 25,373 acres (USFWS, 2005 a). The critical habitat is 

designated in the Central Coast, Livermore, and Carrizo vernal pool regions (USFWS, 

2005 a). 

48
1. Haystack Hill Unit, Monterey County:

Unit 3 includes 3,665 acres and represents the center of the Central Coast region 

and the northwestern area of the Central Coast vernal pool region (USFWS, 2005 

a). This unit is bounded to the south by Soledad, to the west by Paloma Ridge, to 

the east by Jamesberg, and to the north by Carmel Valley (USFWS, 2005 a). The 

land in this unit is a mixture of privately owned land and Hastings Natural History 

State Reserve land (USFWS, 2005 a). 

2. Choice Valley, Kern and San Luis Obispo Counties:

This unit includes 9,233 acres and represents the southernmost extension of the 

CTS’s range in the Central Coast region and is the only critical habitat unit in the 

Carrizo vernal pool region (USFWS, 2005 a). This unit is bordered to the south 

by the Carrisa Highway, to the west by Antelope Valley, to the north by 

Cottonwood, and to the east by Shandon. The land in this unit is privately owned 

(USFWS, 2005 a). 

5.4.3 Santa Barbara DPS: 

Critical habitat was designated for the Santa Barbara DPS of the CTS on November 24, 

2004 (69 FR 68568). This designation was based on the following PCEs, which are 

identical to the PCEs forming the basis of the critical habitat designation for the central 

CTS. 

1. Aquatic habitat: standing freshwater bodies including: natural and man- 

 made (stock) ponds, vernal pools, and dune ponds, and other ephemeral or 

 permanent water bodies that become filled with water during the winter rains and 

 maintain this water for a minimum of 12 weeks (USFWS, 2004b) 

2. Upland (non-breeding) habitat: accessible (barrier-free) uplands near the breeding 

 ponds that contain small mammal burrows (USFWS, 2004b) 

3. Dispersal habitat: upland areas located between breeding areas and areas 

 containing small mammal burrows that allow for the dispersal of the CTS 

 between sites. (USFWS, 2004b) 

Santa Barbara CTS Critical Habitat Units: 

About 11,180 acres of critical habitat comprising six units in northern Santa Barbara 

County were designated for the Santa Barbara County DPS in 2004 (USFWS, 2004b). 

About 2,740 acres of privately-owned land were excluded from this designation 

(USFWS, 2004b). These units are described below: 

1. Western Santa Maria/Orcutt:

This unit consists of 4,135 acres west and southwest of the city of Santa Maria, 

predominantly in unincorporated areas of the county and the community of Orcutt 

(USFWS, 2004b). This critical habitat unit includes known breeding locations from 

the Casmalia Hills in the south to the Santa Maria Airport in the north and the area 

west of Black Road east to Highway 135 (USFWS, 2004b). This unit includes seven 

of the 19 natural vernal pools that are found in Santa Barbara County (USFWS, 

49
2004b). The West Orcutt metapopulation occurs on grazing and agricultural land and 

vernal pools in this area have been lost or adversely affected by development in the 

Santa Maria Valley (USFWS, 2000). About 78% of the CTS upland habitat in the 

West Santa Maria subpopulation has been lost or separated from breeding ponds 

(USFWS, 2004b). Remaining development projects in this area threaten the rest of 

the remaining habitat (USFWS, 2004b). 

2. Eastern Santa Maria:

This unit includes 2,909 acres and is bordered by State Highway 101 to the west, the 

Solomon Hills to the south, the Sisquoc River to the east, and the Santa Maria 

floodplain to the north (USFWS, 2004b). The four known breeding pools in this unit 

are vernal pools (USFWS, 2004b). The Bradley-Dominion metapopulation in 

southeastern Santa Maria Valley is surrounded by oil production and grazing land 

(USFWS, 2000). It has been determined that this is the most at-risk metapopulation 

because of the intense agricultural development (USFWS, 2000). 

3. Western Los Alamos/Careaga:

Part of this unit was excluded from the final critical habitat designation because it is 

already actively managed for protection and enhancement of the CTS habitat 

(USFWS, 2004a). This unit includes 1,451 acres to the west of Highway 101 and is 

bordered on the west by the Careaga Divide (USFWS, 2004a). This unit is known to 

contain some of the highest quality natural breeding areas for the CTS and also large 

sections of continuous upland habitat (USFWS, 2004a). The land surrounding this 

unit is mostly used for cattle grazing (USFWS, 2004a). 

4. Eastern Los Alamos:

Part of this unit was excluded from the final critical habitat designation because it is 

already actively managed for protection and enhancement of the CTS habitat 

(USFWS, 2004a). This unit is comprised of two separate parcels, one is 27 acres and 

the other is 63.7 acres for a total of 90 acres (USFWS, 2004a). This unit is located 

south of Highway 101 and southeast of Los Alamos and is the easternmost location of 

the CTS in Santa Barbara County (USFWS, 2004a). This metapopulation consists of 

three small ponds in open savannah grassland in an area that was used for cattle 

grazing but has been proposed for vineyard installation (USFWS, 2000). 

5. Purisima Hills:

Part of this unit was excluded from the final critical habitat designation because it is 

already actively managed for protection and enhancement of the CTS habitat 

(USFWS, 2004a). This unit includes 1,957 acres along the crest and south slope of 

the Purisima Hills (USFWS, 2004a). The portion of this unit that contains habitat 

suitable for the CTS lies on the lower Careaga Formation, which is bordered to the 

east-southeast by outcrops of the Sisquoc Formation and to the west-northwest by 

“badlands topography of sandier horizons within the upper Careaga Formation” 

(USFWS, 2004a). The breeding ponds, all stock ponds, range in elevation from 500 

to 1400 feet (152 to 427 m) (USFWS, 2004a). This critical habitat unit is the most 

remote and has the fewest documented threats within the Santa Barbara County 

50
population (USFWS, 2004a). This unit is unique because the terrain in this location 

is steeper and more densely vegetated (USFWS, 2004a). The vegetation in this 

location consists of coastal sage chaparral, and this unit is the only one known to 

contain CTS breeding ponds completely surrounded by this type of vegetation 

(USFWS, 2004a). 

The Purisima Hills metapopulation consists of six small ponds and the surrounding 

upland habitat on the crest of the Purisima Hills is in an area of cattle grazing 

(USFWS, 2000). The CTS in this metapopulation may provide evidence of a historic 

genetic link between the Los Alamos and Santa Rita Valley metapopulations 

(USFWS, 2000). This metapopulation is the least threatened of the six Santa Barbara 

County metapopulations (USFWS, 2000). 

6. Santa Rita Valley:

This unit includes 638 acres and comprised the southernmost location for the CTS in 

Santa Barbara County (USFWS, 2004a). This unit is bisected by Highway 246, 

which is the main threat to the CTS found in this unit (USFWS, 2004a). Two 

confirmed breeding locations, a total of three ponds, are located in the Santa Rita 

Valley (USFWS, 2004a). This unit contains the only remaining subpopulation in the 

Santa Rita Valley (USFWS, 2004a). This metapopulation, the westernmost area 

occupied by the CTS, has been affected by grading, conversion to row crops, and 

livestock facilities (USFWS, 2000). 

5.5 Diet 

Larval CTS eat algae, snails, zooplankton, small crustaceans, and aquatic larvae and 

invertebrates, including mosquito larvae for about six weeks after hatching (Hurt, 2000; 

and USFWS, 2000, 2003 a, 2005 b). CTS larvae switch to larger prey after this initial 

period, including smaller tadpoles of Pacific tree frogs, California red-legged frogs 

(CRLF), western toads, and spadefoot toads, as well as aquatic insects and other aquatic 

invertebrates (USFWS, 2000 and 2003 a). The CTS larvae may also eat each other 

(USFWS, 2000). Adult CTS eat terrestrial invertebrates, insects, frogs, and worms 

(USFWS, 2005 b). The juvenile and adult CTS eat very little during the summer and fall 

when they are aestivating (USFWS, 2003 a). However, during the fall and winter rains, 

the CTS emerge from their burrows to feed (USFWS, 2003 a). Adult and subadult CTS 

feed at night when relatively humidity is high (USFWS, 2004a). 

5.6 Life History and Reproduction 

Subadult and adult CTS spend the summer and fall months in a state of dormancy or 

inactivity (estivation). They estivate in the burrows of small mammals. CTS emerge 

from their burrows during the fall and winter rains (November through June) and migrate 

to the breeding ponds to mate and lay eggs (USFWS, 2004 a). The breeding migration 

typically takes place at night during a rainstorm when there is little threat of desiccation 

(Hurt, 2000 and USFWS, 2000). Adult CTS may migrate up to 2 km (1 mile) from their 

burrows to the breeding pond (USFWS, 2003 a). Males migrate before females and 

51
generally stay at the breeding pond five to six weeks longer than the females (USFWS, 

2003 a). Males typically remain in the ponds for an average of 6 to 8 weeks, while the 

females only stay for 1 to 2 weeks (USFWS, 2003 a). If the weather is hot and dry, the 

CTS may not stay at the breeding ponds for very long (USFWS, 2003 a). If the rains 

occur late in the season, or if a drought occurs, CTS may not breed at all (USFWS, 2000 

and 2003 a). 

The adults mate and the females lay their eggs in the pond (USFWS, 2003 a). Female 

CTS in the East Bay area may lay eggs twice, once in December and a second time in 

February (USFWS, 2004a). The females lay their eggs singly, or on rare occasions, in 

small groups of two to four (USFWS, 2003 a). Females lay between 400 and 1300 eggs 

each breeding season (USFWS, 2000). These eggs are attached to grass or vegetation at 

the edge of the breeding ponds, if available. Rocks, branches, or other submerged debris 

are used if no vegetation is available (USFWS, 2003 a). After breeding the adults return 

to their burrows, although they may continue to emerge from the burrow at night for the 

next two weeks in order to feed (USFWS, 2003 a). 

Salamander eggs typically hatch after 10 to 14 days (USFWS, 2003 a). The larval stage 

is aquatic and typically lasts three to six months, until the ponds dry out. Some larvae in 

Contra Costa and Alameda counties may remain in their breeding sites over the summer 

(USFWS, 2004 a). The larvae must reach a critical body size, about two to three inches 

in length, before they metamorphose into the terrestrial life-stage (Hurt, 2000 and 

USFWS, 2003 a). During their metamorphosis CTS larvae lose their gills and develop 

lungs and legs. Larvae metamorphose and leave the breeding pools 60 to 94 days after 

the eggs are laid (USFWS, 2003 a). Larvae develop faster in smaller pools because these 

pools dry out faster. The longer the pond contains water, the larger the larvae and 

metamorphose juveniles are able to grow, and the more likely they are to survive and 

reproduce (USFWS, 2003 a). The snout to vent length of newly metamorphosed CTS 

juveniles ranges from 41 to 78 mm (1.6 to 3.1 inches) (USFWS, 2000). 

Once the larvae metamorphose into the terrestrial life-stage in late spring or early 

summer, they migrate to their own small mammal burrows (USFWS, 2003 a). Juveniles 

have been observed migrating up to 1.6 km (1 mile) from the breeding ponds to their 

aestivation sites (typically burrows) (USFWS, 2003 a). An estimated 50% of juveniles 

do not survive their first summer (USFWS, 2003 a). Juveniles typically do not return to 

the breeding pools until they reach sexual maturity (USFWS, 2003 a). Preliminary data 

suggest that most CTS become sexually mature after two years (USFWS, 2003 a). 

