Amphibian Research and Monitoring 

Initiative: Concepts and Implementation

By Paul Stephen Corn, Michael J. Adams, William A. Battaglin, Alisa L. Gallant, 

Daniel L. James, Melinda Knutson, Catherine A. Langtimm, and John R. Sauer

Prepared in cooperation with the

National Park Service, 

U.S. Fish and Wildlife Service, and

Bureau of Land Management

Scientific Investigations Report 2005–5015

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2005

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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Any use of trade, product, or firm names in this publication 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:

Corn, Paul Stephen, Adams, Michael J., Battaglin, William A., Gallant, Alisa L., James, Daniel L., Knutson, Melinda, 

Langtimm, Catherine A., Sauer, John R., 2005, Amphibian Research and Monitoring Initiative—Concepts and implementation: U.S. Geological Survey Scientific Investigations Report 2005–5015, 23 p.
iii

Acknowledgments

Many people have contributed to the development of the Amphibian Research and Monitoring

Initiative (ARMI), contributing time and ideas to numerous meetings and discussions. We thank 

Dennis B. Fenn and Susan D. Haseltine, particularly, for their support and encouragement. 

Senior U.S. Geological Survey herpetologists Bruce Bury, Gary Fellers, and Ken Dodd were 

instrumental in promoting the issue of amphibian decline and paving the way for the ARMI. 

We thank Bob Alverts, Chauncy Anderson, Jim Collins, Ken Dodd, Robin Jung, Carol Meteyer, 

Brian Todd, Ralph Tramontano, and Susan Walls for comments and review of various versions 

of this report.
v

Executive Summary

This report provides the basis for discussion and subsequent articulation of a national plan for the 

Amphibian Research and Monitoring Initiative (ARMI). The authors were members of a task force 

formed from within the U.S. Geological Survey (USGS) that included scientists with expertise in 

biology, cartography, hydrology, and statistics. The assignment of the task force was to extend 

work begun by the National Amphibian Leadership Group. This group, composed of senior USGS 

scientists, managers, and external authorities, met in Gainesville, Florida, in February 20001. The 

product of this meeting was a document outlining the framework for a national program to monitor amphibian populations and to conduct research into the causes of declines. 

The ARMI program has the following objectives:

• Establish a network designed to monitor the status and changes in the distributions 

and abundance of amphibian species and communities in the U.S. and its territories 

(for example, Puerto Rico and the U.S. Virgin Islands).

• Identify and monitor environmental conditions known to affect amphibians and document 

their differences across the Nation. 

• Conduct research that identifies causes of amphibian population change and malformations.

• Provide information to managers, policymakers, and the public in support of amphibian 

conservation. 

The task force began its deliberations with the pyramid model for research and monitoring outlined in the national framework document. The framework can be conceptualized as a pyramid 

with extensive and necessarily coarse measurements at many sites across the country (the 

base of the pyramid), intensive research efforts at a relatively small number of sites throughout 

the country (the top of the pyramid), and mid-level efforts at a moderate number of sites (the 

middle of the pyramid). Integration of the three levels would be achieved through research and 

modeling.

Monitoring will occur at all levels of the pyramid, but emphasis will be at the middle level. This 

level is characterized by a definable study area (for example, a national park), from which a statistical sample of study sites can be chosen. From these sites and for each species studied, population 

trends will be tracked by changes in site occupancy. Species richness will be another response 

variable in systems with high numbers of species. Occupancy incorporates the probability of detection, which allows unbiased estimates of annual occurrence and of trends. Monitoring at the apex 

of the pyramid consists of intensive population studies at a small group of selected sites designed 

to determine demographic and life-history characteristics of key species, to relate environmental 

change to changes in demographic and life-history characteristics over time, and to study causeeffect relationships and(or) evaluate new methods and protocols. Gathering useful data at the base 

of the pyramid will be more difficult, because this level involves lands that the Department of the 

Interior (DOI) does not manage. Existing programs that collect data at this scale also have methodological problems and are managed by several different groups.

 Attendees at this meeting included Bill Battaglin, Viginia Burkett, Norita Chaney, Steve Corn, Ken Dodd, Alisa Gallant, Russ Hall, 

Sue Haseltine, Dan James, Doug Johnson, Karen Kaye, Cathy Langtimm, Carol Meteyer, Dave Pyke, Tom Stohlgren, and Gary Williams.
vi

Studies of the causes of amphibian declines and deformities will be based on hypotheses generated by monitoring data and by the expert opinion of USGS scientists. Hypotheses also will be 

generated using a tiered approach of increasing complexity, consisting of (1) an initial assessment and monitoring of potential stressors in ARMI study areas; (2) experimental research to 

isolate causality between potential stressors and declining occupancy or frequent malformation 

of individual amphibian species; and (3) modeling to evaluate relations among potential stressors and individual species occupancy and malformation rates, overall species richness, and 

relative susceptibility of various amphibian species to changes in environmental conditions or 

potential stressors; and (4) model validation using an iterative process of continued monitoring 

and experimentation.

Methods development and protocol description are expected to be a continuing process. Existing methods need to be adapted and new methods developed to initiate the program. Continued 

development is anticipated because of the adaptive nature of the research program. As results 

accumulate, new research directions are expected to emerge requiring adjustments to existing 

methods and protocols. To maintain the ARMI at “state of the science” and at the forefront of 

monitoring technology, appropriate new techniques, analysis, and models will need to be incorporated into the ARMI program as they become available. Because amphibians and amphibian 

habitats are highly diverse nationally, most protocol development must occur at the regional 

level. The ARMI, however, will continually strive to coordinate and scale up the regional efforts. 

For example, the techniques used to monitor occupancy necessarily vary both within and among 

regions, but the unbiased nature of the estimator allows regional and national comparison, 

synthesis, and analysis of trends in occupancy.

Photograph by Priya Nanjappa

Two national databases are associated with the ARMI program: a 

relational database that houses 

the ARMI field-survey data and 

the ARMI Atlas for Amphibian

Distributions, a county- or 

subcounty-level compendium of 

historic and current species presence, documented for all amphibian species known to occur in the 

U.S. An integrated national database of survey data will benefit 

ARMI investigators, cooperators, 

DOI and other Federal land managers, and scientists worldwide with 

an interest in amphibian status 

and global conservation issues.

A variety of analyses will be conducted to assess the status and 

trends of amphibian populations, 

to determine biotic and abiotic 
vii

stressors, and to improve 

understanding of the relations 

between amphibians and environment. Different mechanisms 

for reporting these results can 

be used to provide regional and 

national syntheses; to provide 

feedback for determining 

whether changes in protocols, 

monitoring strategies, and(or) 

research activities should be 

considered (adaptive research 

and monitoring); and to provide 

decision-support tools for land 

managers and policymakers.

Photograph by William Battaglin

Partnerships are important at every level of the monitoring pyramid. As a first priority, the 

ARMI is developing strategies for the mid-level of the pyramid and working with DOI landmanagement partners to identify Federal land areas and objectives for USGS monitoring efforts. 

As the program matures, a major task of the ARMI will be to develop collaborative relationships 

with agencies, universities, and organizations possessing long-term intensive data and expertise 

and to integrate this information into regional and national status and trends reports for amphibians. International partnerships can provide an important context for the information collected 

by the ARMI program and can prove fruitful in the investigation of problems of global concern.

The conceptual designs outlined for each component of the ARMI already are in various stages 

of implementation and, in some instances, have been in operation for some time. We have an 

active national program, with research and monitoring proceeding across the U.S. and at all 

three levels of the pyramid. Integration, however, will be key to realizing a larger and greater 

value above the excellent value already coming out of the ARMI’s functioning parts. Integration 

needs to proceed in multiple directions—across regions, across disciplines, and across the three 

levels of research and monitoring within the pyramid. Coordinating the component parts into a 

well-integrated national program will require the full-time efforts of more than one individual. 

As partners come into the program and data accumulate for processing, analysis, and reporting, 

the integration of the program will become even more complex. It is critical to anticipate the 

needs of the ARMI for the near and distant future and to begin to establish now an infrastructure for national coordination and integration.
ix

Contents

Acknowledgments ....................................................................................... iii

Executive Summary ....................................................................................... v

History, Objectives, and Organization of the Amphibian Research and 

Monitoring Initiative ........................................................................... 1

Concepts and Design of Amphibian Monitoring ...................................................... 2

A Hierarchical Framework ........................................................................ 2

Monitoring at the Mid-Level of the Pyramid ................................................... 2

Objectives for Mid-Level Monitoring ...................................................... 3

The Occupancy Approach .................................................................. 3

Estimating Site Occupancy .................................................................. 6

Field Implementation ........................................................................ 7

Monitoring at the Base of the Pyramid ......................................................... 8

The Amphibian Research and Monitoring Initiative National 

Atlas for Amphibian Distributions ................................................ 8

North American Amphibian Monitoring Program ....................................... 9

Frogwatch USA .............................................................................. 9

North American Reporting Center for Amphibian Malformations ..................... 10

Implementation of Base-Level Monitoring ................................................ 10

Monitoring at the Apex of the Pyramid ......................................................... 10

Research on Causes of Declines ........................................................................ 11

Tier 1 Assessments ................................................................................. 11

Tier 2 Assessments ................................................................................. 13

Tier 3 Assessments ................................................................................. 13

Methods and Protocol Development .................................................................. 13

Database Development ................................................................................. 15

Analysis and Reporting ................................................................................. 15

Partners and Leadership ................................................................................. 17

Integration ................................................................................................ 19

References Cited .......................................................................................... 20

Glossary ................................................................................................... 23

Figures

1. Map showing regional organization of the Amphibian Research and 

Monitoring Initiative ........................................................................... 2

2. The pyramid conceptual model applied to the Amphibian Research 

and Monitoring Inititative ..................................................................... 3

3. Species distribution map for A, Wood frog (rana sylvatica); B, American 

bullfrog (rana catesbeiana); C, Eastern newt (notophthalmus viridescens); 

and D, Tiger salamander (ambystoma tigrinum) .......................................... 9
History, Objectives, and Organization 

of the Amphibian Research and 

Monitoring Initiative

Amphibian decline has been recognized as a global issue 

since the meeting of the First World Congress of Herpetology

in England in 1989. The rapidly growing literature on the status 

of amphibians and the causes of declines has been the subject 

of several reviews, including Collins and Storfer (2003), Linder 

and others (2003), and Semlitsch (2003). Two recent analyses 

suggest that the problem of amphibian declines may be accelerating (Stuart and others, 2004; Thomas and others, 2004). The 

increasing interest and demand for information to better understand the status and the underlying causes for declines and malformations prompted the U.S. Congress to fund the Amphibian 

Research and Monitoring Initiative (ARMI) in 2000. ARMI is 

a national program coordinated by the U.S. Geological Survey 

(USGS), the science and research bureau for the Department 

of the Interior (DOI). The goals of the program are to implement a plan to monitor trends in amphibian populations on 

DOI lands and to study the causes for declines, should they be 

detected. This program includes cooperation with the National 

Park Service (NPS), the U.S. Fish and Wildlife Service 

(USFWS), and the Bureau of Land Management (BLM). The 

USGS is uniquely qualified to develop and provide scientific 

leadership for such an effort. It has a long record of studies on 

amphibian life history, sampling techniques, toxicology, and 

health-related issues, and it has the responsibility for many 

natural-resources monitoring programs at regional, national, 

and continental scales.

