Overview of Threatened and Endangered 

Species Studies in the Tijuana River 

Watershed

Chris Brown and Robert Fisher

San Diego Field Station

Western Ecological Research Center

USGS
Who Is WERC?

http://www.werc.usgs.gov
• What are the regional patterns of diversity across southern 

California?

• What is the autecology of some of the sensitive species?

• How can we best maintain the diversity on reserve lands?

• What species may need additional regulatory attention, and 

which species are adequately protected in the current 

planning of permanently preserved habitats?

What we do...
Fragmentation of Terrestrial Systems
Sampling Design

• Use standard sampling protocols

• Identify wildlife crossing sites along 

highways

• Quantitatively describe vegetation 

communities 

• Quantitative measurement of wildlife 

species richness and relative abundance

• Repeated long-term sampling at fixed 

sample points
Inventory and Monitoring Data

•Monitoring Protocol Development

•Reptile and amphibians (terrestrial)

•Bats, carnivores, birds, ants

•Amphibians and fish (aquatic)

•Data Management Needs/Requirements

•Use of PDA’s

•Consistent forms

•Database structure
Riparian Habitat
>95% Riparian Habitat Lost
Population Ecology and Demography of 

Endangered Birds

Least Bell’s Vireo

Southwestern Willow Flycatcher
Brown-headed Cowbird Parasitism

© VIREO
Research Focus

• Habitat requirements

• current distribution

• breeding habitat

• wintering habitat

• Ecology and behavior

• foraging ecology (Miner 1989)

• territory size (Newman 1993)

• vocalizations and song repetoire (Embree 1992, Beck 1996)

• mating system (Spiegelberg 1997)
Research Focus

(continued)

• Life History and Demography

• reproductive success and productivity (Peterson in prog.)

• impact of cowbird parasitism (Sharp in prog.)

• recruitment and dispersal

• population viability

• Data management

• repository for annual survey data

• maintain statewide database
Habitat Restoration
Habitat Restoration
Number of Territories

< 5

5 - 10

11 - 25

> 25

Owens Valley

Kern River

Mojave River

San Bernardino Mtns.

Temecula Creek

Upper San

Luis Rey River

Sweetwater River

San Dieguito River

Lower San Luis Rey River

Camp Pendleton

Prado Basin

Santa Clara River

Santa Ynez River

Southwestern Willow Flycatcher Numbers in California: 2000
Least Bell’s Vireo Population

1986 2000

300 males 2500+ males
Amphibian 

Research 

and 

Monitoring
Aquatic Amphibians Being Monitored
Reptile and 

Amphibian 

Diversity—

Inventory and 

Monitoring
Long-term Monitoring

• Trigger points for adaptive management

– Changes in diversity of snakes

– Reduction in recruitment in reptiles

– Lack of recruitment in amphibians

– Occurrence of exotics that may effect native species

– Reduced counts of sensitive species
Results:

• 46 species captured (18 families represented)

• >36,000 captures

• Study sites have 9 - 33 species present

• Arrays have up to 22 species present
Results:

• 13 species occur at 24 - 31 sites (type 1)

represented by 220 - >8800 captures

• 12 species occur at 10 - 19 sites (type 2)

represented by 42 - 730 captures

• 17 species occur at 1 - 8 sites (type 3)

represented by 1 - 130 captures
Comparison of large “core” areas to 

fragments (established reserves)

Can use snakes of San Diego County

Excellent historic record from Klauber

(collected 1920’s-1940’s)
0

10,000,000

20,000,000

30,000,000

40,000,000

50,000,000

60,000,000

70,000,000

80,000,000

90,000,000

100,000,000

1938 1975 1995 2015

Source: Klauber 1939; SANDAG 1998

Mile

s

/

d

a

y

Vehicle Miles Driven per day

in San Diego County
San Diego County Sites Only

Camp Marron Rancho Elliot Little Torrey Chula Tijuana Chula Point

Pend WAP Valley SD Reserve Cedar Pines Vista II Estuary Vista I Loma Klauber

Total # 34 Arrays 20 Arrays 9 Arrays 10 Arrays 17 Arrays 9 Arrays 15 Arrays 9 Arrays 15 Arrays 7 Arrays 17 Arrays number Difference 

Species of sites 80 days 130 days 105 days 95 days 135 days 94 days 80 days 90 days 10 days 90 days 90 days of sites Hist/present