However, most individuals do not breed until they are four or five years old (USFWS, 

2005 b). CTS usually go back to their natal pond to breed but one study showed that 

20% of CTS were re-captured at ponds other than their natal pond (USFWS, 2000). 

Studies have also correlated dispersal distance with precipitation with CTS traveling 

farther in wetter years (USFWS, 2000). 

Although CTS are generally long-lived, some may live up to 10 years, many individuals 

only reproduce once in their lifetime and others may not reproduce at all (USFWS, 2004 

a). Individual animals may not survive to sexual maturity and others may not find a pond 

52
in which to mate. It has been estimated that less than 50% of CTS breed more than once 

in their lifetime (USFWS, 2000). In some populations, it has been determined that less 

than 5% of juveniles survive to breeding adults (USFWS, 2005 b). One study found that 

the average female CTS breeds 1.4 times and produces 8.5 young that survive to 

metamorphosis per reproductive effort (USFWS, 2005 b). The result of this finding is 

that over the lifetime of a female only about 11 metamorphic offspring are produced 

(USFWS, 2005 b). 

5.7 References 

Hammerson, G. 2004. Ambystoma californiense. In: IUCN 2007. 2007 IUCN Red List 

of Threatened Species. Available online at: www.iucnredlist.org (Accessed on 

March 16, 2009). 

Hurt, R. 2000. The Elusive California Tiger Salamander. Tideline. 20 (2):1-3. 

Available online at: 

http://www.fws.gov/desfbay/Archives/CTSalam/CaTigSal.htm (Accessed on 

March 16, 2009). 

U.S. Fish and Wildlife Service (USFWS). 2000. Endangered and threatened wildlife and 

plants: final rule to list the Santa Barbara County distinct population of the 

California tiger salamander as endangered. Federal Register 65 (184):57242-

57263. Available online at: http://frwebgate.access.gpo.gov/cgibin/getdoc.cgi?dbname=2000_register&docid=00-24173-filed.pdf (Accessed on 

March 16, 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 March 16, 

2009). 

U.S. Fish and Wildlife Service (USFWS). 2003 a. 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 March 16, 

2009). 

U.S. Fish and Wildlife Service (USFWS). 2003 b. Endangered and threatened wildlife 

and plants: listing of the central California distinct population segment of the 

California tiger salamander; proposed rule. Federal Register 68 (100):28648-

28670. Available online at: http://ecos.fws.gov/docs/federal_register/fr4102.pdf

(Accessed on March 16, 2009). 

53
U.S. Fish and Wildlife Service (USFWS). 2004 a. 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 March 16, 

2009). 

U.S. Fish and Wildlife Service (USFWS). 2004 b. Endangered and threatened wildlife 

and plants: designation of critical habitat for the California tiger salamander 

(Ambystoma californiense) in Santa Barbara County. Federal Register 69 

(226):68568-69609. Available online at: 

http://edocket.access.gpo.gov/2004/pdf/04-25775.pdf (Accessed on March 16, 

2009). 

U.S. Fish and Wildlife Service (USFWS). 2005 a. Endangered and threatened wildlife 

and plants: designation of critical habitat for the California tiger salamander, 

Central population. Federal Register 70 (162):49380-49458. Available online at: 

http://a257.g.akamaitech.net/7/257/2422/01jan20051800/edocket.access.gpo.gov/

2005/pdf/05-16234.pdf (Accessed on March 16, 2009). 

U.S. Fish and Wildlife Service (USFWS). 2005 b. Endangered and threatened wildlife 

and plants: designation of critical habitat for the Sonoma County distinct 

population segment of the California tiger salamander. Federal Register 70 

(239):74138-74163. Available online at: 

http://a257.g.akamaitech.net/7/257/2422/01jan20051800/edocket.access.gpo.gov/

2005/pdf/05-23701.pdf (Accessed on March 16, 2009). 

U.S. Fish and Wildlife Service (USFWS). 2005 c. 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 March 16, 2009). 

U.S. 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 March 16, 2009). 

Sacramento Zoo Website. Available online at: www.sac.zoo (Accessed on March 16, 

2009). 

54
6: DELTA SMELT 

6.1 Species Listing Status 

The delta smelt (Hypomesus transpacificus) was listed as threatened on March 5, 1993 

(58 FR 12854) by the U.S. Fish and Wildlife Service (USFWS) (USFWS, 2007 a). A 

recovery plan for the Sacramento/San Joaquin Delta Native Fishes, including the delta 

smelt, was approved by the USFWS on November 26, 1996 (USFWS, 1995). A 5-year 

review was published by the USFWS on March 31, 2004 (USFWS, 2004 a). 

6.2 Description and Taxonomy 

Delta smelt are slender-bodied, nearly transparent steely blue fish that typically reach 60-

70 millimeters (2.4-2.8 inches) standard length, although a few may reach 120 

millimeters (5.1 inches) standard length (USFWS, 1995 and 2007 a). This species 

typically lives only about one year (USFWS, 1993 and 2007 a). 

6.3 Distribution and Status 

Delta smelt occur only in Suisun Bay and the Sacramento-San Joaquin estuary (known as 

the Delta) near San Francisco Bay, in Contra Costa, Sacramento, San Joaquin, Solano 

and Yolo counties California (USFWS, 1993,1995, 2004 b and 2007 a and b). The Delta 

is the uppermost part of the system, where the Sacramento and San Joaquin Rivers meet, 

and is largely a tidal freshwater system (USFWS, 1995). Delta smelt are now known to 

spawn in the Napa River; however, it is unclear if these delta smelt are self perpetuating 

or if frequent recolonization from the delta is necessary to maintain a population in that 

location (USFWS, 2004 a). 

Delta smelt abundance from year to year has fluctuated greatly in the past, and between 

1982 and 1992 their population was consistently low (CDFG, 2008 b; and USFWS, 1995 

and 2004 b). At the time of listing, the Delta smelt were under a high degree of threat 

from the severe drought in California between1987and 1992. The species persisted in 

small numbers and rebounded to pre-decline levels in 1993 (USFWS, 2004 a). Annual 

changes in the population appear to be affected by the amount of outflow from the upper 

Sacramento-San Joaquin Estuary which varies from year to year due to precipitation and 

water management (CDFG, 2008 a and b). The analysis of 22 years of monthly sampling 

data from the Suisun Marsh shows that the delta smelt have still not recovered to their 

former abundance, although there has been a general increase in numbers since their low 

point during the long period of drought (USFWS, 2004 a). 

55
6.4 USFWS Critical Habitat 

Critical habitat was designated for the delta smelt on December 19, 1994 (59 FR 65256) 

(USFWS, 1994 and 2007 a). The designation of critical habitat is based on habitat areas 

that provide essential life-cycle needs of the species or areas that contain primary 

constituent elements (PCEs). Critical habitat is designated in the following geographic 

area – areas of all water and all submerged lands below ordinary high water and the entire 

water column bounded by and contained in Suisun Bay (including the contiguous Grizzly 

and Honker Bays); the length of Goodyear, Suisun, Cutoff, First Mallard (Spring 

Branch), and Montezuma sloughs; and the existing contiguous waters contained within 

the Delta. Thus, critical habitat for the delta smelt is contained within Contra Costa, 

Sacramento, San Joaquin, Solano, and Yolo Counties, California (USFWS, 1994). 

The PCEs essential to the conservation of the delta smelt are physical habitat, water, river 

flow, and salinity concentrations required to maintain delta smelt habitat for spawning, 

larval and juvenile transport, rearing, and adult migration (USFWS, 1994). The specific 

geographic areas identified for each habitat condition represent the maximum possible 

range of each of these conditions. Depending on the water-year type (i.e., wet, above 

normal, normal, below normal, dry, critically dry), each of the habitat conditions 

specified below requires fluctuation (within-year and between-year) in the placement of 

the 2 parts per thousand (ppt) isohaline (a line drawn to connect all points of equal 

salinity) around three historical reference points (USFWS, 1994). These three points are 

the Sacramento-San Joaquin River confluence, the upstream limit of Suisun Bay at 

Chipps Island, and in the middle of Suisun Bay at Roe Island. The actual number of days 

that the 2 ppt isohaline is maintained at the three points varies according to water-year 

type (USFWS, 1994). In addition, the number of days at each reference point must 

simulate that which historically existed in 1968. This year represents a period of time 

when the delta smelt was abundant (USFWS, 1994). The PCEs are organized by habitat 

conditions required for each life stage which are as follows: 

• Spawning Habitat: Shallow, fresh or slightly brackish backwater sloughs and 

edgewaters are required for spawning (USFWS, 1994). These areas must also 

provide suitable water quality (i.e., low concentrations of pollutants) and 

substrates for egg attachment (e.g., submerged tree roots and branches and 

emergent vegetation) to ensure egg hatching and larval viability. Specific areas 

that have been identified as important delta smelt spawning habitat include 

Barker, Lindsey, Cache, Prospect, Georgiana, Beaver, Hog, and Sycamore 

sloughs and the Sacramento River in the Delta, and tributaries of northern Suisun 

Bay (USFWS, 1994). 

• Larval and Juvenile Transport: Adequate river flow is necessary to transport 

larvae from upstream spawning areas to shallow, productive rearing or nursery 

habitat in Suisun Bay. The 2 ppt isohaline must be located westward of the 

Sacramento-San Joaquin River confluence during the period when larvae or 

juveniles are being transported, according to the historical salinity conditions 

which vary according to water-year type to ensure that suitable rearing habitat is 

56
available in Suisun Bay (USFWS, 1994). Maintenance of the 2 ppt isohaline will 

produce the high plankton and zooplankton densities that characterize most 

healthy estuarine ecosystems that ensure suitable rearing habitat. The specific 

season when habitat conditions identified above are important for successful 

larval transport varies from year to year, depending on when peak spawning 

occurs and on the water-year type (USFWS, 1994). 

• Rearing Habitat: Maintenance of the 2 ppt isohaline according to the historical 

salinity conditions described above and suitable water quality within the upper 

Sacramento-San Joaquin Estuary is necessary to provide delta smelt larvae and 

juveniles a shallow, protective, food-rich environment in which to mature into 

adulthood. An area extending eastward from Carquinez Strait, Honker Bay, 

Montezuma Slough and its tributary sloughs, up the Sacramento River to its 

confluence with Three Mile Slough, and south along the San Joaquin River 

including Big Break, defines the specific geographic area critical to the 

maintenance of suitable rearing habitat. Protection of rearing habitat conditions 

may be required from the beginning of February through the summer (USFWS, 

1994). 

• Adult Migration: Adult delta smelt must be provided unrestricted access to 

suitable spawning habitat in a period that may extend from December to July. 

Adequate flow and suitable water quality may need to be maintained to attract 

migrating adults in the Sacramento and San Joaquin River channels and their 

associated tributaries. These areas should be protected from physical disturbance 

and flow disruption during migratory periods (USFWS, 1994). 

6.5 Habitat 

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 (68-72 degrees Fahrenheit) in 

the summer (USFWS, 1995 and 2004 b). When not spawning, they tend to be 

concentrated near the zone where incoming salt water and out flowing freshwater mix 

(mixing zone). This area has the highest primary productivity and is where zooplankton 

populations (on which delta smelt feed) are usually most dense. At all life stages, delta 

smelt are found in greatest abundance in the top 2 meters of the water column and usually 

not in close association with the shoreline (USFWS, 1995 and 2004 b). 