The goal of ARMI is to better understand the dynamics 

of amphibian population trends, including causes of declines, 

so that DOI agencies and other land managers have the most 

accurate information from which to develop effective ways to 

manage and conserve amphibian populations. Specific objectives include:

• Establish a network designed to monitor the status and 

changes in the distributions and abundance of amphibian species and communities in the U.S.

• Identify environmental conditions known to affect 

amphibians and document their differences across 

the Nation.

• Conduct research that identifies causes of amphibian 

population change and malformations.

• Provide information to managers, policymakers, 

and the general public in support of amphibian 

conservation.

To take advantage of regional knowledge and expertise, 

the U.S. has been divided into seven blocks of States that are 

the focus of regional herpetological investigations (fig. 1). 

The monitoring program is coordinated in each region by 

USGS herpetologists who collaborate with USGS hydrologists. ARMI-sponsored research is conducted by USGS 

scientists nationally. Data are managed jointly by the Patuxent 

Wildlife Research Center and the Western Ecological Research 

Center. A Web site, Geographical Information Systems (GIS) 

resources, an interactive Web-based mapping tool, and other 

remote-sensing resources are overseen by the National Center 

for Earth Resources Observation and Science (EROS) Data 

Center. Oversight is provided by a steering committee, with 

members from within the USGS and from a number of major 

government environmental agencies and nongovernment 

organizations.

Amphibian Research and Monitoring Initiative: 

Concepts and Implementation

By Paul Stephen Corn, Michael J. Adams, William A. Battaglin, Alisa L. Gallant, Daniel L. James, 

Melinda Knutson, Catherine Lagtimm, and John R. Sauer Photograph by Michael Adams
2 Amphibian Research and Monitoring Initiative: Concepts and Implementation

Concepts and Design of Amphibian 

Monitoring

A Hierarchical Framework

One of the greatest challenges to developing this national 

monitoring plan is the highly regional nature of amphibians 

in North America. With the exception of the woodfrog (Rana 

sylvatica), which ranges from Georgia to Alaska but does not 

occur in most of the West, and the bullfrog (R. catesbeiana), 

which is nonindigenous west of the Great Plains (Bury and 

Whelan, 1984), there are no species of U.S. amphibians with 

truly continental distributions. Amphibians occupy diverse 

habitats that require specialized sampling techniques. No single 

technique is capable of sampling amphibians across the country, 

and the factors affecting amphibians differ among regions. This 

diversity argues for a highly regionalized approach to amphibian 

monitoring and research; however, it also is important to integrate these regional programs in a way that allows for a national 

synthesis and for analysis at a wide range of spatial scales.

A design modified from the Committee on Environment

and Natural Resources (CENR) report “Integrating the 

Nation’s Environmental Monitoring and Research Networks 

and Programs—A Proposed Framework” (CENR, 1997) is 

the model used by the USGS to offer leadership in amphibian 

monitoring and research and to achieve regional and national 

assessments of status and trends. The framework describes a 

pyramid (fig. 2). At the base, extensive but necessarily coarse 

measurements are made at many sites across the country. 

At the apex of the pyramid, intensive research and population monitoring is conducted at a relatively small number of 

sites throughout the country. At the mid-level of the pyramid, 

monitoring directed toward detecting change in occurrence and 

abundance of species across the landscape is conducted at a 

moderate number of sites.

Monitoring at the Mid-Level of the Pyramid

This is the level of monitoring where ARMI and its 

partners will come together in a national monitoring effort. 

USGS monitoring on protected DOI lands, as mandated by

U.S. Congress, will provide the core framework, while Federal, 

State, and private partners collaborating with the USGS extend 

the effort to non-DOI land units to make it a truly national 

program. By necessity, the design and implementation of this 

framework is modular. Land areas currently being monitored 

by USGS investigators were chosen by subjective criteria 

such as previous monitoring efforts or perceived importance 

of the habitat. New areas will be incorporated as managers or 

stewards of selected areas willingly enter the program. Because 

new monitoring areas will not be randomly chosen from available areas, statistical inference will be focused on each land 

Figure 1. Regional organization of the Amphibian Research and Monitoring Initiative. Puerto Rico and the U.S. Virgin Islands 

are in the Southeast Region, Alaska is in the Pacific Northwest Region, and Hawaii is in the Southwest Region. Amphibian 

species richness based on data in the Amphibian Research and Monitoring Initiative National Atlas for Amphibian Distributions.

Number of Amphibian 

Species

Pacific

Northwest

Rocky Mountains

North Central

South Central

Northeast

Southeast

Southwest
unit and will provide substantial information to managers and 

stewards of the selected areas. Statistical inference at a regional 

and national level will be limited, although monitoring in these 

areas can and will inform at broader landscape levels.

Objectives for Mid-Level Monitoring

• Provide geographic and temporal information on 

change at the scale of the individual park, refuge, 

or other land unit (mid-level monitoring area).

• Provide estimates of change within strata of management interest within the park, refuge, or land unit.

• Provide information for modeling amphibian and 

environment-stressor associations at the mid-level 

monitoring area and for mapping these associations 

at the regional level.

The Occupancy Approach

Amphibian monitoring on Federal lands will emphasize 

estimation of well-defined parameters using statistical procedures that can be applied to a variety of species in different regions. All sampling will be based on a defined sample 

frame with a specified target population and will incorporate 

a method of estimating the detection probability of each 

species sampled (Box A). Because estimating abundance of 

wildlife populations, including amphibians, can be difficult 

and expensive, use of raw counts or other indices such as 

relative abundance is sometimes suggested (Caughley and 

Sinclair, 1994; Alford and Richards, 1999; Engeman, 2003). 

Although Smith and Petranka (2000) found that counts of terrestrial salamanders were highly predictive of population sizes 

estimated from capture-recapture data, indices usually rely on 

assumptions about detection probabilities that are difficult to 

Figure 2. The pyramid conceptual model applied to the Amphibian Research and Monitoring Initiative.

Concepts and Design of Amphibian Monitoring 3

APEX

MONITORING

MID-LEVEL

MONITORING

BASE ASSESSMENTS

A small

numbers of study sites

established to track changes

in abundance and to answer sitespecific questions about demographics

or factors that might affect populations

A defined area where the proportion of area

occupied by amphibians will be monitored long term.

Mid-level monitoring areas typically encompass dozens to hundreds

of amphibian breeding sites and are the primary focus of ARMI monitoring.

Regional assessments of the distribution and status of species. These assessments provide a

snapshot of distribution or status over broad areas (for example, the Great Basin). They could serve as a

baseline for future comparison. A subset of the assessments involve visiting sites that are known to have had

amphibians in the past and that provide a rapid assessment of large-scale changes in amphibian distribution.

RANGE OF INFERENCE

NUMBER OF SITES

INTENSITY
4 Amphibian Research and Monitoring Initiative: Concepts and Implementation

satisfy. Therefore, indices are very likely to result in biased 

estimates of abundance and change in abundance (Anderson, 

2001, 2003; MacKenzie and Kendall, 2002; Schmidt, 2003; 

Storfer, 2003). Instead, ARMI will apply statistical methods 

that use species presence-absence data from a sample of sites 

to estimate the proportion of sites occupied by each species 

and species richness. In collecting and analyzing presenceabsence data, it is recognized that “absence” pertains to two 

possible conditions: (1) The species is truly absent from the 

site, or (2) the species is present but undetected. By estimating detection probabilities, the naïve estimate of occupancy 

is adjusted to provide an unbiased estimate of the proportion 

of sites truly occupied, allowing comparisons among studies 

with differing methods or level of effort (Bailey and others, 

2004). The methods and conceptual designs of ARMI were 

developed through discussions held at several organizational 

meetings and through the deliberations of ARMI herpetologists, hydrologists, geographers, and biometricians representing three disciplines within the USGS.

Why an approach based on presence-absence data?—

Amphibians pose a number of difficulties when designing 

surveys to determine long-term trends. An ideal survey would 

Key Elements of ARMI Regional Monitoring at Each Level of the Pyramid

Mid-Level of the Pyramid.—It may seem strange to start in the middle, but this will be the core of ARMI. 

Most integration will occur at the scale of individual mid-level monitoring areas. Each ARMI region will establish two to three mid-level monitoring areas using the following guidelines:

• A defined sample frame is essential. This implies that the investigator maps the boundary or boundaries 

of the mid-level monitoring area, divides it into sampling units, and chooses which units to sample via a 

probabilistic scheme.

• Occupancy is the primary response variable. This estimator, which incorporates detection probability, will 

be employed whenever possible. This requires multiple visits within a season to at least a subset of sites in 

each mid-level monitoring area. Regional coordinators will produce annual estimates of occupancy and its 

variance for a subset of species of their choosing for each mid-level monitoring area each year.

• Disease screening is integral to data collection. Data will be collected at each mid-level monitoring area 

according to procedures developed by the USGS National Wildlife Health Center.

• Water data are necessary. Regional coordinators will work with a hydrologist to identify and monitor basic 

water parameters at a subset of mid-level monitoring sites.

• Mid-level data will be used to guide research and monitoring of stressors related to amphibian decline. 

Regional coordinators, with input from ARMI specialists in hydrology, geography, chemistry, and biology, will identify potential stressors and determine if additional data related to those stressors can and 

should be collected.

• Partnerships are strongly encouraged. Mid-level monitoring areas need to be established in partnership with 

client agencies. The NPS, in particular, should be a primary partner because they also are establishing longterm monitoring. Monitoring areas funded solely by the USGS should be located strategically to address 

specific questions related to amphibian decline, or to increase coverage of poorly represented habitats.

Apex of the Pyramid.—Apex monitoring consists of intensive population monitoring and research at 

handpicked sites. Apex monitoring does not provide broad inference. Apex monitoring often will consist of egg 

counts, population estimates, demographic studies, or other detailed population-scale work. Each region will 

identify one to three apex monitoring sites.

Base of the Pyramid.—Funding constraints and the logistics of emphasizing DOI lands prevent ARMI 

regions from working effectively at this level. Partnerships with other broad-scale efforts such as the North 

American Amphibian Monitoring Program (NAAMP) or Frogwatch USA will be encouraged.

• Regional coordinators are encouraged to seek matching funds to conduct broad-scale inventories that 

incorporate historic site revisits when feasible and when deemed that such information is needed. This 

is a good way to obtain quick information about amphibian status at a broad scale and to provide the information most sought after by many of our partners. Depending on regional priorities and resources, regional 

coordinators also may fund basic research on causes of amphibian decline that have broad regional or

national relevance.

A
Photograph by Priya Nanjappa

include unbiased estimates of population size at every location 

studied. Unfortunately, population estimates of most amphibians are difficult and expensive to obtain, limiting their feasibility. Many amphibian surveys employ indices as surrogates to 

population estimates, but a useful index must provide unbiased 

estimates of changes in abundance. To provide such unbiased 

estimates of population change, the numbers of adults, tadpoles, or egg masses recorded must reflect a constant proportion of the true population size among study sites and among 

years at the same study site; however, satisfying this condition 

is likely to be difficult for most studies.