Lampropeltis getulus 11 X X X X X X X X X X X 11 0

Crotalus viridis 11 X X X X X X X X X X X 11 0

Pituophis melanoleucas 11 X X X X X X X X X X 11 0

Masticophis lateralis 11 X X X X X X X X X X X 11 0

Crotalus ruber * 8 X X X X X X X X 11 3

Rhinocheilus lecontei 6 X X X X X X 11 5

Thamnophis hammondii * 7 X X X X X X X 10 3

Masticophis flagellum 7 X X X X X X X X 10 3

Lichanura trivirgata * 5 X X X X X 10 5

Diadophis punctatus * 7 X X X X X X X 9 2

Hypsiglena torquata 7 X X X X X X X 8 1

Salvadora hexalepis * 5 X X X X X 6 1

Coluber constrictor 3 X X X 5 2

Leptotyphlops humilis 6 X X X X X X 4 -2

Crotalus mitchellii 4 X X X X 4 0

Tantilla planiceps 6 X X X X X X 3 -3

Trimorphodon biscutatus 3 X X X 3 0

Arizona elegans 1 X 3 2

Thamnophis sirtalis * 1 X 2 1

Lampropeltis zonata * 0 1 1

Total number of species present = 19 19 16 14 12 12 10 8 8 9 6 6

Total number of species historic = 20 19 18 15 15 14 15 16 12 13 11 10

Difference = 0 2 1 3 2 N/A 8 4 4 5 4

* = considered sensitive or protected by USFWS or CDFG

Sites in green are core areas; sites in red are isolated or fragments

Recent and historic occurrence of snakes at 

San Diego Study sites
Comprehensive Biodiversity Studies
Carnivore Track Station
•Management Implications

–Importance of Monitoring (examples from field studies)

–Point Loma/Torrey Pines/Tijuana River
Response and Recovery of Plants and Animals to 

2003 and 2007 San Diego Wildfires: Research 

Objectives and Management Implications

U.S. Department of the Interior

U.S. Geological Survey
Background

Massive 2003 southern California wildfires

• Burned approximately 750,000 acres of mostly 

wildlands in southern California

• 300,000 acres in Cedar and Otay Fires, San Diego

County

• Large portion of San Diego County MSCP reserve 

area
Followed by 

Massive 2007 

Southern 

California 

Wildfires 
Background (cont.)

Short and long term impacts on plants, 

invertebrates, and vertebrates

• Direct mortality, habitat loss, loss of plant and 

animal food resources, soil erosion and stream 

siltation (loss of amphibian breeding habitat)

• Habitat conversion

– Shrublands converted to grasslands

– Closed vs. open habitats

– Natives displaced by non-natives
Research Objectives: Overview

Measure response/recovery of plants, 

invertebrates, and vertebrates

•Pre-burn data from fire footprint

– Pitfall Arrays

– Focused T & E species studies

– Multi-taxa studies

•Controls 
Research Objectives: Overview (cont.)

•Ground-dwelling vertebrate and invertebrate 

communities in San Diego County

•Nesting and migratory birds in San Diego County

•Foraging and roosting bats in San Diego County
Conclusions and Management 

Implications

• Fire as ecosystem driver

• Time scales necessary for recovery

•Effects on reserve design; covered species

– Viability of reserve(s)

– Local, state, and federal governments legal 

requirements

– Adaptive management

– Alter reserve design if necessary
P re P o s t P re P o s t P re P o s t P re P o s t

C o mmo n N a m e S c i e n t i fi c N a m e

W e s t e rn T o a d B u fo b o reas 209 3 1 279 2 7 6 1 2 1 4 0

S o u t h w e s t e r n To a d B u fo c a l i fo rn i c u s 2

P a c ifi c C h o ru s F r o g Hyla r e g i lla 113 6 8 0 8 1 2 1 2

B u llfr o g R a na c a t e s b e iana 9 1 1

W e s t e rn S p adefoot S c aphiopus h a m m o ndi i 4 7 1 2 6

A fric an C la w ed F ro g X e nopus laevi s 1

O range-T h r o a t ed L i z a r d C n e m i d ophoru s h y p e r y t h ru s 5 3 9 2 331 226 2 2 1 9 6

W e s t e rn W h i p t a i l C n e m i d ophoru s tig ri s 5 3 114 3 2 5 3 1 1 3 3 2 5 3 3

