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Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red-legged frog (Rana draytonii) has undergone extensive declines in urban-plagued southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east-west trending axis. We studied the genetic structure and diversity of these front-line populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the ‘abundant-center’ model, we found that diversity, admixture and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some populations due to recent fire-flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.

In the southeastern U.S., changes in temperature and precipitation over the last three decades have been the most dramatic in winter and spring seasons. Continuation of these trends could negatively impact pond-breeding amphibians, especially those that rely on winter and spring rains to fill seasonal wetlands, trigger breeding, and ensure reproductive success. From 2009 to 2012, we monitored aquatic stages (larval and paedomorphic, gilled adult) of a winter-breeding amphibian (the mole salamander, Ambystoma talpoideum) and used a single-species, multi-season model to estimate occupancy, detection probability, local colonization and extinction. Annual estimates of occupancy, corrected for imperfect detection, ranged from 9.9 to 23.1%, with the rate of change in occupancy probabilities between sampling seasons fluctuating over time. Our best supported model suggested that this change in occupancy was driven by an increase in estimates of extinction probabilities which, in turn, corresponded with an increase in drought over time. In contrast, colonization was low and less variable. A future climate change scenario of severe, prolonged drought could result in regional losses of seasonal wetlands and a concomitant change in the occupancy dynamics of aquatic amphibians.

A study by the U.S. Geological Survey (USGS) evaluated the hydrologic response to different projected carbon emission scenarios of the 21st century using a hydrologic simulation model. This study involved five major steps: (1) setup, calibrate and evaluated the Precipitation Runoff Modeling System (PRMS) model in 14 basins across the United States by local USGS personnel; (2) acquire selected simulated carbon emission scenarios from the World Climate Research Programme’s Coupled Model Intercomparison Project; (3) statistical downscaling of these scenarios to create PRMS input files which reflect the future climatic conditions of these scenarios; (4) generate PRMS projections for the carbon emission scenarios for the 14 basins; and (5) analyze the modeled hydrologic response. This report presents an overview of this study, details of the methodology, results from the 14 basin simulations, and interpretation of these results.<br />
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A key finding is that the hydrological response of the different geographical regions of the United States to potential climate change may be different, depending on the dominant physical processes of that particular region. Also considered is the tremendous amount of uncertainty present in the carbon emission scenarios and how this uncertainty propagates through the hydrologic simulations.

A method for the determination of the widely used herbicide diuron, three degradates of diuron, and six neonicotinoid insecticides in environmental water samples is described. Filtered water samples were extracted by using solid-phase extraction (SPE) with no additional cleanup steps. Quantification of the pesticides from the extracted water samples was done by using liquid chromatography with tandem mass spectrometry (LC/MS/MS).<br />
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Recoveries in test water samples fortified at 20 nanograms per liter (ng/L) for each compound ranged from 75 to 97 percent; relative standard deviations ranged from 5 to 10 percent. Method detection limits (MDLs) in water ranged from 3.0 to 6.2 ng/L using LC/MS/MS. The method was applied to water samples from two streams in Georgia, Sope Creek and the Chattahoochee River. Diuron and 3,4-dichloroaniline (3,4-DCA) were detected in 100 and 80 percent, respectively, of the samples from the Chattahoochee River, whereas Sope creek had detection frequencies of 15 percent for diuron and 31 percent for 3,4-DCA. Detection frequencies for the neonicotinoid insecticide, imidacloprid, were 60 percent for the Chattahoochee River and 85 percent for Sope Creek. Field matrix-spike recoveries for each compound, when averaged over four water samples, ranged from 79 to 100 percent. The average percentage difference between replicate pairs for all compounds detected in the field samples was 10.1 (± 4.5) percent.