Another complication is that amphibians tend to have 

highly variable populations. This inherent variability means 

that even if adequate population estimates or reliable indices 

were available, the power to detect changes will be low and 

long-term data will be required. The problem may be exacerbated by the pattern of annual variation. Alford and Richards 

(1999) observed that population dynamics of pond-breeding 

amphibians are based on variation in recruitment from the 

larval stage, which is much greater than variation in adult 

survival. This results in populations that have the potential for 

rapid changes in abundance. Populations that are more or less 

stable over the long term may exhibit large increases in abundance that are balanced by more frequent, small decreases. 

This could explain the observations from several long-term 

studies of amphibian abundance that recorded declines, 

sometimes lasting for several years, followed by increases in 

abundance back to or greater than the population size before 

the decline began (Pechmann and others, 1991; Semlitsch and 

others, 1996; Meyer and others, 1998). For several groups 

(ranid frogs, toads, ambystomatid salamanders), Alford and 

Richards (1999) found that it was significantly more likely to 

observe a decline in population size than an increase in any 

one year.

Green (2003) analyzed a variety of amphibian population time series and also found declines to be more frequent 

than increases, but the magnitude of declines and increases 

did not differ. This does not support the scenario proposed by 

Alford and Richards (1999), but it does support the analyses by 

Houlahan and others (2000) that shows a global trend of declining population size since the 1950s. Alford and others (2001), 

however, pointed out that the data used for these analyses are 

not randomly distributed geographically, and that the data were 

collected for a variety of purposes other than detecting trends 

in population size. Furthermore, some of these data are simple 

counts of individuals or egg masses. Without detection probabilities, these data are inadequate to assess trends, because the 

changes observed could be due to changes in detection instead 

of changes in abundance (MacKenzie and Kendall, 2002).

Habitat availability and attractiveness of water bodies as 

breeding sites change over time, which may compromise use 

of single sites for monitoring long-term trends (Alford and 

Richards, 1999; Skelly and others, 1999). Furthermore, the 

precision of population estimates (hence, the power for detecting change) depends on sampling intensity, with single visits 

(index data) providing the least useful information for detecting changes.

The inadequacy of existing data on amphibian populations suggests that a new approach is necessary. Green (1997) 

provided a useful framework for amphibian populations that 

deals with sampling problems and low power for detecting 

changes. Green distinguished between declines in size of 

populations and declines in numbers of populations:

A decline is the condition whereby the local loss 

of populations across the normal range of a species 

so exceeds the rate at which populations may be 

established, or reestablished, that there is a definite 

downward trend in population number.

The approach of monitoring changes in site occupancy 

of species based on presence-absence data allows for the 

estimation of several parameters that can be used to study 

population and community dynamics, estimate extinction 

and colonization probabilities, and test hypotheses concerning 

environmental factors affecting those dynamics. Research in 

wildlife estimation theory seeks to incorporate measures of 

detection probability in the estimation procedures and reduce 

unknown bias due to some species invariably being missed or 

overlooked during surveys. In one class of estimators, species richness is the state variable of interest (Boulinier and 

others, 1998, 2001; Nichols and others, 1998a, b; Cam and 

others, 2000). In the other class of estimators, the proportion 

of patches or area occupied is the state variable of interest 

(Erwin and others, 1998; MacKenzie and others, 2002). Thus 

far, these new estimators have been applied primarily to data 

from bird surveys, but they hold considerable promise for 

amphibian surveys (MacKenzie and others, 2002, 2003).

In addition to the strength of this approach for biological and statistical reasons, there are considerable logistical 

benefits. Presence-absence data are more reliably and easily 

Concepts and Design of Amphibian Monitoring 5
6 Amphibian Research and Monitoring Initiative: Concepts and Implementation

collected than data necessary for estimates of population 

size and do not require marking animals. The methods do not 

require technically sophisticated field surveys, and protocols 

are potentially transferable to persons who are not specialists in amphibian biology, although technical proficiency and 

experience in amphibian field techniques and species identification are imperative.

Obviously, no single approach can cover all species or all 

objectives in a national monitoring program. Other approaches 

will be developed as needed, but this approach offers the best 

possibility for immediate and successful implementation, with 

subsequent data analysis providing reliable indication of the 

status of selected amphibian species.

Estimating Site Occupancy

Estimating occupancy yields species-specific statistical 

inferences with regard to the proportion of discrete sample sites 

(for example, ponds, caves, wetlands, stream reaches, terrestrial 

quadrats) that are occupied by a species. Pond-based surveys 

and inferences already are accepted in the amphibian literature 

(Kareiva and others, 1997; Skelly and others, 1999; Joly and 

others, 2001; Marsh and Trenham, 2001), and the conceptual 

transition to terrestrial sample plots is easily made. As populations increase in abundance they should expand into available 

habitat with a concomitant increase in occupancy. As populations decrease in size, distributions should shrink, with fewer 

species in the sampling units and a concomitant decline in 

occupancy. Thus, the occupancy estimator can provide indirect information on temporal and spatial variations in species 

abundance. With simultaneous monitoring at sampling sites of 

environmental variables and stressors that can affect amphibians, 

correlation with possible causes of change can be established 

and studied. For ARMI, surveys based on occupancy are attractive because of the ease of implementation and the potential for 

general application to all regions and amphibian habitats. Field 

methods can be tailored for different kinds and configurations of 

habitats, landscapes, and amphibian communities.

The occupancy approach also can be used to address 

issues of metapopulation dynamics, which may be important 

to many amphibian species (Alford and Richards, 1999). 

Metapopulations are networks of subpopulations that occupy 

discrete habitat patches but are united by migration (Hanski

and Gilpin, 1996). Metapopulation theory is particularly 

applicable to pond-breeding amphibians (but has not been 

demonstrated to apply to terrestrial salamanders). Research on 

salamanders and anurans generally supports the existence of 

semi-isolated subpopulations centered around breeding ponds 

and linked by migration (Gill, 1978; Berven and Grudzien, 

1990; Sinsch, 1992; Sinsch and Seidel, 1995). In amphibian 

metapopulations, migration among nearby ponds is relatively 

frequent, but more isolated sites have less contact with other 

populations, have decreased rates of occupancy, and have 

increasing probability of extinction (Sjögren, 1991; Sjögren 

Gulve, 1994; Vos and Stumpel, 1996). A focus on metapopulation systems could increase the efficiency of fieldwork (by 

sampling randomly selected groups of sites instead of random 

individual sites spread over large, inaccessible landscapes). 

Not all groups of amphibian populations in a landscape may 

function as metapopulations, and changes in the surrounding terrestrial environment may have significant influence on 

extinction rates (Joly and others, 2001; Marsh and Trenham, 

2001). The assessment of trend from occupancy data, however, 

does not depend on metapopulation dynamics.

Using the occupancy approach, models of system dynamics will be parameterized by local extinction and colonization 

rates. Long-term data (10 years or more) will provide more 

reliable estimates, but only 2 years of data are required to 

begin the analysis of system dynamics. Declines will be manifested by local extinctions that exceed colonizations. Patterns 

of habitat occupancy will allow for some inferences with only 

a single year of data by testing the hypothesis that occupancy 

is related to isolation (for example, high rates of vacancy in 

groups of nearby ponds may indicate a decline). Sampling 

clusters of sites also will allow for more efficient sampling 

and analysis of environmental factors that may be related to 

declines.

A statistical framework and associated software for estimating occupancy and rates of local extinction and colonization have been developed in collaboration with researchers 

at the USGS Patuxent Wildlife Research Center (MacKenzie 

and Kendall, 2002; MacKenzie and others, 2002, 2003). This 

framework allows for modeling with covariates to test hypotheses about environmental effects on the presence or detection 

probability of species within the sampling unit of interest (for 

example, ambient temperature effects on the mean estimate 

of detection probability, presence of fish or bullfrogs, hydrology pattern, fertilizers, proximity to a source population on 

the presence of species). Note that some index methods do 

not permit the separation of environmental covariate effects 

on detection probability and animal presence, precluding 

reasonable interpretation of results (Schmidt, 2003). Variations in occupancy estimates are expected. The challenge 

Photograph by William Battaglin

is to isolate variation in occupancy due to natural stressors 
(rainfall patterns, temperature patterns, good or bad year for 

prey populations) from variation that may result from anthropogenic causes (pollution, habitat loss, parasite infestations, 

management actions), keeping in mind the complication that 

humans have changed the weather (land use affects temperature and precipitation). Covariate analysis can help determine 

where population dynamics fall within expected patterns of 

variation explained by known factors of change and where 

variation does not follow explainable patterns (Box B). This 

is an essential step in testing hypotheses to explain amphibian 

declines, but it is a step that few entities have the capability 

to address at a broad scale. With adequate time series, extinction and recolonization probabilities at sampling sites within a 

sample frame with a defined area of inference can be estimated for species.

Field Implementation

Each mid-level monitoring area will present unique 

sampling challenges for implementing occupancy estimation. 

ARMI is addressing this challenge through annual meetings 

and workshops that provide opportunities for the regional 

coordinators, biometricians, and others to meet and resolve 

their unique challenges. The basic components of implementation are as follows:

1. Define a sample frame with a known range of inference.—

Investigators routinely cannot apply survey or monitoring 

techniques over the entire sample frame. In such situations, 

a subset of sample units is chosen from which to pick sample 

sites and make statistical inferences. All sites in that sample 

unit need to have an equal chance of selection for sampling. If 

sites are selected arbitrarily, the monitoring results only reflect 

what is happening at those sites and cannot be extrapolated to 

the rest of the sample frame.

Sample frames will be tailored to the species and landscape of interest. Sample frames need not be one contiguous 

unit and, for example, may be a network of USFWS refuges 

on the lower Mississippi River. Conversely, it may be appropriate to have more than one sample frame within a park or 

refuge. For example, at Okefenokee National Wildlife Refuge 

in Georgia, there are six different wetland types that harbor 

different species and amphibian assemblages.

Example 1.—As a species goes from high to low abundance, which sample units lose the species first? 

Which sample units consistently maintain the species? Which sample units are reoccupied first? Why? Is the pattern of loss or gain consistent each time occupancy increases or decreases? Are these patterns consistent for the 

same species across different mid-level monitoring areas? If there is a change from a consistent pattern does that 

mean that there is a problem? Are differences among populations on DOI and non-DOI lands in the same area a 

cause for concern? Is a consistent declining trend in occupancy by a species indicative of a problem?

Example 2.—As abundance varies, which species within a different mid-level monitoring area show the 

same patterns of change in occupancy? Which species differ? Are those patterns consistent among different midlevel monitoring areas within an ARMI region? Is one species more vulnerable than another, and why might that 

be? Are populations that inhabit one habitat type more vulnerable than those inhabiting another?

Example 3.—Within a given species range in the U.S., are there patterns in occupancy that can be identified 

with geographic gradients such as latitude, elevation, climate variables, known stressors, or periphery versus core 

of its geographic range?

Applications of Occupancy Analysis: Questions

Photograph by Wendy Palen

Concepts and Design of Amphibian Monitoring 7

B
8 Amphibian Research and Monitoring Initiative: Concepts and Implementation

2. Apply appropriate field survey techniques.—Appropriate 

and feasible methods for detecting all targeted species in a 

sample frame will be consistently applied in all sample units. 

