Herpetological Monitoring Using a Pitfall Trapping 

Design in Southern California

Techniques and Methods 2–A5

U.S. Department of the Interior

U.S. Geological Survey

Chapter 5 of 

Section A, Biological Science

Book 2, Collection of Environmental Data
Cover: Pitfall trap arrays have been used in southern California to document reptile and amphibian species. Photograh taken by 

U.S. Geological Survey, date unknown.
Herpetological Monitoring Using a Pitfall 

Trapping Design in Southern California

By Robert Fisher, Drew Stokes, Carlton Rochester, Cheryl Brehme, and Stacie 

Hathaway, U.S. Geological Survey; and Ted Case, University of California

Chapter 5 of 

Section A, Biological Science 

Book 2, Collection of Environmental Data

Techniques and Methods 2–A5

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

For product and ordering information:

World Wide Web: http://www.usgs.gov/pubprod

Telephone: 1-888-ASK-USGS

For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, 

natural hazards, and the environment:

World Wide Web: http://www.usgs.gov

Telephone: 1-888-ASK-USGS

Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. 

Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Fisher, Robert; Stokes, Drew; Rochester, Carlton; Brehme, Cheryl; Hathaway, Stacie; and Case, 

Ted,2008,Herpetological monitoring using a pitfall trapping design in southern California: U.S. Geological Survey 

Techniques and Methods 2-A5, 44 p.
iii

Contents

Abstract...........................................................................................................................................................1

1.0 Introduction...............................................................................................................................................1

2.0 Background and Justification ...............................................................................................................1

3.0 Array Design ............................................................................................................................................2

3.1 Trap Labeling/ Numbering.............................................................................................................4

4.0 Array Materials and Trap Construction................................................................................................4

4.1 Drift Fencing.....................................................................................................................................4

4.2 Pitfall Traps ......................................................................................................................................4

4.2.1 Pitfall Trap Cover.................................................................................................................4

 4.3 Equipment within Pitfall Traps .....................................................................................................5

4.4 Funnel Traps ....................................................................................................................................5

4.4.1 Funnel Traps with Pitfall Trap Retreats ........................................................................10

4.5 Weather Stations ..........................................................................................................................12

5.0 Array Installation ...................................................................................................................................13

5.1 Personnel, Equipment, and Logistics ........................................................................................13

5.2 Installation Instructions...............................................................................................................13

5.2.1 Pitfall Arrays ......................................................................................................................13

5.2.2 Weather Stations ..............................................................................................................14

6.0 Array Operation .....................................................................................................................................14

6.1 Survey Scheduling........................................................................................................................14

6.2 Personnel, Equipment, and Logistics ........................................................................................15

6.2.1 Safety Precautions ...........................................................................................................16

6.3 Survey Methods (Checking Traps).............................................................................................16

6.4 Field Identification .......................................................................................................................16

6.5 Processing Specimens ................................................................................................................16

6.5.1 Processing Lizards, Turtles, Frogs, Toads, Salamanders, and Newts 

(Limbed Animals)..........................................................................................................17

6.5.2 Processing Snakes and Other Limbless Specimens ..................................................20

6.5.3 Incidental Captures and Observations..........................................................................22

6.6 Vegetation Surveys.......................................................................................................................22

7.0 Survey Data Management....................................................................................................................24

7.1 Data Collection and Entry ...........................................................................................................24

7.1.1 Pitfall Capture Data ..........................................................................................................24

7.1.2 Megafauna Data ...............................................................................................................26

7.1.3 Weather Data ....................................................................................................................26

7.2 Quality Assurance/Quality Control.............................................................................................29

7.3 Data Organization and Summarization......................................................................................29

7.4 Data Analysis.................................................................................................................................36

8.0 Acknowledgments.................................................................................................................................36

9.0 References Cited....................................................................................................................................39

Appendix 1. Materials and supplies needed to build, maintain, and sample a pitfall 

trapping array. ...............................................................................................................................43

Appendix 2. Species codes and abbreviatoins. ................................................................................44
iv

Figures

Figure 1. Pitfall array (A) overhead view and (B) side view design .............................. 3

Figure 2. Pitfall trap design diagram.................................................................. 5

Figure 3. Assembly of funnel (snake) trap body diagram .......................................... 6

Figure 4. Preparing hardware cloth for funnel (snake) trap end cone design .................. 7

Figure 5. Assembly of funnel (snake) trap and cone diagram .................................... 8

Figure 6. Completed funnel (snake) trap assembly diagram....................................... 9

Figure 7. Funnel (snake) trap shade cover and position .......................................... 9

Figure 8. Desert funnel (snake) trap with pitfall trap retreat .................................... 10

Figure 9. Desert funnel (snake) trap with pitfall trap retreat .................................... 11

Figure 10. Front view (A) and top view (B) of weather station .................................... 12

Figure 11. The cumulative number of species detected by pitfall array surveys for 

three study sites in San Diego County, California ....................................... 15

Figure 12. Measure each animal from snout to vent ................................................ 17

Figure 13. Numbering reptile toe clips ............................................................... 18

Figure 14. Numbering amphibian toe clips............................................................ 18

Figure 15. Numbering snake scale clips ............................................................ 20

Figure 16. Paper data form for recording animal captures ....................................... 24

Figure 17. Handheld computer form for recording animal capture data ........................ 25

Figure 18. Paper data form for recording megafauna captures.................................... 26

Figure 19. Paper data form for recording weather conditions .................................... 27

Figure 20. Handheld computer data form for recording weather conditions ..................... 27

Figure 21. Tabular and graphical displays of temperature patterns for a sampling period ... 28

Figure 22. Example site map. ........................................................................... 32

Tables

Table 1. Reptile and amphibian toe-clip numbers ................................................ 19

Table 2. Snake scale-clip numbers.................................................................. 21

Table 3. Vegetation data spreadsheet. ............................................................ 23

Table 4. Reptile and amphibian data spreadsheet ............................................. 30

Table 5. Small mammal data spreadsheet ......................................................... 31

Table 6. Site location file ........................................................................... 33

Table 7. Summary of small mammal species captured at each pitfall array .................. 34

Table 8. Summary of reptile and amphibian species captured at each pitfall array ......... 35

Table 9. Capture rate ................................................................................. 37

Table 10. Average capture rate table ............................................................... 38
v

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Volume

gallon (gal) 3.785 liter (L) 

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg) 

SI to Inch/Pound

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

Volume

liter (L) 0.2642 gallon (gal)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound, avoirdupois (lb)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32

Datum

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
vi

This page intentionally left blank.
Herpetological Monitoring Using a Pitfall Trapping 

Design in Southern California

By Robert Fisher1, Drew Stokes1, Carlton Rochester1, Cheryl Brehme1, Stacie Hathaway1, and Ted Case2

Abstract

The steps necessary to conduct a pitfall trapping survey 

for small terrestrial vertebrates are presented. Descriptions 

of the materials needed and the methods to build trapping 

equipment from raw materials are discussed. Recommended 

data collection techniques are given along with suggested data 

fields. Animal specimen processing procedures, including toeand scale-clipping, are described for lizards, snakes, frogs, and 

salamanders. Methods are presented for conducting vegetation 

surveys that can be used to classify the environment associated 

with each pitfall trap array. Techniques for data storage and 

presentation are given based on commonly use computer 

applications. As with any study, much consideration should be 

given to the study design and methods before beginning any 

data collection effort.

1.0 Introduction

Due to its mild climate, complex topography, and rich 

geologic and biogeographic history, southern California 

supports a high diversity of reptiles and amphibians (Stebbins, 

1985; Fisher and Case, 1997). Most species can be rather 

inconspicuous, making them difficult to survey at the 

community level. Because of this, much of their ecology and 

habitat affinities are not well known. For researchers and 

land managers to be able to answer ecological questions and 

address management needs of the local herpetofauna, it is 

necessary to identify a cost-effective field survey technique 

that detects all or most of the species in a given area with 

minimal sampling bias. The technique that is the most 

accommodating to these needs is drift fences with pitfall and 

funnel traps. 

Drift fences are barriers that act to intercept and guide 

small terrestrial animals into pitfall or funnel traps placed 

along the fences. Pitfall traps are open containers that are 

buried in the ground such that the tops of the containers are 

level with the ground. Small terrestrial animals fall into the 

containers as they move across the ground. Funnel traps are 

elongated traps that have funnels at one or both ends that allow 

animals to pass easily into them through the large end of the 

funnels. The animals, once inside the traps, have difficulty 

finding their way out through the small end of the funnels and 

are trapped. 

Since initiation of large-scale pitfall trapping in coastal 

southern California in 1995, this technique has proven to 

be effective at sampling a high diversity of reptiles and 

amphibians, invertebrates and small mammals (Fisher and 

Case, U.S. Geological Survey, written commun., 2000; 

Case and Fisher, 2001; Laakonen and others, 2001). This 

report describes, in detail, all of the elements of our pitfall 

trapping protocol with specific descriptions of how to process 

reptiles (lizards, snakes, and turtles) and amphibians (frogs, 

toads, salamanders, and newts). The purpose of this report 

is to describe trap array design, materials used, sampling 

schedules, personnel needs, equipment requirements, logistical 

considerations, trap installation and operating procedures, 

safety precautions, specimen identification and processing, site 

characterization (weather and vegetation), data collection and 

entry, and data management and analysis. 

2.0 Background and Justification

Monitoring biological diversity is a current priority for 

researchers, land managers, and resource managers. It is 

important to have sampling and monitoring techniques that are 

comprehensive, cost effective, and standardized (Dodd, 1994). 

Sampling reptiles and amphibians can be difficult 

because of their size, behavior, and cryptic coloring. To 

meet this task, numerous techniques have been employed by 

researchers. Singly or in combination, these methods include 

time-constrained searches, surveys of wood debris and cover 

boards, quadrate searches, road “cruising”, pitfall trapping, 

and funnel trapping (Scott, 1982; Heyer and others,1994). 

The latter techniques may be used in combination with drift 

fencing. Comparison studies of different sampling techniques 

have revealed that each technique has its own advantages, 

disadvantages, and set of sampling biases (Campbell and 

1

 U.S. Geological Survey.

2

 Department of Biology, University of California at San Diego.
2 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Christman, 1982; Vogt and Hine, 1982; Corn and Bury, 1990; 

Rice and others, 1994; Fair and Henke, 1997; Jorgensen and 

others, 1998; Ryan and others, 2002). In order to directly 

compare data collected over multiple sites or times, it is 

important to use a standardized sampling method. This 

method should minimize the amount of observer bias while 

maximizing the number of species documented. Time 

constrained searches, quadrat searches, and road cruising may 

introduce a significant amount of bias due to the different 

skill levels of observers. A technique that has been identified 

as being the most effective for trapping a wide variety of 

species with the least amount of observer bias in various 

habitats of southern California is the use of drift fences with a 

combination of pitfall and funnel traps (Case and Fisher, 2001; 

Ryan and others, 2002). In order to validate the effectiveness 

of the pitfall trapping technique, Case and Fisher (2001) 

compared results with several other survey techniques. At 

the same sites that pitfall traps were operated, professional 

herpetologists conducted timed walking transects, timed 

visual surveys of search plots, high intensity herpetological 

searching, and passive observing surveys. None of these 

techniques yielded results as substantial as the pitfall trapping 

design for determining diversity or relative abundance of the 

local herpetofauna (Case and Fisher, 2001). 

Pitfall traps, funnel traps, and drift fencing have been 

used to trap herpetofauna since the 1940s. Early studies 

typically used traps alone or in simple linear fence arrays 

to collect and document herpetofauna (Imler, 1945; Fitch, 

1951; Banta, 1957; Banta, 1962; Medica, 1971). The shape 

of the trapping array has since been adapted to meet specific 

habitat types and study objectives. Traditional fences with 

large pitfall traps are effective for sampling squamate reptiles 

(Imler, 1945; Gloyd, 1947; Woodbury, 1951, 1953; Nelson and 

Gibbons, 1972; Semlitsch and others, 1981; Enge, 2001; Ryan 

and others, 2002). Fences made of various materials with or 

without pitfall traps are effective for sampling turtles (Bennett 

and others, 1970; Gibbons,1970; Wygoda, 1979; Burke and 

others, 1998). Funnel traps placed alongside drift fences have 

proven effective at capturing amphibians and reptiles (Enge, 

2001). In order to study population and community dynamics 

around ponds and ephemeral aquatic habitats, fenced arrays 

have been modified to encircle the water, thus catching all 

incoming and outgoing species (Storm and Pimental, 1954; 

Gibbons and Bennett, 1974; Dodd and Scott,1994). The 

effectiveness of terrestrial arrays has been increased by 

changing the shape from a linear array to an “X” or “Y” shape 

with trap arms protruding from a center pitfall trap (Campbell 

and Christman, 1982). 

In addition to collecting and documenting herpetofauna, 

these methods have been used for studies of habitat use 

(Bostic, 1965; Loredo and others, 1996) and population 

dynamics of individual species (Pearson, 1955; Parker, 1972; 

Fisher and Shaffer, 1996) and communities (Storm and 

Pimental, 1954; Gibbons and Bennett, 1974; Dodd, 1992). 

More recently, the scope of these studies has increased to 

address current ecological issues. Arrays have been replicated 

over multiple sites to look at variation within and between 

multiple habitats (DeGraaf and Rudis, 1990) and to study the 

effects of human induced impacts on the relative abundance 

and diversity of herpetofauna. These include effects of grazing 

(Jones, 1981), forestry practices (Rudolph and Dickson, 1990), 

mining (Ireland and others, 1994), water supplementation of 

desert habitats (Burkett and Thompson, 1994), and habitat 

fragmentation (McCoy and Mushinsky, 1994).

To date, many studies are limited to use of one type 

of trap, a short time frame, and (or) are conducted over a 

localized geographical region. We have used a standardized 

array of pitfall traps, funnel traps, and drift fencing to 

perform long-term research over a wide geographic area 

with replicates within and between site localities, habitats, 

and environments (Fisher and Case, 2000; Fisher and Case, 

U.S. Geological Survey, written commun., 2000; Rochester

and others, U.S. Geological Survey, written commun., 

2001). The large scope of the trapping effort over southern 

California has enabled us to evaluate not only the effect of 

local landscape features on herpetofauna assemblages, but 

also the effects of larger area geographical variables such as 

latitude, altitude, and climate (Fisher and Case, 2000; Fisher 

and Case, U.S. Geological Survey, written commun., 2000). 

We have used the data to study autecology of sensitive species, 

effects of habitat fragmentation and introduced species on 

native wildlife, regional patterns of herpetofaunal diversity, 

and historic versus current species distributions (Case and 

Fisher, 2001; Laakkonen and others, 2001; Fisher and others, 

2002). By collecting tissue samples from animals captured 

in the traps, we have enabled researchers to study phylogeny 

and population genetics of individual species (Maldonado 

and others, 2001; Jockusch and Wake, 2002; Richmond and 

Reeder, 2002; and Mahoney and others, 2003). The purpose of 

this report is to provide valuable data for both the theoretical 

and applied sciences as well as for conservation planning.

3.0 Array Design 

Array designs can be variable. Compared with fourarmed arrays, three-armed arrays yield comparable results, 

(Heyer and others, 1994), use less material, and take less time 

to construct. Our array design consists of three 15-m arms 

of drift fence with seven pitfall traps and three funnel traps 

(fig. 1). One pitfall trap is placed in the center of the array with 

each of the three arms of drift fence extending outward from 

the center trap. The angle formed by the array arms around the 

center trap should be approximately 120 degrees. Pitfall traps 

are placed in the middle and at the end of each arm of fencing. 

One funnel trap is placed along each arm approximately 

halfway between the middle and end pitfall traps on the right 

side of each arm when looking from the center trap toward the 

end trap. The funnel traps are placed consistently on the same 

side of the fence at an array to ensure that funnel trapping 

results are comparable among arrays. 
3.0 Array Design 3

A.