The mountainous areas of Colorado are used for tourism and recreation, and they provide water storage and supply for municipalities, industries, and agriculture. Recent studies suggest that water supply and tourist industries such as skiing are at risk from climate change. In this study, a distributed-parameter watershed model, the Precipitation-Runoff Modeling System (PRMS), is used to identify the potential effects of future climate on hydrologic conditions for two Colorado basins, the East River at Almont and the Yampa River at Steamboat Springs, and at the subbasin scale for two ski areas within those basins.<br />
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Climate-change input files for PRMS were generated by modifying daily PRMS precipitation and temperature inputs with mean monthly climate-change fields of precipitation and temperature derived from five general circulation model (GCM) simulations using one current and three future carbon emission scenarios. All GCM simulations of mean daily minimum and maximum air temperature for the East and Yampa River basins indicate a relatively steady increase of up to several degrees Celsius from baseline conditions by 2094. GCM simulations of precipitation in the two basins indicate little change or trend in precipitation, but there is a large range associated with these projections. PRMS projections of basin mean daily streamflow vary by scenario but indicate a central tendency toward slight decreases, with a large range associated with these projections.<br />
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Decreases in water content or changes in the spatial extent of snowpack in the East and Yampa River basins are important because of potential adverse effects on water supply and recreational activities. PRMS projections of each future scenario indicate a central tendency for decreases in basin mean snow-covered area and snowpack water equivalent, with the range in the projected decreases increasing with time. However, when examined on a monthly basis, the projected decreases are most dramatic during fall and spring. Presumably, ski area locations are picked because of a tendency to receive snow and keep snowpack relative to the surrounding area. This effect of ski area location within the basin was examined by comparing projections of March snow-covered area and snowpack water equivalent for the entire basin with more local projections for the portion of the basin that represents the ski area in the PRMS models. These projections indicate a steady decrease in March snow-covered area for the basins but only small changes in March snow-covered area at both ski areas for the three future scenarios until around 2050. After 2050, larger decreases are possible, but there is a large range in the projections of future scenarios. The rates of decrease for snowpack water equivalent and precipitation that falls as snow are similar at the basin and subbasin scale in both basins. Results from this modeling effort show that there is a wide range of possible outcomes for future snowpack conditions in Colorado. The results also highlight the differences between projections for entire basins and projections for local areas or subbasins within those basins.

Water and bed-sediment samples were collected by the U.S. Geological Survey (USGS) in 2009 and 2010 from 11 sites within California and 18 sites total in Colorado, Georgia, Idaho, Louisiana, Maine, and Oregon, and were analyzed for a suite of pesticides by the USGS. Water samples and bed-sediment samples were collected from perennial or seasonal ponds located in amphibian habitats in conjunction with research conducted by the USGS Amphibian Research and Monitoring Initiative and the USGS Toxic Substances Hydrology Program. Sites selected for this study in three of the states (California, Colorado, and Orgeon) have no direct pesticide application and are considered undeveloped and remote. Sites selected in Georgia, Idaho, Louisiana, and Maine were in close proximity to either agricultural or suburban areas. Water and sediment samples were collected once in 2009 during amphibian breeding seasons. In 2010, water samples were collected twice. The first sampling event coincided with the beginning of the frog breeding season for the species of interest, and the second event occurred 10–12 weeks later when pesticides were being applied to the surrounding areas. Additionally, water was collected during each sampling event to measure dissolved organic carbon, nutrients, and the fungus, Batrachochytrium dendrobatidis, which has been linked to amphibian declines worldwide. Bed-sediment samples were collected once during the beginning of the frog breeding season, when the amphibians are thought to be most at risk to pesticides. Results of this study are reported for the following two geographic scales: (1) for a national scale, by using data from the 29 sites that were sampled from seven states, and (2) for California, by using data from the 11 sampled sites in that state.<br />
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Water samples were analyzed for 96 pesticides by using gas chromatography/mass spectrometry. A total of 24 pesticides were detected in one or more of the 54 water samples, including 7 fungicides, 10 herbicides, 4 insecticides, 1 synergist, and 2 pesticide degradates. On a national scale, aminomethylphosphonic acid (AMPA), the primary degradate of the herbicide glyphosate, which is the active ingredient in Roundup®, was the most frequently detected pesticide in water (16 of 54 samples) followed by glyphosate (8 of 54 samples). The maximum number of pesticides observed at a single site was nine compounds in a water sample from a site in Louisiana. The maximum concentration of a pesticide or degradate observed in water was 2,880 nanograms per liter of clomazone (a herbicide) at a site in Louisiana. In California, a total of eight pesticides were detected among all of the low and high elevation sites; AMPA was the most frequently detected pesticide, but glyphosate was detected at the highest concentrations (1.1 micrograms per liter).<br />
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Bed-sediment samples were analyzed for 94 pesticides by using accelerated solvent extraction, gel permeation chromatography for sulfur removal, and carbon/alumina stacked solid-phase extraction cartridges to remove interfering sediment matrices. In bed sediment, 22 pesticides were detected in one or more of the samples, including 9 fungicides, 3 pyrethroid insecticides, p,p’-dichlorodiphenyltrichloroethane (p,p’-DDT) and its major degradates, as well as several herbicides. Pyraclostrobin, a strobilurin fungicide, and bifenthrin, a pyrethroid insecticide, were detected most frequently. Maximum pesticide concentrations ranged from less than their respective method detection limits to 1,380 micrograms per kilogram (tebuconazole in California). The number of pesticides detected in samples from each site ranged from zero to six compounds. The sites with the greatest number of pesticides were in Maine and Oregon with six pesticides detected in one sample from each state, followed by Georgia with four pesticides in one sample. For California, a total of 10 pesticides were detected among all sites, and 4 pesticides were detected at both low and high elevation sites; tebuconazole and pyraclostrobin were the two most frequently detected pesticides in California. For the other six selected states, the most frequently detected pesticides in bed sediment were pyraclostrobin (detected in 17 of 42 samples), bifenthrin (detected in 14 of 42 samples), and tebuconazole (detected in 10 of 42 samples).<br />
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The fungus, Batrachochytrium dendrobatidis (Bd), was detected in water samples in sites from four of the seven states during 2009 and 2010, and the number of zoospore equivalents per liter of water in samples where Bd was detected ranged from 1.6 to 343. Bd was not detected in water samples from sites in Georgia, Louisiana, and Oregon.