Multiple survey techniques will be applied to increase the 

probability of detection (for example, visual survey, auditory 

surveys, PVC pipes, cover boards). If field techniques, such as 

calling surveys, are employed that are not capable of detecting certain species in the area (noncalling anurans), then those 

species cannot be considered as targets for sampling and estimation. Each investigator will decide which species to target.

An important component of survey techniques is the timing of surveys. Surveys must be designed to maximize detectability of the species studied, and this is generally specific to 

individual study areas or regions. Appropriate timing may vary 

from year to year because of variable weather conditions.

3. Perform repeat surveys of sampling sites.—Repeat visits 

during a field season are used to estimate detection probability. 

Detection probability refers to the near-universal situation in 

animal population monitoring in which survey methods do not 

detect all populations present in a study area. The occupancy 

estimator is designed to incorporate data from repeat site visits 

so that estimated changes in occupancy reflect true changes in 

occupancy and not simply changes in detection probability.

4. Estimate Species Richness.—Species richness (fig. 1) 

provides community-level parameter estimates that can be 

used to monitor spatial and temporal changes in targeted communities. Estimating variation in species richness through time 

and among sample units is one means of tracking the status of 

amphibians as a group and adds another level of information. 

Furthermore, detection of a change in species richness can 

alert biologists and managers to potential problems that may 

require more focused study.

Statistical methods recently have been developed that 

account for variation in detection probabilities that estimate 

species richness, standard error, and confidence intervals 

(Nichols and Conroy, 1996). The data collected and the sampling schemes employed are similar to those used to estimate 

occupancy, and the same data set often can be used to estimate 

both species richness and occupancy. Development in this 

area of estimation research has been intense, and the initial 

approach and method have been extended to estimate several 

vital rates in community dynamics important to identifying 

amphibian declines—rate of increase in species richness, local 

extinction rates, local species turnover, annual extinction and 

recolonization probabilities, and probability of species cooccurrence (Nichols and others, 1998a; Hines and others, 

1999). Additional methods have been developed to test hypotheses concerning environmental factors affecting temporal 

(Boulinier and others, 1998) and spatial variation (Nichols and 

others, 1998b) in species richness, which will be important to 

identify cause-effect relationships. Methods development was 

based principally on data supplied by the USGS Breeding Bird 

Survey (BBS), but the statistical techniques hold promise for 

amphibians. Application, however, may be limited to regions 

of high diversity, as the estimator performs best when applied 

to communities with a relatively large number of species.

Monitoring at the Base of the Pyramid

Because ARMI has an explicit mandate to monitor 

amphibians and assess status and trends on DOI lands, extensive monitoring efforts on a continental scale at the base of 

the pyramid currently must be a peripheral component of the 

program. It is clear, however, that efforts on DOI lands will 

not provide landscape-level data comparable to those obtained 

from the BBS or from State amphibian atlases. Landscapelevel data are needed for documenting change at regional 

or landscape levels. Because DOI lands form a nonrandom 

selection of areas within any region, extensive surveys at the 

base of the pyramid form a stratum of areas not covered by 

mid-level monitoring, and they are a critical component of any 

nationwide summary of amphibian populations.

ARMI intends to collaborate with ongoing landscapelevel programs to provide more intensive information to augment data collected in these programs, to provide methods and 

analysis advice that can improve these programs, and to assist 

the coordinators of these programs with data management 

and summary, whenever possible. Here, we briefly describe 

three ongoing program elements that have been identified as 

possible contributors to base-level monitoring, note limitations 

that could compromise their use as base-level monitoring programs, discuss what information they could bring to an ARMI 

collaboration as they exist now, and identify what modifications would be needed for the programs to provide valid inferences of distributions and change on a continental scale.

The Amphibian Research and Monitoring 

Initiative National Atlas for Amphibian 

Distributions

The atlas is a county-level compendium of current 

and historic records of amphibian occurrences compiled 

by Dr. Michael Lannoo, Ball State University, and his students. A copy of the atlas has been obtained by ARMI 

(http://www.pwrc.usgs.gov/armiatlas). The species records 

are from published, peer-reviewed scientific literature; 

museum records; State and regional herpetological atlases; 

and other confirmed and validated observations. The atlas 

includes geographic distribution data (see examples in fig. 3) 

for all amphibian species currently recognized in the U.S., 

along with a list of the supporting references used for each 

species. The atlas is not a monitoring effort and cannot provide 

the basis for statistical comparisons over regions or times, but 

it has value as a geographic summary of survey efforts and is 

useful for illuminating data gaps. The atlas also has considerable value for application with GIS tools to analyze patterns 

of species distributions, in concert with patterns of known and 

potential stressors, to develop research hypotheses and provide 

a first assessment of risk. The atlas provides a convenient 

structure for future summaries of information at the county 

level.
North American Amphibian Monitoring Program

The North American Amphibian Monitoring Program 

(NAAMP) is a project in the Inventory and Monitoring 

Branch of the Patuxent Wildlife Research Center. NAAMP 

was designed to be directly analogous to the BBS in that it has 

roadside survey routes and collects an index to animal abundance based on ordered categorical data collected at a series 

of stops along these routes. The survey approach is limited 

to regions with calling frogs and is currently implemented 

in the Midwest and the Northeast regions. Data are collected 

by volunteers who are recruited by State agencies. Although 

NAAMP data have the potential to represent broad population 

patterns operating at the landscape scale, the geographic scope 

and survey design limit the general applicability of the survey 

and statistical inference. As with the ARMI National Atlas for 

Amphibian Distributions, NAAMP can provide information to 

develop research and monitoring hypotheses and first qualitative assessments.

Frogwatch USA

Frogwatch USA is an educational frog and toad monitoring program coordinated by the USGS and the National 

Wildlife Federation (http://www.nwf.org/frogwatchUSA/). 

Volunteers collect data on breeding calls by amphibians 

throughout the country. Frogwatch USA lacks a defined 

sampling frame, and counting procedures are designed to 

provide minimal data from a series of volunteers who vary 

greatly in competence. Data entry is Web based and relies on 

repeated counts by volunteers. Frogwatch USA could be an 

extremely effective public outreach program, and the goals of 

the program are mainly educational. With some modification 

in design, it could provide some valid statistical inference to 

broader landscapes (MacKenzie and others, 2002).

Figure 3. Species distribution map for A, wood frog (rana 

sylvatica); B, American bullfrog (rana catesbeiana); C, Eastern

newt (notophthalmus viridescens); and D, tiger salamander 

(ambystoma tigrinum).

Photograph by Chauncey Anderson

Concepts and Design of Amphibian Monitoring 9

A

B

C

D
10 Amphibian Research and Monitoring Initiative: Concepts and Implementation

As these three program elements now stand, they could 

bring to ARMI the following:

• Considerable outreach to the public and professionals 

who contribute to these programs.

• Frameworks to organize information about actual datacollection activities in the U.S.

• Qualitative data about distribution patterns that could 

be used to develop research hypotheses and provide a 

first cut at qualitative assessments of risk and trend.

None of the program elements, however, provide information appropriate for the base-level monitoring needs of ARMI. 

Base-level requirements include defined sample frames and 

some means to estimate detection probability. All of the program 

elements, however, have components that could form the basis 

of base-level monitoring. ARMI could influence their development by providing protocols for data collection and summary. In 

particular, the occupancy estimation procedure has application in 

NAAMP and Frogwatch USA, and Frogwatch USA coordinators 

are experimenting with this technique in their replicate counts.

North American Reporting Center for Amphibian 

Malformations

The USGS Northern Prairie Wildlife Research Center

initiated citizen reporting of amphibian malformations 

through the Web-based North American Reporting Center 

for Amphibian Malformations (NARCAM). This site is now 

hosted by the National Biological Information Infrastructure 

and managed by the University of Georgia’s Savannah River 

Ecology Laboratory (http://frogweb.nbii.gov/narcam/).

probability, and to assess changes over time. The occupancy 

and species richness estimation procedures used at ARMI midlevel monitoring sites could be implemented at the level of 

either counties (as in an atlas, with multiple participants collecting information in replicate checklists), NAAMP-style survey routes, or in Frogwatch USA-style nonrandom sites. Also, 

ongoing State atlases could be incorporated into a dynamic 

nationwide atlas. All of these approaches have varying levels 

of scientific control and representation, so their relative roles 

would have to be specified. Providing an appropriate sample 

frame and estimation procedure, however, will greatly enhance 

the quality of information, and the existing administrative 

structures can be used in these enhanced surveys.

Monitoring at the Apex of the Pyramid

Monitoring at the apex of the pyramid includes intensive 

population studies at a small group of selected sites, which, 

at this stage of implementation, are located on DOI lands, or, 

if on other lands, receive outside funding. The objectives of 

these studies will vary, but four types are anticipated:

• Determining demographic and life-history characteristics of key species. Data from these studies will 

provide information for population modeling efforts 

targeted to elucidate fundamental population processes 

specific to species rather than locations. Results from 

these studies are intended to provide the basic biological information necessary to inform research and 

monitoring at all levels.

• Relating environmental change to changes in demographic and life-history characteristics over time. 

These studies are intended to provide the basic biological information necessary to inform research and 

monitoring at all levels.

• Doing cause-effect studies. As locations with disease, 

malformations, nonindigenous species, or declines are 

identified, these sites will provide for progressively 

more intensive research to identify specific causes. 

ARMI also anticipates emerging research needs at 

this level, as resource managers implement management plans and question resultant effects on amphibian 

populations. Some apex sites already incorporate controlled manipulations designed to determine the effects 

of potential stressors on amphibian populations. This 

approach effectively merges the research and monitoring components of ARMI.

• Developing protocol and techniques. Considerable 

information is needed on the techniques appropriate 

for sampling some groups of amphibians, and research 

is necessary before effective monitoring of some species can begin.

Photograph by Priya Nanjappa

Implementation of Base-Level Monitoring

ARMI base-level monitoring will consist of a replicate 

checklists approach in which some national sampling frame is 

chosen (counties, blocks of area of specified dimensions, and 

so forth) and well-defined sampling schemes are implemented 

to provide adequate spatial representation across the landscape 

and to provide temporal representation to estimate detection 
that foster these stressors involve complex interactions among 

environmental conditions, including human land management. 

For example, although acid deposition can cause direct mortality of embryos of some species, other species are quite tolerant of acid conditions. Acidification, however, also increases 

the degradation of humic acids in water that normally protect 

aquatic organisms from ultraviolet radiation (Schindler and others, 1996), leading to the possibility that tolerant species could 

nonetheless be harmed by increased acid deposition. ARMI 

hopes to gain an understanding of these complexities by bringing together biological, hydrological, geographical, geological, 

toxicological, and statistical expertise to ensure access to a 

broad set of analytic approaches and tools.

ARMI will link the monitoring data collected with available and new information about environmental conditions in 

amphibian habitats and potential sources of amphibian stress 

(Little and others, 2003). A three-level approach of increasing 

complexity is proposed to determine relations among environmental conditions, stressors, and amphibian population 

declines. This approach includes tier 1—an initial survey of 

environmental conditions and potential stressors; tier 2—

experimentally based causal research to evaluate the effects 

of stressors on amphibians, with emphasis on evaluation of 

multiple stressors; and tier 3—evaluations of the relative risk 

from multiple stressors and recommendations for remediation.