Arm 1 Arm 2 

Arm 3

5-1B 

5-C 

5-2B 

5-2A 

5-3A 

5-3B 

5-1A 

5-ST-3 

5-ST-1

5-ST-2 

Drift Fence 

Funnel Trap 

15 meters 

B.

Pitfall Trap 

Funnel Trap

Drift Fence 

Pitfall Trap 

Figure 1. Pitfall array (A) overhead view and (B) side view design.
4 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

3.1 Trap Labeling/ Numbering

For identification purposes, each array at a given study 

site is assigned a number. Each array arm is assigned a number 

1, 2, or 3 in a clockwise direction beginning with the arm 

arbitrarily designated as arm number 1 (usually the arm first 

encountered on the trail is assigned the number 1). The pitfall 

containers are labeled A, B, and C for outer, middle, and 

center buckets, respectively. All of the traps making up an 

array are first identified by the number of the array followed 

by the number of the arm along which the container lies. For 

example, the middle container at array five of arm three would 

be identified as 5-3B. The center container of array five would 

be identified as simply 5-C. The funnel traps, also called 

“snake traps” or “ST”, are identified by the arm number along 

which they lie, 1–3. For example, the funnel trap located along 

arm two of array five would be identified as 5-ST2 (fig. 1). 

4.0 Array Materials and Trap 

Construction

Below is a complete description of materials needed 

for the pitfall array design and instructions for making 

individual traps. Measures are presented in metric units with 

the exception of materials commonly available in Standard 

English units. Background information on traps and materials 

is presented also. A complete supply list for array construction 

and operation is provided in appendix 1.

4.1 Drift Fencing

A variety of different materials can serve as effective 

drift fencing and should be chosen to suit the substrate(s) 

and weather conditions within the study area. For instance, 

a porous material should be used in areas with high winds to 

prevent winds from tearing out fences. Other materials that 

have been used in various studies include clear roll plastic, 

silt fencing, wooden boards with bronze window screen, 

aluminum flashing, hardware cloth, and galvanized metal 

(Milstead, 1953; Storm and Pimental, 1954; Pearson, 1955; 

Gibbons and Semlitsch, 1981; Campbell and Christman, 1982; 

Bury and Corn, 1987; Murphy, 1993; Enge, 1997; Jorgensen 

and others, 1998; Zug and others, 2001). We use 30-cm tall 

nylon shade cloth. The length of drift fence is 15 m per array 

arm (7.5 m between each pitfall trap). Wooden stakes 

(1- × 2- × 24-in.) are used to secure the drift fence upright. 

The drift fence is secured to the stakes by using heavy-duty 

staples and a heavy-duty staple gun. Ten to 15 stakes are used 

per 15-m arm of fencing. See installation section in this report 

for procedures. Gibbons and Semlitsch (1981) discussed the 

advantages and limitations of the drift fence technique and 

considered aluminum flashing to be superior to other fencing 

materials in their area because it is more difficult for animals 

to bypass and it does not deteriorate or rust. We use the shade 

cloth in rocky areas with many surface irregularities.

4.2 Pitfall Traps

Various containers have been used as pitfall traps such as 

19-L (5-gal) plastic buckets, coffee cans, metal buckets, “lard” 

cans, local pottery water containers, and 208-L (55-gal) drums 

(Pearson, 1955; Banta, 1957, 1962; Gibbons and Bennet, 

1974; Gibbons and Semlitsch, 1981; Campbell and Christman, 

1982; Vogt and Hine, 1982; Yunger and others,1992; Corn, 

1994; and Zug and others, 2001). Larger containers generally 

capture more animals (Vogt and Hine, 1982), while smaller 

(more shallow) containers increase the likelihood for escape. 

The double-pit systems may aid in trapping larger reptiles 

(Friend, 1984), although smaller containers may be useful 

if the target is smaller and there is no need to capture the 

larger animals (Shoop, 1965; Gill, 1978; Douglas, 1979). 

Additionally, fitting a plastic collar to the top of pitfall traps 

may prevent some animals from escaping the container (Vogt 

and Hine, 1982). 

Containers should be buried such that the rim is flush 

with the ground. The containers should have small drain holes 

in the bottom to minimize flooding during rain events while 

traps are open. We typically use white plastic 19-L (5-gal) 

buckets. At desert sites, we use 23-L (6-gal) buckets because 

they are deeper and provide increased insulation from heat. 

Crawford and Kurta (2000) found that black plastic buckets 

trapped frogs and shrews more effectively than did white 

plastic buckets. However, black buckets may experience high 

internal temperatures when exposed to intense sunlight for 

long periods. This could result in damage to the containers and 

increased trap mortality. Dodd (1992) used slanting pegboards 

to partially shade the black buckets in Florida. 

4.2.1 Pitfall Trap Cover

All pitfall traps should have some form of top cover when 

open to shield animals from the elements. We use an inverted 

lid design set on top of the trap with wooden spacers (fig. 2). 

This design prevents most litter, sunlight, and precipitation 

from entering the open bucket while allowing sufficient space 

for small animals to enter. 

To construct the top cover, cut three 6.4-cm-long pieces 

of 2- × 2-in. construction-grade wood at a 35-degree angle. 

Attach these, facing outward, around the top of the bucket lid 

using 1.25-in. drywall screws with SAE #10 washers. Make 

vertical cuts approximately every 15 cm around the outer 

perimeter of the lid. This will allow easier opening and closing 

of the traps. When the traps are open, the lid is turned over 

with the spacers resting on top of the bucket (fig. 2). Animals 

and wind occasionally remove the container lids while in the 

open position. When necessary, bungee cords may be used to 

keep the lids on. To attach the bungee cords to the pitfall traps, 

drill three holes, with diameters similar to the bungee cords, in 
4.0 Array Materials and Trap Construction 5

 ecneF tfirD nedooW

Stakes

Bucket Lid with 

Wooden Legs 

Soil

Surface

5-gal Pitfall

Bucket

Buried Drift

Fence

Soil

Figure 2. Pitfall trap design diagram (gal, gallon).

the sides of the bucket. The holes should be evenly spaced and 

approximately 8 cm down the container sides. Next, cut three 

12-in. bungee cords in half. Feed the cord ends through the 

holes from the inside of the container and tie a knot at the end 

of the cord outside the container. Attach the cords by pulling 

out the hook ends and fastening onto the lid while it rests on 

the wooden feet. There should be enough tension in the cord 

that it takes considerable force to remove the lid from its 

resting position without unhooking the bungee cord. Wooden 

boards that attach to the pitfall containers using bolts and eyesockets may also be used to keep container lids on while they 

are being sampled (Fellers and Pratt, 2002). 

 4.3 Equipment within Pitfall Traps

Cover should be provided within the pitfall traps for 

captured animals. We use two segments of differently sized 

PVC pipes, a 6-in. long piece of 1.5-in. diameter pipe and 

an 8-in. long piece of 1-in. diameter pipe. Some form of 

insulation such as synthetic batting or foam material should 

be provided in the PVC pipes if small mammals are likely to 

be captured. We place a section of closed foam pipe insulation 

within the 1.5-in. diameter piece of pipe. 

Placing a wet sponge in the pitfall trap is recommended 

to help keep amphibians hydrated. The sponges should be 

wetted on a daily basis when traps are opened. The use of 

sponges is discontinued in southern California during the dry 

months, as they usually attract ants. A large number of ants 

can kill or seriously injure small vertebrates in the traps.

4.4 Funnel Traps 

A variety of materials can be used to make funnel traps 

but 0.125-, 0.25-, or 0.33-in.-mesh hardware cloth has been 

the material of choice in herpetological studies (Imler, 1945; 

Gloyd, 1947; Fitch, 1951; and Milstead, 1953). The traps 

should be sturdy yet lightweight. We used 0.25-in. hardware 

cloth for the studies documented in this report. 

To construct the funnel traps, first cut 100-ft rolls of 

36-in. hardware cloth into 18-in. wide sections. For each 

cylinder body, roll one 36- × 18-in. section of hardware cloth 

along the 18-in. edge into a cylinder and fasten with hog-rings. 

Plastic zip-ties or cable ties can be used (fig. 3). Under field 

conditions, the metal hog-rings have a longer life than do the 

plastic zip-ties, which tend to last for only 1 year in southern 

California sun. The same hardware cloth is used to make 

the funnel ends. To make funnel ends, cut a 24-in. diameter 

circle of hardware cloth into four equal sections (fig. 4). Each 

piece is rolled into a funnel shape and serves as one end of 

the trap. Cut the small end of the funnel to have an opening 

of approximately 2-in. in diameter, which will allow animals 

including large snakes to enter into the cylinder. Fit two 

funnel ends into each cylinder with the small ends pointing 

inwards. Evenly cut the overhanging material in five places 

to the edge of the cylinder body to form flaps (fig. 5). Fold 

the overhanging flaps over the edge of the cylinder so that the 

funnels fit snugly onto the cylinder. Finally, fasten the funnels 

to the cylinder with medium-sized binder clips, two per funnel 

end (fig. 6). Trim off all sharp points and edges during the 

cutting process to prevent injury to captured animals and field 

personnel. 
6 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

18 in

36 in

Step 1. Step 2.

1 in

Hog rings or plastic cable ties

 Seams

Step 4. 

Step 3. 

Figure 3. Assembly of funnel (snake) trap body diagram (in, inch).
4.0 Array Materials and Trap Construction 7

Step 3. Step 4.

 24 in

.1 petS .2 petS 24 in

Figure 4. Preparing hardware cloth for funnel (snake) trap end cone design (in, inch).
8 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Step 1. 

Hog rings or plastic zip ties

 Seams

Step 2. 

Step 3. 

Step 4. 

Figure 5. Assembly of funnel (snake) trap and cone diagram.
4.0 Array Materials and Trap Construction 9

Burlap Cover (Optional) 

End Cone 

End Cone 

Binder Clips 

Figure 6. Completed funnel (snake) trap assembly diagram.

Fence

Snake trap

Wooden

shingles

In the field, position the funnel traps with the seams 

of both the body and end cones facing upwards to prevent 

animals from becoming injured on any rough edges of the 

hardware cloth. Binder clips should be placed on the sides of 

the cones rather than top and bottom.

The funnel trap should be covered at all times to avoid 

exposure to sunlight and precipitation. We use shingle boards 

to cover the funnel traps (fig. 7). A shingle board is placed 

Figure 7. Funnel (snake) trap shade cover and position.

beneath the funnel trap also to shield it from extreme substrate 

temperatures. In the desert and high wind areas, 2- × 2-ft 

squares of 0.75-in. plywood substitute for shingle boards. 

A 6-in.-long piece of 1.5-in. PVC pipe with 2 in. of foam 

insulation is placed inside each funnel trap for additional 

cover.
10 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

4.4.1 Funnel Traps with Pitfall Trap Retreats 

In areas having extreme temperatures, such as desert 

sites, it may be necessary to provide a more substantial 

secondary retreat within funnel traps. This can be done by 

installing a 6-gal pitfall trap under, and attached to, the funnel 

trap (fig. 8). 

Cut-away side view 

6 gal bucket 

1.5-in PVC connector

1.5-in PVC “T” joint Bailing wire

Body of funnel trap

Lid with 2.25-in 

hole drilled through

36 in

Pitfall traps, lids

 with wooden legs

Drift fence

“B” Bucket “A” Bucket

Funnel trap PVC “T” joint

to “C” Bucket

Pit fall trap, lid with 2.25-in 

hole drilled through

Overhead view 

To construct this retreat, install a pitfall trap under 

the intended location of the funnel trap. Before rolling 

the hardware cloth into a cylinder, cut a hole in it using a 

sharpened steel pipe of appropriate diameter (fig. 9). Connect 

the funnel trap to the buried bucket by placing a 1.5-in. PVC 

“T” joint inside the funnel trap cylinder. Insert an 8- × 1.5-in. 

Figure 8. Desert funnel (snake) trap with pitfall trap retreat (in, inch; gal, gallon).
4.0 Array Materials and Trap Construction 11

 36 in

18 in

Steel pipe with

sharpened end

Hammer

PVC “T” Joint

PVC “T” Joint

Bailing Wire

Step 1.

Step 2.

Step 3.

piece of PVC pipe into the trunk end of the “T” joint (fig. 8). 

The trunk end will extend down through the hole in the bottom 

of the funnel trap and into the hole cut in the top of the lid of 

the buried bucket. Cut the holes in the funnel trap cylinder 

and bucket lid just large enough to accommodate the “T” joint. 

Secure the “T” joint to the funnel trap cylinder with bailing 

wire. This design allows captured animals to seek cover in the 

buried bucket by way of the “T” joint pipe.

Figure 9. Desert funnel (snake) trap with pitfall trap retreat.
12 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

4.5 Weather Stations

Weather stations are designed to record ambient 

temperature data at a height of 1 m off the ground (fig. 10). To 

construct the weather station, attach an inverted 5-gal bucket to 

a 2- × 2-in. × 2-ft long piece of construction-grade wood using 

a wood bolt with a wing nut and washer. Cut away a piece 

from the side of the bucket that will allow for easy access to 

the thermometer or temperature probe (fig. 10). Insert a small 

wood screw into the wooden post a few inches below the top 

on the side of the post exposed by the section of bucket cut 

Hood

(Inverted Bucket)

Thermometer

Post

Sleeve

A.

N

B.

Cutaway

Substrate Stand

Figure 10. Front view (A) and top view (B) of weather station.

away in the previous step. A thermometer may be hung on 

the small screw. Alternatively, a data logger device, such as 

HOBO (Onset Computer Corporation), may be wrapped in a 

plastic bag, attached to a medium-sized binder clip, and hung 

on the screw. Attach a piece of 2-in. diameter PVC pipe to the 

bottom of the wooden post using wood screws. This acts as 

a sleeve adapter to allow the entire station to be attached to a 

same sized wooden post (2- × 2- × 24-in.) buried in the ground 

at the selected pitfall array. If necessary, the top portion of the 

weather station can be moved between study sites.
5.0 Array Installation 13

5.0 Array Installation 

5.1 Personnel, Equipment, and Logistics

The time it takes to install a set of arrays can vary 

depending on conditions of the substrate and terrain. In 

general, a four-person team can install a single array in 

about 1 hour, not including the time it takes to load/unload 

equipment and driving time. Considering these and other 

factors, usually no more than five arrays can be installed by 

a four-person team in 1 workday at any given study site. The 

equipment needed for a four-person team to install a set of 

pitfall trap arrays includes the following: 

1. Fifty-m measuring tape to measure out array arm lengths 

2. Two to three shovels

3. At least one pry-bar if working in rocky substrate or, 

if very rocky, a hammer drill may be necessary with a 

portable generator 

4. (Optional) an auger with a 14-in. bit for digging holes for 

the pitfall traps (5- or 6-gal buckets)

5. One to two pick axes with flat blade ends to dig the 

trenches where the drift fencing will be placed 

6. Small sledge hammer (3–5 pounds) for pounding in the 

wooden stakes used to support the drift fencing 

7. Heavy duty staple gun and staples to attach drift fence to 

stakes 

8. Tin snips to clip bucket lid rims 

9. Scissors to cut the drift fence 

10. Brush removal equipment to form trails to arrays and 

clear space for array arms as needed

11. At least one vehicle, with four-wheel drive if necessary, 

to transport the installation team and equipment to and 

around the study site.

Site selection involves landowner permission and (or) 

permits for the study in addition to any required state or 

federal permits for the use of this technique on the target 

species. Often site permits require archeological clearance 

that needs to be completed prior to final site selection and 

construction. It is better to select more sites than necessary 

in case some need to be abandoned during the permitting 

process.

5.2 Installation Instructions

5.2.1 Pitfall Arrays

During site reconnaissance, flag each of the pitfall array 

locations at the position of the center bucket. Measure the first 

array arm out 15 m from the location of the center pitfall trap. 