This study documents the occurrence of fungicides in select U.S. streams soon after the first documentation of soybean rust in the U.S. and prior to the corresponding increase in fungicide use to treat this problem. Water samples were collected from 29 streams in 13 States in 2005 and/or 2006, and analyzed for 12 target fungicides. Nine of the 12 fungicides were detected in at least one stream sample and at least one fungicide was detected in 20 of 29 streams. At least one fungicide was detected in 56% of the 103 samples, as many as 5 fungicides were detected in an individual sample, and mixtures of fungicides were common. Azoxystrobin was detected most frequently (45% of 103 samples) followed by metalaxyl (27%), propiconazole (17%), myclobutanil (9%), and tebuconazole (6%). Fungicide detections ranged from https://0.002 to https://1.15 ug/L. There was indication of a seasonal pattern to fungicide occurrence, with detections more common and concentrations higher in late summer and early fall than in spring. At a few sites, fungicides were detected in all samples collected suggesting the potential for season-long occurrence in some streams. Fungicide occurrence appears to be related to fungicide use in the associated drainage basins, however, current use information is generally lacking and more detailed occurrence data are needed to accurately quantify such a relation. Maximum concentrations of fungicides were typically one or more orders of magnitude less than current toxicity estimates for fresh-water aquatic organisms or humans however gaps in current toxicological understandings of the effects of fungicides in the environment limit these interpretations.

More than 25 years ago, scientists began to identify unexplained declines in amphibian populations around the world. Much has been learned since then, but amphibian declines have not abated and the interactions among the various threats to amphibians are not clear. Amphibian decline is a problem of local, national, and international scope that can affect ecosystem function, biodiversity, and commerce. This fact sheet provides a snapshot of the state of the amphibians and introduces examples to illustrate the range of issues in the United States.