W e s t e rn B a nded L i z a r d C o l e ony x va rie gat u s 8 4

S o u t hern A l lig a t o r L i z a rd E lgari a m u lt i c a rin a t a 5 0 1 3 7 5 2 2 4 1 2 2 8 4 7

G i l b e rt 's S k i n k E u m e c e s g i l b e rt i 7 9 3 3

W e s t e rn S k i n k E u m e c e s ski l t onianus 9 1 2 1 146 4 8 1 5 3 7 3 5 3 3

C o a s t H o rned L i z a r d P h r y nos o m a c o r o nat u m 155 2 5 2 7 1 3 2 2

W e s t e rn F e n c e L i z a r d S c e loporu s o ccident a l i s 296 292 264 318 9 9 263 170 271

G ranit e S p in y L i z a rd S c e loporu s o r c u t t i 2 1 2 2 5 8 1 1 5 2

S ide-B lo t c h ed L i z a r d U t a s t ans buri a n a 3 6 102 5 5 8 6 4 2 6 0 1 3 2 4

G ranit e N i g h t L i z a rd X a n t u s i a h ens haw i 1 1 4

G a r d en S lender S a la m ander B a t ra c hos eps p a c i fi c u s 8 4 6 5 3 0 1 6

M o n t e re y S a la m ander E n s a t ina e s c h sch o lt z i i 1 8 1 5

R a c e r C o l u ber c ons t ri c t o r 1 5 9 1 2 6 6

S p e c k led R a ttle s nak e C ro t a lu s m i t c h e l lii 2 2

R e d D ia m ond R a ttle s nak e C ro t a lu s ruber 1 4 4 1

W e s t e rn R a ttle s nak e C ro t a lu s virid i s 1 0 4 1 1 8 1 4 4

R ingnec k S n a k e D iadophis punc t a t u s 6 1 4 3 1 1 3 1

N ight S nak e Hyp s ig lena t o r q uat a 7 4 4 1 1 1

C o mmo n K ings nak e Lam p ropelt i s get u lu s 1 8 3 2 3 1 2 5 1 4 2 4

W e s t e rn B l i n d S n a k e Lept o t y p h lops h u m ilis 8 1 3 1 3 3 2

R o sy B o a L i c h anura t rivirg a t a 1

C o a c h w h ip M a s t i c ophis flagel l u m 3 1 3 3 6

C a lifo rn ia W h i p s n a k e M a s t i c ophis l a t e r a lis 1 9 1 4 2 2 2 0 1 1 1 3

G o pher S nak e P it u ophis c a t e n ife r 2 0 5 2 5 5 3 1 1 1 6

Long-N o s e d S n a k e R h i n o c hei l u s l e c o n t e i 4 1 1 1 1

W e s t e rn P a t c hed-N o s e d S n a k e S a lva dora hex a lepis 1 6 6

C a lifo rn ia B la c k -H e aded S n a k e T a n t illa p l a n i c e p s 1 1 1 0 1 3 1 5

T w o -S t rip ed G a r t e r S nak e T h a m nophis ham m o ndi i 6 2 6 5 1

L y r e S nak e T ri m o rphodon b i scu t a t u s 1

F ro g L i z a rd S a l. S n a k e

CHA P C S S GRASS W R Reptile and 

Amphibian 

Captures—

Pre vs. Post 

Burn by 

Habitat
Reptile and Amphibian Diversity
Arroyo Toad Response to Fire

4 Watersheds

•San Dieguito

•San Diego

•Sweetwater

•Tijuana
Arroyo 

Toad in 

Tijuana 

River
Below Tecate Creek
No Fish

No Amphibians
Cottonwood Creek 

above Tecate Creek
3 Fish

4 Amphibians
Arroyo Toad in Tijuana River

Extent of arroyo Habitat indicated toad detections as suitable pre-2008 burn

Dynamic 

system...

What happens 

with a border 

fence?
What’s Next?

Continued monitoring

Other toads have shown initial positive response to 

fire, then disappear (Hossack 2007)

Document aquatic habitat change over time (where 

does suitable habitat appear/disappear)
Acknowledgements:

•Barbara Kus (riparian bird information)

•Carlton Rochester/Drew Stokes (post fire 

overview)

•Tritia Matsuda, Meg Snyder, Denise Clark 

(SDFS Project and Field Support)