Tier 1 Assessments

The objectives of tier 1 assessments are to evaluate existing information related to potential stressors at ARMI baselevel, mid-level, and apex monitoring sites. This will begin the 

process of evaluating stressors that may cause harm to amphibian populations. The focus of tier 1 assessments will be an evaluation of potential stressors (Little and others, 2003) conducted 

at mid-level and apex monitoring areas across the Nation.

Tier 1 assessments will include both desktop and onsite 

activities. From the desktop, ARMI regional coordinators will 

have access to existing Federal and non-Federal data, including information on land use and land cover, climate, chemical 

use, soils, and sources of pollution (Box C). These data will be 

accessed via a GIS-enabled Web application that will make it 

easy for ARMI researchers to view, query, and download information for the monitoring areas or sampling units of interest. 

The benefits of a Web-served tier 1 database are: (1) New data 

and updates are readily available to users; (2) functionality of the 

Web application can continue to grow with advances in interactive Web technology; (3) physical data media (for example, CDs 

and DVDs) and associated costs for production and distribution are avoided; and (4) dynamic access to external data sets is 

possible through a worldwide digital geographic data network. 

These benefits are particularly important for a monitoring program, where data collection is a continuing process.

Tier 1 assessments also can include in-the-field measurement of a range of environmental variables, including current 

habitat and weather conditions, water quality, and surveys 

Apex monitoring sites will not be chosen randomly. 

Some apex sites will be locations where population data 

already have been collected annually over the past several 

years. For new apex sites, selection should be based on several 

criteria. Locations with multiple species are desirable, but 

single species may be important for compelling reasons (for 

example, an endangered species). Single breeding sites probably should be avoided in favor of clusters of sites so that 

metapopulation processes (migration) can be studied. Sites 

should be generally representative of local amphibian habitats 

(artificial habitats should be avoided), and some sites should 

be chosen where potential exists for influences from known or 

suspected stressors. Logistics for reaching and monitoring the 

sites also should be a consideration. Apex monitoring sites are 

good candidates for intensive water-quality monitoring or any 

monitoring activities that are too expensive to conduct at midlevel monitoring sites.

Research on Causes of Declines

The causes of amphibian declines are varied and can be 

complex, and different approaches will be necessary if ARMI 

is to contribute to this rapidly developing field. Some research 

will be tactical—short-term research with a well-defined question to address a known problem for persistence of amphibian 

populations. However, because there are still significant gaps in 

our knowledge of what is causing the declines of many species, 

a major, multidisciplinary effort will be necessary to determine 

environmental factors responsible for the decline or malformation of amphibians. Stresses on amphibian populations come 

from a variety of sources, both natural and anthropogenic 

(Halliday and Heyer, 1997; Kiesecker and others, 2001; Krest 

and others, 2003; Lannoo and others, 2003), and the effects can 

depend upon life history and habitat of the affected species. The 

types of stressors amphibians experience and the conditions 

Photograph by William Battaglin

Research on Causes of Decline 11
12 Amphibian Research and Monitoring Initiative: Concepts and Implementation

In December 2001, the ARMI task force on stressors research presented a report outlining a three-tiered 

approach to investigate potential environmental factors contributing to amphibian declines and malformations. 

The broadest tier suggested a synoptic evaluation of existing environmental data to identify factors exhibiting 

spatial autocorrelation with geographic patterns of declines. This coarse-level evaluation would support development of research hypotheses through the compilation of a national database of amphibian decline response and 

potential predictor variables within a GIS framework. The ARMI program funded this approach in August 2002, 

and an environmental stressors team was formed. The team members are: Carl Korschgen and Jennifer Hamilton, 

Columbia Environmental Research Center; Alisa Gallant, EROS Data Center; William Battaglin, USGS Colorado 

Water Science Center; and Pat Anderson, Biological Status and Trends.

The objectives of the team are to: (1) Assist in coarse-filter analysis of relations between amphibian declines 

and environmental stressors, (2) compile a geospatial database of potential amphibian stressor predictor and 

response variables that will support this effort and more intensive analyses, and (3) develop a Web-enabled 

application to facilitate database analysis by providing user-interactive mapping and data download capabilities. 

Candidate stressors include:

Tier 1 Investigation into Stressors Associated with Amphibian Declines

Stressor Category—Habitat

Habitat quality

Extent and fragmentation of habitat

Water supply (hydroperiod)

Food web

Land-cover and land-use changes

Urbanization

Agriculture Silva and culture

Water source and quality

Wildland fires

Construction (for example, roads, agriculture,

 private or commercial development)

Stressor Category—Climate

Historic and long-term climate

 Departures from long-term averages for:

 Precipitation

 Temperature

 Snow Accumulation

 Timing of freeze/thaw

Current climatic conditions

 Departures from monthly mean precipitation 

 and temperature

 Increase/decrease in mean temperature

 Winter degree days, number of days above

 freezing

 Dates of first freeze and thaw

 Prevailing wind direction

 Humidity

Frequency and amount of rainfall

Flooding, droughts, and other extreme events

Ultraviolet radiation

Changes in cloud cover

Presence of vegetative cover or shading

Climate-change effects

Stressor Category—Biotic

Interspecific competition

Nonindigenous species

Native species

Predation

Disruption of food chain

Loss of food-chain organisms

Disruption of community dynamics

Regulating processes

Keystone species

Commensalism

Stressor Category—Disease

Infectious diseases

Known distribution factors that increase the 

 success of the pathogen

Carrier stages or carrier organisms

Stressor Category—Chemical

Chemical usage

Proximity to contaminant sources (for example, 

 agricultural crops, town dumps)

Influence from point source pollution (for 

 example, proximity to industrial area)

Aquatic pathways

Water-quality characteristics

Nutrients, pH, acid-neutralizing capacity, ions

Turbidity and dissolved organic carbon content 

 of water

Geologic characteristics

Soils, sediments, metals, pH

Air quality

Acid deposition

Smoke, smog

C
for nonindigenous species and disease or parasitism. Tier 1 

assessments will be conducted at selected monitoring sites in 

mid-level and apex-level monitoring areas, providing the basis 

for developing hypotheses about causes of amphibian decline 

or malformation. If resources permit, tier 1 assessments also 

will be extended to base-level monitoring sites, providing a 

foundation for data analysis at the regional or national scale.

Tier 2 Assessments

The objectives of tier 2 assessments are to determine the 

cause(s) of observed amphibian declines or malformations, to 

identify the stressors that lead to the harmful conditions, and 

to propose a management strategy to mitigate the problem. 

The analysis of tier 2 assessments will result in the definition 

of new or critical variables to be collected at mid-level and 

apex monitoring sites. Tier 2 assessments will include manipulative laboratory and field experiments, comparative monitoring, and analysis of amphibian data in conjunction with information on local or regional stressors (Little and others, 2003).

Tier 2 assessments will consist of hypotheses-driven 

experimental research in each region (for example, do chemicals that have sublethal effects on individual animals affect the 

persistence of populations?). Targeted stressors data will be 

collected concurrently with amphibian data to test the hypotheses. Tier 2 assessments will emphasize the evaluation of 

multiple stressors, each of which may cause harm to amphibian populations. This process will result in the identification 

of a large number of potential stressors and will attempt to 

determine their relative importance. Once a particular stressor 

is implicated in amphibian decline, that stressor will be incorporated into ARMI’s broader scale monitoring efforts.

Identification of potential stressors from tier 1 studies 

will be followed up by more specific studies of greater complexity. Likewise, the monitoring of potential stressors would 

begin with rapid, low-cost methods, such as toxicity tests with 

common test species or enzyme-linked immunosorbent assays 

(ELISA) to detect pesticide residues, and then proceed to more 

complex or costly methods.

Tier 3 Assessments

The objective of tier 3 assessments is to provide models 

that predict when and where amphibian species or habitats are 

at risk at a local, regional, or national scale. Tier 3 assessments 

will build on the information and understanding gained from 

tier 1 and tier 2 assessments. Information generated by the 

research will be used to develop and test habitat restoration 

or management strategies. Tier 3 assessments will provide an 

iterative decision-support process that will include probabilistic risk-assessment models of stressor effects on amphibian 

species, margins of error for injury, and focused monitoring of 

previously identified amphibian stressors. This type of analysis can be used to evaluate the relative risk of injury posed 

by a specified change in some environmental condition to all 

species in a sampling frame.

Although ARMI currently devotes funding to studies 

into the causes of declines, these studies are limited by the 

funding available to short-term, highly focused research on 

limited topics. Implementing the broader strategic research 

described herein will be difficult without additional funding 

(Box D).

Methods and Protocol Development

Sound methods for monitoring, assessing, and synthesizing information on amphibian populations are needed to meet 

ARMI objectives. As new methods are implemented, protocols should be documented to ensure consistency in application. Methods and protocols are important products to offer 

potential partners to help expand monitoring beyond DOI 

lands.

Methods development and protocol documentation will 

be a continuing process as ARMI evolves (Box E). Due to the 

diversity of amphibians, habitats, and risk factors, development of methods and protocols for an integrated program is 

complex. As results accumulate, new research directions are 

expected to emerge requiring adjustments to existing methods and protocols. To maintain the ARMI at the forefront of 

amphibian monitoring, appropriate new techniques, technology, analyses, and models will be incorporated into the 

program.

Methods development in the ARMI is in progress in 

eight categories: (1) Amphibian monitoring; (2) stressors 

monitoring; (3) trend analysis and correlation; (4) population, 

landscape, and stressors modeling; (5) geospatial information applications; (6) management decision-support tools; 

(7) database management structure, input, and output; and 

(8) metadata. Communication among the various groups 

developing methods and protocols will be critical to the integration of ARMI. Methods and protocols should be structured 

to enable researchers to meet ARMI goals. It should be clear 

how the methods and protocols contribute to the ability to 

Photograph by Priya Nanjappaaddress questions such as: What is the expected information 

Methods and Protocol Development 13
14 Amphibian Research and Monitoring Initiative: Concepts and Implementation

Recommended Actions

• Develop tier 1 assessment procedures to ensure uniformity in the evaluation of habitat conditions relative 

to physical, chemical, and biotic variables that are potentially harmful to amphibians. Identify sources of 

information and create a database tool to organize, manage, and serve the data to ARMI researchers.

• Initiate prototype projects that focus on amphibian habitats that appear to be impacted by a dominant 

stressor, such as contamination, disease or parasitism, physical habitat alteration, and(or) nonindigenous 

species. Use these projects to illustrate how to diagnose a multiple stressor problem. Form research teams to 

assist ARMI coordinators with site assessments and to conduct studies in support of the prototype projects.

• Form a working group(s) to identify, prepare, and organize protocols for research methods, such as for 

pathogens, contaminants, biotic indices of injury, and so forth.

Challenges to Implementation

• Funding for research in the ARMI program is limited, and allocation of resources in the most efficient 

way will require considerable oversight and evaluation. Evaluation of any stressor at ARMI sites across 

the nation will be expensive.

• DOI lands may not be the ideal location for some causal research because they lack some stressors (for 

example, urban development or agricultural use) that are common on non-DOI lands.

Stressors and Causal Research: Recommendations and Challenges

Recommended Actions

• Form a technical committee to facilitate communication, feedback, and consistency in methods development.