The delta smelt is a euryhaline species (species adapted to living in fresh and brackish 

water) that occupies estuarine areas with salinities typically below 2 grams per liter (parts 

per thousand), but have been found in waters up to 18.5 ppt (USFWS, 1993, 1994, and 

1995). Delta smelt live along the freshwater edge of the mixing zone (entrapment zone - 

saltwater-freshwater interface), where the salinity is approximately 2 ppt for a large part 

of their one-year life span (USFWS, 1994, 2004 b, and 2007 a). However, it should also 

be noted that the point in the estuary where the 2 ppt salinity is located does not 

57
necessarily regulate delta smelt distribution in all years (USFWS, 1995). In wet years, 

when abundance levels are high, their distribution is normally very broad. (USFWS, 1995 

and 2004 b). In some cases food availability may also influence delta smelt distribution 

(USFWS, 1995). During years with wet springs (such as 1993), delta smelt may continue 

to be abundant in Suisun Bay during summer even after the 2 ppt isohaline has retreated 

upstream (USFWS, 1995). 

 

6.6 Activity, Movement, and Behavior 

 

Although delta smelt swim together in schools, they are unsteady, and are intermittent, 

slow speed swimmers (USFWS, 2004 a, USFWS, 2004 b and 2007 a). Delta smelt are 

unable to swim against the current for any substantial distance, and therefore are more 

susceptible to impingement and entrainment at major water diversions than other similar 

sized fish species (USFWS, 2004 a). 

6.7 Diet 

The most important food organism for all sizes of the delta smelt seems to be the 

euryhaline copepod and Eurytemora affinis (USFWS, 1995 and 2004 b). The primary 

food for all life stages of the delta smelt are the nauplius, copepodite, copepodid, and 

adult stages of the euryhaline copepod Eurytemora affinis. 

 

6.8 Life History and Reproduction 

The spawning season varies from year to year and may occur from late winter to early 

summer (USFWS, 1994 and 2004b). Gravid adult smelt have been collected from 

December to April, although ripe delta smelt were most common in February and March 

(USFWS, 1994 and 2004b). Delta smelts spawn in shallow, fresh or slightly brackish 

water upstream of the mixing zone (USFWS, 1994, 2004b, and 2007a) at temperatures 

ranging 7-22 degrees Celsius (44-72 degrees Fahrenheit) (USFWS, 1995 and 2004b). 

Most spawning happens in tidally influenced backwater sloughs and channel edgewaters 

in the upper Delta including Barker, Lindsey, Cache, Georgiana, Prospect, Beaver, Hog, 

and Sycamore sloughs, and in the Sacramento River above Rio Vista. (USFWS, 1994, 

1995, and 2007a). 

Delta smelt are broadcast spawners that spawn in a current, usually at night, distributing 

their eggs over a local area (USFWS, 1994). The eggs are demersal (i.e., they sink to the 

bottom) and contain an adhesive-like substance causing them to stick to hard substrates 

such as rock, gravel, tree roots or submerged branches, and submerged vegetation 

(USFWS, 1994, 1995, 2004b, and 2007a). Delta smelt reach their full length in 7-9 

months and are considered to be sexually mature adults at this point (USFWS, 1993, 

1995, and 2004b). Delta smelt have a low fecundity compared to two other species of 

Osmeridae occurring in California (USFWS, 1993). Based on observations, delta smelt 

58
greater than 1.97 inches found throughout their range when spawning season is over is 

rare indicating that adult delta smelt may die after spawning (USFWS, 1993). 

6.9 References 

California Department of Fish and Game (CDFG). 2008 a. Bay-Delta Region: Delta 

Smelt (Hypomesus transpacificus). Available online at: 

http://www.delta.dfg.ca.gov/baydelta/monitoring/delta.asp (Accessed on April 21, 2008). 

California Department of Fish and Game (CDFG). 2008 b. Bay-Delta Region: Delta 

Smelt. Available online at: http://www.delta.dfg.ca.gov/gallery/dsmelt.asp (Accessed on 

April 21, 2008). 

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 28, 2008). 

U.S. Fish and Wildlife Service (USFWS). 1994. Endangered and Threatened Wildlife 

and Plants: Critical Habitat Determination for the Delta Smelt. Federal Register 59 

(242):65256-65279. Available online at: 

http://ecos.fws.gov/docs/federal_register/fr2751.pdf (Accessed on January 28, 2008). 

U.S. Fish and Wildlife Service (USFWS). 1995. 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 28, 

2008). 

U.S. Fish and Wildlife Service (USFWS). 2004 a. 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 28, 2007). 

U.S. Fish and Wildlife Service (USFWS). 2004 b. 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 28, 2007). 

U.S. Fish and Wildlife Service (USFWS). 2007 a. Species Account: Delta Smelt 

(Hypomesus transpacificus). Sacramento Fish and Wildlife Office. Available online at: 

59
http://www.fws.gov/sacramento/es/animal_spp_acct/delta_smelt.pdf (Accessed on 

January 28, 2008). 

U.S. Fish and Wildlife Service (USFWS). 2007 b. Species Account – Kid-Friendly: 

Delta Smelt. Sacramento Fish and Wildlife Office. Available online at: 

http://www.fws.gov/sacramento/es/animal_spp_acct/delta_smelt_kf.htm (Accessed on 

January 28, 2008). 

60
7: SALT MARSH HARVEST MOUSE 

7.1 Species Listing Status 

The salt marsh harvest mouse (SMHM) (Reithrodontomys raviventris) was listed as 

endangered on October 13, 1970 (35 FR 16047) by the U.S. Fish and Wildlife Service 

(USFWS). This species has been protected by the Endangered Species Act since it was 

enacted in 1973. A recovery plan for the SMHM was approved by USFWS on November 

16, 1984 (USFWS 1984). 

7.2 Description 

The SMHM weighs between 8-14 grams (Goals Project 2000; Massicot 2005; CDPR 

website), and has a head to body length of 69-74 mm, with a total length (including tail) 

of 118-175 mm (Goals Project 2000; Massicot 2005; CDPR website). The lifespan of the 

SMHM is generally less than eight months, though can range up to one year, with the 

maximum observed lifespan being 18 months in the wild (Shellhammer 1998; Massicot 

2005). 

7.3 Distribution 

There are two subspecies of the SMHM. The northern subspecies (R. r. halicoetes) is 

found in Marin, Sonoma, Napa, Solano, and Contra Costa counties (CDPR website). It 

lives in the Petaluma and Napa marshes, as well as marshes of the San Pablo and Suisun 

Bays (Goals Project 2000; Brylski 1999). The southern subspecies (R. r. raviventris) is 

found mainly in San Mateo, Alameda, and Santa Clara counties, with some isolated 

populations in Marin and Contra Costa counties (CDPR website). It occupies the marshes 

of Corte Madera, Richmond, and South San Franciso Bay, which are generally more 

highly developed areas (USFWS 1984; USFWS 2007a; Goals Project 2000). 

SMHMs are currently found in tidal and non-tidal salt marshes in San Francisco, San 

Pablo, and Suisun Bays (USFWS 2007a; CDFG website). Currently, the highest 

consistent SMHM populations are found in large marshes along the eastern edge of San 

Pablo Bay that are or will be included in the San Francisco Bay National Wildlife Refuge 

(SFBNWR) (Goals Project 2000). The SMHM is also sustaining itself in a few marsh 

areas in the SFBNWR, including Calaveras and Dumbarton Points, Greco Island, and 

New Chicago Marsh (Shellhammer 1998). 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). 

61
7.4 USFWS Critical Habitat 

There is no federally designated critical habitat for the SMHM (USFWS, 2007a). 

7.5 Habitat 

Salt marshes have three zones: a low marsh that receives maximum submergence 

comprised of cordgrass (Spartina foliosa) or tules (Scirpus spp.); a middle marsh zone 

comprised of pickleweed (Salcornia virginica), alkali bulrush (Scirpus robustus), or 

cattails (Typha spp.); and a high marsh dominated by peripheral halophytes (salt-tolerant 

plants) that receives infrequent to no tidal coverage (USFWS 1984; Shellhammer 1998). 

Other halophyte species include gum-plant (Grindelia spp.), salt grass (Distichlis 

spicata), jaumea (Jaumea carnosa), and alkali heath (Frankenia grandifolia) (USFWS 

1984). 

SMHM prefer habitat in the middle and upper parts of the marsh dominated by 

pickleweed (Salicornia virginica) and peripheral halophytes, as well as similar vegetation 

found in diked wetlands adjacent to the San Francisco Bay, and depend on dense, 

perennial cover (USFWS 1984; USFWS 2007a; Goals Project 2000; Brylski 1999; 

Shellhammer 1998). SMHM prefer pickleweed to salt grasses and alkali bulrush, as 

pickleweed provides more cover (USFWS 1984). The northern subspecies of the SMHM 

is usually found in brackish marshes with a wide range of salinities but an average of 

moderately saline, and the southern subspecies lives in marshes with an average salinity 

that is relatively high and stable (USFWS 1984). Diverse brackish marshes composed of 

various rushes, cattails and pickleweed support SMHM populations (USFWS 1984). 

Although pickleweed is its primary habitat, SMHM also utilize non-submerged salttolerant vegetation in the upper marsh zone for escape during high tide, and may also 

spend a considerable amount of their lives there (Brylski 1999; USFWS 1984; USFWS 

2007a). During the highest winter tides, SMHMs can move into adjoining grasslands 

(USFWS 1984; USFWS 2007a). SMHM also use grasslands in spring and summer when 

they provide maximum cover, though these movements represent daily activity and not 

complete shifts in habitat (Goals Project 2000; Brylski 1999; CDPR website).

7.6 Diet 

SMHMs consume leaves, seeds, and plant stems (USFWS 1984; USFWS 2007a; Brylski 

1999). They may also occasionally eat insects (Massicot 2005). Seasonal variation has 

been observed in SMHM stomach contents (Brylski 1999). They seem to prefer fresh 

green grasses in winter and pickleweed and saltgrass during the rest of the year (USFWS 

1984; USFWS 2007a; CDPR website; Brylski 1999). The northern subspecies of SMHM 

can drink salt water for long periods of time but prefers fresh water, while the southern 

subspecies cannot subsist on salt water but prefers moderately salty water over fresh 

(USFWS 1984; USFWS 2007a; Brylski 1999; Shellhammer 1998). 

62
7.7 Life History and Reproduction 

SMHMs are active year-round (CDPR website; Massicot 2005). They are primarily 

nocturnal but are occasionally active during the day (USFWS 1984; USFWS 2007a; 

CDPR website; Massicot 2005). The southern subspecies of SMHM has been described 

as becoming torpid in the early morning but the northern subspecies does not become 

torpid (Brylski 1999). In general, SMHM are not extremely active and depend on cover 

for predator escape (USFWS 1984). 

Roads or small open areas (10 meters wide) can act as homerange barriers to SMHM 

(USFWS 1984), so individual SMHMs do not seem to move between marshes (Brylski 

1999). However, as adept swimmers and floaters, SMHM can sometimes re-colonize 

marshes separated by water after local extinctions by swimming or rafting to the new 

marsh (USFWS 1984). 

SMHMs do not burrow (USFWS 1984; Brylski 1999; CDPR website; Goals Project 

2000); however, Massicot (2005) suggested that “some winter nests are constructed in 

burrows and small crevices.” SMHM nests are minimal and are often built over old birds’ 

nests, including those of song sparrows (USFWS 2007a; Massicot 2005; CDPR website). 

SMHMs may also use Suisun shrew nests, after the young shrews have dispersed (Goals 

Project 2000). SMHM nests often consist of a loose ball of dry grasses and other 

vegetation, about 150 to 175 mm in diameter, built on the ground surface or up in the 

pickleweed, and may be abandoned at the next high tide (USFWS 1984; Massicot 2005; 

Goals Project 2000). The southern subspecies usually does not even make a nest, 

although it may construct a loosely organized structure of dry grasses (USFWS 2007a; 

Brylski 1999).