The ability to track individual animals is crucial in many field studies and often requires applying marks to captured individuals. Toe clipping has historically been a standard marking method for wild amphibian populations, but more recent marking methods include visual implant elastomer and photo identification. Unfortunately, few studies have investigated the influence and effectiveness of marking methods for recently metamorphosed individuals and as a result little is known about this life-history phase for most amphibians. Our focus was to explore survival probabilities and mark retention and migration in postmetamorphic Boreal Chorus Frogs (Psuedacris maculata) in a laboratory setting. Three treatments were assigned randomly among 147 individuals: frogs were either marked with visual implant elastomer, toe clipped, or left unmarked as controls. Growth and mortality were recorded for one year and resulting data were analyzed using known-fate models in Program MARK. Model selection results suggested that survival probabilities of frogs varied with time and showed some variation among marking treatments. We found that frogs with multiple toes clipped on the same foot had lower survival probabilities than individuals in other treatments, but individuals can be marked by clipping a single toe on two different feet without any mark loss or negative survival effects. Individuals treated with visual implant elastomer had a mark migration rate of 4% and mark loss rate of 6% and also showed very little negative survival impacts relative to control individuals.

We conducted surveys for the endangered Sierra Madre yellow-legged frog (Rana muscosa) throughout southern California to evaluate their current distribution and status. Surveys were conducted between 2000 and 2009 at 150 unique streams and lakes within the San Gabriel, San Bernardino, San Jacinto, and Palomar mountains of southern California. Of the 150 survey locations only nine small, geographically isolated, populations were detected across the four mountain ranges. The nine R. muscosa populations all tested positive for the amphibian chytrid fungus (Batrachochytrium dendrobatidis). Our data show that when R. muscosa is known to be present, it is highly detectable (89%) from a single visit during the frogs active season. We estimate there were only 166 adult frogs that remained in the wild in 2009. From our research, it appears that R. muscosa populations in southern California are extremely vulnerable to natural and stochastic events and may become extirpated in the near future without intervention.

Stream ecosystems are particularly sensitive to urbanization, and tolerance of water-quality parameters is likely important to population persistence of stream salamanders. When combined with climate change forecasts, significant changes in stream flow, chemical composition, and temperature of streams are expected in coming decades. Protected areas where landscape alterations are minimized will therefore become increasingly important for salamander populations. We surveyed 29 streams at three National Parks in the highly urbanized greater metropolitan area of Washington, D.C. We investigated relationships between water-quality variables and occupancy of three species of stream salamanders (Desmognathus fuscus, Eurycea bislineata, and Pseudotriton ruber). Using a set of site-occupancy models, and accounting for imperfect detection, we found that stream water temperature limits salamander occupancy. There was substantial uncertainty about the effects of the other water-quality variables, although both specific conductance (SC) and pH were included in competitive models. Our estimates of occupancy suggest that temperature, SC, and pH have some importance in structuring stream salamander distribution. When climate and landscape changes are joint stressors on a population, the interactive effects of increased temperatures under urbanization and climate change may drive local extinctions.

1. Recently, interest in species distribution modeling has increased following the development of new methods for the analysis of presence-only data and the deployment of these methods in user-friendly and powerful computer programs. However, reliable inference from these powerful tools requires that several assumptions be met, including the assumptions that observed presences are the consequence of random or representative sampling and that detectability during sampling does not vary with the covariates that determine occurrence probability.<br />
2. Based on our interactions with researchers using these tools, we hypothesized that many presence-only studies were ignoring important assumptions of presence-only modeling. We tested this hypothesis by reviewing 108 articles published between 2008 and 2012 that used the MAXENT algorithm to analyze empirical (i.e., not simulated) data. We chose to focus on these articles because MAXENT has been the most popular algorithm in recent years for analyzing presence-only data.<br />
3. Many articles (87%) were based on data that were likely to suffer from sample selection bias, however, methods to control for sample selection bias were rarely used. In addition, many analyses (36%) discarded absence information by analyzing presence-absence data in a presence-only framework, and few articles (14%) mentioned detection probability. We conclude that there are many misconceptions concerning the use of presence-only models, including the misunderstanding that MAXENT, and other presence-only methods, relieve users from the constraints of survey design.<br />
4. In the process of our literature review, we became aware of other factors that raised concerns about the validity of study conclusions. In particular, we observed that 83% of articles studies focused exclusively on model output (i.e. maps) without providing readers with any means to critically examine modeled relationships, and that MAXENT’s logistic output was frequently (54 % of articles) and incorrectly interpreted as occurrence probability.<br />
5. We conclude with a series of recommendations, foremost that researchers analyze data in a presence-absence framework whenever possible, because fewer assumptions are required and inferences can be made about clearly defined parameters such as occurrence probability.

