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Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and an estimate of FST (FST = 0.0675, P-value < 0.0001) also supports the genetic differentiation of the two clusters. Migration rates among the two subpopulations were small. Though we found support for a pattern of genetic isolation-by-distance, other processes also may have affected levels of genetic differentiation. Genetic variability in the population is low relative to other studies. However, we found no evidence that a recent bottleneck was responsible for the low variation. Conservation of the population of wood frogs would be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

Climate change is expected to increase the frequency and severity of drought and wildfire. Aquatic and moisture-sensitive species, such as amphibians, may be particularly vulnerable to these modified disturbance regimes because large wildfires often occur during extended droughts and thus may compound environmental threats. However, understanding of the effects of wildfires on amphibians in forests with long fire-return intervals is limited. Numerous stand-replacing wildfires have occurred since 1988 in Glacier National Park (Montana, U.S.A.), where we have conducted long-term monitoring of amphibians. We measured responses of 3 amphibian species to fires of different sizes, severity, and age in a small geographic area with uniform management. We used data from wetlands associated with 6 wildfires that burned between 1988 and 2003 to evaluate whether burn extent and severity and interactions between wildfire and wetland isolation affected the distribution of breeding populations. We measured responses with models that accounted for imperfect detection to estimate occupancy during prefire (0–4 years) and different postfire recovery periods. For the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), occupancy was not affected for 6 years after wildfire. But 7–21 years after wildfire, occupancy for both species decreased &#8805;25% in areas where >50% of the forest within 500 m of wetlands burned. In contrast, occupancy of the boreal toad (Anaxyrus boreas) tripled in the 3 years after low-elevation forests burned. This increase in occupancy was followed by a gradual decline. Our results show that accounting for magnitude of change and time lags is critical to understanding population dynamics of amphibians after large disturbances. Our results also inform understanding of the potential threat of increases in wildfire frequency or severity to amphibians in the region.

Understanding the relationship between climate-driven habitat conditions and survival is key to preserving biodiversity in the face of rapid climate change. Hydroperiod—the length of time water is in a wetland—is a critical limiting habitat variable for amphibians as larvae must metamorphose before ponds dry. Changes in precipitation and temperature patterns are affecting hydroperiod globally, but the impact of these changes on amphibian persistence is poorly understood. We studied Boreal Chorus Frog (Pseudacris maculata) tadpole response to simulated hydroperiods (i.e. water level reductions) in the laboratory using individuals collected from ponds spanning a range of natural hydroperiods (Colorado Front Range, USA). To assess the effects of experimental hydroperiod reduction, we measured mortality, time to metamorphosis, and size at metamorphosis. We found that tadpoles grew at rates reflecting the hydroperiods of their native ponds, regardless of experimental treatment. Tadpoles from permanent ponds metamorphosed faster than those from ephemeral ponds across all experimental treatments, a pattern which may represent a predation selection gradient or countergradient variation in developmental rates. Size at metamorphosis did not vary across experimental treatments. Mortality was low overall but varied by pond of origin. Our results suggest that adaptation to local hydroperiod and/or predation and temperature conditions is important in P. maculata. Moreover, the lack of a plastic response to reduced hydroperiods suggests that P. maculata may not be able to metamorphose quickly enough to escape drying ponds. These results have important implications for amphibian persistence in ponds predicted to dry more quickly due to rapid climate change.

1) Epidemiological studies are crucial for understanding the distribution and dynamics of emerging infectious diseases. To accurately assess infection states in wild populations, researchers need to account for observational uncertainty. We focus on two sources of uncertainty when estimating epidemiological parameters: non-detection of infection in sampled individuals and sampling error when quantifying infection intensity for infected individuals. <br />
2) We developed new analytical methods to simultaneously estimate prevalence and the distribution of infection intensities based on repeated sampling of individuals in the wild. The methods are an extension of those used for occupancy estimation and address both sources of observation error. At the same time, we account for heterogeneity in detection probability that results from individual variation in infection intensity. <br />
3) We use two estimation approaches to account for detection. The first is to use the complete likelihood in a hierarchical Bayesian model, fit using Markov chain Monte Carlo sampling. The second is to estimate the detection relationship using a mark-recapture abundance estimator and uses those results to calculate weighted estimates for prevalence and mean infection intensities.<br />
4) We use data from a field survey of Batrachochytrium dendrobatidis (Bd) in Illinois amphibians to test these methods. We show that detection probability using quantitative PCR is strongly related to infection intensity, measured in zoospore equivalents. Sites in the study varied greatly in estimated prevalence and to a lesser extent in mean infection intensities of infected individuals. We did not find evidence of a relationship of snout-vent-length to infection intensity or prevalence. Naïve estimates of prevalence that do not account for detection were smaller than estimates for either of our methods, which yielded similar prevalence values for most sites. <br />
5) Uncertainty when assessing disease state is a characteristic of most diagnostic tests. The estimators presented here account for this uncertainty and thus, can improve accuracy when assessing the relationship of ecological factors to prevalence and infection intensity.