At 7.5 and 15.0 m, mark locations of pitfall traps by setting 

bucket lids on the ground. Measure out the remaining two 

arms from the center trap approximately 120 degrees apart. 

All three fence arms should be as straight as possible, but 

could bend to avoid large rocks, trees, and other barriers, as 

necessary.

At the marked locations of the pitfall traps, two or three 

crew members should begin digging separate holes using the 

most appropriate tools for the substrate (shovels, pick axes, 

pry bars). Dig the holes just large enough to accommodate the 

pitfall trap containers. When installing containers in substrate 

types that don’t drain easily, it is recommended to dig the 

holes deeper than the depth of the containers and to place a 

layer of rocks below the containers before they are buried. 

Combined with the 0.125-in. holes drilled in the bottom of the 

containers, this will allow water to drain from the containers 

if they should become flooded during rain events. If the holes 

are not drilled in the bottom of the bucket then the buckets will 

pop out of the ground if they are closed during a rain event. 

If they are open during a rain event without holes, they will 

flood, killing most of the trapped animals.

Before burying the buckets, it is recommended that the 

rims of the bucket lids be clipped vertically in four or five 

places to make them easier to remove when opening the traps. 

Set the buckets into the holes with the covers on. Use dirt from 

the excavation to fill in the space between the outside of the 

bucket and the hole until the top of the bucket is flush with the 

ground. Having the lid on the bucket during back filling will 

help to maintain the shape of the bucket. Without the lid, the 

shape of the bucket may become deformed, making it difficult 

to secure the lid later. It is important to firmly compact the 

soil around the buried containers so that stakes put in at the 

edges of the buckets have a solid foundation. Next, use a pick 

axe to dig 3- to 5-in. deep trenches where drift fencing will be 

installed to connect the pitfall traps.

After all seven pitfall containers with lids are in place and 

the trenches are completed, install the drift fence. First, lay 

the appropriate length of fence along the trench. The number 

of stakes needed per array arm can vary, but is typically 10 to 

15. For each array arm, place one stake each at the center and 

end containers, two stakes at the container in the middle of the 

array arm (one on either side), and one stake approximately 

every meter along the fence in between the containers. If it 
14 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

is necessary for the array arm to change direction or make a 

turn, place a stake at the inside of each turn. When the array 

is built on a slope, place the stakes on the down hill side of 

the trench for stability. Next, pound the stakes into the ground 

along the edge of the trench deep enough to be secure, but 

not so deep so that the top of the drift fence is higher than the 

top of the stakes. The stakes next to the containers should not 

be pounded into the ground until ready to attach the fencing. 

Pound each stake located at the edge of the container as close 

to the container as possible to maximize trapping efficiency, 

but not so close that it indents the side of the bucket.

Once the stakes are installed, set the drift fencing along 

the middle of the trench along the stakes. It is recommended 

that the fence be anchored to the end stakes (stakes at bucket 

edges) first. To attach the fence to an end stake, cut a 4- to 

6-in. horizontal slit approximately 2 in. from the bottom of 

the fencing. Wrap the lower strip around the stake and staple 

it in place so that the top edge of the fence extends straight 

to and above the edge of the bucket. This flap is used to help 

guide animals towards the pitfall traps. Starting with the 

stake at the center container and keeping the fence as tight 

as possible, fasten the drift fence with heavy-duty staples to 

each stake working from the bottom of the stake to the top. 

Alternating sides where the stakes are stapled to the fence may 

be beneficial; this helps to keep the fence in place should the 

staples fail. Additionally, if a fence line must curve around an 

obstacle, the stake should be to the inside of the curve. If the 

fence is stapled to the inside of the curve, it often puts stress 

on the staples to the point of pulling out the staples and the 

fence falls down. When the fence has reached the container 

in the middle of the array arm, it should be cut such that the 

fence edge is extending just beyond the edge of the container 

and attached as described for the first end stake. Start the fence 

again on the other side of the middle container and fasten to 

the remaining stakes until the end container is reached. Install 

the fences of the other two array arms in this same manner 

until all three are in place.

Replace and pack the substrate along the drift fence such 

that the bottom of the fence is buried completely and all of 

the pitfall container rims are flush with the ground. Set the 

funnel traps in place along the drift fence between the pitfall 

containers in the middle and the outer end of the array arms. 

The funnel traps are placed along the right side of each arm 

when viewed from the center bucket (fig. 1). Close all bucket 

lids and remove funnel trap ends until sampling begins. 

5.2.2 Weather Stations

Choose a location for the weather station that best 

represents the study site. Pound a wooden post (2- × 2 

× 24-in.) into the ground at the chosen location. Leave 1 ft of 

the stand exposed above the substrate (fig. 10) so that when 

the weather station is affixed, the thermometer or data logger 

is approximately 1 m above the ground. Affix the weather 

station by sliding the exposed PVC sleeve over the top of the 

ground stand. Orient the station such that the cutaway portion 

(exposing thermometer or data logger) is facing north in 

the Northern Hemisphere to prevent sunlight from reaching 

the thermometer or data logger. This setup allows for the 

collection of ambient temperature at the study site. 

It may be necessary to have more than one weather 

station per study site, depending on the topographic diversity 

in the area and different microclimate zones encompassed 

within the study site. The weather stations can be installed at 

the study site when arrays are opened and then removed at the 

end of the sample period.

6.0 Array Operation 

6.1 Survey Scheduling

The timing of surveys will vary depending on the 

research objectives. For instance, if surveying exclusively 

for amphibians, it is recommended that traps be opened 

after rainfall to maximize captures. However, this type 

of opportunistic trapping may be logistically difficult. 

Rain events can be unpredictable and can create access 

problems where use of dirt roads is required to get to the 

traps. Alternately, continuous trapping reveals seasonal and 

weather-related variations in animal activity but requires more 

personnel and may affect resident animals. 

In our protocol, traps at any given study site are sampled 

for 4 consecutive days and then closed (for example, opened 

on Monday, sampled daily Tuesday through Friday, and 

closed on Friday). This is referred to as a sample period. 

Sample periods are scheduled every 4–5 weeks for a given 

site, resulting in 10–12 sample periods a year. This sampling 

schedule allows for target information to be collected, 

including seasonal activity patterns of reptiles and amphibians. 

Based on our analysis of species accumulation curves, it is 

recommended that a site be sampled 3–5 consecutive years 

to increase the probability of detecting rare species (fig. 11). 

The probability of detecting rare species also depends on the 

number of trapping arrays at any given site. We usually place 

arrays in multiple representative habitats within a site and 

include replicates within habitat types, as funding permits.
6.0 Array Operation 15

0

5

10

15

20

25

30

35

1/1/1995 1/1/1996 12/31/1996 12/31/1997 12/31/1998 12/31/1999 12/30/2000 12/30/2001

Date

CUMULATIVE NUMBER OF SPECIES DETECTED

Wild Animal Park Pt Loma Mission Trails

Figure 11. The 

cumulative number of 

species detected by 

pitfall array surveys 

for three study sites 

in San Diego County, 

California.

6.2 Personnel, Equipment, and Logistics

In general, a single person can operate a set of 20–30 

pitfall trap arrays a day. Following the 4-day sampling 

schedule, a single person working full time can operate 

4 sets of 20 pitfall trap arrays on a rotational basis. Some 

circumstances, such as long distances between arrays or 

personnel safety concerns, may warrant the need for a twoperson team for array operation.

Each person or team operating a set of pitfall trap arrays 

will need a field kit that consists of a portable carrying case, 

such as a backpack and (or) tackle, tool, or ammunition box 

plus several items for processing animals and recording data. 

The processing equipment needed includes

1. Gloves for handling reptiles, small mammals, and (or) 

invertebrates.

2. A set of appropriately sized spring scales; typically 10-g, 

30-g, 60-g, 100-g, and 1-kg scales will accommodate 

most small vertebrates 

3. At least one small bag for weighing small animals 

(re-closable plastic bag)

4. At least one large bag for weighing larger animals (a bag 

or pillow case for weighing a snake)

5. Clear plastic, metric ruler

6. Cloth or plastic, 2-m measuring tape for measuring large 

snakes

7. Large and small forceps

8. Small scissors for toe- and scale-clipping

9. Lab marker

10. 5-mL microcentrifuge tubes containing 95-percent ethanol 

for storing small pieces of tissue (toe, tail, and scale clips) 

or ectoparasites

11. Box with dividers for storing 5-mL tubes containing 

95-percent ethanol

12. 50-mL centrifuge tubes containing 95-percent ethanol for 

storing larger pieces of tissue

13. Large and small plastic bags for storing dead specimens 

that are too large for either 5- or 50-mL tubes (specimens 

in plastic bags should be placed immediately on ice)

14. Cooler containing dry ice or ice packs for temporary 

storage of dead specimens to be immediately transferred 

to freezer

15. Small spatula or cup for clearing out debris from within 

pitfall traps; a cup may also be needed to bail water out of 

pitfalls during rain events

16. Field identification guide to help identify captured 

animals

Equipment needed for recording data includes

1. Data book (small three-ring binder or hand-held 

computer) with appropriate data forms

2. Write-in-rain pen for recording data

3. A permanent marker for writing on plastic tissue tubes 

and bags
16 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

6.2.1 Safety Precautions

Safety precautions that should be considered when 

operating pitfall traps. When trapping in areas where 

venomous snakes occur, it is recommended that persons 

operating the traps wear some form of protection for their legs 

and ankles, such as “snake chaps.” The handling of venomous 

snakes is described in the “Processing of Specimens” section 

of this report. In addition to venomous snakes, many other 

stinging or biting invertebrates and vertebrates are often 

trapped and warrant careful handling.

Precautions also should be taken in areas where the 

occurrence of communicable diseases, such as Hantavirus 

or Bubonic plague, is probable or confirmed in the rodent 

populations. Rodents are often caught in both pitfall and 

funnel traps. It is recommended that persons operating the 

traps wear latex and (or) thick leather gloves and some form of 

respiratory protection. Project leaders should check with local 

public health authorities before initiating fieldwork. The traps 

may be washed and sterilized with a diluted bleach solution as 

deemed necessary. It is important to ensure that the traps are 

rinsed thoroughly if bleach is used.

6.3 Survey Methods (Checking Traps)

 The sample period starts by opening the pitfall and 

funnel traps at each array to be sampled. The PVC pipes and 

sponges placed into the traps should be washed in soapy water, 

sterilized in a diluted bleach solution (5 percent or less), and 

rinsed thoroughly before being brought to the site. To open 

pitfall traps, remove the lids from the containers. Turn over 

the lids and place them so that the wooden “feet” sit on the 

container rim. As each trap is opened, remove dirt and debris 

with a spatula or cup. Place one 6- × 1.5-in. diameter pipe with 

foam insulation, one 8- × 1-in. pipe, and one clean sponge in 

each pitfall trap as it is opened. Place one shingle board under 

each funnel trap. Place one 6- × 1.5-in. diameter PVC pipe 

with insulation inside each funnel trap and cover the entire 

trap with the shingle boards. Open funnel traps by fastening 

both funnel ends to the cylinder body using the binder clips.

After opening, the traps are then checked for 4 

consecutive days, usually during the early morning hours. 

To check the pitfall traps, remove the open lids and visually 

inspect the inside of the containers, including inside the PVC 

pipes, under the sponge, and under any debris such as leaf 

litter and soil. During the wet season, wet the sponges daily. 

To check funnel traps, first visually inspect for venomous 

snakes, then pick up one end of the trap and inspect the inside 

of the trap, including inside the PVC pipe. It is usually not 

necessary to remove an end funnel to see inside the trap. 

In desert sites, the funnel traps that are connected to pitfall 

containers (fig. 8) should be lifted so that the inside of the 

pitfall container can also be inspected. All of the arrays at a 

study site should be checked and all animals processed and 

released before daytime temperatures reach levels that could 

result in animal mortality. If a fast moving snake (for example, 

Masticophis) or lizard (for example, Cnemidophorus) is 

captured, it may be easiest to empty the end of the trap 

directly into a cloth bag or pit-trap to capture the specimen for 

processing.

On the last day of the sample period, close the traps after 

checking and processing animals. To prevent animals from 

being captured in the traps between sample periods, remove 

both ends of each funnel trap and tightly attach all lids to the 

pitfall containers in the closed position. It may be necessary 

to place small rocks on top of the closed container lids to 

prevent them from being removed by animals or wind. Rocks 

that are too large will eventually break through older lids that 

have become brittle due to sun exposure. If periods between 

sampling are long or if arrays are in sites subject to vandalism, 

pitfall traps should be checked periodically to ensure they are 

intact between sample periods. 

6.4 Field Identification 

Persons operating the pitfall trap arrays should be trained 

to identify all of the focal species potentially trapped in the 

study area and should be aware of other species that might 

be trapped incidentally. This can be done by studying field 

guides, museum specimens, and (or) by training with an 

experienced field biologist. It is important that the person 

checking the traps is also able to identify the sex, relative age, 

and reproductive condition, when possible, of trapped animals. 

It may be helpful to carry field identification guides while 

sampling. If the field technician cannot positively identify an 

animal, the animal may be photographed or brought in from 

the field, when appropriate, for further examination.

6.5 Processing Specimens

All animals trapped alive are processed and released 

immediately. Processing captured animals involves handling, 

recording relevant data, and marking. Dead animals are 

preserved as voucher specimens. They may be collected in 

clean, re-closable plastic bags, 50-mL centrifuge tubes, or 

other appropriately sized air tight containers. The specimens 

can be preserved immediately in 95-percent ethanol or 

temporarily stored on ice in a small ice chest and transported 

to a freezer. The container should be appropriately labeled 

with site, trap, species, date, and a unique identifier such as 

a record identification number, if possible. Photographs of 

representative species can be taken also and will serve as 

vouchers for reports and publications. 
6.0 Array Operation 17

6.5.1 Processing Lizards, Turtles, Frogs, 

Toads, Salamanders, and Newts (Limbed 

Animals)

To process a limbed reptile or amphibian, first 

record the array and trap number in which the animal 

was trapped. Record the species, age (juvenile/ adult), 

any unusual markings, deformities and (or) injuries. 

Record the sex and reproductive status, if possible. 

Measure the length of lizards, newts, or salamanders 

by placing a ruler on the ventral side of the animal and 

measuring the length from the tip of the snout to the vent 

(fig. 12). Frogs and toads are measured from the tip of 

the snout to the end of the urostyle. The length of the 

carapace is recorded for turtles and tortoises. All length 

measurements should be made to the nearest millimeter. 

Before recording the weight, tare the spring scale to 

the attached weighing bag. Place the animal into the 

weighing bag and record the weight as accurately as the 

spring scale displays.

All limbed species, except turtles and extremely 

small salamander species, are toe-clipped for 

identification purposes. A combination of toes are 

clipped, a maximum of one toe per foot, such that no 

two individuals of a species at a study site are marked 

with the same combination (figs. 13, 14). Toes are 

assigned numbers by looking at the individual from 

the top or dorsal side with head facing up or in the 

12 o’clock position. All numbers are assigned in a 

clockwise direction beginning with the toes of the left 

front foot being assigned the numbers 1–5 (or 1–4; frogs, 

toads). The toes of the right front foot are assigned the 

numbers 10–50 (or 10–40). The toes of the right hind 

foot are assigned the numbers 100–500 and the toes of 

the left hind foot are assigned the numbers 1,000–5,000. 

The accelerator toes on the hind feet (toe numbers 400 

and 2,000) of lizards are not clipped. Similarly, thumbs 

of frogs and toads (toe numbers 4 and 10) should not be 

clipped, as they are important for amplexus. Alternate 

numbering systems may be used (Heyer and others, 

1994).