SMHMs breed from spring through fall (USFWS 2007; CDPR website). Male SMHMs 

are reproductively active from April through September, although some males appear to 

be active year-round (USFWS 1984). Females SMHMs have a longer breeding season 

that extends from as early as March through November (USFWS 1984). The northern 

subspecies of SMHM breeds from May to November and the southern subspecies breeds 

from March to November (Brylski 1999). Each female typically only has one or two 

litters per year with an average litter size of about three or four young per litter (USFWS 

2007a; Shellhammer 1998; CDPR website). Brylski (1999) suggests that the southern 

subspecies may have two litters per year whereas the abbreviated breeding season for the 

northern subspecies may indicate only one litter per year. Reported gestation periods for 

the genus Reithrodontomys are 21 – 24 days (Massicot 2005).

7.8 References 

Brylski, P. 1999. M114-Salt-marsh Harvest Mouse. California Wildlife Habitat 

Relationships System, a database of the California Department of Fish and Game 

63
(CDFG), in cooperation with the California Interagency Wildlife Task Group. 

Database version 8.1. http://www.dfg.ca.gov/biogeodata/cwhr/lha/lha_M114.pdfl;

http://sibr.com/mammals/M114.html. (Website accessed: December 10, 2007). 

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

http://www.dfg.ca.gov/habcon/cgibin/read_one.asp?specy=mammals&idNum=47 (Website accessed: December 11, 

2007). 

California Department of Pesticide Regulation (CDPR). Salt Marsh Harvest Mouse

(Reithrodontomys raviventris). 

http://www.cdpr.ca.gov/docs/endspec/espdfs/smhm1.pdf and 

http://www.cdpr.ca.gov/docs/endspec/espdfs/smhmall.pdf (Website accessed: 

December 10, 2007).

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 (Website accessed: December 

10, 2007). 

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

raviventris). http://www.animalinfo.org/species/rodent/reitravi.htm#IUCN

(Website accessed: December 10, 2007). 

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. 

http://www.fws.gov/desfbay/Archives/Salty/salty.htm (Website accessed: October 

3, 2007). 

U.S. Fish and Wildlife Service (USFWS). 1984. Salt Marsh Harvest Mouse and 

California Clapper Rail Recovery Plan. USFWS, Portland, Oregon. 141 pp. 

http://ecos.fws.gov/docs/recovery_plans/1984/841116.pdf 

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

Mouse (Reithrodontomys raviventris). Sacramento Fish and Wildlife Office. 

http://www.fws.gov/sacramento/es/animal_spp_acct/salt_marsh_harvest_mouse. 

htm (Website accessed: December 10, 2007). 

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

Mouse (Reithrodontomys raviventris). 

http://ecos.fws.gov/speciesProfile/SpeciesReport.do?spcode=A03Y (Website 

accessed: October 3, 2007).

64
8: SAN FRANCISCO GARTER SNAKE 

8.1 Species Listing Status 

The San Francisco Garter Snake (SFGS) (Thamnophis sirtalis tetrataenia) was listed as 

endangered on March 11, 1967 (32 FR 4001; USFWS 1967) by the U.S. Fish and 

Wildlife Service (USFWS) and was grandfathered under the Endangered Species Act 

(ESA) when it was signed into law in 1973. A Recovery Plan for the SFGS was 

approved by the USFWS on September 11, 1985 (USFWS, 1985). In addition, a 5-year 

review, which provides an updated life history for the SFGS, was published by the 

USFWS in September of 2006 (USFWS, 2006). 

8.2 Description 

The SFGS is a thin and colorful snake in the Colubridae family, which includes most of 

the species of snakes found in the western U.S. (USFWS, 2007). SFGSs range in length 

from 46 to 131 cm (18 to 51 inches) (USFWS, 1985 and Woodland Park Zoo). Female 

SFGS typically weigh about 8 oz. (227 g), whereas, males are usually smaller than 

females and can be half the length and weight of females (SF Zoo and Woodland Park 

Zoo). Garter snakes are usually about two inches in girth (Kaplan, 2002). Neonate 

snakes are 18 to 20 cm in length and disperse immediately after they are born. Juvenile 

SFGS grow quickly during their first year and spend most of their time feeding. These 

snakes are typically considered to be mature at two years of age when the males are about 

46 cm and the females are about 55 cm; however, some snakes take longer to mature and 

may not reach maturity until they are three years old. It is estimated that SFGS live 

between 8 and 15 years (Woodland Park Zoo and Goals Project, 2000). 

8.3 Distribution 

SFGSs are endemic to the San Francisco Peninsula and San Mateo County and were 

historically found from San Francisco to Santa Cruz (USFWS, 1985 and 2005), including 

the San Francisco Peninsula from just north of the San Francisco-San Mateo County line 

near Lake Merced south along the eastern and western bases of the Santa Cruz 

Mountains, to the Upper Crystal Springs Reservoir, along the coast south to Ano Nuevo 

Point, in San Mateo County, and Waddell Creek, in the extreme northern portion of Santa 

Cruz County (USFWS, 1985, 2006, and 2007). However, the findings of SFGS in 

Waddell Creek in Santa Cruz County may be questionable (Goals Project, 2000) due to 

the reported presence of hybrid species in the area. 

65
SFGS populations are thought to have primarily occupied habitat areas in the Buri Buri 

Ridge along the San Andres Rift Zone from near Pacifica, southeast to the Pulgas Water 

Temple, and in an arc from the San Georgio-Pescadero highlands west to the coast, and 

south to Ano Nuevo (USFWS, 2006 and Goals Project, 2000). Red-sided garter snake 

(RSGS) and SFGS hybrids have been found in eastern San Mateo County (southeast of 

the Pulgas Water Temple) and in the extreme western part of Santa Clara County (Goals 

Project, 2000). The hybrids range from the Pulgas region near Upper Crystal Springs 

Reservoir south to Palo Alto (USFWS, 2006). 

The extreme northeastern part of the SFGS’s range may have been represented by a 

population at San Bruno Mountain; however, it is possible that this population has been 

extirpated (USFWS, 2006). This population may not be natural as individual SFGSs may 

have been moved here in an attempt to protect them because this area is protected under a 

Habitat Conservation Plan (HCP) (USFWS, 2006). It is possible that these attempted 

conservation methods were also used farther south, resulting in the population at Half 

Moon Bay (USFWS, 2006). 

The historic range of the SFGS may have extended as far south as Stanford in Santa Clara 

County (USFWS, 2006). This assumption is based on observations of hybrids of the 

SFGS and other garter snake species in this area (USFWS, 2006). The USFWS also 

believes that areas on the coast west of the Santa Cruz Mountains may be inhabited by 

the SFGS; however, this cannot be confirmed because this area is privately owned 

(USFWS, 2006). 

Historically, SFGSs were found in sag ponds, small seasonal ponds along the San 

Andreas Fault in the northern part of the San Francisco Peninsula (USFWS, 1985). Some 

believe that the purest SFGS populations were found on the coast around Sharp Park in 

Laguna Salada and along the ridge of the San Francisco Peninsula east of Sharp Park 

(USFWS, 1985). Habitat areas in the northern and eastern portions of the SFGS’s 

historical range have been destroyed by urbanization and development, including the 

SFGS population co-located with the sag ponds along the ridge of the San Francisco 

Peninsula east of Sharp Park (USFWS, 1985). 

Although the SFGS’s geographical range seems extensive, field surveys performed by the 

USFWS and the California Department of Fish and Game (CDFG) indicate that their 

range is limited to and localized within San Mateo County (USFWS, 1985). Six areas are 

known to contain significant populations of SFGS: 1) Ano Nuevo State Reserve (ANSR), 

2) Pescadero Marsh Natural Preserve, 3) San Francisco State Fish and Game Refuge 

(including both Upper and Lower Crystal Springs Reservoirs), 4) Sharp Park (Laguna 

Salada), 5) Cascade Ranch, and 6) Milbrae or West of Bayshore (near the San Francisco 

Airport) (USFWS, 1985). 

The current distribution of the SFGS is unknown because most of their historic range is 

now privately owned; however, it appears that the SFGS can still be found in much of its 

historic range (USFWS, 2006 and 2007). SFGSs were found in Upper Crystal Springs 

Reservoir and Mud Dam in 1998 (San Francisco Planning Department, 2001). They 

66
were also observed at “San Andreas Reservoir and in a sag pond between San Andreas 

and Crystal Springs” (San Francisco Planning Department, 2001). Regardless, the 

number of locations that previously maintained healthy populations of the SFGS has 

declined and SFGS have been extirpated from individual locations within their historic 

range (USFWS, 2007). Currently, wild SFGS populations are limited to coastal San 

Mateo County and other small pockets (USFWS, 2005). 

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

over 500 adults were 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). 

8.4 USFWS Critical Habitat 

 

No critical habitat for the SFGS has been designated by the USFWS (2007) to date. 

8.5 Habitat 

Successful SFGS breeding populations are typically found in densely vegetated ponds 

near open hillsides where they can sun themselves, feed, and find shelter in rodent 

burrows; however, less ideal habitats can also be occupied (USFWS, 2007). These sites 

usually include emergent vegetation for cover, basking sites, food sources, upland 

hibernation sites, and corridors which allow for movement between the feeding grounds 

and the hibernation sites (USFWS, 1985 and 2007). SFGSs prefer shallow marshlands 

with emergent vegetation and breeding populations of both Pacific tree frogs and 

California red-legged frogs (CRLF) as well as open grassy uplands (USFWS, 2006). 

Breeding populations of SFGS are not known to exist where amphibians are not found 

(USFWS, 2006). 

SFGSs are usually observed near standing open water, including ponds, lakes, marshes, 

slow-moving streams, and sloughs; however, they are also observed at temporary pools 

including stock ponds, channelized sloughs, and reservoirs (USFWS, 1985 and 2007; 

NatureServe, 2007; Kaplan, 2002; and Goals Project, 2000). It is speculated that SFGS 

remain close to open water to retain proximity to anuran species, their preferred prey 

(USFWS, 2006). These snakes avoid brackish water because their preferred prey, the 

CRLF, cannot survive in saline water (USFWS, 2007). In addition, Pacific tree frogs and 

their larvae cannot survive in water with a salinity of 7.0 ppt or greater (USFWS, 2006). 

However, SFGS may use ditches influenced by the tides as “migration corridors between 

disconnected areas of freshwater wetland habitat” (Powers, 2003). 

67
Shallow water near the shoreline is required from May to July, to allow the anuran prey 

to hatch and metamorphose (USFWS, 2006); SFGSs are unable to capture their prey 

effectively in water that is more than 5 cm deep (USFWS, 2006). Shallow water also 

exposes rocks, algal mats, and floating vegetation found around the edges of the pond 

which the SFGSs use as basking sites (USFWS, 2006). These sites may also be used by 

the anurans and allows the SFGS greater access to their prey (USFWS, 2006). 

SFGS prefer emergent vegetation, including cattails, bulrushes, spike rushes, and water 

plantain, for cover (USFWS, 1985 and 2007); however, they will also seek cover in the 

water if necessary (USFWS, 1985). If these types of vegetation are not available, SFGSs 

can be found in aquatic areas surrounded by willow trees as long as there is only a small 

distance between the overhanging vegetation and the ground (USFWS, 2006). SFGSs 

sun themselves at the edges of ponds or streams and will also use the area between the 

aquatic habitat required for their prey and the grasslands where they aestivate (become 

inactive or dormant) for basking (USFWS, 1985). 

