National efforts, which include database development, geospatial environmental correlative studies, and identification and design of nationally meaningful, regionally calibrated amphibian monitoring variables.
	Regional efforts, which include statistical design of field surveys, development of field protocols, geospatial environmental correlative studies, and analysis of amphibian and habitat data.
	Local efforts, which include effects research, amphibian population research, and development of field protocols.
	Laboratory efforts, which include health, disease, and malformations research.

National Efforts

Database Development - Development of a national amphibian database is an important ARMI Program component.

Geospatial Environmental Correlative Studies - Comparisons of broad-scale patterns of amphibian distributions with current and historic patterns of environmental characteristics are underway to facilitate the development of hypotheses about influences on amphibian distributions and support efforts toward amphibian conservation. An example of the latter is shown in Figure 1, which illustrates that regions of the country having the greatest diversity in amphibian species are also regions of high rates of land-cover and land-use change.

Monitoring Variables - While all amphibian monitoring is being conducted at the regional and local levels in ARMI, considerable research is being invested in developing and testing variables whose interpretation can be integrated at the national level. Focus is currently on an estimator called "Percent Area Occupied" (PAO), which evaluates the fraction of the landscape that is occupied by an amphibian species, rather than a species' actual abundance across the landscape. Benefits of the PAO estimator are that:

	It yields species-specific, statistically valid information about the proportion of sampling areas - for example, caves, ponds, wetlands, or terrestrial habitat - that a species occupies and uses.
	It was designed to estimate and account for the fact that a species may be present but undetected during a survey. Without compensating for this unavoidable type of error, researchers can underestimate the true occurrence of a species and inaccurately conclude that the species has declined.
	The number and location of sites to be monitored are chosen with statistical approaches, that ensure adequate assessments across the landscape.
	This approach allows scientists to better estimate the rate of change in the amount of land occupied by a species over space and time and to directly estimate status and trends.
	With the simultaneous monitoring of environmental factors at sites it is possible to assess the evidence for potential causes of a species decline.
	Field methods can be tailored to different kinds of habitats, landscapes, and amphibian communities.

Back to Top

Regional Efforts

Statistical Design of Field Surveys - Amphibians pose a number of difficulties for designing surveys to determine long-term trends. An ideal survey would include unbiased estimates of population size at every location studied. Unfortunately, population estimates for most amphibians are difficult and expensive to obtain. Many amphibian surveys employ indices as surrogates to population estimates, but a useful index must provide unbiased estimates of changes in abundance. In order to provide unbiased estimates, the numbers of adults, tadpoles, or egg masses recorded must reflect a constant proportion of the true population size, both among study sites and among years at the same study site. Otherwise, variation in the proportion detected should be accounted for using covariates (e.g., weather conditions) that are known to affect detection probability but not abundance, itself. It is doubtful that indices arising from simple counts during amphibian surveys meet these requirements.

ARMI is implementing statistical methods that use information on presence/absence of species at a collection of sites to estimate a population-level parameter, proportion of area occupied by each species (PAO), and a community-level parameter, species abundance. The fact that amphibian populations tend to have high interannual variability will complicate the interpretation of such data, but interpretation will improve with cumulative collection over years.

The sample frame used for determining where to collect field data must be tailored to the species and landscape of interest. For example, the monitoring area need not be one contiguous unit, but a network of refuges. Alternatively, the framework might be based on a stratification of habitats within a single park or refuge. [See an example of a sample frame design]

Field survey techniques should include all appropriate and feasible methods for detecting species in the area and should be applied consistently on all the defined sample units (e.g., ponds, stream reaches, terrestrial quadrats). Repeated surveys on the sample units during a field season will be used to estimate detectability, which refers to the near-universal situation in animal population monitoring in which survey methods do not detect all animals present in the sampled area. The PAO estimator is designed to incorporate data from repeated samples such that the estimated changes in PAO reflect true changes in occupancy and not simply changes in detectability.

While the PAO approach provides species-specific parameter estimates, the species richness approach 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 different locations is one means of tracking the status of amphibians as a group, and can add another level of information to that garnered from the PAO approach. Furthermore, detection of a change in species richness can alert biologists and managers to potential problems that may require more focused study.

Back to Top

Development of Field Protocols - Sound methods for monitoring, assessing, and synthesizing information on amphibian populations are needed to meet ARMI objectives. As methods are implemented, protocols are described to ensure consistency in application. Documentation of protocols is particularly important because of the degree to which ARMI relies on partnerships in order to expand monitoring beyond Department of Interior lands.

Due to the diversity of amphibians, habitats, and risk factors, development of protocols is complex. Existing methods are adapted and new methods are developed. As results accumulate, new research directions are expected to emerge, requiring adjustments to existing protocols. The variety of protocols needed is wide, spanning the statistical design for selecting monitoring sites, field measurements and handling of samples, stressors monitoring, analysis and reporting of data, database management, and data documentation.

ARMI provides information on protocols through multiple venues. Those accessible through the internet include our “Products” page, which has listings of publications and hotlinks to some protocol descriptions and field guides, and the web sites for several of the USGS Centers participating in ARMI. For example, the National Wildlife Health Center already has a set of Standard Operating Procedures available online for the handling of amphibian samples; the Southeast ARMI Region provides information about biosecurity for field sampling; and the Northeast ARMI Region provides descriptions of the survey protocols they follow for sampling of vernal pond and stream amphibians.