Occupancy statistical models which account for imperfect detection have proven very useful in several areas in ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, during which it is assumed the species is either absent or present and available for detection while each sample is taken. However, for some species individuals are only present or available for detection seasonally. We present a statistical model that relaxes the closure assumption within a season by permitting staggered entry and exit times for the species of interest at each site. Based on simulation, our open model eliminates bias in occupancy estimators and in some cases increases precision. The power to detect the violation of closure is high if detection probability is reasonably high. In addition to providing more robust estimation of occupancy, this model permits comparison of phenology across sites, species, or years, by modeling variation in arrival or departure probabilities. In a comparison of four species of amphibians in Maryland we found that two toad species arrived at breeding sites later in the season than a salamander and frog species, and departed from sites earlier.

Disturbances are often expected to magnify effects of disease, but these effects may depend on the ecology, behavior, and life history of both hosts and pathogens. In many ecosystems, wildfire is the dominant natural disturbance and thus could directly or indirectly affect dynamics of many diseases. To determine how probability of infection by the aquatic fungus Batrachochytrium dendrobatidis (Bd) varies relative to habitat use by individuals, wildfire, and host characteristics, we sampled 404 boreal toads (Anaxyrus boreas boreas) across Glacier National Park, Montana (USA). Bd causes chytridiomycosis, an emerging infectious disease linked with widespread amphibian declines, including the boreal toad. Probability of infection was similar for females and the combined group of males and juveniles. However, only 9% of terrestrial toads were infected compared to >30% of aquatic toads, and toads captured in recently burned areas were half as likely to be infected as toads in unburned areas. We suspect these large differences in infection reflect habitat choices by individuals that affect pathogen exposure and persistence, especially in burned forests where warm, arid conditions could limit Bd growth. Our results show that natural disturbances such as wildfire and the resulting diverse habitats can influence infection across large landscapes, potentially maintaining local refuges and host behaviors that facilitate evolution of disease resistance.

The status of the California red-legged frog (Rana draytonii), a federally listed threatened species, has long been uncertain in the Sierra Nevada range in eastern California, USA. We examined museum collections and historical records, and conducted 213 field surveys at 151 sites over 21 years to evaluate the status of this frog in the Sierra Nevada. We documented only 20 Sierra Nevada localities and one Cascades Mountains locality where R. draytonii occurred between 1916 and 1975, extending from Tehama County southeast about 405 km to Madera County. the elevation range of most of the historical localities was 200 to 900 m (about 40 km from lower to upper elevation), but three apparently extirpated populations that may have originated from deliberate translocations occurred at 1,500 to 1,536 m elevation in Yosemite National Park. We surveyed directly or within 5 km of 20 of the 21 historical Sierra Nevada/Cascades R. draytonii localities and found that at least one of these historical populations persists today, in large numbers. We also discovered or confirmed six new Sierra Nevada R. draytonii populations and individual frogs at three additional new sites, for a total of seven recent populations and three recent single-specimen occurrences extending from Butte County southeast about 275 km to Mariposa County. Historically, R. draytonii in the Sierra Nevada probably bred in stream pools, which tend to be small with limited forage and thus may have constrained the historical size and number of Sierra Nevada R. draytonii populations. since the 1850s, manmade ponds sometimes capable of supporting large R. draytonii populations have supplemented stream pool breeding habitat. Excluding the southernmost and Yosemite historical localities, the current range of Sierra Nevada R. draytonii differs little from the historical range, and further surveys may reveal additional surviving Sierra Nevada R. draytonii populations. Sierra Nevada R. draytonii are threatened primarily by habitat modification and loss related to human population increase.