• Maintain an interactive Web site that stores information about currently applied data-collection and management protocols and reports of ongoing research on new methods and protocols.

• Allocate funding to support development of observational, statistical, and analytical techniques for 

amphibian monitoring.

• Provide an outlet for publishing data-collection protocols and metadata.

Challenges to Implementation

• Limited communication between the ARMI components and disciplines impedes collaboration.

• Diversity of amphibian life histories and habitats makes application of uniform and unbiased methods 

difficult.

• Diversity of the range and types of methods and protocols in this program (for example, in the eight areas 

identified) makes it difficult to keep everyone abreast of the most current information.

Methods and Protocols Development: Recommendations and Challenges

D

E
content of the data collected? How can the data be analyzed? 

How can the analyses address the major questions? How can 

all available analyses and information be synthesized into 

a broader understanding of amphibian issues? What are the 

limitations of the data, analyses, and syntheses in addressing amphibian issues? To integrate new collaborators, ARMI 

will strive to anticipate and develop methods and protocols 

compatible with the needs of our partners. Therefore, it also 

will be important to structure methods and protocols such that 

ARMI can adapt to emerging amphibian issues and incorporate new techniques that can better analyze and interpret 

historical and future monitoring data.

Database Development

Two national databases are associated with ARMI. One, 

the ARMI National Database, is a relational database that 

houses the ARMI field-survey data (Box F). This database 

will store amphibian survey data, including information about 

sampling methods, species observed, habitat, water chemistry, 

and additional related parameters. The database will feature 

Web-based data retrieval, allowing researchers, cooperators, 

and the public to view these data via the Web. Another database, the ARMI Atlas for Amphibian Distributions, represents 

a county-level (subcounty level for some States) compendium 

of historic to current species presence documented for all 

amphibian species known to occur in the U.S. Construction 

of amphibian distribution maps for the atlas began in 1999, 

with the compilation of documented records of presence from 

scientific literature, museum records, and regional expertise, to accompany the book “Amphibian Declines—The 

Conservation Status of United States Species” (Lannoo, 2005). 

A copy of this original database was acquired by ARMI. The 

ARMI Atlas Web site features photographs and distribution 

maps for all amphibian species known to occur in the U.S. 

(http://www.pwrc.usgs.gov/armiatlas/).

An integrated national database will have several benefits. ARMI investigators will have fewer data-management 

responsibilities—the relational database will be created and 

maintained for them. The ability to easily query these data sets 

should expedite data analyses. This data-management process 

should facilitate collaborative efforts among ARMI investigators and between ARMI scientists and the herpetological 

research community. Investigators will be able to readily identify the locations and goals of ongoing studies so that duplicity can be avoided while activities at nearby locations can be 

better coordinated. The availability of new results frequently 

leads to additional questions that require more research, 

allowing investigators to quickly add components to ongoing 

studies that would address these questions. Improved communication among investigators should result in faster response to 

management needs.

For land managers and administrators, this datamanagement process should improve access to timely information. Rapid access to information is becoming a necessity, 

allowing managers to more effectively initiate proper conservation and management activities on the ground, to the benefit 

of the amphibian communities. Amphibian populations have 

been shown to change dramatically during relatively short 

periods of time, and access to current information can be critical for identifying and implementing appropriate management 

actions for these taxa.

Analysis and Reporting

Analyses will be conducted to assess the status and 

trends of amphibian populations, to determine biotic and 

abiotic stressors, and to improve understanding of the relations 

between amphibians and the environment (Box G). Different 

mechanisms for reporting these results can be used to provide 

regional and national syntheses; to provide feedback for determining whether changes in protocols, monitoring strategies, 

and(or) research activities should be considered; and to provide 

decision-support tools for land managers and policymakers. 

Recommended Actions

• The national database must have the 

flexibility to allow differences among 

regions in the types of data collected 

and to allow a variety of different analyses. During the continuing development 

of the database, other models, such as 

a modular network (Baker and others, 

2000), needs to be given consideration.

• ARMI principal investigators need to 

take an active role in developing the 

implementation of the database.

• ARMI database developers need to be in 

frequent communication with principal 

investigators.

Challenges to Implementation

• The variety of data collected among the 

different regions means that the database 

will be complex and difficult to manage.

• Assimilation of regional data sets has 

been slower than anticipated.

Databases

Analysis and Reporting 15

F
16 Amphibian Research and Monitoring Initiative: Concepts and Implementation

Recommended Actions

• The team of national ARMI coordinators need to take leadership for coordinating analysis and reporting 

activities. This interdisciplinary team will determine how to integrate biological, hydrological, geographical, and statistical components into analyses and reports.

• National coordinators need to establish milestones and deliverables with the regional coordinators. Likewise, the regional coordinators need to establish who is responsible for what products and when those 

products will be available. Data ownership and the schedule for making data available to partners, managers, and the general public also need to be defined.

• Annual national meetings and more frequent conference calls or cyber meetings need to occur to achieve 

the required level of communication. A national, multidisciplinary program requires frequent communication among participants in order to ensure that program activities support program objectives. 

• Periodic external review of program activities and outputs need to be instituted to maintain program relevance and defensibility. ARMI currently has a steering committee comprised of members both external 

and internal to the USGS that can address this need.

Challenges to Implementation

• Perhaps the greatest challenge to implementing broad-scale analysis and reporting on amphibian status 

and trends is the multidimensional complexity of the task. Amphibian monitoring methods can differ by 

region, by species, and by stage of development, so nationally consistent data-collection methodology is 

not feasible. Accordingly, sample designs will vary across the country, making consistency in reporting a 

challenge.

• Communication among ARMI participants is insufficient to meet program objectives. Because of the 

many responsibilities placed on regional coordinators, communication outside the region has not been 

given a priority. ARMI national coordinators should work with regional coordinators to decide how best 

to effect more frequent communication among regional and national coordinators.

Analysis and Reporting: Recommendations and Challenges

Reports will include descriptions of field and laboratory 

research, regional and national status and progress reports, 

methods and protocol documentation, field-survey raw data and 

summaries, and administrative summaries regarding operational 

challenges and integration of partners. Forms of reporting will 

include peer-reviewed journal articles, USGS publications, 

administrative reports, maps, factsheets, oral presentations, 

posters, and Web pages.

ARMI regional coordinators will be responsible for conducting analyses and compiling reports. Regional differences 

in environmental complexities, site availability and(or) access, 

species richness, and complexity in sample designs virtually 

ensure that the scope of these responsibilities and the analyses 

will vary by region. Communication among regional coordinators, national coordinators, and the ARMI steering committee 

is essential if information collected by ARMI is to be integrated across spatial scales and disciplines.

Some activities will produce nonroutine publications 

from current ARMI-sponsored research on specific stressorsspecies interactions and from comparison of coarse-scale 

species distribution patterns with patterns of environmental 

characteristics. These publications, together with routine 

summary reports, will provide a broader understanding of 

factors operating at different scales that affect amphibian 

conservation.

It will require several years for ARMI to have a fully operational field component and routine analysis and reporting procedures, but the current design is producing immediate results 

and information. Of the approximately 290 amphibian species 

in the U.S., and as of the field season of 2003, ARMI has been 

studying 61 species in mid-level monitoring areas and 62 species at apex monitoring sites—monitoring 84 species overall. 

In some cases, there are sufficient data to begin examining 

change in occupancy with time; how many and which species 

increased, decreased, or remained the same; and if the direction 

of change can be predicted by environmental conditions at the 

local level (rainfall, drought, habitat loss). With longer monitoring, ARMI will begin to address ecological processes, including 

the identification of true declines, stressor effects on population 

dynamics, and metapopulation dynamics.

G
Integrating data from a variety of sources presents a challenge for national reporting, but the data can be interpreted 

and summarized using an ecoregion framework (Omernik, 

1995). Ecoregions are useful environmental units for interpretation and reporting because they represent areas where there 

are more environmental homogeneity in characteristics such 

as climate, terrain, geology, soils, vegetation, and land use 

than occurs across units, and they can be hierarchically scaled 

as needed. Selection of an appropriate ecoregion framework 

will stratify the broader scale environmental and human factors affecting amphibians. The ecoregions provide a geographic context for generalizing or extrapolating environmental or stressor data collected at specific monitoring locations 

to amphibian and environmental data collected elsewhere or 

at other times within an ecoregion. An ecoregional framework 

also can be used to establish sites for long-term monitoring 

and research. Various ecoregion maps have been developed 

(Bailey, 1995; Omernik and Bailey, 1997; Griffith and others, 

1999), but the framework developed by Omernik (1995) best 

incorporates the human interaction with the environment. A 

challenge facing ARMI is that Federal lands are generally not 

representative of the ecoregion where they occur. Most Federal 

lands were so designated because they are unique in some 

way and were not perceived to be amenable to early economic 

development.

Despite the necessity of using a wide variety of sampling techniques and designs, ARMI monitoring data will be 

comparable across the country for mid-level and apex monitoring areas. For mid-level monitoring areas, direct estimates 

of occupancy only will be comparable among monitoring 

areas that use the same sampling units (for example, ponds). 

Trends in occupancy, however, can be compared and summarized among all species and all mid-level monitoring areas 

across the country. This will allow both regional and national 

tabulations on the proportion of species that are declining in 

mid-level monitoring areas. These tabulations, in turn, can be 

compared over time to track the status of amphibians regionally and nationally. Similarly, trends in amphibian abundance 

in apex monitoring areas can be summarized and tracked 

despite a wide range of methodology.

Some ARMI reporting will encourage participation by 

collaborators. By widely sharing information on the methods 

and protocols developed for ARMI, the program can indirectly influence the way in which data are collected by other 

researchers. The ARMI public Web site (http://armi.usgs.gov/) 

is available to encourage information sharing.

ARMI also will encourage partnerships through reciprocal exchange. While ARMI collects data on amphibians at 

sites under the jurisdiction of the partners, the partners will 

gain access to protocols that ARMI has developed and(or) to 

the ancillary environmental data that ARMI has compiled for 

the partners’ sites. Additionally, ARMI’s broader geographic 

scope will provide the partners with a regional or national 

context from which to compare their own sites.

Partners and Leadership

Building relationships with partners is a major component of the ARMI program (Box H). ARMI partners in the 

DOI, the USFWS, the NPS, and the BLM, have long looked 

to the USGS for assistance with monitoring amphibians on 

Federal lands. These agencies also need status and trends 

information about U.S. amphibians to set land-management 

policy. Other Federal partners, such as the U.S. Environmental 

Protection Agency (USEPA), the USDA Forest Service, and 

the USDA Natural Resources Conservation Service, and 

State partners also can utilize the information ARMI collects to make decisions about environmental regulations, land 

management, conservation incentive policies, and landowner 

education needs. Implementation of the ARMI will be greatly 

enhanced by cooperative relationships with State agencies 

(Departments of Natural Resources), State herpetological 

societies, and amphibian education and conservation organizations such as the Declining Amphibian Populations Task Force 

(http://www.open.ac.uk/daptf/) and Partners for Amphibian 

and Reptile Conservation (http://www.parcplace.org/). There 

are a multitude of organizations, academic institutions, and 

agencies concerned with amphibian conservation (see Web 

Photograph by William Battaglinsites listed above).