Upland grassy hillsides near ponds are also used for basking (USFWS, 1985). It is 

thought that SFGS may prefer hillsides that face south or west because they receive more 

sun (USFWS, 2006). Coyote bush, wild oat, wild barley, and other brome species may 

be found in the SFGS’s upland habitat (USFWS, 2006). SFGS “prefer a grassland/shrub 

matrix with brush densities ranging from 1 averaged sized bush/30 square meters to 1 

large bush/20 square meters” (USFWS, 2006). This mix provides both cover from 

predators and also exposed surfaces to allow the SFGS sun themselves, an important part 

of their thermoregulation (USFWS, 2006). The preferred brush to grassland ratios are 

maintained or can be achieved by allowing livestock grazing (USFWS, 2006). Large 

SFGS populations have been found to coincide with areas of land that are used for cattle 

grazing (USFWS, 2006). Gopher activity, which moves nitrogen-poor subsoil to the 

surface, has also been shown to stimulate early successional conditions (open grassland) 

required by the SFGS (USFWS, 2006). Although grazing appears to have a positive 

impact on the SFGS, overgrazing can be detrimental to this species as SFGS habitat may 

no longer be useful if the vegetative cover falls below 20 cm (USFWS, 2006). 

Rodent burrows and thick grass mats near the ponds are used for shelter and aestivation 

when the ponds become dry (USFWS, 1985 and 2007 and NatureServe, 2007). SFGSs 

may also forage for amphibians in the rodent burrows during the summer (Goals Project, 

2000). These burrows are also used for hibernation, since SFGSs found along the coast 

will hibernate during the winter (USFWS, 2006 and 2007). However, SFGS have been 

observed emerging from their burrows to bask in the winter indicating that SFGS may not 

truly hibernate (USFWS, 2006). This could also be due to the relatively warm climate of 

the San Francisco Bay area (USFWS, 2006). SFGSs that are farther inland are more 

likely to be active year-round (USFWS, 2007). 

Recapture studies have indicated that SFGS have small home ranges that are determined 

by the availability of food and cover (USFWS, 1985). Most individuals remain within 

one or two hundred meters of their aquatic and upland habitats (USFWS, 2006). 

However, some snakes may be able to travel up to two km or more in a short period of 

68
time (Goals Project, 2000). Although SFGS typically do not travel far, they may follow 

their prey to new areas (USFWS, 2006). It is in pursuit of their prey that SFGS may be 

adversely affected by creek channelization, removal of vegetation, and other flood 

control measures that are sometimes implemented in riparian areas (USFWS, 2006). 

Garter snakes are typically found from sea level to 2400 m (8000 feet) (Morey, 2005). 

8.6 Diet 

Newborn and juvenile SFGS prey almost exclusively on Pacific tree frogs in temporary 

pools during the spring and early summer (USFWS, 2006 and 2007). Juvenile SFGS 

may capture metamorphosed Pacific tree frogs in upland habitats; however, they 

primarily feed on the newly metamorphosed frogs once the temporary pools begin to dry 

up and the frogs begin to disperse (USFWS, 2006). A laboratory experiment performed 

using juvenile SFGS showed that Pacific tree frogs elicited the highest response rate out 

of all of the common prey items that were tested (USFWS, 2006). Observations at one 

SFGS site have shown that anuran numbers decreased during dry years with a subsequent 

decrease in the survival of SFGS juveniles (USFWS, 2006). This observation indicates 

that the SFGS may be so dependent on their anuran prey that they are not able to switch 

to other available prey sources if necessary to survive (USFWS, 2006). SFGS under 500 

mm snout-to-vent length (SVL) require Pacific tree frogs in various stages of 

metamorphosis, whereas individuals over 500 mm SVL can consume Pacific tree frog, 

CRLF, and bullfrog tadpoles and adults (USFWS, 2006). 

The main diet of adult SFGS consists of CRLF, which are listed as a threatened species 

(USFWS, 1985 and 2007). Adult SFGSs consume CRLFs in the late summer when they 

metamorphose (USFWS, 2006). The emergence of the CRLF in the late summer allows 

the adult SFGS to continue feeding after the Pacific tree frogs have left the drying 

wetland areas (USFWS, 2006). This observed behavior likely explains the high activity 

level of SFGSs in the late summer (USFWS, 2006). Adult SFGSs may also feed on 

juvenile non-native bullfrogs (Rana catesbeiana), but are unable to consume the larger 

adults (USFWS, 2007). Bullfrogs are known to be found in degraded habitats and it is 

thought that bullfrogs may allow SFGS to colonize areas where Pacific tree frogs or 

CRLF cannot exist (USFWS, 2006). Although bullfrogs may be consumed by SFGSs, 

captive SFGS often regurgitate them indicating that they may be undigestable, and that 

bullfrogs may not be consumed by wild SFGS populations (USFWS, 2006). 

Immature California newts (Taricha torosa), California toads (Bufo boreas halophilus) 

recently metamorphosed western toads (Bufo boreas), threespine stickleback 

(Gasterosteus aculeatus), and non-native mosquito fish (Gambusia affinis) are also 

known to be consumed by SFGS (USFWS, 1985). SFGS are one of the few animals 

known to eat the California newt without suffering the toxic effects of this organism 

(USFWS, 2007). Small mammals, reptiles, amphibians, possibly invertebrates, and some 

fish species may also be consumed by the SFGS if they can be captured in shallow water 

(USFWS, 1985 and 2006). Captive SFGS have been found to consume earthworms; 

however, some individuals will starve instead of eating them (USFWS, 2006). 

69
Earthworms may also not be readily available in the wild, further indicating that wild 

populations of SFGS may not prey on these animals (USFWS, 2006). 

8.7 Life History and Reproduction 

SFGSs mate in the spring (March and April) and fall (September through November); 

however, mating is “concentrated in the first few warm days of March” (USFWS, 1985 

and 2006 and Goals Project, 2000). The increased mating in the spring is correlated with 

SFGSs emerging from their burrows and congregating at the aquatic feeding areas 

(USFWS, 2006). Aggregations of mating adult SFGSs have also been observed on open 

grassy slopes on warm sunny mornings in late October and early November (USFWS, 

1985). It is thought that the female’s role in mating is relatively passive. Females release 

pheromones to attract males, males actively seek out the females primarily using scent, 

and several males may court the same female simultaneously. These types of behaviors 

have been identified in other subspecies of the common garter snake (USFWS, 1985 and 

SF Zoo). Female SFGS can store the male’s sperm over the winter and can retain viable 

sperm for periods ranging from 3 to 53 months (USFWS, 1985 and Goals Project, 2000). 

Ovulation in the common garter snake typically occurs in late spring with pregnancy 

resulting in early summer (USFWS, 1985). The young are typically born about three to 

four months after successful mating (Woodland Park Zoo). SFGS are ovoviviparous 

meaning that the eggs hatch within the female’s body and the young are born live 

(USFWS, 1985 and SF Zoo). Female SFGSs give birth from June through September 

with young typically born in July or August (USFWS, 2007; NatureServe, 2007; and 

Goals Project, 2000). However, young can be born as late as early September (Goals 

Project, 2000). The number of young can range from three to 85 but are more typically 

in the range of 12 to 24 (USFWS, 1985). Most often around 16 young are produced 

(USFWS, 2007; SF Zoo; and Goals Project, 2000). 

The young are typically born in the upland areas near the aquatic feeding habitats. 

Neonate snakes are 18 to 20 cm in length and disperse immediately after they are born 

(Woodland Park Zoo and Goals Project, 2000). Juvenile SFGS grow quickly during their 

first year and spend most of their time feeding (Goals Project, 2000). These snakes are 

typically considered to be mature at two years of age when the males are about 46 cm and 

the females are about 55 cm; however, some snakes take longer to mature and may not 

reach maturity until they are three years old (Woodland Park Zoo and Goals Project, 

2000). 

8.8 References 

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. 

70
Available online at: http://sfep.abag.ca.gov/pdf/speciescommunity/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). 

Morey, S. 2005. R061-Common Garter Snake. 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: 

nrm.dfg.ca.gov/FileHandler.ashx?DocumentVersionID=2814 (Accessed on 

November 5, 2007). 

NatureServe. 2007. NatureServe Explorer: An online encyclopedia of life [web 

application]. Version 6.2. NatureServe, Arlington, Virginia. Available online at: 

http://www.natureserve.org/explorer/servlet/NatureServe?searchName=Thamnop

his+sirtalis+tetrataenia. (Accessed: October 15, 2007). 

Powers, D.J., and Associates, Inc. 2003. Environmental Constraints Analysis for the San 

Bruno Grade Separation Project (MP 10.8 to 12.0). Available online at: 

http://www.caltrain.org/pdf/SB_L.pdf (Accessed on October 25, 2007). 

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). 

SF Zoo website. Available online at: 

http://www.sfzoo.org/openrosters/ViewOrgPageLink.asp?LinkKey=13516&orgke

y=1821 (Accessed on November 2, 2007). 

U.S. Fish and Wildlife Service (USFWS). 1967. Native Fish and Wildlife, Endangered 

Species (32 FR 4001). Washington, D.C. 

USFWS. 1985. Recovery Plan for the San Francisco Garter Snake (Thamnophis sirtalis 

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

online at: http://ecos.fws.gov/docs/recovery_plan/850911.pdf

(Accessed on October 16, 2007) 

USFWS. 2005. San Francisco garter snake returns to its namesake city. June 2005. 

Available online at: 

http://www.fws.gov/sacramento/ea/feature_stories/SFGS_returns_mediaevent.ht

m (Accessed on October 16, 2007). 

71
USFWS. 2006. 5-Year Review: Summary and Evaluation for the San Francisco Garter 

Snake (Thamnophis sirtalis tetrataenia). U.S. Fish and Wildlife Service, 

Sacramento Field Office, Sacramento, California. 42 pp. Available online at: 

http://www.fws.gov/sacramento/es/documents/San%20Francisco%20Garter%20S

nake%205%20Year%20Review.FINAL.pdf

(Accessed on October 25, 2007 ) 

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). 

Woodland Park Zoo website. Available online at: 

http://www.zoo.org/factsheets/garter_snake/sanFransiscoGarterSnake.html#

(Accessed on November 5, 2007). 

72
9: SAN JOAQUIN KIT FOX 

9.1 Species Listing Status 

The San Joaquin kit fox (Vulpes macrotis mutica) was listed as endangered on March 11, 

1967 (32 FR 4001) by the U.S. Fish and Wildlife Service (USFWS) (USFWS, 1967). A 

recovery plan for upland species of the San Joaquin Valley was approved by the USFWS 

on September 30, 1998 (USFWS, 1998). 

9.2 Description 

The kit fox is the smallest species in North America in the Canidae family, and on 

average adult males weigh 2.3 kilograms (5 pounds) and adult females weigh 2.1 

kilograms (4.6 pounds) (USFWS, 1998). 

9.3 Distribution 

Historical Range 

Prior to 1930, kit foxes inhabited most of the San Joaquin Valley from southern Kern 

County north to Tracy, San Joaquin County (and possibly as far as Contra Costa County 

to the west) and near La Grange, Stanislaus County (to the east) (USFWS, 1998 and 

2008). By 1930, the kit fox range had been reduced by more than half, with the largest 

portion remaining in the southern and western parts of the Valley (USFWS, 1998 and 

2008). 