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Short-comings of many existing empirical approaches for these questions include a reliance on patterns of occurrence at a single time point, failure to properly account for imperfect detection, and treating the environment as a static variable. <br />
2. We fit detection and non-detection data collected from repeat visits using a dynamic site occupancy model that simultaneously accounts for the temporal dynamics of a focal prey species, its predators, and its habitat. Our objective was to determine how disturbance and species interactions affect the co-occurrence probabilities of an endangered toad and recently introduced non-native predators in stream breeding habitats. To do this we determined support for alternative processes that could affect co-occurrence frequency in the system. <br />
3. Co-occurrence probabilities of toads with non-native predators in high-disturbance ephemeral streams and low-disturbance perennial streams were directly related to the differences disturbance regimes in each of the stream types. If predators were established at a site, they were rarely lost from the site except in cases when the site dried out. Once a dry site became suitable again, toads colonized them much more rapidly than predators, creating a period of predator-free space.<br />
4. We attribute the dynamics to a ‘storage effect’ where toads persisting outside of the stream environment during periods of drought rapidly colonized sites when they become suitable again. Our results demonstrate that, even in a highly connected stream network, temporal disturbance can structure frequencies with which breeding amphibians encounter non-native predators.<br />
5. Dynamic site occupancy models are a powerful tool for quantifying inter-species and species-habitat interactions. In contrast to previous methods that infer dynamic processes based on static patterns in occupancy, the approach we take allows the dynamic processes that determine species-species and species-habitat interactions to be directly estimated.

False positive errors are a significant component of many ecological data sets, which in combination with false negative errors, can lead to severe biases in conclusions about ecological systems. We present results of a field experiment where observers recorded observations for known combinations of electronically broadcast calling anurans under conditions mimicking field surveys to determine species occurrence. Our objectives were to characterize false positive error probabilities for auditory methods based on a large number of observers, to determine if targeted instruction could be used to reduce false positive error rates, and to establish useful predictors of among-observer and among-species differences in error rates. We recruited 31 observers, ranging in abilities from novice to expert, that recorded detections for 12 species during 180 calling trials (66,960 total observations). All observers made multiple false positive errors and on average 8.1% of recorded detections in the experiment were false positive errors. Additional instruction had only minor effects on error rates. After instruction, false positive error probabilities decreased by 16% for treatment individuals compared to controls with broad confidence interval overlap of 0 (95% CI: -46 to 30%). This coincided with an increase in false negative errors due to the treatment (26%; -3 to 61%). Differences among observers in false positive and in false negative error rates were best predicted by scores from an online test and a self-assessment of observer ability completed prior to the field experiment. In contrast, years of experience conducting call surveys was a weak predictor of error rates. False positive errors were also more common for species that were played more frequently, but were not related to the dominant spectral frequency of the call. Our results corroborate other work that demonstrates false positives are a significant component of species occurrence data collected by auditory methods. Instructing observers to only report detections they are completely certain are correct is not sufficient to eliminate errors. As a result, analytical methods that account for false positive errors will be needed, and independent testing of observer ability is a useful predictor for among-observer variation in observation error rates.

We studied growth, development, and metamorphic traits of Polypedates braueri tadpoles in Taiwan to elucidate the cause of tadpole overwintering in man-made water containers in lowland orchards on the Bagua Terrace. Polypedates braueri bred from March to August, but tadpoles were present year round. Laboratory experiments demonstrated that tadpole overwintering was facultative; low temperatures and limited food retarded both growth and development, resulting in overwintering in the tadpole stage. Tadpoles at the lowest experimental temperature (15uC) never reached metamorphosis. A field experiment demonstrated that 78, 28, and 4% of tadpoles raised in high, medium, and low food regimes, respectively, metamorphosed before the onset of winter. Tadpoles that did not metamorphose by fall continued to grow slowly and either metamorphosed during the winter or the following spring. These findings indicate that food availability plays a key role in inducing overwintering in tadpoles. Jumping performance of metamorphs was positively correlated with food regimes, but body lipid content was significantly higher in metamorphs raised with either low or high food regimes than in those with medium levels of food. Overwintering by P. braueri tadpoles has not been previously reported; however, agricultural activities have created new breeding habitats(i.e., man-made bodies of water), some of which are sufficiently food-limited that tadpoles overwinter to complete development and metamorphosis. An understanding of the survivorship, life history traits,and physiology of these frogs is needed to shed light on how man-made breeding sites affect the population
dynamics of native frog populations.