Some animals may be missing toes due to natural 

causes. In these cases, the animal can be assigned the 

number corresponding to its missing toes. If more than 

one toe is missing per foot, the highest numbered toe per 

foot is used by default, with all missing toes recorded 

in the notes. For example, if an animal was missing 

the number 1 and 2 toes on the front left limb, and the 

number 40 and 50 toes on the front right limb, it would 

be identified as 0052 with recapture status as unknown 

and the notes would read “missing toes 1, 2, 40 and 50”. 

It is not always possible to distinguish these animals 

from toe-clipped individuals. 

Turtles can be individually marked by making 

notches on the edges of the marginal scutes or 

by painting the shells, depending on the level of 

Figure 12. Measure each animal from snout to vent.

0

1

2

3

4

5

Snout 

Vent 

permanency needed in the study (Cagle, 1939; Woodbury, 1953). 

If the marginal scutes are going to be marked, this should be 

coordinated with other researchers that are studying these species 

in the area or have done so in the past to share numbering schemes 

and data for already marked individuals. This is more important 

for turtles than many other reptiles due to their longevity and 

the possibility of multiple research efforts detecting the same 

individuals many years apart. Different researchers have used angle 

files or scissors to mark smaller turtles, but larger ones will need 

to be marked using a hacksaw blade or grinder (Woodbury, 1953). 

The numbering scheme that is used needs to be well documented 

in the study and associated metadata. Because of the endangered 

or threatened status of many turtles, we have taken measures to 

reduce the capture of these species. Where study sites overlap 

the distribution of Gopherus agassizii, bungee cords are used to 

secure the opened lids in place on top of the pitfall traps, reducing 

the size of the opening. Thus, we have been able to study reptile 

communities without the risk of harm to this species or the need for 

permits for it.
18 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

 The toe-clip or shell-marked numbers are 

tracked on a clip chart. A newly captured individual is 

assigned the next available number for its species and 

that number is marked off of the clip chart (table 1). 

Used numbers can be removed later from the clip 

chart as shown in table 1 for Elgaria multicarinata 

(ELMU), Cnemidophorus hyperythrus (CNHY), 

Sceloporus occidentalis (SCOC), Sceloporus orcutti 

(SCOR), and Uta stansburiana (UTST) , which 

start at higher numbers than those species which 

have never been captured. Alternatively, toe-clip or 

shell–marked numbers can be tracked on a handheld 

computer which removes numbers.

Toes should be clipped with very sharp scissors 

at the distal knuckle. To acquire more tissue, 5 to 

10 mm of tail tip (of tailed specimens) may be clipped 

also. Applying pressure to the wound can reduce any 

bleeding. Submersing the animal in a jar of sand is 

reported to be effective also (Medica, U.S. Geological 

Survey, oral commun., 1995). 

The toes and tail tissue can be placed into 

a 1.5-mL micro centrifuge tube filled with 

95-percent ethanol to preserve for later genetic or 

skeletochronology analysis. Label the tubes with 

the species code, date, site, array, arm, trap, toe-clip 

number, and a unique identifier, such as a record 

identification number, if possible. Release the 

processed animal into nearby vegetation or cover 

to prevent predation and exposure. Some animals, 

though limbed, are unsuited for toe-clipping due to 

one or more aspects of the animal’s anatomy. In the 

case of slender salamanders, their toes often are too 

small to distinguish one from another, let alone toeclip.

At a new study site, captured animals will be 

unmarked. Record these animals as new captures 

and mark accordingly. On subsequent visits to the 

site, examine captured animals for marks. Note any 

marked individuals as recaptures and record the 

identification number of each toe-clipped or shellmarked animal. 

1

2

3 4

5

1 0

2 0 3 0

4 0

5 0

1 000

1 00

2 0 0

3 0 0

4 00*

5 00

5000

4 000

3 000

2 000 *

1

2

3 4*

1 0*

2 0 3 0

4 0

1 00

2 0 0

3 0 0

4 00

5 00

1 000

5000

4 000

3 000

2 000

Figure 13. Numbering 

reptile toe clips.

Figure 14. Numbering 

amphibian toe clips.
6.0 Array Operation 19

Table 1. Reptile and amphibian toe-clip numbers.[Toe-clip numbers for reptiles and amphibians are listed by scientific name and species code. For all species, as numbers are used in the field, each number is marked off, as indicated below by the strikethrough, and later removed to prevent repeating the same number. Strikethroughs indicate used toe-clip or shell-marked numbers. Certain combinations of toe-clip numbers should be avoided, such as those including the 4 and 10 toes for amphibians and the 400 and 2,000 toes for lizards. Certain species, such as both Batrachoseps species, may be incompatible with toe-clipping due to characteristics of the species and are only included to present the processing code information. Processing codes are 1- toe-clip, weigh, measure all individuals; 2- toe-clip, weigh, measure all adults and 20 juveniles each sample period; 3- take tail tip from these.]

Scientific Name Species Code Processing Code* Toe-Clip Number

Batrachoseps nigriventris BANI 3

Batrachoseps pacificus BAPA 3

Aneides lugubris ANLU 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Ensatina eschscholtzii ENES 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Taricha torosa TATO 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Hyla cadaverina HYCA 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Hyla regilla HYRE 2 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Bufo boreas BUBO 2 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Bufo californicus BUMI 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Bufo punctatus BUPU 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Rana aurora RAAU 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Rana catesbeiana RACA 2 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Scaphiopus hammondii SCHA 1 1 2 3 20 21 22 23 30 31 32 33 40 41 42 43 100 101

Coleonyx variegatus COVA 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Xantusia henshawi XAHE 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Xantusia vigilis XAVI 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Anniella pulchra ANPU 3 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Elgaria multicarinata ELMU 2 510 512 513 514 515 520 521 522 523 524 525 530 531 532 533 535 541

Eumeces gilberti EUGI 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Eumeces skiltonianus EUSK 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Cnemidophorus 

hyperythrus

CNHY 1 3,045 3,051 3,052 3,053 3,054 3,055 3,100 3,101 3,102 3,103 3,104 3,105 3,110 3,111 3,114 3,115 3,120

Cnemidophorus tigris CNTI 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Sceloporus occidentalis SCOC 2 3,153 3,154 3,155 3,200 3,201 3,202 3,203 3,204 3,205 3,210 3,211 3,212 3,213 3,214 3,215 3,220 3,221

Sceloporus orcutti SCOR 1 30 31 32 33 34 35 40 41 42 43 44 45 50 51 52 53 54

Uta stansburiana UTST 2 3,202 3,212 3,214 3,215 ,3220 3,224 3,225 3,230 3,231 3,232 3,233 3,234 3,235 3,240 3,241 3,242 3,243

Phrynosoma coronatum PHCO 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25

Gambelia wislizenii GAWI 1 1 2 3 4 5 10 11 12 13 14 15 20 21 22 23 24 25
20 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

6.5.2 Processing Snakes and Other Limbless 

Specimens

To process limbless reptiles, first record the array and 

trap in which the animal is captured. Record the species, age 

(juvenile/adult), any unusual markings, deformities, and (or) 

injuries. Record the sex and reproductive status, if possible. 

Measure the length by placing a ruler on the ventral side 

of the animal and measuring the length from the tip of the 

snout to the vent. A measuring tape may be needed when 

measuring most adult snakes. Length is measured to the 

nearest millimeter. Before weighing an animal, make sure that 

the spring scale has been tared to correct for the weight of the 

weighing bag. Record the weight as accurately as the spring 

scale allows.

Most snakes are marked by scale-clipping. Venomous 

snakes (see below), blind snakes, and legless lizards typically 

are not marked. Snakes are marked by clipping their post-anal 

scales such that no two individuals of a species at a study site 

are marked with the same number (fig. 15). The post-anal 

scales are located on the ventral side of a snake’s tail, posterior 

to the vent or anal plate. Some snakes have divided post-anal 

scales while some have undivided post-anal scales. The scales 

are assigned numbers by looking at the individual from the 

bottom or ventral side with the head up in the 12 o’clock 

position. For snakes with divided post-anal scales, the two 

columns of scales are numbered 1 to 9 beginning with the 

scales closest to the vent and working towards the end of the 

tail. The left side represents 100s and the right side represents 

10s. Snakes with undivided post-anal scales are treated like 

snakes with divided scales. The left and right halves of the 

same scale are clipped in the same manner as separate left and 

right scales. The first two scales on each side (10, 20, 100, and 

200) are not clipped to reduce the chance of infection near the 

vent area. 

All species (except venomous snakes) are inspected 

for markings upon capture. Marked individuals are noted as 

recaptures. A newly captured individual is assigned a new 

number in sequence. The number is marked as used on the 

scale-clip chart and later removed (table 2). Alternatively, 

scale-clip numbers can be tracked on a handheld computer 

with numbers removed automatically after use.

Vent 

1

2

3

4

5

6

7

8

1

8

5

4

3

6

7

2

Left

100s

g

Right

10s 

Figure 15. Numbering snake scale clips.
6.0 Array Operation 21

Table 2. Snake scale-clip numbers.[Scale-clip numbers for snakes are listed by scientific name and species code. For all species, as numbers are used in the field, the number is marked off and removed to prevent repeating the same number. Certain combinations of scale-clip numbers should be avoided, such as combinations including the 1 and 2 scale. Certain species, such as Leptotyphlops humilis, may be incompatible with scale-clipping due to characteristics of the species and are only included to present the processing code information. Processing codes for snakes are 1- Not individually tail-clipped, but scales along the side of the tail removed for scarring and saved for tissue. 2- Scales under tail not divided, but remove either from right or left sides. 3- Scales divided, and easy to clip. Also remove 0.5- to 1-inch of tail tip for tissue. 4- Scales divided, but hard to clip. Also remove 0.5- to 1-inch of tail tip for tissue. 5- Do not clip scales, weigh, or measure, release, and record species and approximate size. Snake scale-clip numbers are recorded in the data book with the left side as the 100s digit and the right side the 10s (that is, 3L 4R would be recorded as 340 for scale-clip number).]

Scientific name Species code Processing code Scale-clip number L R L R L R L R L R L R L R L R L R L R L R L R L R L R

Leptotyphlops humilis LEHU 1

Lichanura trivirgata LITR 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Arizona elegans AREL 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Charina bottae CHBO 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Coluber constrictor COCO 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Diadophis punctatus DIPU 4 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Hypsiglena torquata HYTO 4 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Lampropeltis getula LAGE 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Lampropeltis zonata LAZO 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Masticophis flagellum MAFL 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Masticophis lateralis MALA 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Pituophis catenifer PIME 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Rhinocheilus lecontei RHLE 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Salvadora hexalepis SAHE 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Tantilla planiceps TAPL 4 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Thamnophis elegans THEL 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Thamnophis hammondii THHA 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Thamnophis sirtalis THSI 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Trimorphodon biscutatus TRBI 3 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Crotalus mitchellii CRMI 5 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Crotalus ruber CRRU 5 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9

Crotalus viridis CRVI 5 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 3 4 4 4 5 4 6 4 7 4 8 4 9
22 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

To perform a scale clip, use small sharp scissors to clip 

the outer corners of the scales. It is important to clip deeply 

enough so that the scute does not regenerate. Extra scales on 

the belly or 5 to 10 mm of tail tip can be clipped to acquire 

extra tissue from medium and large snakes for genetic 

material. Five to 10 mm of tail tip can be collected from 

animals with scales too small to clip, such as small snakes and 

limbless lizards. Place the clipped scales and (or) tail tip into a 

1.50-mL microcentrifuge tube filled with 95 percent ethanol. 

Label the tubes with the species, date, site, array, arm, trap, 

scale-clip number, and a unique identifier, such as a record ID 

#, if possible. Finally, the animal can be released into nearby 

vegetation or cover.

Due to safety concerns with large crews of field 

technicians, venomous snakes are not weighed or measured. 

Length, age, and sex may be approximated without handling 

the animals. Venomous snakes in pitfall traps can be removed 

carefully by using a snake stick if they are not large enough 

to get out themselves. Venomous snakes can be removed from 

funnel traps by carefully removing one end of the trap, tipping 

the snake out a few meters away from the array, and allowing 

it to find cover away from the researcher. 

6.5.3 Incidental Captures and Observations

Many non-targeted species may be trapped or observed 

on site incidentally. How these animals are recorded and 

processed depends on the research objectives. For our studies, 

the focal animal types are herpetofauna. Small mammals 

and invertebrates captured in the pitfall traps are treated 

as incidentals. We identify small mammals to the species 

level, if possible, and record the observation. Relative age 

and gender of specimens are noted also. Live animals are 

released and dead animals are collected as vouchers. Direct 

observations of megafauna at study sites are recorded daily 

while traps are being sampled. The term “megafauna” is used 

to refer to any animal other than the reptiles, amphibians, 

and small mammals normally found in the pitfall traps. For 

our purposes, this includes ground birds, large carnivores, 

and large herbivores observed at the site. Direct observations 

and signs from megafauna, such as tracks and scat, may be 

recorded also. Invertebrates are not identified in the field but 

are collected from pitfall traps on the last day of sampling. 

Forceps are used to collect the animals and put them into an 

appropriate container filled with 70-percent ethanol for storage 

and future analysis.

6.6 Vegetation Surveys

Vegetation is surveyed at each pitfall trap array through 

the use of a point-intercept transect technique (Sawyer and 

Keeler-Wolf, 1995) and recorded on a vegetation data sheet 

(table 3). Data are collected for species composition, canopy 

height, substrate, leaf litter depth, as well as incidental plant 

species, slope and aspect.

A 50-m transect is sampled for each array and data 

are recorded at points every 0.5 m along the transect. To 

perform a survey transect, run a 50-m line that is centered 

on the midpoint of the array (center bucket) in a north-south 

orientation. The line will extend 25 m north and 25 m south 

of the center bucket. Begin at the northernmost point of the 

transect. Line 1 of the data sheet always refers to the northernmost point of the transect. Place a telescoping measuring rod 

vertical to the ground at each 0.5-m survey point. First, record 

the tallest vegetation height (canopy height) on the vegetation 

data sheet (table 3). Record the plant species under one of 

three height classifications: tree, shrub, or herb. Tree refers to 

any plant taller then 3 m. Shrub refers to any plant between 

0.5- and 3-m. Herb refers to any plant less than 0.5 cm. After 

recording the tallest plant height and species, record any 

additional species that touch the telescoping rod and their 

height classifications (without recording numerical height). 

At each point, also record substrate type and leaf litter depth. 

After completing the transect, record any incidental plant 

species around the array that were not recorded at any point 

on the transect. For each array location, note the slope, aspect, 

GPS coordinates, and date. 

 These transects are completed once at each array unless 

there is a substantial change in vegetation, usually due to 

disturbance such as fire. In such an instance, the transect 

technique may be repeated. Vegetation surveys may be 

performed more frequently depending on the nature of the 

research and the questions they are intended to answer.
6.0 Array Operation 23

Table 3. Vegetation data spreadsheet. 