Current Range 

The current distribution of kit foxes in California includes all or portions of Alameda, 

Contra Costa, Fresno, Kern, Kings, Madera, Merced, Monterey, San Benito, San Joaquin, 

San Luis Obispo, Santa Barbara, Santa Clara, Stanislaus, Tulare and Ventura counties 

(SJCOG, 2008). Kit foxes currently inhabit some areas of suitable habitat on the San 

Joaquin Valley floor and in the surrounding foothills of the coastal ranges, the Sierra 

Nevada, and Tehachapi Mountains, from southern Kern County north to Contra Costa, 

Alameda, and San Joaquin Counties on the west, and 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 

also 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). 

73
According to the recovery plan (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, Ciervo-Panoche 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” (p. 124). 

The SJKF population is fragmented, particularly in the northern part of the range due to 

limited suitable habitat (USFWS, 2008). No evidence of recent kit fox occupancy was 

found in a recent survey in Contra Costa County and Alameda Counties (East Contra 

Costa County HCP/NCCP, 2006). Although this does not prove an absence of kit fox in 

these counties, it does suggest that kit fox density is low or their occurrence is periodic in 

the northern part of the kit fox range (East Contra Costa County HCP/NCCP, 2006). 

9.4 USFWS Critical Habitat 

No critical habitat for the SJKF has been designated by the USFWS (2008) to date. 

9.5 Habitat 

The SJKF occurs in a variety of habitats, including grasslands, scrublands (e.g., chenopod 

scrub and sub-shrub scrub), vernal pool areas, oak woodland, alkali meadows and playas, 

and an agricultural matrix of row crops, irrigated pastures, orchards, vineyards, and 

grazed annual grasslands (East Contra Costa County HCP/NCCP, 2006; USFWS, 1998). 

These habitats are found as relatively small patches in scattered locations, and, in general, 

do not provide good denning habitat for kit foxes because all have moist or waterlogged 

clay or clay-like soils. However, where they are interspersed with more suitable kit fox 

habitats these areas provide food and cover (USFWS, 1998). According to the recovery 

plan (USFWS, 1998): 

“Kit foxes use some types of agricultural land where uncultivated land is 

maintained, allowing for denning sites and a suitable prey base. Kit foxes also 

74
den on small parcels of native habitat surrounded by intensively maintained 

agricultural lands and adjacent to dryland farms” (p. 129). 

Denning sites are used for temperature regulation, shelter from adverse environmental 

conditions, reproduction, and escape from predators (USFWS, 1998 and 2008). Kit fox 

dens are found on virtually every soil type, but the kit foxes seem to prefer loose-textured 

soils. Dens are rarely found in areas with shallow soils because of the proximity to 

bedrock, high water tables, or impenetrable hardpan layers. Kit foxes dig their own dens, 

modify and use those already constructed by other animals (ground squirrels, badgers, 

and coyotes), or use human-made structures (culverts, abandoned pipelines, or banks in 

sumps or roadbeds) (USFWS, 1998 and 2008). 

Although den characteristics vary across the SJKF range, the majority of dens are found 

in relatively flat terrain or gently sloping hills (with a slope of less than 40 degrees), in 

washes, drainages, and roadside berms in open areas with grass or grass and scattered 

brush, and only rarely occur in areas with thick brush (Cal. EPA Dept. of Pesticide 

Regulation, 2002). Natal and pupping dens are limited to flatter ground with slopes of 

about 6 degrees (USFWS, 1998). 

Kit foxes change dens often and many dens may be used throughout the year likely to 

avoid potential predation by coyotes (USFWS, 1998 and 2008). Radio-telemetry studies 

found that foxes (of both sexes) use individual dens for only a median of 2 days (mean of 

3.5 days) (USFWS, 1998). More dens are used during the dispersal season than during 

the breeding or pup-rearing seasons (East Contra Costa County HCP/NCCP, 2006). 

9.6 Diet 

The diet of the SJKF varies geographically, seasonally and annually, based on variation 

in abundance of potential prey (USFWS, 1998). According to the recovery plan 

(USFWS, 1998): 

“In the southern part of the range, one-third of the kit fox diet consists of 

kangaroo rats (Dipodomys spp.), pocket mice (Perognathus spp.), white-footed 

mice (Peromyscus spp.) and other nocturnal rodents. Kit foxes in this area also 

prey on California ground squirrels (Spermophilus beecheyi), black-tailed hares 

(Lepus californicus), San Joaquin antelope squirrels (Ammospermophilus 

nelsoni), desert cottontails (Sylvilagus audubonii), ground-nesting birds and 

insects... Vegetation and insects occur frequently in feces. Grass is the most 

commonly ingested plant material... In the central portion of their geographic 

range, defined here as Kings, Tulare, Fresno, Madera, San Benito, Merced, 

Stanislaus, and Monterey Counties, known prey species include white-footed 

mice, insects, California ground squirrels, kangaroo rats, San Joaquin antelope 

squirrels, black-tailed hares, and chukar (Alectoris chukar), listed in approximate 

proportion of occurrence in fecal samples... In the northern part of their range, 

defined here as San Joaquin, Alameda and Contra Costa Counties, kit foxes most 

75
frequently consume California ground squirrels... Cottontails, black-tailed hares, 

pocket mice, and kangaroo rats are also eaten” (p. 124). 

9.7 Life History and Reproduction 

Kit foxes are predominantly, although not strictly, nocturnal with most above-ground 

activities beginning near sunset and continuing sporadically throughout the night 

(USFWS, 1998). In addition to some populations preying on diurnal ground squirrels, kit 

foxes are commonly seen during the day during late spring and early summer (USFWS, 

1998). 

Based on observations at the Elk Hills Naval Petroleum Reserves in California, kit foxes 

move an average of 9.6 miles nightly during the breeding season which is longer than the 

average nightly movements during the breeding and pup-rearing seasons (6.5 and 6.3 

miles, respectively) (USFWS, 1998). 

Kit fox home ranges are generally between 1-3 square miles, but they can be as large as 

12 square miles (SJCOG and USFWS, 1998). Home ranges in non-urban areas tend to be 

larger than those in urban areas (Ralls, 2007). Differences in home range size tend to be 

related to prey abundance (USFWS, 1998). 

Kit foxes reach reproductive age at 1-year, although they may not breed during their first 

year of adulthood. Breeding pairs remain together in the same home range (although not 

necessarily the same den) all year. In the fall (Sept. – Oct.) adult females begin to 

prepare (clean and/or enlarge) pupping dens, selecting those with multiple openings. 

Breeding takes place between Dec. and March. Gestation is estimated to range from 48 – 

52 days and most litters (of 2 – 6 pups) are born between Feb. and late March. While the 

adult female is lactating, the adult male provides most of the food for the adult female 

and her pups. Pups emerge from their dens at about 1-month of age and may begin to 

disperse after 4 – 5 months usually in Aug. or Sept. However, offspring may remain with 

their parents throughout the following year to help raise a subsequent litter (USFWS, 

1998 and 2008). Pups disperse on aver 5 miles (and up to 25 miles) from their pupping 

dens. 

9.8 References 

Bell, H. 1995. San Joaquin Kit Fox. Tideline. Vol. 15 No. 3 1-3. Available online at: 

http://www.fws.gov/desfbay/Archives/Fox/KitFox.htm (Accessed on October 3, 

2007). 

Cal EPA. Dept. of Pesticide Regulation. 2002. San Joaquin Kit Fox (Vulpes macrotis 

mutica). Available online at: 

http://www.cdpr.ca.gov/docs/endspec/espdfs/sjkfall.pdf (Accessed on April 4, 

2008). 

76
East Contra Costa County HCP/NCCP. 2006. San Joaquin Kit Fox (Vulpes macrotus 

mutica). Available online at: http://www.co.contracosta.ca.us/depart/cd/water/HCP/archive/hcp_nccp_content/hcp_nccp/app_figs/A

pp%20D%20components/App_D-02a_San_Joaquin_kit_fox_profile_1-18-05.pdf

(Accessed on April 3, 2008). 

List, R. and B.L. Cypher. 2004. Kit fox (Vulpes macrotis). Pages 105-109 in C. SilleroZubiri, M. Hoffmann, D. W. Mac Donald, editors. Canids: Foxes, Wolves, Jackals 

and Dogs. Status Survey and Conservation Action Plan. Cambridge, UK: 

IUCN/SSC Canid Specialist Group. Available online at: 

http://www.canids.org/species/Kit_fox.pdf (Accessed on April 4, 2008). 

Ralls, K. B. Cypher, and L.K. Spiegel. 2007. Social monogamy in kit foxes: formation, 

association, duration, and dissolution of mated pairs. Journal of Mammalogy 

88(6):1439-1446. Available online at: http://www.bioone.org/archive/1545-

1542/88/6/pdf/i1545-1542-88-6-1439.pdf (Accessed on April 3, 2008). 

Ridgley, H. 2007. Foxy City. Defenders Magazine. Defenders of Wildlife. Available 

online at: 

http://www.defenders.org/newsroom/defenders_magazine/fall_2007/foxy_city.ph

p (Accessed on April 3, 2008). 

San Joaquin County Multi-Species Habitat Conservation and Open Space Plan (SJCOG) 

Available online at: 

http://www.sjcog.org/Programs%20&%20Projects/Habitat_files/Species/San%20

Joaquin%20Kit%20Fox.pdf (Accessed on April 3, 2008) 

U.S. Fish and Wildlife Service (USFWS). 1967. Native Fish and Wildlife, Endangered 

Species. Washington, D.C. Available online at: 

http://ecos.fws.gov/docs/federal_register/fr18.pdf (Accessed on April 16, 2008). 

U.S. Fish and Wildlife Service (USFWS). 1998. Recovery Plan for Upland Species of 

the San Joaquin Valley, California. U.S. Fish and Wildlife Service, Portland, 

Oregon. 319 pages. Available online at: 

http://ecos.fws.gov/docs/recovery_plans/1998/980930a.pdf (Accessed on March 

31, 2008). 

U.S. Fish and Wildlife Service (USFWS). 2008. Species Account: San Joaquin Kit Fox 

(Vulpes macrotis mutica). Sacramento Fish and Wildlife Office. Available 

online at: http://www.fws.gov/sacramento/es/animal_spp_acct/sj_kit_fox.htm 

(Accessed on March 31, 2008). 

White, P. J., W. H. Berry, J. J. Eliason, and M. T. Hanson. 2000. Catastrophic decrease 

77
in an isolated population of kit foxes. Southwestern Naturalist 45(2):204–211. 

(Only the abstract was viewed and used). Available online at: 

http://www.jstor.org/pss/3672462 (Accessed on April 3, 2008). 

78
10: VALLEY ELDERBERRY LONGHORN BEETLE 

10.1 Species Listing Status 

The valley elderberry longhorn beetle (VELB) (Desmocerus californicus dimorphus) was 

listed as threatened on August 8, 1980 (45 FR 52803) by the U.S. Fish and Wildlife 

Service (USFWS). A recovery plan for the VELB was approved by the USFWS on June 

28, 1984 (USFWS, 1984). A 5-year review, which provides an updated life history for 

the VELB, was published by the USFWS in September of 2006. The USFWS announced 

its recommendation to remove the VELB from the endangered species list on October 2, 

2006 (USFWS, 2007 a). This recommendation was based on the slowing of the loss of 

the habitat for this species, the protection of 50,000 acres of riparian (riverside) habitat, 

and the restoration of 5,100 acres of VELB habitat (USFWS, 2007 a and Environmental 

Defense, no date). 