Partners and Leadership 17
18 Amphibian Research and Monitoring Initiative: Concepts and Implementation

Recommended Actions

• Priorities should be set to identify individuals responsible for national components of the program and to 

set time lines for implementation and deliverables. Resouces should be allocated according to established 

priorities.

• Communication should be initiated by ARMI regional coordinators with the partners in each region, and 

periodic meetings should be held to share information on research and monitoring activities to advance 

the understanding of status, trends, and threats to amphibians.

• Products should be developed, such as Web sites and a survey database, that will engage the partner agencies and States in contributing to the monitoring effort.

• Information should be exchanged by ARMI with other Federal agencies engaged in monitoring efforts. 

Information on the experiences, successes, and failures of other national monitoring programs could save 

valuable resources.

• University research partners with herpetological expertise should be sought out by ARMI. ARMI coordinators can facilitate amphibian research through funding opportunities regionally and nationally.

• A unified set of methods and analyses for all amphibian monitoring and research in the USGS should be 

developed to increase communication within and outside of ARMI.

Challenges to Implementation

• The wide diversity of potential partners, within and across regions, will challenge the organizational and 

communication skills of the ARMI coordinators.

• Building an integrated partner network will require effort from all partners, including USGS, and will take 

time to develop.

• The responsibility for protection and conservation of amphibian populations resides with the States and 

must be respected and recognized by ARMI. All research and monitoring efforts must abide by State laws 

for scientific research permits, specimen collection, and reporting.

• Many ARMI researchers have other research or administrative duties that keep ARMI duties from being a 

first priority.

Partnerships, Leadership, and Integration: Recommendations 

and Challenges

Partnerships are important at every level of the monitoring pyramid. As a first priority, ARMI is working with 

DOI land-management partners to identify Federal lands for 

establishing mid-level monitoring areas. As ARMI matures, 

non-Federal partners, such as States and nongovernmental 

organizations, may choose to participate by collecting 

similar data from a broad range of Federal and non-Federal 

sites.

At the base of the pyramid, partnerships are critical 

for collecting information on status and trends of amphibian populations across the landscape. State agencies have the 

primary responsibility for managing amphibian populations, 

except for those species federally listed as threatened or endangered. These agencies, therefore, are important partners for 

broad-based data collection. Many State agencies already are 

engaged in amphibian atlas projects or are implementing frog 

and toad calling surveys in collaboration with the NAAMP. The 

public can directly contribute observations that may provide 

useful monitoring information via the Frogwatch USA project 

or report on amphibian malformations using NARCAM. At the 

apex of the pyramid are intensive, long-term monitoring sites 

and sites with long-term active research. Some of these include 

the PRIMENET sites located within the national parks (http://

www.forestry.umt.edu/research/MFCES/programs/primenet/). 

The NPS and the USEPA have been engaged in long-term 

monitoring of national parks for ecosystem stressors since 

1996. Universities and other individuals and agencies also have 

engaged in intensive research, and occasionally, monitoring of 

specific sites (Lannoo, 1996).

H
The ARMI will develop collaborative relations with 

agencies and organizations possessing valuable broad-based 

data and expertise and will explore ways to integrate this 

information into regional and national status and trends reports 

for amphibians. Information developed through the ARMI 

program should be relevant and useful to partner agencies and 

organizations charged with land management and conservation 

of amphibian populations.

International partnerships may provide an important context for the information collected within ARMI. Many factors 

contributing to amphibian disease, declines, and malformations may not be limited to the U.S. or North America (Green, 

1997).

Because of its strong commitment to partnerships, 

the ARMI has convened a steering committee composed 

of members from academia, State and Federal research and 

resource-management agencies, and other interested organizations (see http://armi.usgs.gov/region.asp#nationalsteering). 

The steering committee will advise and provide recommendations to the ARMI program and its principal investigators on 

the direction of the program, research and monitoring priorities, reporting requirements, and development of partnerships. 

The chairperson will be the principal liaison between the 

steering committee and the Assistant Wildlife and Terrestrial 

Resources Program Coordinator, who is the ARMI Program 

Coordinator. The ARMI Program Coordinator will work with 

the ARMI coordinators for Biology, Water, and Mapping to 

provide oversight and leadership for the program.

Integration

The objectives and scope of ARMI are ambitious and 

complex, but they are necessary to address the complex ecological and management issues of amphibians. The conceptual 

designs outlined by this report are in various stages of implementation and, in some instances, have been in operation for 

several years. Integration will be the key to realizing a fully 

functional ARMI program.

Photograph by Robin Jung

Integration must proceed in multiple directions—across 

regions, across disciplines, across the levels of the ARMI 

pyramid, and across time. Ideally, ARMI will evolve into an 

integrated and adaptive research and monitoring program, 

working continuously to refocus, refine, or redirect its questions as results accumulate or new issues emerge. A designated science coordinator at the national level would ensure 

that these needs are met and could help maintain an appropriate scientific balance between continuation of past monitoring 

efforts and flexibility for implementation of new directions.

Photograph by William Brian Hughes

The conceptual designs described in this report for 

amphibian monitoring and stressors research should give 

ARMI the flexibility to become an adaptive program. Amphibian monitoring is focusing on a national approach at the 

mid-level of the pyramid using methods and protocols that 

allow regional principal investigators to tailor their activities 

to local amphibian communities and habitats, while providing 

comparable amphibian metrics and easy transferability to new 

partners. The proposed statistical estimators address key biological issues and use stressors data to model and test hypotheses of cause-effect. Stressors monitoring and research are 

focused on a tiered approach to first broadly identify stressors 

at a national and regional level, then focus investigations at 

the local level to the most likely candidates, and finally apply 

hypotheses-driven research and modeling efforts. This tiered 

approach to identifying the causes of decline or malformations 

has considerable flexibility and adaptability.

Achieving integration, however, will not be easy due to 

the complexity of the Initiative. Coordinating the component 

parts into a well-integrated national program will require the 

full-time efforts of more than one individual. As partners come 

into the program and data accumulate for processing, analysis, and reporting, the integration of the program will grow in 

complexity. It is critical to anticipate ARMI needs for the near 

and distant future and to begin to strengthen the infrastructure 

for national coordination and integration.

Partners and Leadership 19
20 Amphibian Research and Monitoring Initiative: Concepts and Implementation

References Cited

Alford, R.A., Dixon, P.M., and Pechmann, J.H.K., 2001, 

Global amphibian population declines: Nature, v. 412, 

p. 499–500.

Alford, R.A., and Richards, S.J., 1999, Global amphibian 

declines—A problem in applied ecology: Annual Review 

of Ecology and Systematics, v. 30, p. 133–165.

Anderson, D.R., 2001, The need to get the basics right in 

wildlife field studies: Wildlife Society Bulletin, v. 29, 

p. 1294–1297.

Anderson, D.R., 2003, Response to Engeman—Index values 

rarely constitute reliable information: Wildlife Society Bulletin, v. 31, p. 288–291.

Bailey, L.L., Simons, T.R., and Pollock, K.H., 2004, Estimating site occupancy and species detection parameters for 

terrestrial salamanders: Ecological Applications, v. 14, 

p. 692–702.

Bailey, R.G., 1995, Description of the ecoregions of the 

United States, 2d ed.: Washington, D.C., USDA Forest 

Service, Miscellaneous Publication 1391.

Baker, K.S., Benson, B.J., Henshaw, D.L., Blodgett, D., Porter, 

J.H., and Stafford, S.G., 2000, Evolution of a multisite network information system—The LTER information management paradigm: BioScience, v. 50, p. 963–978.

Berven, K.A., and Grudzien, T.A., 1990, Dispersal in the wood 

frog (Rana sylvatica)—Implications for genetic population 

structure: Evolution, v. 44, p. 2047–2056.

Boulinier, T., Nichols, J.D., Hines, J.E., Sauer, J.R., Flather, 

C.H., and Pollock, K.H., 1998, Higher temporal variability 

of forest breeding bird communities in fragmented landscapes: Proceedings of the National Academy of Sciences, 

U.S.A., v. 95, p. 7497–7501.

Bury, R.B., and Whelan, J.A., 1984, Ecology and management 

of the bullfrog: Washington, D.C., USDI Fish and Wildlife 

Service, Resource Publication 155, 23 p.

Cam, E., Nichols, J.D., Sauer, J.R., Hines, J.E., and Flather, 

C.H., 2000, Relative species richness and community 

completeness—Avian communities and urbanization in 

the mid-Atlantic states: Ecological Applications, v. 10, 

p. 1196–1210.

Caughley, G., and Sinclair, A., 1994, Wildlife ecology 

and management: Cambridge, Massachusetts, Blackwell 

Science.

Collins, J.P., and Storfer, A., 2003, Global amphibian declines—

Sorting the hypotheses: Diversity and Distributions, v. 9, 

p. 89–98.

Committee on Environment and Natural Resources, 1997, 

Integrating the Nation’s environmental monitoring and 

research networks and programs—A proposed framework: 

National Science and Technology Council’s Committee 

on Environment and Natural Resources Report, 103 p. 

Accessed February 2001 at http://www.epa.gov/cludygxb/

pubs.html

Engeman, R.M., 2003, More on the need to get the basics 

right—Population indices: Wildlife Society Bulletin, v. 31, 

p. 286–287.

Erwin, R.M., Nichols, J.D., Eyler, T.B., Stotts, D.B., and 

Truitt, B.R., 1998, Modeling colony-site dynamics—A 

case study of gull-billed terns (Sterna nilotica) in coastal 

Virginia: The Auk, v. 115, p. 970–978.

Gill, D.E., 1978, The metapopulation ecology of the redspotted newt, Notophthalmus viridescens (Rafinesque): 

Ecological Monographs, v. 48, p. 145–166.

Green, D.M., 1997, Perspectives on amphibian population 

declines—Defining the problem and searching for answers, 

in Green, D.M., ed., Amphibians in decline—Canadian 

studies of a global problem: St. Louis, Missouri, Society 

for the Study of Amphibians and Reptiles, Herpetological 

Conservation, v. 1, p. 291–308.

Green, D.M., 2003, The ecology of extinction—Population 

fluctuation and decline in amphibians: Biological Conservation, v. 111, p. 331–343.

Griffith, G.E., Omernik, J.M., and Woods, A.J., 1999, Ecoregions, watersheds, basins, and HUCs—How state and Federal agencies frame water quality: Journal of Soil and Water 

Conservation, v. 54, p. 666–677.

Halliday, T.R., and Heyer, R., 1997, The case of the vanishing 

frogs: Accessed March 2000 at http://www.techreview.com/

articles/mj97/halliday.htm

Hanski, I., and Gilpin, M.E., eds., 1996, Metapopulation 

biology—Ecology, genetics, and evolution: San Diego, 

California, Academic Press.

Hines, J.E., Boulinier, T., Nichols, J.D., Sauer, J.R., and 

Pollock, K.H., 1999, COMDYN—Software to study the 

dynamics of animal communities using a capture-recapture 

approach: Bird Study 46 (suppl.), S209–S217.

Houlahan, J.E., Findlay, C.S., Schmidt, B.R., Meyer, A.H., 

and Kuzmin, S.L., 2000, Quantitative evidence for global 

amphibian population declines: Nature, v. 404, p. 752–755.