[At each pitfall array, vegetation data are collected at 0.5-meter intervals along a 50-meter north/south transect, centered on the center pitfall trap. In 

cases where the data will be available to the public, asterisks may be used to show the precision of the coordinate positions were reduced to protect 

the equipment in the field. The four letter species codes consist of the first two letters of the genus and the species. See appendix 2 for a translation of 

species codes and descriptions of substrate abbreviations. location date, date when the coordinate data was collected; cm, centimeter; m, meter]

Site Name: POINT LOMA Array #: 13 Location: 32.669** N 117.241*** W

Slope: (N-S) -30, -25 (E-W) -7, -3 Location date: 01-24-96 Transect date 01-24-96

Incidental Species

N

Canopy

height 

(m)

Species Litter

depth 

(cm) Tree Tree Shrub Shrub Shrub Herb Herb Substrate

1 0.19 DULA ARCA OR 0.0

2 0.00 SS 0.0

3 0.00 SS 0.0

4 0.00 SS 0.0

5 0.00 BR 0.0

6 0.44 ARCA LL 0.5

7 0.49 ARCA LL 0.5

8 0.47 ARCA ENCA LL 0.5

9 0.50 ARCA ENCA LL 0.5

10 0.53 ARCA ENCA NNG OR 0.0

11 0.56 ARCA LL 0.5

12 0.60 ARCA LL 1.0

13 0.73 ARCA LL 1.0

14 0.70 ARCA LL 1.0

15 0.60 ARCA LL 2.0

16 0.00 LL 11.0

17 0.00 LL 8.0

18 0.20 ARCA LL 4.0

19 0.31 ARCA LL 4.0

20 0.74 RHIN SS 0.0

21 0.90 RHIN LL 0.5

22 1.05 RHIN ARCA LL 0.5

23 0.71 ARCA LL 1.0

24 0.72 ARCA LL 1.0

25 0.83 ARCA LL 3.0

26 0.63 ARCA LL 3.0

27 0.97 RHIN ARCA LL 1.0

28 0.60 RHIN LL 2.0

29 0.95 RHIN LL 2.0

30 0.81 RHIN LL 2.0

31 0.53 RHIN LL 2.0

32 0.75 RHIN LL 3.0

33 0.75 ERFA RHIN LL 3.0

34 0.70 RHIN ERFA LL 3.0

35 0.84 RHIN LL 2.0
24 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

7.0 Survey Data Management

7.1 Data Collection and Entry 

Data are recorded onto standardized data forms on either 

paper or on a handheld computer. Data collected in the field 

can be grouped into one of several categories, such as animals 

captured in the pitfall arrays, megafauna, or weather. When 

collecting data on paper, each category has a separate form. 

On the handheld computer, the “megafauna” category has been 

incorporated into the animal data form. 

7.1.1 Pitfall Capture Data

The majority of data fields recorded for each captured 

animal are the same whether data are collected on paper or on 

the handheld computer (figs. 16 and 17).

 Data fields and definitions are

Date: recorded as the present date. On the handheld 

computer, this field automatically is generated based on 

the handheld’s preset, internal clock.

Site Name: referring to the overall study area and its 

components. Those collecting data on the handheld 

computers need to enter the site name only at the start 

of the fieldwork; it will automatically be carried over to 

subsequent records until the collector changes the site 

name.

Array Number: within a site, there are multiple pitfall/

funnel trap study plots, each with an individual 

identification number.

Bucket Number: each pitfall trap (fig. 1) has a 

preassigned, unique identification based on the arm 

along which it occurs and its position along that arm. 

Using the handheld computer, the collector selects the 

bucket number from a predefined list of entries.

Snake Trap #: as with Bucket Number, each funnel/snake 

trap has a preassigned, unique number based on the arm 

along which it is located. To facilitate entry, a pop-up list 

(fig. 17) is used on the handheld to enter the snake trap 

number.

Species: entered as a four-letter code, consisting of 

the first two letters of both the genus and the species. 

Examples of these codes would be SCOC for the western 

fence lizard (Sceloporus occidentalis) and RHLE for 

the long-nosed snake (Rhinocheilus lecontei). To aide 

in data entry on the handheld computers, species names 

and codes have been predefined and appear as a pop-up 

list from which the collector selects the desired species 

code. The entry of a species code is further aided by an 

additional data field on the handheld computer described 

below.

Sex: M / F / ?, (Male, Female, Unknown) as determined 

by physical characteristics, appearing as a pop-up list on 

the handheld computer.

Date 7/29/2001 Date January 6, 2001 Date 4/23/2001 Date 

Site Name Pt. Loma Site Name Torrey Pines Site Name JoshuaTree Site Name

Array Number 15 Array Number 8 Array Number 13 Array Number

Bucket Numbe 1B Bucket Number Bucket Numbe C Bucket Number

# parT ekanS # parT ekanS 1 # parT ekanS # parT ekanS

Species CNHY Species MALA Species SCOR Species

Sex M / F / ? A / J / ? Sex M / F / ? A / J / ? Sex M / F / ? A / J / ? Sex M / F / ? A / J / ?

Wt (gms.) 6.5 Wt (gms.) 60 Wt (gms.) ---- Wt (gms.)

Length (mm) m 62 Length (mm) 360 Length (mm) ---- Length (mm)

skraM skraMliat gnissim skraM ---- skraM

Toeclip numbe 0034 Toeclip numbe 0450 Toeclip numbe ---- Toeclip number

Recap? yes / no / ? Recap? yes / no / ? Recap? yes / no / ? Recap? yes / no / ?

Collector DS Collector SH Collector RH, SL Collector

Disposition released / dead/ Disposition released / dead/ Disposition released / dead/ Disposition released / dead/

depacse depacse depacse depacse

Tissue sample yes / no Tissue sample yes / no Tissue sample yes / no Tissue sample yes / no

Figure 16. Paper data form for recording animal captures.
7.0 Survey Data Management 25

Age: A / J / ?, (Adult, Juvenile, Unknown) which can 

be established by size and appearance, appearing as a 

pop-up list on the handheld computer.

Weight: the weight is recorded in grams, as accurately as 

the spring scale displays.

Length: as measured from snout to vent for lizards, 

snakes, and salamanders, or snout to urostyle for frogs 

and toads. Record carapace length for turtles or tortoises. 

Record all length measurements in millimeters.

Marks or Notes: any unusual markings, injuries, 

deformities, and reproductive status can be recorded 

in this data field. This field also allows for the 

documentation of any outstanding features of the 

specimen. For example, the amount of tail regeneration 

in lizards, scars, or additional missing toes may be 

recorded for general information. For handheld computer 

users, a list of commonly used phrases can be accessed 

to minimize manual input on the computer.

Toe-clip number: listed as a four-digit figure, for 

consistency, even if only one toe on one foot has been 

cut. Number 5 would be documented on the paper data 

sheet or handheld computer as 0005. If study sites are 

sufficiently far apart, toe-clip, scale-clip, and shellmarked numbers are not carried over from one site to the 

next. Each site has its own independent set of numbers. 

Recap: Y / N / ?, (Yes, No, Unknown) the question mark 

often is used in the case of amphibians. Recaptures of 

some amphibians can be identified accurately within 

a sample period. However, since some species can 

regenerate toes, it may be impossible to tell whether they 

have been trapped in previous sample periods, based 

on these criteria. “Unknown” may indicate animals that 

have lost toes naturally. Each recap needs to be evaluated 

carefully.

Collector: typically recorded as the initials of the 

observer(s). An effort should be made to ensure that each 

observer has unique initials, using the middle initial as 

necessary. Full names with a key for initials should be 

maintained in the laboratory. 

Disposition: released / dead / escaped. Once all relevant 

data have been gathered, most animals, if alive, are freed. 

If an animal is found dead in the traps, weight and length 

are still recorded and the body is saved for a voucher and 

tissue sample. If the specimen is in poor condition, these 

measurements can be skipped. Occasionally, an animal 

is resourceful enough to escape from the hand of the 

researcher, resulting in incomplete data for that animal.

Tissue: yes / no. The processing codes, as explained in 

tables 1 and 2, outline whether or not a tissue sample 

is collected from an animal. In addition to the toes and 

scales that are clipped to tag the specimens, a piece 

of the tail may be collected for the purpose of a tissue 

sample. For turtles, the tail tip will be the only tissue 

sample collected. A new tissue sample will not be 

collected if an animal is a recapture. 

Date: ________________

Site: ________________

Array: ________________

Bucket:

Snaketrap: 

TYPE: 

Species:

Sex:

Age: 

Wt (g): ________________

Len (mm): ______________ 

Toeclip: ________________

Recap:

Collector: _______________

Disposition: 

Tissue:

Notes: 

MOUSE/RAT 

OTHER MAMMAL 

MEGAFAUNA 

FROG

SALAMANDER

LIZARD 

SNAKE

C.

HYCA

HYRE

BUBO

RACA

D.

1A

1B 

2A

2B 

3A

3B 

C

A. B.

Figure 17. Handheld computer form for recording animal capture data.
26 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

In addition to the data fields described above, handheld 

computer users have one more field to enter, “TYPE”. On the 

handheld computer, just above “SPECIES”, is “TYPE”, which 

is a pop-up list used to identify the kind of animal that is 

being processed (fig. 17C). The use of the “TYPE” data field 

acts to reduce the number of species codes from which the 

handheld user has to choose when entering the species code 

in the “SPECIES” field. For example, when the user chooses 

“FROG” from the “TYPE” pop-up list, only a list of frog 

species will appear in the “SPECIES” pop-up list. Likewise, 

when “SNAKE” is selected under “TYPE”, only snake species 

will be shown in the pop-up list for “SPECIES”. There are 

type and species codes for lizards, salamanders, and small 

mammals. The list of options under “TYPE” can be modified 

to include other categories of animals, as necessary for the 

study.

7.1.2 Megafauna Data

Megafauna observations are recorded onto standardized 

megafauna forms on a daily basis on either paper or a 

handheld computer (fig. 18). The term “Megafauna” is used 

here to refer to any animal other than the reptiles, amphibians, 

and small mammals that are found in the pitfall traps. Signs 

from megafauna, such as tracks and scat, also may be 

recorded. Handheld computer users can record the megafauna 

records in a standard animal form by making a check mark 

next to the appropriate species. 

7.1.3 Weather Data

Weather observations are recorded onto standardized 

weather data forms on a daily basis on either paper data 

forms or on a handheld computer (see figs. 19 and 20). Air 

temperatures at a site may be recorded using a “Max/Min” 

thermometer or a temperature sensitive data logger. When 

collecting data on paper, the name of the site is recorded 

across the top of the page. The date and related weather 

variables are recorded in columns. When using the “Max/

Min” thermometers, the high and low temperatures over 

the previous 24 hours are recorded, along with the array 

number and site. The “Max/Min” thermometers must be 

reset daily. When using the data loggers, the unit is put into 

position on the opening day of the sample period and left 

alone for the duration. In addition to temperatures, a general 

weather condition is recorded daily: sunny, foggy, overcast, 

precipitation. The data loggers used to record environmental 

temperatures must be set up and downloaded using a computer 

and the related application (for example, HOBO data logger 

with Boxcar application). In our protocol, the loggers are 

programmed to gather temperature data every 15 minutes. 

At the end of the sample period, the logger is returned to the 

lab to be downloaded. Once the data have been downloaded, 

a graph of the temperatures during the sample period can be 

generated (fig. 21). 

The weather data form on the handheld computer is 

formatted in conjunction with the temperature data loggers. 

Therefore, the data fields are slightly different from those on 

the paper weather-data form. On the handheld computer, the 

:etiS amoL tP :etiS :etiS

Sample Period Start Date: 6/7/00 Sample Period Start Date: Sample Period Start Date:

:revresbO WS :revresbO :revresbO

?tneserP ?tneserP ?tneserP

reed eluM reed eluM reed eluM

etoyoC etoyoC etoyoC

xof yerG xof yerG xof yerG

xof deR xof deR xof deR

tacboB tacboB tacboB

noiL niatnuoM noiL niatnuoM noiL niatnuoM

regdaB regdaB regdaB

tibbarkcaJ tibbarkcaJ tibbarkcaJ

lerriuqs yerG lerriuqs yerG lerriuqs yerG

riuqs dnuorG ler lerriuqs dnuorG lerriuqs dnuorG

rennur daoR rennur daoR rennur daoR

liauQ liauQ5# yarra @ 3 liauQ

lwO gniworruB lwO gniworruB lwO gniworruB

Other Ground Bird Other Ground Bird Other Ground Bird

slammaM rehtO slammaM rehtO slammaM rehtO

Figure 18. Paper data form for recording megafauna captures.
7.0 Survey Data Management 27

Figure 19. Paper data form for recording weather conditions.

Figure 20. Handheld computer data form for recording weather conditions.

Site Pt Loma

Date: 6/8/99 6/9/99 6/10/99

Day: 1234 5 678 9 10

Array# 15

Max 1 25 20 22

Min 1 15 15 13

Array # 8

Max 2 23 22 25

Min 2 12 13 12

Array # 5

Max 3 24 22 23

Min 3 15 15 14

Weather * 1 2 2

* 1= sunny 3= overcast

2= foggy 4= precipitation

Site: Pt Loma___________

Date: _6/7/99_________ 

Conditions Start:

Conditions End: 

Notes: logger #3 @ array 5

sunny

foggy

overcast 

precipitation

data fields are Site, Date, Conditions Start, Conditions End, 

and Notes (fig. 20). On the day that the site is opened, the user 

must enter the name of the site. This name automatically will 

be carried over to the following weather records until the user 

changes the name of the site. The “Date” field is generated 

automatically based on the hand-held computer’s internal 

clock. “Conditions Start” and “Conditions End” are predefined 

pop-up lists from which the user can select a weather 

condition based on the same four categories described above: 

Sunny, foggy, overcast, precipitation. In the “Notes” field, 

those using handheld computers can record which data logger 

was used in the field and its corresponding array location.
28 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

 Date Temperature, 

 Degrees Celsius

8/28/2000 9:58 25.6

8/28/2000 10:13 28.3

8/28/2000 10:28 29.4

8/28/2000 10:43 30.3

8/28/2000 10:58 30.7

8/28/2000 11:13 31.9

8/28/2000 11:28 28.3

8/28/2000 11:43 27.5

8/28/2000 11:58 27.1

8/28/2000 12:13 27.1

8/28/2000 12:28 26.7

8/28/2000 12:43 26.7

8/28/2000 12:58 27.1

8/28/2000 13:13 27.1

8/28/2000 13:28 27.1

8/28/2000 13:43 27.1

8/28/2000 13:58 27.1

8/28/2000 14:13 27.5

8/28/2000 14:28 27.5

8/28/2000 14:43 27.5

8/28/2000 14:58 27.5

8/28/2000 15:13 27.9

8/28/2000 15:28 27.9

8/28/2000 15:43 27.5

8/28/2000 15:58 27.5

8/28/2000 16:13 27.5

8/28/2000 16:28 27.5

8/28/2000 16:43 26.3

8/28/2000 16:58 26.7

8/28/2000 17:13 27.9

8/28/2000 17:28 27.9

8/28/2000 17:43 27.9

8/28/2000 17:58 27.5

8/28/2000 18:13 26.7

8/28/2000 18:28 26.3

8/28/2000 18:43 25.9

8/28/2000 18:58 25.6

8/28/2000 19:13 25.2

8/28/2000 19:28 24.8

8/28/2000 19:43 24.4

8/28/2000 19:58 24.0

8/28/2000 20:13 24.0

8/28/2000 20:28 23.6

8/28/2000 20:43 23.2

8/28/2000 20:58 23.2

8/28/2000 21:13 22.8

8/28/2000 21:28 22.8

8/28/2000 21:43 22.8

8/28/2000 21:58 22.4

Pt. Loma Array #15

0

5

10

15

20

25

30

35

40

8/28/00 8/30/00 9/1/00 9/3/00 9/5/00 9/7/00 9/9/00

Date

Temperature, degrees Celsius

Figure 21. Tabular and graphical displays of temperature patterns for a sampling period.
7.0 Survey Data Management 29

7.2 Quality Assurance/Quality Control

Multiple levels of review ensure a high standard of 

quality assurance and control of field data. First is a sameday review of the data sheets (or handheld forms) by the field 

technician. This should be done immediately after returning 

from the field while the captures from the field day are still 

fresh in the technician’s mind. A second review of the data is 

conducted after the sample period when entering the data into 

a spreadsheet to go into the main database. Data are proofed 

to ensure that the spreadsheet data accurately mirrors the data 

collected from the field. 

 Additional proofing of the data involves checking the 

accuracy of the toe-clip numbers. The species records and 

toe-clip charts are compared to ensure that all numbers that 

were used in the field were marked as used and removed from 

the list. Next, toe-clip numbers are checked for replication. 