10.2 Description 

Three species of the genus Desmocerus occur in North America, “including two species 

that occur in California” (USFWS, 1984). These species “are moderately-sized, brightly 

colored, and sexually dichromatic” (USFWS, 1984). All species in the genus 

Desmocerus use various elderberry species as food plants (USFWS, 1984). Two 

subspecies of Desmocerus californicus, D. c. californicus (California elderberry longhorn 

beetle [CELB]) and D. c. dimorphus (VELB), have been described (USFWS, 1984). 

Longhorn beetles in the family Cerambycidae “are characterized by somewhat elongate, 

cylindrical bodies with long antennae, often more than 2/3 of the body length” (USFWS, 

2007 a). Male VELB are usually about 2 cm (13-21 mm) but can “range in length from 

about 1⁄2 to nearly 1 inch (measured from the front of the head to the end of the abdomen) 

with antennae about as long as their bodies” (USFWS, 2007 a and b and LSA, 2004). 

Female VELB are broader and “slightly more robust than males, measuring about 3⁄4 to 1 

inch, with somewhat shorter antennae” (USFWS, 2007 a and b). Females range in length 

from 18-25 mm (LSA, 2004). 

10.3 Distribution 

Historic Range 

The VELB is “endemic to the Central Valley of California (USFWS, 2006). 

“Historically the beetle ranged throughout the Valley” and could be found “in elderberry 

thickets in moist valley oak woodland along the margins of the Sacramento and San 

Joaquin Rivers” (California’s Endangered Insects and USFWS, 1980). “Although the 

precise historical range of the valley elderberry longhorn beetle can never be known, it is 

79
presumed that the extensive loss of riparian habitat has reduced its distribution 

significantly” (USFWS, 1984). 

Current Range 

The VELB currently occurs in the Central Valley of California “from southern Shasta 

County to Fresno County in the San Joaquin Valley” (USFWS, 2006 and 2007 a). 

However, other sources state that the range “extends from Redding (Shasta County) at the 

northern end of the Central Valley to the Bakersfield area (Kern County) in the south” 

(Barr, 1991 and 1996; and Jones & Stokes, 2004). Still another source states that the 

range extends from “a location along the Sacramento River in Shasta County, southward 

to an area along Caliente Creek in Kern County” (Talley et al., 2006-Biological Opinion). 

 These differences in range could be due to the fact that “the distribution of VELB based 

on sightings or collections of typically colored males is” “smaller than that of exit holes” 

(Talley et al., 2006). “Adults have been taken northward almost to Red Bluff (Tehama 

County), and as far south as Porterville (Tulare County) and an unknown location in Kern 

County (museum specimen, not seen)” (Barr, 1991). Although records exist for Kern 

County,” “no specimens or observations of living beetles exist that support the assertion 

that the species is found there” (USFWS, 2006). A complete description of the VELB’s 

range is discussed in Barr, 1991. 

Another source states that the VELB’s “range extends throughout California’s Central 

Valley and associated foothills from about the 3,000-foot elevation contour on the east 

and the watershed of the Central Valley on the west” (USFWS, 1999). This range 

encompasses all or portions of 31 counties including: “Alameda, Amador, Butte, 

Calaveras, Colusa, Contra Costa, El Dorado, Fresno, Glenn, Kern, Kings, Lake, Madera, 

Mariposa, Merced, Napa, Nevada, Placer, Sacramento, San Benito, San Joaquin, San 

Luis Obispo, Shasta, Solano, Stanislaus, Sutter, Tehama, Tulare, Tuolumne, Yolo, and 

Yuba” (USFWS, 1999). 

“In the foothills of the Sierra Nevada, adult beetles have been found in elevations up to 

2,220 feet and exit holes in elevations up to 2,940 feet” (Jones & Stokes, 2004 and Barr, 

1991). “Along the Coast Ranges, adult beetles have been found up to 500 feet elevation, 

and exit holes have been detected up to 730 feet elevation (Jones & Stokes, 2004 and 

Barr, 1991). About 190 records of VELB have been documented in the Central Valley 

“mostly based on exit holes” (USFWS, 2007 a). 

“To date, no range-wide surveys of VELB have been conducted and therefore the data 

regarding the range distribution of the species, as well as the local distribution, are 

incomplete” (Jones&Stokes, 2002). “It is not possible to accurately assess the species’ 

population status” “because the information on VELB population and distribution is 

limited” (Jones&Stokes, 2002). “However, based on the extent of habitat loss in the 

Central Valley, it is likely that populations have declined” (Jones&Stokes, 2002). 

80
10.4 USFWS Critical Habitat 

Critical habitat was designated for the VELB on August 8, 1980 (45 FR 52803). Two 

critical habitat areas, the Sacramento Zone and the American River Parkway Zone, were 

designated because “these areas include the densest known populations of the beetle” 

(USFWS, 1980, 1991, and 1996). The Putah Creek Zone, “one of the areas proposed as 

Critical Habitat for the beetle in Solano County,” was not designated as critical habitat 

due to a lack of information (USFWS, 1980). However, “although not officially 

designated as critical habitat, portions of Putah Creek and the American River Parkway 

just west of Nimbus Dam are herein considered essential habitat” (USFWS, 1984 and 

1991). “These areas support large numbers of mature elderberry shrubs with extensive 

evidence of use by the beetle” (USFWS, 1996). 

Critical habitat is defined in the ESA as specific areas within the geographic area 

occupied by a species at the time it is listed, containing physical and biological features 

necessary for the conservation of the species, and that may require special management to 

protect the listed species (USFWS, 1980). Critical habitat may also include “specific 

areas outside the geographical area occupied by the species at the time it is listed” if they 

are determined to be “essential for the conservation of the species” (USFWS, 1980). The 

designation of critical habitat is based on habitat areas that provide essential life-cycle 

needs of the species or areas that contain primary constituent elements (PCEs). PCEs 

include, but are not limited to, space for individual and population growth and for normal 

behavior; food, water, air, light, minerals, or other nutritional or physiological 

requirements; cover or shelter; sites for breeding, reproduction, rearing (or development) 

of offspring; and habitats that are protected from disturbance or are representative of the 

historic geographical and ecological distributions of the species (USFWS, 1978). 

Critical habitat areas were designated because the PCEs need additional protection or 

special management to ensure that the areas designated as critical habitat are not 

adversely modified. The threats that may adversely modify the critical habitat and 

require special management include (USFWS, 1980): 

1) “modification of riparian habitats by river channelization” 

2) “construction of buildings, roads, bridges, or parking lots, directly eliminating 

the beetle’s host plant, elderberry (Sambucus sp.).” 

3) “human disturbance, such as vandalism or fire, resulting from increased 

recreational use, which adversely affects the beetle” 

VELB Critical Habitat Units 

Unit 1: Sacramento Zone:

This area is located in the city of Sacramento and is bounded “on the north by the Route 

160 Freeway, on the west and southwest by the Western Pacific railroad tracks, and on 

the east by Commerce Circle and its extension southward to the railroad tracks” 

(USFWS, 1980). “The Sacramento Zone is privately owned” and when it was designated 

as critical habitat, this area consisted of “predominantly riparian woodland” (Talley et al., 

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2006). “Today it remains undeveloped with similar vegetation communities and 

continues to be degraded by homeless encampments, which has been a long-standing 

problem” (Talley et al., 2006). As a result of the encampments, “this section of Critical 

Habitat remains somewhat degraded with the threat of continued and more serious 

degradation (e.g., wild fires, although elderberry often recover from fires)” (Talley et al., 

2006). 

Unit 2: American River Parkway Zone:

This area of the American River Parkway is located “on the south bank of the American 

River” and is bordered “on the north by latitude 30°37’30”N, on the west and southwest 

by Elmanto Drive from its junction with Ambassador Drive to its extension to latitude 

38°37’30”N, and on the south and east by Ambassador Drive and its extension north to 

latitude 38°37’30”N” (USFWS, 1980). This area also includes “Goethe Park, and that 

portion of the American River Parkway northeast of Goethe Park, west of the Jedediah 

Smith Memorial Bicycle Trail, and north to a line extended eastward from Palm Drive” 

(USFWS, 1980). “The American River Parkway Zone remains relatively protected as 

part of the American River Parkway, so is largely unchanged as far as land use and major 

vegetation types” (Talley et al., 2006). 

10.5 Habitat 

“Potential VELB habitat is defined by the presence of mature and immature elderberry 

shrubs (Sambucus spp.)” (Barr, 1991). Elderberries are typically “associated with 

riparian forests which occur along rivers and streams” in California’s Central Valley “and 

in the surrounding foothills up to 3,000 feet in elevation in the east and the entire 

watershed to the west (Jones & Stokes, 2004; and California’s Endangered Insects). 

“Elderberry is a common component of the remaining riparian forests and adjacent 

grasslands of the Central Valley” (Barr, 1991). “The beetle occurs most frequently and is 

most abundant in significant riparian zones” (Talley et al., 2006). 

“Studies have found that the beetle is more abundant in dense native plant communities 

with a mature overstory and a mixed understory” (USFWS, 1999). One study “of 

Sacramento Valley riparian vegetation” published in 1987, showed that “elderberries 

were found with VELB emergence holes (7-10mm in diameter) in four types of overstory 

situations: 

• young-growth riparian stands of cottonwoods and willows on the lower 

terrace; 

• stands of mature and senescent cottonwoods on the lower terrace; 

• mature riparian stands of mixed tree species, including cottonwood, box 

elder, northern California walnut, and valley oak on the higher terrace; and 

• sites without overstory in both higher and lower terrace areas” (Jones & 

Stokes, 2002). 

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Although elderberries are typically associated with riparian habitats, they have also been 

found “growing in several types of situations” and are “not necessarily restricted to 

riparian areas” (Barr, 1991). VELB “were also frequently scattered in Elderberry 

Savannas adjacent to riparian forests, in pastures, and along fencerows” (Barr, 1991). 

Elderberry “often occurs nearly alone in altered and artificial situations such as along 

levees, roadside ditches, and in maintained yards and pastures, and is the characteristic 

woody plant of the Elderberry Savanna” (Barr, 1991). 

Although elderberries “can thrive in riparian and low-lying non-riparian areas in the 

Central Valley,” “the VELB has much reduced occupancy rates in non-riparian habitats” 

(Talley et al., 2006). “VELB are probably more limited by suitable habitat in the nonriparian so tend to stay closer and re-use the same shrubs” (Talley et al., 2006). Riparian 

habitat was higher quality than non-riparian scrub as evidenced by higher occupancy 

rates” (Talley et al., 2006). 

“The VELB was present in all of the communities in which elderberry grew, but it was 

more common in riparian woodlands and savannas” (Barr, 1991). “More occupied 

shrubs than expected” were found in wooded areas whereas “fewer occupied shrubs than 

expected by chance” were found in open and sparsely wooded areas (Talley et al., 2006). 

The VELB is “nearly always found on or close to its host plant, elderberry (Sambucus

species)” throughout its entire life cycle (USFWS, 2007 a and California’s Endangered 

Insects). “The VELB feeds on from one to four species of elderberry and has been 

documented as using both blue and red elderberry in the Central Valley” (Talley et al., 

2006). In addition, “the limited data indicate that one species is not preferred over the 

other” by the VELB and that “the beetle inhabits whichever Sambucus spp.” is available 

(Barr, 1991). 