Joly, P., Miaud, C., Lehmann, A., and Grolet, O., 2001, Habitat matrix effects on pond occupancy by newts: Conservation Biology, v. 15, p. 239–248.
Kareiva, P., Skelly, D., and Ruckelshaus, M., 1997, Reevaluating the use of models to predict the consequences of habitat 

loss and fragmentation, in Pickett, S.T.A., Ostfeld, R.S., 

Shachak, M. and Likens, G.E., eds., The ecological basis 

of conservation: New York, Chapman and Hall, p. 156–166.

Kiesecker, J.M., Blaustein, A.R., and Belden, L.K., 2001, 

Complex causes of amphibian population declines: Nature, 

v. 410, p. 681–684.

Krest, S.K., Linder, G., and Sparling, D.W., 2003, The role of 

multiple stressor causes in declining amphibian populations—

A wingspread workshop summary, in Linder, G., Krest, S., 

Sparling, D., and Little, E., eds., Multiple stressor effects in 

relation to declining amphibian populations: Bridgeport, New 

Jersey, American Society for Testing and Materials STP1443, 

p. 207–218.

Lannoo, M.J., 1996, Okoboji wetlands: Iowa City, University 

of Iowa Press.

Lannoo, M.J., ed., 2005, Amphibian declines—The conservation status of United States species: Berkeley, University of 

California Press.

Lannoo, M.J., Sutherland, D., Jones, P., Rosenberry, D., 

Klaver, R., Hoppe, D., Johnson, P., Lunde, K., Facemire, 

C., and Kapfer, J., 2003, Multiple causes for the malformed 

frog phenomenon, in Linder, G., Krest, S., Sparling, D., and 

Little, E., eds., Multiple stressor effects in relation to declining amphibian populations: Bridgeport, New Jersey, American Society for Testing and Materials STP1443, p. 233–262.

Linder, G., Krest, S.K., and Sparling, D.W., eds., 2003, 

Amphibian decline—An integrated analysis of multiple 

stressor effects: Pensacola, Florida, SETAC Press.

Little, E.E., Bridges, C.M., Linder, G., and Boone, M., 2003, 

Establishing causality in the decline and deformity of 

amphibians—The amphibian research and monitoring 

initiative model, in Linder, G., Krest, S., Sparling, D., and 

Little, E., eds., Multiple stressor effects in relation to declining amphibian populations: Bridgeport, New Jersey, American Society for Testing and Materials STP1443, p. 263–277.

MacKenzie, D.I., and Kendall, W.L., 2002, How should detection probability be incorporated into estimates of relative 

abundance?: Ecology, v. 83, p. 2387–2393.

MacKenzie, D.I., Nichols, J.D., Hines, J.E., Knutson, M.G., 

and Franklin, A.B., 2003, Estimating site occupancy, colonization, and local extinction when a species is detected 

imperfectly: Ecology, v. 84, p. 2200–2207.

Mackenzie, D.I., Nichols, J.D., Lachman, G.B., Droege, S., 

Royle, J.A., and Langtimm, C.A., 2002, Estimating site 

occupancy rates when detection probabilities are less than 

one: Ecology, v. 83, p. 2248–2255.

Marsh, D.M., and Trenham, P., 2001, Metapopulation dynamics and amphibian conservation: Conservation Biology, 

v. 15, p. 40–49.

Meteyer, C.U., 2000, Field guide to malformations of frogs 

and toads: Reston, Virginia, U.S. Geological Survey, 

Biological Science Report USGS/BRD/BSR–2000–0005, 

18 p.

Meyer, A.H., Schmidt, B.R., and Grossenbacher, K., 1998, 

Analysis of three amphibian populations with quartercentury long time-series: Proceedings of the Royal Society 

of London B 265, p. 523–528.

Nichols, J.D., and Conroy, M.J., 1996, Estimation of species 

richness, in Wilson, D.E., Cole, F.R., Nichols, J.D., Rudan, 

R., and Foster, M.S., eds., Measuring and monitoring biodiversity—Standard methods for mammals: Washington, 

D.C., Smithsonian Institution Press, p. 226–234.

Nichols, J.D., Boulinier, T., Hines, J.E., Pollock, K.H., and 

Sauer, J.R., 1998a, Estimating rates of local species extinction, colonization, and turnover in animal communities: 

Ecological Applications, v. 8, p. 1213–1225.

Nichols, J.D., Boulinier, T., Hines, J.E., Pollock, K.H., and 

Sauer, J.R., 1998b, Inference methods for spatial variation in species richness and community composition when 

not all species are detected: Conservation Biology, v. 12, 

p. 1390–1398.

Omernik, J.M., 1995, Ecoregions—A spatial framework for 

environmental management, in Davis, W.S., and Simon, 

T.P., eds., Biological assessment and criteria: Boca Raton, 

Florida, Lewis Publishers, p. 49–62.

Omernik, J.M., and Bailey, R.G., 1997, Distinguishing 

between watersheds and ecoregions: Journal of the American Water Resources Association, v. 33, p. 935–949.

Pechmann, J.H.K., Scott, D.E., Semlitsch, R.D., Caldwell, J.P., 

Vitt, L.J., and Gibbons, J.W., 1991, Declining amphibian 

populations—The problem of separating human impacts 

from natural fluctuations: Science, v. 253, p. 892–895.

Schindler, D.W., Curtis, P.J., Parker, B.R., and Stainton, M.P., 

1996, Consequences of climate warming and lake acidification for UV-B penetration in North American boreal lakes: 

Nature, v. 379, p. 705–708.

Schmidt, B.R., 2003, Count data, detection probabilities, 

and the demography, dynamics, distribution, and decline 

of amphibians: Comptes Rendus Biologies 326 (suppl.), 

p. S119–S124.

Semlitsch, R.D., ed., 2003, Amphibian conservation: Washington, D.C., Smithsonian Press.

Literature Cited 21
22 Amphibian Research and Monitoring Initiative: Concepts and Implementation

Semlitsch, R.D., Scott, D.E., Pechmann, J.H.K., and Gibbons, 

J.W., 1996, Structure and dynamics of an amphibian community evidence from a 16-year study of a natural pond, in

Cody, M.L., and Smallwood, J.A., eds., Long-term studies 

of vertebrate communities: San Diego, California, Academic Press, p. 217–248.

Sinsch, U., 1992, Structure and dynamic of a natterjack 

toad metapopulation (Bufo calamita): Oecologia, v. 90, 

p. 489–499.

Sinsch, U., and Seidel, D., 1995, Dynamics of local and temporal breeding assemblages in a Bufo calamita population: 

Australian Journal of Ecology, v. 20, p. 351–361.

Sjögren, P., 1991, Extinction and isolation gradients in 

metapopulations—The case of the pool frog (Rana 

lessonae): Biological Journal of the Linnean Society, 

v. 42, p. 135–147.

Sjögren Gulve, P., 1994, Distribution and extinction patterns 

within a northern metapopulation of the pool frog, Rana 

lessonae: Ecology, v. 75, p. 1357–1367.

Skelly, D.K., Werner, E.E., and Cortwright, S.A., 1999, Longterm distributional dynamics of a Michigan amphibian 

assemblage: Ecology, v. 80, p. 2326–2337.

Smith, C.K., and Petranka, J.W., 2000, Monitoring terrestrial 

salamanders—Repeatability and validity of area-constrained 

cover object searches: Journal of Herpetology, v. 34, 

p. 547–557.

Storfer, A., 2003, Amphibian declines—Future directions: 

Diversity and Distributions, v. 9, p. 151–163.

Stuart, S.N., Chanson, J.S., Fox, N.A., Young, B.E., Rodrigues, 

A.S.L., Fischman, D.L., and Waller, R.W., 2004, Status and 

trends of amphibian declines and extinctions worldwide: 

Science, v. 306, p. 1783–1786.

Thomas, C.D., Cameron, A., Green, R.E., Bakkenes, M., 

Beaumont, L.J., Collingham, Y.C., Erasmus, B.F.N., 

Ferriera de Siqueira, M., Grainger, A., Hannah, L., Hughes. 

L., Huntley, B., van Jaarsveld, A.S., Midgley, G.F., Miles, 

L., Ortega-Huerta, M.A., Peterson, A.T., Phillips, O.L., and 

Williams, S.E., 2004, Extinction risk from climate change: 

Nature, v. 427, p. 145–148.

Vos, C.C., and Stumpel, H.P., 1996, Comparison of habitatisolation parameters in relation to fragmented distribution 

patterns in the tree frog (Hyla arborea): Landscape Ecology, 

v. 11, p. 203–214.
A

Amphibian decline When the loss of 

amphibian populations across their normal 

range exceeds the rate at which populations 

are established, or reestablished, resulting in a 

downward trend in the number of populations.

Amphibian malformation Primary errors in 

any phase of morphogenesis including cell 

proliferation, cell migration, differentiation, 

programmed cell death, or regression of larval 

structures (Meteyer, 2000).

Apex monitoring area An area, usually a 

Department of the Interior (DOI) land unit, 

that contains one or more apex monitoring 

sites.

Apex monitoring site Handpicked sites 

for intensive monitoring and research often 

consisting of egg counts, population estimates, demographic studies, or other detailed 

population-scale work.

ARMI Amphibian Research and Monitoring 

Initiative, a program funded by the U.S. 

Congress in 2000 to determine the status of 

amphibians in the U.S. and the causes for 

declines.

B

Base-level site A site monitored regularly 

or irregularly for amphibian species presence 

that can be on DOI land or other lands, or part 

of an ARMI-funded study, and may include 

data reported by the public.

C

Causal research Research into the causes of 

amphibian decline or malformation.

D

Detection probability The likelihood that a 

particular species will be detected during one 

visit to a sampling site. Animal population 

monitoring surveys rarely identify all animals 

present at a sampling site.

M

Mid-level monitoring area A defined area 

for which a probabilistic sampling design will 

allow estimates of occupancy to apply. These 

areas may include individual or multiple 

parks, refuges, or any other land units where 

amphibian monitoring will be conducted.

Mid-level monitoring site A site that is 

selected from a set of potential sites within a 

mid-level monitoring area with some known 

probability and is surveyed one or more times 

for the presence of amphibian species.

O

Occupancy An unbiased estimate of the 

proportion of area or sites occupied by a 

particular amphibian species that incorporates 

the detectability of the species.

S

Sample frame An area over which occupancy or species-richness data will be analyzed and interpreted. For most ARMI studies, 

this equates with the mid-level monitoring 

area. The sample frame defines the range of 

inference of the data that will be collected and 

defines the sampling units.

Sample sites and(or) units Individual ponds, 

caves, wetlands, stream reaches, terrestrial 

quadrats, and so forth, that are occupied by 

an amphibian species. For most ARMI studies, sample sites are aggregated within the 

mid-level monitoring sites.

Species richness The number of amphibian species detected. This metric can be used 

to monitor spatial and temporal changes in 

targeted communities and can be applied to 

individual sites or the sample frame. 

Stressor An environmental condition that 

alone or in combination with other conditions 

exceeds the range of an organism’s tolerance 

and results in a decline in the viability of the 

organism and its population.

Glossary of Terms and Abbreviations

Glossary of Terms and Abbreviations 23