If the same toe-clip number was used twice for the same 

species, this is documented in the notes field of each animal. 

Lastly, the data are checked to make sure that the correct 

toe-clip numbers were used with the correct species. Any 

abnormalities are checked with the field technician, noted, and 

(or) corrected. 

The animal data are proofed also, which includes 

reviewing species identifications and measurement data. 

Questions such as “Are weight and length measurements 

appropriate for the species?” or “Was a decimal point put in 

the wrong place?” are answered. The tissue vials are checked 

for accuracy against the animal records.

The remainder of the data are then checked for 

completeness and accuracy. For example, the data are 

checked to verify that each sample day of the sample period 

is represented in the data. If a date is not accounted for, the 

data are reviewed to determine if there were no captures for 

that day. If, indeed, there were no animal captures for a day in 

the sample period, a new record is added to the data set that 

consists of the date, the name of the site, the field technician, 

and the note “No Captures”. This record is needed to maintain 

an accurate account of the effort that has been put forth when 

calculating capture rates.

Once the data have been checked for accuracy, they are 

sorted by animal type (herpetofauna, small mammals, and 

megafauna). The data for each category of animal are added to 

the main database for each animal type.

7.3 Data Organization and Summarization

The data organization and summarization methods 

presented here are based on the use of Microsoft Excel 

spreadsheets and the tools and functions available within them. 

Newer data storage programs are available and should be 

reviewed for their potential advantages.

The reptile and amphibian data for the site are stored 

as Microsoft Excel files. Examples of raw data files for 

animal records are given in tables 4 and 5. A map of the 

study site showing the general location of the arrays can be 

generated using a topographic mapping program such as 

TOPO! (Wildflower Productions, San Francisco, California) 

or other geographic information system program (fig. 22). 

Other metadata important to maintain includes the latitude 

and longitude of each array, the sampling history of the site, 

the number of days the site has been sampled, and a brief 

description of the site (table 6). 

Tables in Microsoft Excel are useful for reviewing and 

summarizing survey data. “Species by Array Tables” can be 

generated to count the number of times that each species has 

been documented at each array. We generate “Species by 

Array Tables” for the small mammals and herpetofauna at 

each study site (tables 7 and 8, respectively). Tables can be 

generated to analyze the captures for a single sampling period 

or from multiple sampling periods. They can be manipulated 

to reflect specific conditions in any of the data fields, such as 

removing and calculating the number of recaptures.

The reptile and amphibian species detected using our 

pitfall trapping technique can be compared with the species 

known to have existed previously at a study site. For example 

in Point Loma, near San Diego, California, a significant 

record exists for just such a comparison (L.M. Klauber, San 

Diego Natural History Museum, unpub. field notes, 1923–40). 

After several years of surveying, we have not captured five 

of the snake species and two of the lizard species that were 

known to occur at the site historically. These seven species of 

reptiles represent over 30 percent of the species documented 

at Point Loma in the 1940s. While it is difficult to say for 

sure that these species have been extirpated from the study 

site, it can be argued that they no longer are present. First, 

to date, there have been 320 sample days at this study site 

(table 6) containing 17 pitfall trap arrays. With seven pitfall 

traps and three funnel traps per array, this is equivalent to 

38,080 pitfall trap days and 16,320 funnel trap days. This 

represents a significant sampling effort using a technique that 

has successfully captured these species at other study sites. 

Second, targeted searches were conducted using specialized 

techniques that still did not detect these species. These types 

of historical comparisons are important for documenting local 

and regional species declines. They serve to bring attention 

to species that may be particularly vulnerable to human 

disturbance or habitat fragmentation. These analyses may 

stimulate further research, monitoring, and protection for 

focal species and aid those responsible for making land- and 

resource-management decisions. 

Additional summarization may include calculating an 

index of relative abundance for each species between arrays 

within a study site or among study sites. The comparison 

within a site can be accomplished by dividing the data in 

table 8 (with animals recaptured within each sample period 

removed) by the number of sampling days from table 6. 
30 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California Table 4. Reptile and amphibian data spreadsheet. [Reptile and amphibian data as transcribed from a paper data sheet are stored in a Microsoft Excel spreadsheet. See the appropriate section within appendix 2 for the abbreviations or codes and their explanations. g, gram; mm, millimeter; CNHY, Cnemidophorus hyperythrus; SCOC, Sceloporus occidentalis; ELMU, Elgaria multicarinata; CRVI, Crotalus viridis; UTST, Uta stansburiana; R, released; D, dead; M, male; F, female; ?, unknown; A, adult; J, juvenile; N, no; Y, yes; SB, Shane Bagnall; SW, Samantha Weber] Date Site name Array No. Bucket Snake trap Species Sex Age Weight (g) Length (mm) Toe-clip No. Recap (?) Collector’s initials Dispo- sition Tissue (?) Sample No. Notes 08-01-95 Point Loma 1 2B CNHY

M

A 6.0 58 0001

N SB-SW

R

Y 1

08-01-95 Point Loma 2 3B SCOC ? J 0.6 26 0001

N SB-SW

R

Y 1

08-01-95 Point Loma 4 1B ELMU ? A 24.0 122 0001

N SB-SW

R

Y 1

08-01-95 Point Loma 5 3 CRVI ? A

N SB-SW

R

N 1 Trapped with 

live shrew

08-01-95 Point Loma 5 3B SCOC

F

A 10.0 65 0004

N SB-SW

R

N 1

08-01-95 Point Loma 5 3B SCOC

M

A 12.0 67 0005

N SB-SW

R

Y 1

08-01-95 Point Loma 6 2A SCOC ? J 0.8 25 0010

N SB-SW

R

Y 1

08-01-95 Point Loma 6 3A UTST

M

A 3.5 46 0001

N SB-SW

R

Y 1

08-01-95 Point Loma 6 3B UTST

M

A 4.5 50 0002

N SB-SW

R

Y 1

08-01-95 Point Loma 8 1B ELMU ? A 34.0 114 0002

N SB-SW

R

Y 1

08-01-95 Point Loma 9 1 CNHY

F

A 6.0 55 0002

N SB-SW

R

Y 1

08-01-95 Point Loma 10

C SCOC ? J 0.8 23 0011

N SB-SW

R

Y 1

08-01-95 Point Loma 11 1B SCOC ? J 1.0 27 0012

N SB-SW

R

Y 1

08-01-95 Point Loma 13 1B SCOC ? J 0.5 29 0002

N SB-SW

R

Y 1

08-01-95 Point Loma 13

C SCOC

M

A 8.0 63 0003

N SB-SW

R

Y 1

08-02-95 Point Loma 3 3C CNHY

F

A 4.5 61 0003

N SB-SW

R

Y 1

08-02-95 Point Loma 4 1A ELMU ? J 14.0 87 0003

N SB-SW

R

Y 1

08-02-95 Point Loma 7 C ELMU ? A 39.5 132 0004

N SB-SW

R

Y 1

08-02-95 Point Loma 14 1A UTST ? A 8.5 48 0003

N SB-SW

R

Y 1

08-03-95 Point Loma 3 2A UTST ? J 0.6 22 0004

N SB-SW

R

Y 1

08-03-95 Point Loma 7 C SCOC

M

A 10.5 71 0013

N SB-SW

R

Y 1

08-03-95 Point Loma 12 1 ELMU ? A 25.0 114 0005

N SB-SW

R

Y 1
7.0 Survey Data Management 31

Table 5. Small mammal data spreadsheet.[Small mammal data are transcribed from a paper data sheet and stored in a Microsoft Excel spreadsheet. See the appropriate section within appendix 2 for the abbreviations or codes and their explanations. g, gram; mm, millimeter; NOCR, Notiosorex crawfordi; PECA, Peromyscus californicus; MICA, Micorotus californicus; AB, Anita Burkett; R, released; D, dead; ?, unknown; A, adult; J, juvenile; N, no; Y, yes]

Date Site name Array No. Bucket Snake trap Species Sex Age Weight (g) Length (mm) Toe-clip No. Recap (?) Collector’s initials Dispo- sition Tissue (?) Sample No. Notes

06/02/98 Point Loma 3 1A NOCR ? ? ? AB R N 16

06/02/98 Point Loma 9 C NOCR ? ? ? AB R N 16

06/02/98 Point Loma 12 C PECA ? ? ? AB R N 16

06/02/98 Point Loma 12 3B PECA ? ? ? AB R N 16

06/03/98 Point Loma 14 1A NOCR ? ? ? AB D Y 16 Eaten

06/03/98 Point Loma 14 1A NOCR ? ? ? AB R N 16

06/03/98 Point Loma 10 1A NOCR ? ? ? AB R N 16

06/03/98 Point Loma 12 2B PECA ? A ? AB R N 16

06/04/98 Point Loma 10 1A NOCR ? ? ? AB D Y 16

06/04/98 Point Loma 14 1A NOCR ? ? ? AB R N 16

06/04/98 Point Loma 1 3A PECA ? ? ? AB R N 16

06/04/98 Point Loma 15 1A NOCR ? ? ? AB R N 16

06/04/98 Point Loma 5 3A NOCR ? ? ? AB R N 16

06/04/98 Point Loma 7 2A NOCR ? ? ? AB R N 16

06/04/98 Point Loma 10 C NOCR ? ? ? AB R N 16

06/04/98 Point Loma 10 2B MICA ? ? ? AB R N 16

06/04/98 Point Loma 9 C NOCR ? ? ? AB R N 16

06/04/98 Point Loma 8 3 PECA ? A ? AB R N 16

06/05/98 Point Loma 9 C NOCR ? ? ? AB R N 16

06/05/98 Point Loma 12 C PECA ? A ? AB R N 16

06/06/98 Point Loma 7 1A NOCR ? ? ? AB R N 16

06/06/98 Point Loma 7 1B NOCR ? ? ? AB R N 16

06/06/98 Point Loma 12 3B PECA ? J ? AB R N 16

06/06/98 Point Loma 12 3B PECA ? J ? AB R N 16

06/06/98 Point Loma 12 C PECA ? ? ? AB R N 16

06/06/98 Point Loma 12 3A NOCR ? ? ? AB R N 16

06/06/98 Point Loma 10 1B NOCR ? ? ? AB R N 16
32 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Figure 22. Example site map.
7.0 Survey Data Management 33

Table 6. Site location file. 

[For each study site, a location file is generated, containing information on the sampling history of the site, array locations, and a brief account of the study site 

and the parties responsible. If the equipment in the field is sensitive or relates to sensitive species, the accuracy of array locations, latitude and longitude, may 

need to be reduced to protect the integrity of the study. In cases where the data will be available to the public, asterisks may be used to show the precision of the 

coordinate positions have been reduced to protect the equipment in the field.] 

Site name: Point Loma Ecological Reserve

County: San Diego

Responsible parties: National Park Service

Contact: ####### #####

Phone: (###) ###-####

Description: Elevation 22–113 meters. This site is a medium size fragment with arrays sampling 116 hectares and is 

isolated by urban areas from any other natural lands. The majority of the habitat present is maritime 

succulent scrub and coastal sage scrub. Some chamise chaparral, grassland and a wash are present 

also. The Point Loma research area is internally subdivided by roads and buildings, and has a lot of 

public activity. Point Loma is part of a joint federal partners planning area.

Start dates for Sample Periods:

08-01-95 02-20-96 02-18-97 02-03-98 01-27-99 02-09-00 02-21-01

09-12-95 04-23-96 04-22-97 03-31-98 04-06-99 04-05-00 06-21-01

11-13-95 06-25-96 06-24-97 06-02-98 06-08-99 06-06-00 07-30-01

08-27-96 09-03-97 08-04-98 08-18-99 08-29-00 08-28-01

10-29-96 10-28-97 10-06-98 11-10-99 11-10-00 10-23-01

11-27-01

12-18-01

Number of Sample Days: 320

Location:

Array Latitude

(N)

Longitude

(W)

Latitude

(N)

dec.

Longitude

(W)

dec.

Elevation

(meter) Datum

1 32°40'**.** 117°14'**.** 32.683** 117.247** 26 NAD 83

2 32°40'**.** 117°14'**.** 32.672** 117.244** 22 NAD 83

3 32°40'**.** 117°14'**.** 32.667** 117.242** 22 NAD 83

4 32°40'**.** 117°14'**.** 32.668** 117.242** 33 NAD 83

5 32°41'**.** 117°14'**.** 32.695** 117.242** 83 NAD 83

6 32°41'**.** 117°14'**.** 32.695** 117.243** 82 NAD 83

7 32°41'**.** 117°14'**.** 32.694** 117.243** 90 NAD 83

8 32°42'**.** 117°15'**.** 32.703** 117.253** 33 NAD 83

9 32°40'**.** 117°14'**.** 32.674** 117.244** 42 NAD 83

10 32°42'**.** 117°15'**.** 32.705** 117.253** 35 NAD 83

11 32°41'**.** 117°14'**.** 32.684** 117.247** 37 NAD 83

12 32°41'**.** 117°14'**.** 32.683** 117.247** 31 NAD 83

13 32°40'**.** 117°14'**.** 32.669** 117.241** 109 NAD 83

14 32°40'**.** 117°14'**.** 32.670** 117.241** 113 NAD 83

15 32°40'**.** 117°14'**.** 32.668** 117.238** 54 NAD 83

16 32°40'**.** 117°14'**.** 32.669** 117.238** 55 NAD 83

17 32°40'**.** 117°14'**.** 32.675** 117.237** 37 NAD 83
34 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Table 7. Summary of small mammal species captured at each pitfall array. 

[Small mammal captures can be viewed as the number of times each species was detected at each array.] 

Species

Array No.

Total

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Woodrat 1 1

Neotoma species

Desert woodrat 1 1

Neotoma lepida

Deer mouse 3 5 6 1 4 9 4 4 4 4 6 1 1 52

Peromyscus species

Deer mouse 2 1 1 3 1 3 1 12

Peromyscus maniculatus

California mouse 6 3 4 12 9 4 6 8 20 3 3 15 12 3 3 5 6 122

Peromyscus californicus

Cactus mouse 4 7 1 2 1 1 7 4 1 2 2 3 1 3 39

Peromyscus eremicus

Desert shrew 3 13 7 10 15 1 32 32 25 29 15 25 8 34 11 9 12 281

Notiosorex crawfordi

Ornate shrew 1 2 1 2 2 1 2 1 1 1 14

Sorex ornatus

Unknown shrew 1 2 2 1 2 13

California vole 1 1 1 2 2 2 4 10 6 9 1 1 1 1 42

Microtus californicus

Western harvest mouse 4 2 4 2 23 5 18 15 15 25 17 12 2 5 3 1 153

Reithrodontomys megalotis

Kangaroo rat 1 1 2

Dipodomys species

Desert cottontail 1 1 2

Sylvilagus audubonii

Pocket mouse 1 2 5 2 1 1 12

Chaetodipus species

California pocket mouse 2 3 1 1 1 8

Chaetodipus californicus

San Diego pocket mouse 1 1 2

Chaetodipus fallax

Little pocket mouse 2 2

Perognathus longimembris

House mouse 1 1 1 3

Mus musculus

Unknown mammal 2 2

Unknown mouse 1 1 1 3 6

Unknown rodent 3 2 2 1 4 6 1 1 2 54

Number of individuals 22 34 25 40 58 16 73 77 76 88 50 70 29 48 32 21 31 827
7.0 Survey Data Management 35

Table 8. Summary of reptile and amphibian species captured at each pitfall array. 

[Reptile and amphibian captures can be viewed as the number of times each species was detected at each array.] 

Species

Array No.