“The valley elderberry longhorn beetle inhabits Sambucus of various sizes, ages, and 

growth forms, and utilizes an assortment of branch sizes for larval development” (Barr, 

1991). However, those plants with exit holes “were most often large, mature plants; 

young stands were seldom infested” (Barr, 1991). “It generally takes five or more years 

for elderberry plants to become large enough to support beetles, and it generally takes 25 

years or longer for riparian habitats to reach their full value” (USFWS, 1996). However, 

other studies have shown that “the majority of adults and larvae infest younger elderberry 

plants with trunk diameters of no more than a few inches” (Barr, 1991). 

The elderberry shrubs “must have stems that are 1.0 inch or greater in diameter at ground 

level” to serve as VELB habitat (USFWS, 2007 a). “VELB exit holes are found on stems 

or branches of 2.5 cm (1 inch) diameter or more and infrequently in smaller stems (1.3-2 

cm)” (Talley et al., 2006). “Full-grown larvae and adults typically are 1.5 to 2.5 cm 

long” which “may restrict them to larger branches and stems on older elderberries 

(USFWS, 1984). VELB seem to prefer elderberry trees with a girth of 15 to 65 cm (6-26 

inches), and “exit holes were anywhere from 10 cm to 3 m” (0.3-10 feet) above the 

ground (USFWS, 1984 and 1991). 

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Elderberries can be “tree-like” or may “form bushy, many-stemmed clumps” (Barr, 

1991). Surveys have also shown that VELB exit holes tend to occur more consistently 

“in clumps of elderberry trees rather than in isolated bushes” (LSA, 2004 and Barr, 

1991). “It should be noted that “elderberry shrubs on average are not particularly longlived” (Talley et al., 2006). 

10.6 Diet 

 

The VELB “feeds on at least one species of elderberry (Sambucus) and perhaps as many 

as three elderberry taxa” including S. glauca, S. caerulea, and S. mexicana (USFWS, 

1984). In 1982, most specimens collected by one researcher were identified as S. 

mexicana; however, “there appears to be extensive phenotypic variability and possibly 

hybridization between S. mexicana and S. caerulea” (USFWS, 1984). VELB adults 

consume elderberry foliage and possibly also the flowers whereas the “larvae are borers 

and feed on the soft pith in stems and roots of the elderberry” (USFWS, 1984 and 2007 b; 

and LSA, 2004). The adults eat from when they emerge in the spring until about June 

when they begin to mate (California’s Endangered Insects). 

10.7 Life History and Reproduction 

Adult VELB are actively feeding and mating from March to June (USFWS, 2007 a and 

LSA, 2004). The adults can sometimes be seen “resting on foliage of the elderberry, or 

actively flying between the trees” (USFWS, 1984). “Female VELB adults tend to be less 

active than males, which are more apt to take flight and move between branches, shrubs, 

or clusters of shrubs” (Talley et al., 2006). “Although adult VELBs can fly, they are 

considered poor fliers, which suggests that they are not migratory; however, there is no 

information about seasonal movements of this beetle” (Jones&Stokes, 2002). “The 

movements of VELB are not well understood, but they probably follow drainage courses 

where elderberry shrubs are most common” (Jones&Stokes, 2002). 

The VELB “appears to be only locally common, i.e., found in population clusters which 

are not evenly distributed across available elderberry shrubs” (Barr, 1991 and 1996). 

“Frequently only particular clumps or trees in the study area were found to harbor the 

beetle” where “other similar ones nearby were unaffected” (Barr, 1991 and 1996). 

“Species that are rare have at least one of the following characteristics: limited 

geographic range, high habitat specificity, or small local populations” (Talley et al., 

2006). “The VELB is especially rare, having all three of these characteristics” (Talley et 

al., 2006). These factors may cause the VELB “to be vulnerable to the negative effects of 

the isolation of small subpopulations due to habitat fragmentation” (LSA, 2004 and 

USFWS, 1996). VELB is also assumed to be “a poor disperser” because of the observed 

minimal spatial distribution of this species (LSA, 2004 and USFWS, 1996). This limited 

dispersal has conservation implications because “there is little chance that VELB 

84
populations would naturally recover following drastic declines or migrate to isolated but 

suitable habitat” (Talley et al., 2006). “Unoccupied drainages were likely to remain 

unoccupied and those that experienced extinction were not likely to be recolonized” due 

to dispersal limitations (Talley et al., 2006). “The dispersal limitation of the VELB along 

with its low densities” and “loss and fragmentation (isolation) of its habitat” “makes it 

highly vulnerable to chance events that could lead to local extirpation” (Talley et al., 

2006). “Local extinctions tend to cause wider separations and thus further isolation of 

remaining populations” (Talley et al., 2006). As a result, “non-fragmented stands of 

elderberries are essential for dispersal corridors for the species and may be necessary to 

maintain long-term gene-flow over large areas” (LSA, 2004). “Large areas of high 

habitat quality” are also important “to avoid the creation of population sinks (low quality 

areas that increase mortality)” (Talley et al., 2006). 

The life cycle of the VELB is divided into four stages: “egg, larva, pupa, and adult” and 

“may require two or more years to complete” (USFWS, 2007 a and LSA, 2004). “The 

life cycle of the VELB has been assumed to encompass two years, but recent information 

from rearing experiments suggests that a one year cycle is possible, if not probable” 

(Barr, 1991). Female VELB lay their eggs “singly or in small groups” on live elderberry 

leaves, in crevices in the bark, at the stem/trunk junctions, or at the stem/petiole junctions 

of the elderberry (Barr, 1991, 2006, and 2007 a; California’s Endangered Insects; and 

Talley, no date). The eggs hatch shortly after they are laid and “bright yellow, soft 

bodied larvae emerge” (Talley et al., 2006). The first instar larvae are exposed on the 

surface of the shrub anywhere from a few minutes to a day before they “bore to the center 

of elderberry stems where they create a characteristic feeding gallery in the pith at the 

center of the stem” (Talley et al., 2006 and Barr, 1991). “The larvae develop for 1 or 2 

years feeding on pith” and create frass, a combination of droppings and wood shavings 

(Talley et al., 2006). 

The last larval stage of the VELB before forming their pupae, the fifth instar, chews 

“through the inner bark, all or most of the way to the surface” to create the exit hole 

which is then plugged with wood shavings and frass (Talley, no date and 2006; and 

USFWS, 2006). The larvae then “move back down the feeding gallery to an enlarged 

pupal chamber packed with frass” (Talley, no date and 2006; and Barr, 1991 and 2006). 

In the pupal chamber, the larvae metamorphose into their pupae between December and 

April (Talley et al., 2006). Pupation is thought to take about one month and the adult 

may remain in the chamber for up to several weeks (Talley et al., 2006). “The adults 

complete the hole in the outer bark,” if necessary, and push “out the plug to emerge from 

the stem center” (Talley, no date and 2006). 

The VELB adults typically emerge “at about the same time the elderberry flowers” 

“between mid-March and mid-June” (USFWS, 1984 and Talley et al., 2006). The adults 

live for a few days to a few weeks between mid-March and early-June (Talley, no date 

and 2006; and USFWS, 1984). However, “most records are for late-April to mid-May” 

(Talley et al., 2006 and USFWS, 1984). During this period, the adults feed on elderberry 

leaves and possibly flowers, and reproduce within the canopy (Talley, no date and 2006). 

The females also lay their eggs during this period (USFWS, 2006). The lifespan of the 

85
adult VELB is unknown; however, it is suspected that they die after reproducing (LSA, 

2004). 

 “Egg production per female appears to be highly variable” (Talley et al., 2006). 

“Records of numbers of eggs per female in captivity vary from several to 180” (Talley et 

al., 2006). “The causes of differences in egg production are unknown but may include 

the lifespan and/or health of the female, whether in captivity or not, and site specificity or 

chance” (Talley et al., 2006). In 2003, one researcher “observed 136 larvae, with an 

additional 44 eggs that never hatched, all from one female” (Talley et al., 2006). 

“Hatching success is 50-68% based on two observations” (Talley et al., 2006). “Survival 

rates of the larvae and subsequent pupae are unknown” (Talley et al., 2006). 

10.8 References 

Barr, C.B. 1991. The Distribution, Habitat, and Status of the Valley Elderberry 

Longhorn Beetle Desmocerus californicus dimorphus Fisher (Insecta: Coleoptera: 

Cerambycidae). 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 December 18, 2007).

California’s Endangered Insects. No date. Valley Elderberry Longhorn Beetle 

(Coleoptera: Cerambycidae). Available online at: 

http://essig.berkeley.edu/endins/desmocer.htm (Accessed on December 18, 2007). 

Environmental Defense. No date. Valley Elderberry Longhorn Beetle. Available online 

at: http://www.environmentaldefense.org/documents/3731_Species_Beetle.pdf

(Accessed on December 18, 2007). 

Jones & Stokes. 2002. Low-Effect Habitat Conservation Plan for Valley Elderberry 

Longhorn Beetle for the University of California, Davis, 2001-2002 Campus 

Projects. June 14, 2004. (J&S 98-275). Sacramento, CA. Available online at: 

http://www.ormp.ucdavis.edu/environreview/onlinedocs/hcp/loweffecthcp.pdf

(Accessed on December 19, 2007). 

Jones & Stokes. 2004. Battle Creek Salmon and Steelhead Restoration Project, Draft 

Action Specific Implementation Plan. April 2004. (J&S 03-035). Sacramento, 

CA. Available online at: http://www.battlecreek.net/docs/restoration/environ_docs/append/AppendixESpecies_Accounts.pdf (Accessed on December 19, 2007). 

LSA Associates, Inc. 2004. Valley Elderberry Longhorn Beetle. Solano HCP/NCCP. 

Solano County Water Agency. Species Descriptions. Available online at: 

86
http://www.scwa2.com/hcp/Final%20Draft%202.0/Appendices/APPX%20BSpecies%20Descriptions/Valley%20Elderberry%20Longhorn%20Beetle.pdf

(Accessed on December 19, 2007). 

Talley, T.S. No date. VELB Info. Available online at: 

http://web.mac.com/tsinicrope/Site/VELB_info/Entries/2006/11/4_Lifecycle.html (Accessed on December 18, 2007). 

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 December 19, 2007). 

U.S. Fish and Wildlife Service (USFWS). 1978. Endangered and Threatened Wildlife 

and Plants: Proposed Endangered or Threatened Status and Critical Habitat for 10 

Beetles. Federal Register 43 (155):35636-35643. Available online at: 

http://ecos.fws.gov/docs/federal_register/fr234.pdf (Accessed on December 18, 

2007). 

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 December 18, 

2007). 

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 December 18, 2007). 

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 December 18, 2007). 

U.S. Fish and Wildlife Service (USFWS). 1999. Conservation Guidelines for the Valley 

Elderberry Longhorn Beetle. U.S. Fish and Wildlife Service, Sacramento Field 

Office, Sacramento, California. July 9, 1999. Available online at: 

87
http://fws.gov/sacramento/es/documents/velb_conservation.htm (Accessed on 

December 18, 2007). 

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 December 

18, 2007). 

U.S. Fish and Wildlife Service (USFWS). 2007 a. Species Account: Valley Elderberry 

Longhorn Beetle (Desmocerus californicus dimorphus). Sacramento Fish and 

Wildlife Office. Available online at: 

http://www.fws.gov/sacramento/es/animal_spp_acct/velb.pdf

(Accessed on December 18, 2007). 

U.S. Fish and Wildlife Service (USFWS). 2007 b. Species Account – Kid-Friendly: 

Valley Elderberry Longhorn Beetle. Sacramento Fish and Wildlife Office. 

Available online at: 

http://www.fws.gov/sacramento/es/animal_spp_acct/valley_elderberry_longhorn_

beetle_kf.htm (Accessed on December 18, 2007). 

88