Projected increases in wildfire and other climate-driven disturbances will affect
populations and communities worldwide, including host–parasite relationships. Research in
temperate forests has shown that wildfire can negatively affect amphibians, but this research
has occurred primarily outside of managed landscapes where interactions with human
disturbances could result in additive or synergistic effects. Furthermore, parasites represent a
large component of biodiversity and can affect host fitness and population dynamics, yet they
are rarely included in studies of how vertebrate hosts respond to disturbance. To determine
how wildfire affects amphibians and their parasites, and whether effects differ between
protected and managed landscapes, we compared abundance of two amphibians and two
nematodes relative to wildfire extent and severity around wetlands in neighboring protected
and managed forests (Montana, USA). Population sizes of adult, male long-toed salamanders
(Ambystoma macrodactylum) decreased with increased burn severity, with stronger negative
effects on isolated populations and in managed forests. In contrast, breeding population sizes
of Columbia spotted frogs (Rana luteiventris) increased with burn extent in both protected and
managed protected forests. Path analysis showed that the effects of wildfire on the two species
of nematodes were consistent with differences in their life history and transmission strategies
and the responses of their hosts. Burn severity indirectly reduced abundance of soil-transmitted
Cosmocercoides variabilis through reductions in salamander abundance. Burn severity also
directly reduced C. variabilis abundance, possibly though changes in soil conditions. For the
aquatically transmitted nematode Gyrinicola batrachiensis, the positive effect of burn extent on
density of Columbia spotted frog larvae indirectly increased parasite abundance. Our results
show that effects of wildfire on amphibians depend upon burn extent and severity, isolation,
and prior land use. Through subsequent effects on the parasites, our results also reveal how
changes in disturbance regimes can affect communities across trophic levels.

Chytridiomycosis, a disease caused by Batrachochytrium dendrobatidis (Bd), has been implicated as a cause of amphibian declines. Susceptibility may be influenced by environmental factors that suppress the immune response. The authors conducted a laboratory study to examine the effect of temperature, insecticide exposure, and Bd exposure during larval anuran development. The authors examined the consequences of exposure to Bd, an insecticide (carbaryl or malathion), and static or fluctuating temperature (15&#8201;°C, 20&#8201;°C, 25&#8201;°C, or 15&#8201;°C to 25&#8201;°C 72-h flux) on larval development through metamorphosis of the Pacific treefrog (Pseudacris regilla). High and fluctuating temperature had negative effects on survival in the presence of Bd. Insecticides inhibited the effects of Bd; time to tail resorption of Pacific treefrogs decreased when tadpoles were exposed to carbaryl.

This is the 2011 annual report for the Amphibian Research and Monitoring Initiative. It includes publication updates and a summary of amphibian monitoring trends.

1. World-wide extinctions of amphibians are at the forefront of the biodiversity crisis, with climate change figuring prominently as a potential driver of continued amphibian decline. As in other taxa, changes in both the mean and variability of climate conditions may affect amphibian populations in complex, unpredictable ways. In western North America, climate models predict a reduced duration and extent of mountain snowpack and increased variability in precipitation, which may have consequences for amphibians inhabiting montane ecosystems.
2. We used Bayesian capture–recapture methods to estimate survival and transition probabilities in a high-elevation population of the Columbia spotted frog (Rana luteiventris) over 10 years and related these rates to interannual variation in peak snowpack. Then, we forecasted frog population growth and viability under a range of scenarios with varying levels of change in mean and variance in snowpack.
3. Over a range of future scenarios, changes in mean snowpack had a greater effect on viability than changes in the variance of snowpack, with forecasts largely predicting an increase in population viability. Population models based on snowpack during our study period predicted a declining population.
4. Although mean conditions were more important for viability than variance, for a given mean snowpack depth, increases in variability could change a population from increasing to decreasing. Therefore, the influence of changing climate variability on populations should be accounted for in predictive models. The Bayesian modelling framework allows for the explicit characterization of uncertainty in parameter estimates and ecological forecasts, and thus provides a natural approach for examining relative contributions of mean and variability in climatic variables to population dynamics.
5. Longevity and heterogeneous habitat may contribute to the potential for this amphibian species to be resilient to increased climatic variation, and shorter-lived species inhabiting homogeneous ecosystems may be more susceptible to increased variability in climate conditions.