Total

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Salamander

Garden slender salamander 5 2 8 5 36 2 19 4 1 3 1 3 89

Batrachoseps major

Lizard

California legless lizard 2 1 3

Anniella pulchra

Southern alligator lizard 10 16 25 17 2 6 4 7 7 13 16 22 8 11 7 3 174

Elgaria multicarinata

Western skink

Eumeces skiltonianus

Orange-throated whiptail 65 28 153 46 1 1 2 19 7 3 1 29 55 24 27 11 472

Cnemidophorus hyperythrus

Western fence lizard 18 13 54 48 30 18 33 25 28 14 23 18 53 65 40 36 36 552

Sceloporus occidentalis

Side-blotched lizard 6 42 39 22 52 80 13 4 6 6 2 3 19 49 43 25 23 434

Uta stanburiana

Coast horned lizard

Phrynosoma coronatum

Snake

California glossy snake

Arizona elegans

Western yellow-bellied racer

Coluber constrictor

Western ringneck snake 1 1 2 2 1 7

Diadophis punctatus

Night snake 1 1

Hypsiglena torquata

California kingsnake 1 2 1 1 5

Lampropeltis getula

Coachwhip/red racer

Masticophis flagellum

Striped racer 3 1 3 1 4 3 4 7 5 1 1 3 3 3 1 43

Masticophis lateralis

San Diego gopher snake 1 1 1 1 1 1 6

Pituophis catenifer

Long-nosed snake

Rhinocheilus lecontei

Red diamond rattlesnake

Crotalus ruber

Southern Pacific rattlesnake 1 2 1 1 1 6

Crotalus viridis

Total Individuals 103 109 280 135 91 101 64 46 106 44 64 43 129 183 122 97 78 1,795

Total Species 6 10 8 6 6 4 6 8 8 8 7 6 8 6 6 6 7 12
36 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

This produces a daily average capture rate for each species 

at each array and across the site as a whole (table 9). In 

this example, the data are averaged for the entire site. For a 

comparison of capture rates between sites, one must consider 

the number of arrays at the sites being compared. For example, 

the Point Loma site has 17 study arrays, Mission Trails 

Regional Park has 5 arrays, and the San Diego Wild Animal 

Park has 20 arrays. To correct for this difference, the total 

capture rate per species per day is divided by the number of 

arrays at the study site. Table 10 shows the comparison of the 

three sites noted above (Point Loma, Mission Trails Regional 

Park, and San Diego Wild Animal Park).

7.4 Data Analysis

Data generated from the described survey methods can 

be used to address a variety of conservation or management 

questions. Because the pitfall array method is a passive 

method of sampling smaller terrestrial vertebrates, the bias 

is eliminated from observer variability. This is particularly 

beneficial for studies over large landscapes and timescales, 

where many people are involved in field sampling. 

Data can be used to learn important demographic and 

life history information for species, such as reproductive 

cycles, age class characteristics, seasonal activity patterns, 

survivorship, species interactions, and habitat associations 

(Fisher and others, 2002; Williams and others, 2002). 

Species-specific mark-recapture models can be assessed to 

understand population dynamics and demography and to test 

specific ecological hypotheses (White and Burnham, 1999; 

Burnham and Anderson, 2002; and Amstrup and others, 

2005). Likewise, single and multi-state occupancy models 

can be used to understand species metapopulation and patch 

occupancy dynamics (MacKenzie and others, 2006).

Multivariate statistics can be used to model small 

terrestrial vertebrate community composition and biodiversity 

patterns (Clarke and Warwick, 2001; McCune and Grace, 

2002; Clarke and others, 2006). Dodd and others (2007) used 

these types of methods to show changes in the reptile and 

amphibian communities of northwest Florida over a 28-year 

period.

Using these and other types of analyses, scientifically 

robust sampling programs can be designed to define suitable 

habitat, as well as to understand the effects of landscape 

characteristics, environmental factors, non-native species, 

large scale disturbance, human effects, and management 

actions on wildlife populations. These programs are useful in 

an adaptive monitoring and management approach. Findings 

from monitoring studies can lead to specific management 

recommendations. In turn, the effectiveness of management 

actions can be tested by continued monitoring, resulting in 

a science-management feedback loop (Williams and others, 

2002). 

The pitfall array, as described in this report, is a proven, 

effective, and unbiased sampling tool that is valuable for a 

multitude of research projects. Before beginning a project, 

it is important to define the research objectives, the study 

design, and the planned analytical treatments. Ecology and 

statistical texts can give more information on experimental 

design and statistical analyses of data (for example, Maxwell 

and Delaney, 2000; Clarke and Warwick, 2001; Williams and 

others, 2002; MacKenzie and others, 2006). 

8.0 Acknowledgments

We thank B. Metts, P. Medica, J. Lovich, E. Muths, 

and A. Backlin for feedback on the earlier versions of this 

manuscript. Their comments and suggestions greatly improved 

the final version of this report.
8.0 Acknowledgments 37

Table 9. Capture rate. [Average capture rate per day can be calculated to show relative abundance of each species at each array and across the study site as a whole.]

Species

Array No.

Total

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

SalamanderGarden slender salamander 0.017 0.007 0.027 0.017 0.122 0.007 0.065 0.014 0.003 0.010 0.003 0.010 0.018

Batrachoseps major

LizardCalifornia legless lizard 0.007 0.003 0.001

Anniella pulchra

Southern alligator lizard 0.034 0.054 0.082 0.054 0.007 0.020 0.014 0.024 0.024 0.041 0.051 0.075 0.027 0.037 0.020 0.010 0.034

Elgaria multicarinata

Western skink

Eumeces skiltonianus

Orange-throated whiptail 0.218 0.095 0.510 0.153 0.003 0.003 0.007 0.061 0.024 0.010 0.003 0.099 0.184 0.082 0.088 0.037 0.093

Cnemidophorus hyperythrus

Western fence lizard 0.058 0.044 0.167 0.143 0.095 0.054 0.105 0.082 0.095 0.044 0.078 0.054 0.177 0.214 0.126 0.119 0.122 0.105

Sceloporus occidentalis

Side-blotched lizard 0.017 0.129 0.119 0.065 0.173 0.255 0.037 0.010 0.007 0.017 0.007 0.007 0.058 0.153 0.129 0.075 0.075 0.078

Uta stanburiana

Coast horned lizard

Phrynosoma coronatum

SnakeCalifornia glossy snake

Arizona elegans

Western yellow-bellied racer

Coluber constrictor

Western ringneck snake 0.003 0.007 0.007 0.003 0.001

Diadophis punctatus

Night snake 0.003 0.000

Hypsiglena torquata

California kingsnake 0.003 0.007 0.003 0.003 0.001

Lampropeltis getula

Coachwhip/red racer

Masticophis flagellum

Striped racer 0.010 0.003 0.010 0.003 0.014 0.010 0.014 0.024 0.017 0.003 0.003 0.010 0.010 0.010 0.003 0.009

Masticophis lateralis

San Diego gopher snake 0.003 0.003 0.003 0.003 0.003 0.003 0.001

Pituophis catenifer

Long-nosed snake

Rhinocheilus lecontei

Red diamond rattlesnake

Crotalus ruber

Southern Pacific rattlesnake 0.007 0.003 0.003 0.003 0.001

Crotalus viridis
38 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Table 10. Average capture rate table. 

[A comparison of average capture rates (per array per day) for 19 species among three study sites. 

Standard errors could be included for statistical comparison.]

Species

Average capture rate per array per day 

Point Loma San Diego Wild 

Animal Park

Mission Trails 

Regional Park

Salamander

Garden slender salamander 0.0178 0.0052

Batrachoseps major

Lizard

California legless lizard 0.0006 0.0018

Anniella pulchra

Southern alligator lizard 0.0338 0.0084 0.0324

Elgaria multicarinata

Western skink 0.0332 0.0324

Eumeces skiltonianus

Orange-throated whiptail 0.0928 0.5100 0.1853

Cnemidophorus 

hyperythrus

Western fence lizard 0.1046 0.0703 0.1118

Sceloporus occidentalis

Side-blotched lizard 0.0784 0.0474 0.0647

Uta stanburiana

Coast horned lizard 0.0215

Phrynosoma coronatum

Snake

California glossy snake

Arizona elegans

Western yellow-bellied racer

Coluber constrictor

Western ringneck snake 0.0012 0.0011

Diadophis punctatus

Night snake 0.0002 0.0002

Hypsiglena torquata

California kingsnake 0.0010 0.0065

Lampropeltis getula

Coachwhip/Red racer 0.0008

Masticophis flagellum

Striped racer 0.0086 0.0189 0.0059

Masticophis lateralis

San Diego gopher snake 0.0012 0.0045

Pituophis catenifer

Long-nosed snake 0.0019

Rhinocheilus lecontei

Red diamond rattlesnake 0.0048 0.0029

Crotalus ruber

Southern Pacific rattlesnake 0.0010 0.0013

Crotalus viridis
9.0 References Cited 39

9.0 References Cited

Amstrup, S.C., McDonald, T.L., and Manly, B.F., 2005, 

Handbook of capture-recapture analysis: Princeton, New 

Jersey, Princeton University Press, 313 p.

Banta, B.H., 1957, A simple trap for collecting desert reptiles: 

Herpetologica, v. 13, p. 174-176.

Banta, B.H., 1962, A preliminary account of the herpetofauna 

of the Saline Valley hydrographic basin, Inyo County, 

California: The Wasmann Journal of Biology, v. 20, 

p. 161-251.

Bennett, D.H., Gibbons, J.W., and Franson, J.C., 1970, 

Terrestrial activity of aquatic turtles: Ecology, v. 51, no. 4, 

p. 738-740.

Bostic, D.L., 1965, Home range of the Teiid lizard, 

Cnemidophorus hyperythrus beldingi: The Southwestern 

Naturalist, v. 10, no. 4, p. 278-281.

Burke, V.J., Rathbun, S.L.. Bodie, J.R., and Gibbons, J.W., 

1998, Effect of density on predation rate for turtle nests in a 

complex landscape: Oikos, v. 83, p. 3-11.

Bostic, D.L., 1965, Home range of the Teiid lizard, 

Cnemidophorus hyperythrus beldingi: The Southwestern 

Naturalist, v. 10, no. 4, p. 278-281.

Burkett, D.W., and Thompson, B.C., 1994, Wildlife 

association with human-altered water sources in semiarid 

vegetation communities: Conservation Biology, v. 8, p. 

682-690.

Burnham, K.P., and Anderson, D.R., 2002, Model selection 

and multimodel inference. A Practical InformationTheoretical Approach (2nd ed.): Springer-Verlag, New 

York, 448 p.

Bury, R.B., and Corn, P.S., 1987, Evaluation of pitfall trapping 

in northwestern forests: Trap arrays with drift fences: 

Journal of Wildlife Management, v. 51, p. 112-119.

Cagle, F.R., 1939, A system for marking turtles for future 

identification: Copeia, v. 1939, p. 170-173.

Campbell, H.W. and Christman, S.P., 1982, Field techniques 

for herpetofaunal community analysis, in Scott, N.J., Jr., 

ed., Herpetological communities: U.S. Fish and Wildlife 

Service Wildlife Research Report 13, p. 193-200.

Case, T.J. and Fisher, R.N., 2001, Measuring and predicting 

species presence: Coastal sage scrub case study, in

Hunsaker, C.T., Goodchild, M.F., Friedl, M.A. and Case, 

T.J., eds., Spatial Uncertainty in Ecology: Springer-Verlag, 

New York, p. 47-71.

Clarke, K.R., Somerfield, P.J., and Chapman, M.G., 2006, 

On resemblance measures for ecological studies, including 

taxonomic dissimilarities and a zero-adjusted BrayCurtis coefficient for denuded assemblages: Journal of 

Experimental Marine Biology and Ecology, v. 330, p. 55-80.

Clarke, K.R., and Warwick, R.M., 2001, Change in marine 

communities. An approach to statistical analysis and 

interpretation, (2nd ed): PRIMER-E, Plymouth, UK, 172 p.

Corn, P.S., and Bury, R.B., 1990, Sampling methods for 

terrestrial amphibians and reptiles: U.S. Department of 

Agriculture Forest Service General Technical Report PNWGTR-256, 34 p.

Corn, P.S., 1994, Straight-line drift fences and pitfall traps, in

Heyer, W.R., Donnelly, M.A., McDiarmid, R.W., Hayek, 

L.C., and Foster, M.S., eds., Measuring and monitoring 

biological diversity—Standard Methods for Amphibians: 

Smithsonian Institution Press, Washington, D.C., 

p. 109-117.

Crawford, E., and Kurta, A., 2000, Color of pitfall affects 

trapping success for anurans and shrews: Herpetological 

Review, v. 31, no. 4, p. 222-224.

DeGraaf, R.M., and Rudis, D.D., 1990, Herpetofaunal species 

composition and relative abundance among three New 

England forest types: Forest Ecology and Management 

v. 32, p. 155-165.

Dodd, C.K., Jr., 1992, Biological diversity of a temporary 

pond herpetofauna in north Florida sandhills: Biodiversity 

and Conservation v. 1, p. 125-142.

Dodd, C.K., Jr., 1994, Monitoring and protecting biotic 

diversity, in Majumdar, S.K., Brenner, F.J., Lovich, J.E., 

Schalles, J.F., and Miller, E.W., eds., Biological diversity—

Problems and challenges: Pennsylvania Academy of 

Science, Easton, Pennsylvania, p. 1-11. 

Dodd, C.K., Jr., Barichivich, W.J., Johnson, S.A., and Staiger, 

J.S., 2007, Changes in a northwestern Florida Gulf Coast 

herpetofaunal community over a 28-y period: American 

Midland Naturalist, v. 158, p. 29-48.

Dodd, C.K., Jr., and Scott, D.E., 1994, Drift fences encircling 

breeding sites, in Heyer, W.R., Donnelly, M.A., McDiarmid, 

R.W., Hayek, L.C., and Foster, M.S., eds., Measuring and 

monitoring biological diversity—Standard methods for 

amphibians: Smithsonian Institution Press, Washington, 

D.C., p. 125-130.

Douglas, M.E., 1979, Migration and sexual selection in 

Ambystoma jeffersonianum: Canandian Journal of Zoology, 

v. 57, no. 12, p. 2303-2310.
40 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Enge, K.M., 1997, Use of silt fencing and funnel traps for drift 

fences: Herpetological Review, v. 28, no. 1, p. 30-31. 

Enge, K.M., 2001, The pitfalls of pitfall traps: Journal of 

Herpetology, v. 35, p. 467-478.

Fair, W.S., and Henke, S.E., 1997, Efficacy of capture methods 

for a low density population of Phrynosoma cornutum: 

Herpetological Review, v. 28, no. 3, p. 135-137. 

Fellers, G.M., and Pratt, D., 2002, Terrestrial vertebrate 

inventory, Point Reyes National Seashore, 1998-2001: 

National Park Service Report. 73 p.

Fisher, R.N., and Case, T.J., 1997, A field guide to the reptiles 

and amphibians of coastal southern California: Lazer Touch, 

San Mateo, California. 46 p.

Fisher, R.N., and Case, T. J., 2000, Distribution of the 

herpetofauna of coastal southern California with reference 

to elevation effects, in Keeley, J.E., Baer-Keeley, M., and 

Fotheringham, C.J., eds., Second interface between ecology 

and land development in California: U.S. Geological Survey 

Open-File Report 00-62, p. 137-143.

Fisher, R.N., and Shaffer, H.B., 1996, The decline 

of amphibians in California’s great central valley: 

Conservation Biology, v. 10, p. 1387-1397.

Fisher, R.N., Suarez, A.V., and Case, T.J., 2002, Spatial 

patterns in the abundance of the coastal horned lizard: 

Conservation Biology, v.16, p. 205-215.

Fitch, H.S., 1951, A simplified type of funnel trap for reptiles: 

Herpetologica, v. 7, p. 77-80.

Friend, G.R., 1984, Relative abundance of two pitfall-drift 

fence systems for sampling small vertebrates: Australian 

Zoologist, v. 21, no. 5, p. 423-434.