Geospatial Environmental Correlative Studies - As with national-level correlative studies, efforts are also underway to conduct such research at the regional level. ARMI scientists have compiled a geospatial database to support assessment of associations between amphibian declines and environmental stressors. This type of assessment will be used to generate hypotheses for future research and to refine the types and locations of ARMI survey data collected in the field. The classes of environmental predictor variables included in the database are: 1) land cover/use, 2) climate and weather, 3) agricultural chemicals, 4) transportation routes, 5) percent impervious surface, and 6) fire potential. Internet links to additional data on potential stressors, such as for air, water, and terrestrial contaminants, have been catalogued and provided to ARMI investigators.

Analysis of Amphibians and Habitat Data - To improve their understanding of amphibian-habitat relations, ARMI scientists also record detailed descriptive habitat characteristics as well as amphibian species data at every field site. Subsequent statistical analyses help illuminate associations between species and vegetation cover (e.g., community type, ground/canopy cover, duff layer), land use, terrestrial settings (e.g., elevation, aspect, slope, substrate), and weather conditions (e.g., air temperature, wind speed, precipitation). Data collected for aquatic habitats include variables for water chemistry (e.g., hardness, conductivity, pH), physical parameters (e.g., size and depth of waterbody, flow rates, substrate), and aquatic vegetation (e.g., species, density, height above water). [ Visit the USGS Toxic Substances Hydrology Program web site for further information on water quality investigations for the ARMI Program.]

Back to Top

Local Efforts

Effects Research- The intensive data requirements for assessing the status of specific amphibian populations and the associated effects of potential environmental stressors can most reasonably be carried out at the local level. At this level, often working with cooperators from other agencies (e.g., the National Park Service, the U.S. Forest Service, and the Environmental Protection Agency), USGS scientists can focus research on particular stressors of concern. Topics include investigation of UV doses in amphibian habitats [read about an example in the western U.S.], the effects of introduced species [read about the impacts of fish-stocking on amphibians], pesticides [read about an example of airborne pesticides] and other contaminants, alteration of hydrologic regime, climate change, disease, land use, migration barriers, and many other themes. Download Adobe Acrobat Reader

Amphibian Populations Research - Amphibians are often elusive, making it difficult for biologists to characterize populations. Significantly greater field efforts are required for population studies than can be accommodated by large-area surveys, yet it is at the population level where the relations between environment and species can best be disentangled. Additionally, the concept of metapopulations is a recurring theme in amphibian research, conferring an even greater challenge to biologists trying to understanding amphibian-environment relations.

One example of how information gained from population analyses can be applied toward amphibian conservation is a study in the Midwest. In this analysis, scientists sought to identify farm management practices that best sustained amphibian populations. Measures of amphibian individual, population, and community health were assessed within the context of farm pond characteristics and the land uses surrounding farm ponds. The results point to farm management practices associated with sustainable amphibian populations, high diversity, and low incidence of deformities. [Read more ...]

Field Protocols - Development of field-level protocols is particularly important in ARMI, as the broad survey goals of the Program rely on field data from cooperators for information on non-Department of Interior lands. Development of ARMI protocols has progressed across the country. Program scientists have posted some protocols on web pages to enable easy access by cooperators and other interested parties. Information on proper implementation of survey techniques, biosecurity, and collection and preservation of amphibians are three examples. [learn more about this].

Back to Top

Laboratory Efforts

Malformations and Disease Research - Multiple limbs, missing limbs, and facial abnormalities are the striking hallmarks of developmental malformations seen in frogs. The broad geographic distribution of malformations, now reported from most states, and the high percentage of malformations in some frog populations (up to 50% malformed individuals in some locations) warrant attention. The USGS National Wildlife Health Center is collaborating with ARMI regional herpetologists, as well as with biologists from other agencies, to conduct integrated studies to determine the causes of these malformations. USGS scientists have modified and expanded their diagnostic capabilities and field investigation methods to accommodate the unique life histories and habitats of amphibians. These new capabilities are particularly important in determining whether infectious agents play a role in causing the observed malformations. The National Wildlife Health Center has developed a Field Guide to Malformations of Frogs and Toads to assist field biologists in appropriately identifying and describing observed malformations.

Statistical Efforts

Advances in Ecological Statistics - ARMI is supporting a number of important advances in statistical methodology. While these techniques are highly relevant for monitoring amphibian populations, they will also be applicable to a wide range of other taxa and are sure to become notable contributions to ecological statistics.

One of the most important advances has been the development of new methods for estimating the proportion of area occupied (PAO), and related parameters. These address ARMI's mid-level monitoring efforts. The PAO estimator explicitly accommodates the fact that amphibian species may often go undetected, even when present at a sampling location. Initial development of the estimator enabled unbiased estimation for a single year and enabled relations between occupancy and site covariates to be modeled within a statistically rigorous framework. Further development has extended the model in two directions: to multiple years, accommodating direct estimation of colonization and local extinction probabilities, and to multiple species, addressing questions about patterns of species co-occurrences to be address.

Another area of active research is multi-state mark-recapture models where one or more of the states are unobservable. This is a common dilemma in amphibian studies, as most sampling takes place at breeding sites where only adult breeders are captured. Adults that skip breeding opportunities or post-metamorphic individuals who have not yet recruited into the breeding population remain unobservable. Multistate models have been developed to deal with these types of situations, allowing researchers to estimate demographic parameters such as breeding, survival, and movement probabilities between states (either geographically or demographically defined). Drs. Bill Kendall and Larissa Bailey have been involved in this research and its application extends beyond amphibians.