Gibbons, J.W., 1970, Terrestrial activity and the population 

dynamics of aquatic turtles: American Midland Naturalist, 

v. 83, no. 2, p. 404-414.

Gibbons, J.W. and Bennett, D.H., 1974, Determination of 

anuran terrestrial activity patterns by a drift fence method: 

Copeia, v. 1, p. 236-243.

Gibbons, J.W., and Semlitsch, R.D., 1981, Terrestrial drift 

fences with pitfall traps—An effective technique for 

quantitative sampling of animal populations: Brimleyana, 

v. 7, p. 1-16.

Gill, D.E., 1978, The metapopulation ecology of the redspotted newt, Notophthalmus viridescens (Rafinesque): 

Ecological Monographs, v. 48, no. 2, p. 145-166.

Gloyd, H.K., 1947, Some rattlesnake dens of South Dakota: 

Chicago Naturalist v. 9, p. 87-97.

Heyer, W.R., Donnelly, M.A., McDiarmid, R.W., Hayek, 

L.C., and Foster, M.S., 1994, Measuring and monitoring 

biological diversity—Standard methods for amphibians: 

Smithsonian Institution Press, Washington, D.C., 364 p.

Imler, R.I., 1945, Bullsnakes and their control on a Nebraska 

wildlife refuge: Journal of Wildlife Management v. 9, no. 4, 

p. 265-273. 

Ireland, T.T., Wolters, G.L., and Schemnitz, S.D., 1994, 

Recolonization of wildlife on a coal strip-mine in 

northwestern New Mexico: Southwestern Naturalist, v. 39, 

p. 53-57.

Jockusch, E.L., and Wake, D.B., 2002, Falling apart 

and merging—Diversification of slender salamanders 

(Plethodontidae—Batrachoseps) in the American West: 

Biological Journal of the Linnean Society, v. 76, p. 361-391.

Jones, K.B., 1981, Effects of grazing on lizard abundance and 

diversity in western Arizona: Southwestern Naturalist, v. 26, 

p. 107-115.

Jorgensen, E.E., Vogel, M., and Demarais, S. A., 1998, A 

comparison of trap effectiveness for reptile sampling: Texas 

Journal of Science, v. 50, no. 3, p. 235-242. 

Laakkonen, J., Fisher, R.N., and Case, T.J., 2001, Effect of 

land cover, habitat fragmentation, and ant colonies on the 

distribution and abundance of shrews in southern California: 

Journal of Animal Ecology, v. 70, p. 776-788.

Loredo, I., Vuren, D.V., and Morrison, M. L., 1996, 

Habitat use and migration behavior of the California 

tiger salamander: Journal of Herpetology, v. 30, no. 2, 

p. 285-288.

MacKenzie, D.I., Nichols, J.D., Royle, J.A., Pollock, K.H., 

Bailey, L.L., and Hines, J.E., 2006, Occupancy estimation 

and modeling—Inferring patterns and dynamics of species 

occurrence: Elsevier, San Diego, California, 324 p.

Mahoney, M.J., Parks, D.S.M., and Fellers, G.M., 2003, 

Uta stansburiana and Elgaria multicarinata on the 

California Channel Islands—Natural dispersal or artificial 

introduction: Journal of Herpetology, v. 37, p. 586-591.

Maldonado, J. E., Vila, C., and Wayne, R.K., 2001, Tripartite 

genetic subdivisions in the ornate shrew (Sorex ornatus): 

Molecular Ecology, v. 10, p. 127-147.

Maxwell, S.E., and Delaney, H.D., 2000, Designing 

experiments and analyzing data: Lawrence Erlbaum 

Associates, Inc., Mahwah, New Jersey, 902 p.

McCoy, E.D. and Mushinsky, H.R., 1994, Effects of 

fragmentation on the richness of vertebrates in the Florida 

scrub habitat: Ecology, v. 75, p. 446-457.
9.0 References Cited 41

McCune, B., and Grace, J.B., 2002, Analysis of ecological 

communities: MJM Press, Gleneden Beach, Oregon, 300 p.

Medica, P.A., Hoddenbach, G.A., and Lannom Jr., J.R., 1971, 

Lizard sampling techniques: Rock Valley Miscellaneous 

Publications no. 1, 55 p.

Milstead, W.W., 1953, Ecological distributions of the lizards 

of the La Mota Mountain region of Trans-Pecos Texas: 

Texas Journal of Science, v. 5, p. 403-415.

Murphy, C.G., 1993, A modified drift fence for capturing 

treefrogs: Herpetological Review, v. 24, no. 4, p. 143-145.

Nelson, D.H., and Gibbons, J.W., 1972, Ecology, abundance, 

and seasonal activity of the scarlet snake, Cemophora 

coccinea: Copeia, v. 1972, no. 3, p. 582-584.

Parker, W.S., 1972, Aspects of the ecology of a sonoran 

desert population of the western banded gecko, Coleonyx 

variegatus (Sauria, Eublepharinae): The American Midland 

Naturalist, v. 88, no. 1, p. 209-224.

Pearson, P.G., 1955, Population ecology of the spadefoot toad, 

Scaphiopus h. holbrooki (Harlan): Ecological Monographs, 

v. 25, no. 3, p. 233-267.

Richmond, J.Q. and Reeder, T.W., 2002, Evidence for 

parallel ecological speciation in the scincid lizards of the 

Eumeces skiltonianus species group (Squamata: Scincidae): 

Evolution, v. 56, p. 1498-1513.

Rice, C.G., Jorgensen, E.E., and Demarais, S., 1994, A 

comparison of herpetofauna detection and capture 

techniques in southern New Mexico: Texas Journal of 

Agriculture and Natural Resources, v. 7, p. 107-113.

Rudolph, D.C., and Dickson, J.G., 1990, Streamside zone 

width and amphibian and reptile abundance: The Southwest 

Naturalist, v. 35, p. 472-476.

Ryan, T.J., Philippi, T., Leiden, Y.A., Dorcas, M.E., Wigley, 

T.B., and Gibbons, J.W., 2002, Monitoring herpetofauna in 

a managed forest landscape—Effects of habitat types and 

census techniques: Forest Ecology and Management, v. 167, 

p. 83-90.

Sawyer, J.O., and Keeler-Wolf, T., 1995, A manual of 

California vegetation: California Native Plant Society, 

471 p.

Scott Jr., N.J., 1982, Herpetological communities—A 

symposium of the Society for the Study of Amphibians and 

Reptiles and the Herpetologists’ League, August 1977: U.S. 

Department of Interior Wildlife Research Report 13, 239 p.

Semlitsch, R.D., Brown, K.L., and Caldwell, J.P., 1981, 

Habitat utilization, seasonal activity, and population size 

structure of the southeastern crowned snake Tantilla 

coronata: Herpetologica, v. 37, no. 1, p. 40-46.

Shoop, C.R., 1965, Orientation of Ambystoma maculatum—

movements to and from breeding ponds: Science, v. 149, 

no. 3683, p. 558-559.

Stebbins, R.C., 1985, A field guide to western reptiles and 

amphibians: Houghton, Mifflin Co., Boston, Mass., 336 p.

Storm, R.M., and Pimental, R.A., 1954, A method for studying 

amphibian breeding populations: Herpetologica, v. 10, 

p. 161-166. 

Vogt, R.C., and Hine, R.L., 1982, Evaluation of techniques 

for assessment of amphibian and reptile populations 

in Wisconsin, in Scott, N.J., Jr. (ed), Herpetological 

Communities: U.S. Fish and Wildlife Service Wildlife 

Research Report 13, p. 201-217.

White, G.C. and Burnham, K.P., 1999, Program MARK: 

Survival estimation from populations of marked animals: 

Bird Study 46 Supplement, p. 120-138. Also available at 

http://www.warnercnr.colostate.edu/~gwhite/mark/mark.

htm

Williams, B.K., Nichols, J.D., and Conroy, M.J., 2002, 

Analysis and management of animal populations: Modeling, 

estimation, and decision making: Academic Press, San 

Diego, California, 817 p.

Woodbury, A.M., 1951, Symposium: A snake den in 

Tooele County, Utah—Introduction-a ten year study: 

Herpetologica, v. 7, no. 1, p. 4-14.

Woodbury, A.M., 1953, Methods of field study in reptiles: 

Herpetologica, v. 9, no. 2, p. 87-92.

Wygoda, M.L., 1979, Terrestrial activity of striped mud turtles, 

Kinosternon baurii (Reptilia, Testudines, Kinosternidae) in 

west-central Florida: Journal of Herpetology, v. 13, no. 4, 

p. 469-480.

Yunger, J.A., Brewer, R., and Snook, R., 1992, A method 

for decreasing trap mortality of Sorex: Canadian FieldNaturalist, v. 106, p. 249-251.

Zug, G.R., Lhon, W.Z., Min, T.Z., Kyaw, K., Thin, T., Win, H., 

Nyein, M.T.D., Aung, K., and Tin, K.T., 2001, Durability 

of silt-fencing for drift-fence arrays at a tropical site: 

Herpetological Review, v. 32, p. 235-236.
42 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

This page intentionally left blank.
Appendix 1 43

Appendix 1. Materials and supplies needed to build, maintain, and sample a pitfall trapping array. 

[in, inch; mm, millimeter; cm, centimeter; m, meter; gal, gallon; L, liter; max, maximum; min, minimum; %, percent] 

Site and equipment construction supplies

Funnel Trap

1.25-in. (32-mm) binder clips steel hog rings

0.25-in. (0.635-cm) mesh hardware cloth, 36-in. × 100-ft roll 

(91.45 cm × 30.48 m)

shake shingles, medium untreated or 0.75-in. (1.91-cm) plywood for 

desert sites

0.25-in. (0.635-cm) mesh hardware cloth, 24-in. × 100-ft roll 

(60.69 cm × 30.48 m)

tin snips

bailing wire

PVC "T" joint, 1.5-in. (3.81-cm) SSS for desert sites

hog ringer pliers

Drift Fence

shade cloth, 12-in. (30.48-cm) tall

staples

wooden stakes, 1 × 2 × 24 in. (2.54-cm × 5.08-cm × 60.96-cm)

heavy duty staple gun

scissors

Buckets and Lids

2- × 2-in. lumber (5.08 cm × 5.08 cm) 1.25-in. (3.18-cm) drywall screws 

5-gal (18.9-L) buckets SAE washers #10

6-gal (22.7-L) buckets bungee cords for desert site

plastic bucket lids marker to label buckets and lids

Tools

gloves pry bar/digging bar

spade shovel electric drill

pick axe circular saw

sledge hammer Phillips head drill bit

50-m tape measure 0.5-in. (1.27-cm) drill bit for desert sites

0.125-in. (0.318-cm) drill bit 2.25-in. (5.72-cm) drill bit for desert sites

Site Operation

cellulose sponges

max-min thermometer or temperature data logger

1.5-in. (3.81-cm) PVC pipe with foam insulation

1-in. (2.54-cm) PVC pipe

Field Kit Supplies

notebook selection of appropriately sized metric spring scales

lab marker snake bag

carrying case snake hook

large Tweezers small Tweezers

small re-closable plastic bags handheld computer

metric tape measure large re-closable plastic bags

straight microscissors appropriate data forms

water bottle for sponges ice chest with ice packs

50-ml tissue tubes with 70% ethanol clear plastic, metric ruler

fiberboard storage box and dividers fade resistant, water proof pen

1.5-ml tissue tubes with 95% ethanol appropriate wildlife field guides

extra snake bags or appropriate animal containers small spatula or cup for cleaning out debris from within pitfall traps 

or bailing out water

Weather Station

wood bolt, wood thread on one end and machine threat on the other

wing nut and washer to fit wood bold

2-in. PVC pipe
44 Herpetological Monitoring Using a Pitfall Trapping Design in Southern California

Category Code Scientific name Common name

Species

 Reptiles

Lizards

ANPU Anniella pulchra California Legless Lizard 

CNHY Cnemidophorus hyperythrus Orange-Throated Lizard

CNTI Cnemidophorus tigris Western Whiptail

COVA Coleonyx variegatus Western Banded Lizard

ELMU Elgaria multicarinata Southern Alligator Lizard

EUGI Eumeces gilberti Gilbert's Skink

EUSK Eumeces skiltonianus Western Skink

GAWI Gambelia wislizenii Long-Nosed Leopard 

Lizard

PHCO Phrynosoma coronatum Coast Horned Lizard

SCOC Sceloporus occidentalis Western Fence Lizard

SCOR Sceloporus orcutti Granite Spiny Lizard

UTST Uta stansburiana Side-Blotched Lizard

XAHE Xantusia henshawi Granite Night Lizard

XAVI Xantusia vigilis Desert Night Lizard

Snakes

AREL Arizona elegans Glossy Snake

CHBO Charina bottae Rubber Boa

COCO Coluber constrictor Racer

CRMI Crotalus mitchellii Speckled Rattlesnake

CRRU Crotalus ruber Red Diamond Rattlesnake

CRVI Crotalus viridis Western Rattlesnake

DIPU Diadophis punctatus Ringneck Snake

HYTO Hypsiglena torquata Night Snake

LAGE Lampropeltis getula Common Kingsnake

LAZO Lampropeltis zonata California Mountain 

Kingsnake

LEHU Leptotyphlops humilis Western Blind Snake

LITR Lichanura trivirgata Rosy Boa

MAFL Masticophis flagellum Coachwhip

MALA Masticophis lateralis California Whipsnake

PIME Pituophis catenifer Gopher Snake

RHLE Rhinocheilus lecontei Long-Nosed Snake

SAHE Salvadora hexalepis Western Patched-Nosed 

Snake

Appendix 2. Species codes and abbreviatoins. 

[A list of the species codes and abbreviations used throught the text and their explanations.]

Category Code Scientific name Common name

Species

 Reptiles—Cont.

Lizards

TAPL Tantilla planiceps California Black-Headed 

Snake

THEL Thamnophis elegans Western Terrestrial Garter 

Snake

THHA Thamnophis hammondii Two-Striped Garter Snake

THSI Thamnophis sirtalis Common Garter Snake

TRBI Trimorphodon biscutatus Lyre Snake

 Amphibians

 Frogs

BUBO Bufo boreas Western Toad

BUMI Bufo californicus Southwestern Toad

BUPU Bufo punctatus Red Spotted Toad

HYCA Hyla cadaverina California TreeFrog

HYRE Hyla regilla Pacific Chorus Frog

RAAU Rana aurora Red-Legged Frog

RACA Rana catesbeiana Bullfrog

SCHA Spea hammondii Western Spadefoot

 Salamanders

ANLU Aneides lugubris Arboreal Salamander

BANI Batrachoseps nigriventris Black-Bellied Salamander

BAPA Batrachoseps pacificus Garden Slender Salamander

ENES Ensatina eschscholtzii Monterey Salamander

TATO Taricha torosa California Newt

 Plants

ARCA Artemisia californica California Sagebrush

DUED Dudleya edulis Ladies' Fingers

DULA Dudleya lanceolata Coastal/Lanceleaf Dudleya

ENCA Encelia californica California Encelia

ERFA Eriogonum fasciculatum California Buckwheat

NNG – Unknown Non-native Grass

RHIN Rhus integrifolia Lemonadeberry

 Small Mammals

MICA Microtus californicus California Vole

NOCR Notiosorex crawfordi Grey Shrew

PECA Peromyscus californicus California Mouse 

Category Code Description

Sex ? Unknown

F Female

M Male

Age ? Unknown

A Adult

J Juvenile

Recap ? Unknown

N No

Y Yes

Category Code Description

Disposition ? Unknown

D Dead

E Escaped

R Released

Tissue ? Unknown

N No

Y Yes

Substrate BR Bare rock

LL Leaf litter

OR Organic soil

SS Sandy soil

Fisher and others— Herpetological Monitoring Using a Pitfall Trapping Design in Southern California —TM 2–A5