Native to Cuba, the Bahamas and the Cayman Islands, the Cuban Treefrog (CTF) is an invasive species in Florida, with the ability to inflict serious ecological damage to invaded habitats. By examining the diet of the CTF, a known predator of native frogs, better predictions may be made on the impacts on native species and ecosystems. From 2002 – 2003, CTF diet was investigated in south Florida at four sites, two each within pine rockland and mangrove habitat. Within each habitat, one site exhibited a low density of CTFs and the other a high density of CTFs. CTFs were captured in PVC pipes attached to trees and stomach contents were examined after euthanasia. Beetles were the most numerous and widely consumed prey item among sites; roaches, orthopterans, spiders, ants, and caterpillars were also major dietary components. There were significant differences in the proportion of taxa consumed by CTFs between low and high density populations within each habitat, with the low density site in every instance having the higher proportion. Across habitats, ants comprised a significantly higher proportion of the diet in mangroves, whereas beetles, orthopterans, and snails comprised a significantly higher proportion of the diet in pine rocklands. Approximately 3.5% of all stomachs examined contained anuran remains. Though not significant, CTFs from low density sites consumed a higher proportion of frogs than those at high density sites. Corroborating previous research, the data show the CTF to be a generalist feeder, consuming a wide variety of invertebrate prey, with anurans playing only a minor role in the overall diet.

The ability to accurately predict patterns of species’ occurrences is fundamental to the successful management of animal communities. To determine optimal management strategies, it is essential to understand species-habitat relationships and how species habitat use is related to natural or human-induced environmental changes. Using five years of monitoring data in the Chesapeake and Ohio Canal National Historical Park, Maryland, USA, we developed four multi-species hierarchical models for estimating amphibian wetland use that account for imperfect detection during sampling. The models were designed to determine which factors (wetland habitat characteristics, annual trend effects, spring/summer precipitation, and previous wetland use) were most important for predicting future habitat use. We used the models to make predictions of species occurrences in sampled and unsampled wetlands and evaluated model projections using additional data. Using a Bayesian approach, we calculated a posterior distribution of receiver operating characteristic area under the curve (ROC AUC) values, which allowed us to explicitly quantify the uncertainty in the quality of our predictions and to account for false negatives in the evaluation dataset. We found that wetland hydroperiod (the length of time that a wetland holds water) as well as the occurrence state in the prior year were generally the most important factors in determining occupancy. The model with only habitat covariates predicted species occurrences well; however, knowledge of wetland use in the previous year significantly improved predictive ability at the community level and for two of 12 species/species complexes. Our results demonstrate the utility of multi-species models for understanding which factors affect species habitat use of an entire community (of species)<br />
and provide an improved methodology using AUC that is helpful for quantifying the uncertainty in model predictions while explicitly accounting for detection biases.

Monitoring of natural resources is crucial to ecosystem conservation, and yet it can pose many challenges. We developed an amphibian monitoring program as a means for examining ecological conditions in Yellowstone and Grand Teton National Parks. Annual surveys for amphibian breeding occupancy were conducted over a 4-yr period (2006 – 2009) at two scales: catchments (portions of watersheds) and individual wetland sites. Catchments were selected in a stratified random sample with habitat quality and ease of access serving as strata. All known wetland sites with suitable habitat were surveyed within selected catchments. Changes in breeding occurrence of tiger salamanders, boreal chorus frogs and Columbia-spotted frogs were assessed using multi-season occupancy estimation. Numerous a priori models were considered within an information theoretic framework including those with catchment and site-level covariates. Habitat quality was the most important predictor of occupancy. Boreal chorus frogs demonstrated the greatest change (increase) in breeding occupancy at the catchment level. Tiger salamander breeding occurrence increased slightly and Columbia-spotted frogs decreased slightly over the 4-yr period. Larger changes for all 3 species were detected at the finer site-level scale. Use of covariates (e.g., connectivity of sites) offered improvements over simpler models, and may improve understanding of the dynamic processes occurring among wetlands within this ecosystem. Our results suggest monitoring occupancy at two spatial scales within large study areas such as ours is feasible and informative.

Sensitivity analysis is a useful tool for the study of ecological models that has many potential applications for patch occupancy modeling. I use the rich foundation of existing methods for Markov chain models to demonstrate new methods for sensitivity analysis of the equilibrium state dynamics of occupancy models. Estimates from three previous studies are used to illustrate the utility of the sensitivity calculations: a joint occupancy model for a prey species, its predators, and habitat used by both; occurrence dynamics from a well-known metapopulation study of three butterfly species (Hanski 1994); and golden eagle occupancy and reproductive dynamics (Martin et al. 2009a). I show how to deal efficiently with multistate models and how to calculate sensitivities involving derived state variables and lower level parameters. In addition, I extend methods to incorporate environmental variation by allowing for spatial and temporal variability in transition probabilities. The approach used here is concise and general and can fully account for environmental variability in transition parameters. The methods can be used to improve inferences in occupancy studies by quantifying the effects of underlying parameters, aiding prediction of future system states, and identifying priorities for sampling effort.

Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of variation in the response that may occur when there are dependence structures such as smaller sampling units that are nested within larger sampling units. We used multilevel Bayesian occupancy modeling to handle dependence structures and partition sources of variation in occupancy of sites by terrestrial salamanders (family Plethodontidae) within and surrounding an earlier wildfire in western Oregon, USA. Comparison of model fit favored a spatial N-mixture model that accounted for variation in salamander abundance over models that were based on binary detection/non-detection data. Though catch per unit effort was higher in burned areas than unburned, there was strong support that this pattern was due to a higher probability of capture for individuals in burned plots. Within the burn the odds of capturing an individual given it was present were https://2.06 times the odds outside the burn, reflecting reduced complexity of ground cover in the burn. There was weak support that true occupancy was lower within the burned area. While the odds of occupancy in the burn were https://0.49 times the odds outside the burn among the five species, the magnitude of variation attributed to the burn was small in comparison to variation attributed to other landscape variables and to unexplained, spatially autocorrelated random variation. While ordinary occupancy models may separate the biological pattern of interest from variation in detection probability when all sources of variation are known, the addition of random effects structures for unexplained sources of variation in occupancy and detection probability may often more appropriately represent levels of uncertainty.

Chemical contamination may influence host-pathogen interactions, which has implications for amphibian population declines. We examined the effects of four insecticides alone or as a mixture on development and metamorphosis of Pacific Treefrogs (Pseudacris regilla) in the presence or absence of the amphibian chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Bd exposure had a negative impact on tadpole activity, survival to metamorphosis, time to metamorphosis, and time of tail absorption (with a marginally negative effect on mass at metamorphosis); however, no individuals tested positive for Bd at metamorphosis. The presence of sublethal concentrations of insecticides alone or in a mixture did not impact Pacific Treefrog activity as tadpoles, survival to metamorphosis, or time and size to metamorphosis. Insecticide exposure did not influence the effect of Bd exposure. Our study did not support our prediction that effects of Bd would be greater in the presence of expected environmental concentrations of insecticide(s), but it did show that Bd had negative effects on responses at metamorphosis that could reduce the quality of juveniles recruited into the population.

We found amphibian chytrid fungus (Bd = Batrachochytrium dendrobatidis) to be widespread within a coastal watershed at Point Reyes National Seashore, California and within two high elevation watersheds at Yosemite National Park, California. Bd was associated with all six species that we sampled (Bufo boreas, B. canorus, Pseudacris regilla, Rana draytonii, R. sierrae, and Lithobates catesbeianus). For those species sampled at 10 or more sites within a watershed, the percent of Bd-positive sites varied from a low of 20.7% for P. regilla at one Yosemite watershed to a high of 79.6% for P. regilla at the Olema watershed at Point Reyes. At Olema, the percent of Bd-positive water bodies declined each year of our study (2005-2007). Because P. regilla was the only species found in all watersheds, we used that species to evaluate habitat variables related to the sites where P. regilla was Bd-positive. At Olema, significant variables were year, length of shoreline (perimeter), percent cover of rooted vegetation, and water depth. At the two Yosemite watersheds, water depth, water temperature, and silt/mud were the most important covariates, though the importance of these three factors differed between the two watersheds. The presence of Bd in species that are not declining suggests that some of the amphibians in our study were innately resistant to Bd, or had developed resistance after Bd became established.

Prevalence of the pathogen Batrachochytrium dendrobatidis (Bd), implicated in amphibian population declines worldwide, is associated with habitat moisture and temperature, but few studies have varied these factors and measured the response to infection in amphibian hosts. We evaluated how varying humidity, contact with water, and temperature affected the manifestation of chytridiomycosis in boreal toads Anaxyrus (Bufo) boreas boreas and how prior exposure to Bd affects the likelihood of survival after re-exposure, such as may occur seasonally in long-lived species. Humidity did not affect survival or the degree of Bd infection, but a longer time in contact with water increased the likelihood of mortality. After exposure to ~10^6 Bd zoospores, all toads in continuous contact with water died within 30 d. Moreover, Bd-exposed toads that were disease-free after 64 d under dry conditions, developed lethal chytridiomycosis within 70 d of transfer to wet conditions. Toads in unheated aquaria (mean = 15°C) survived less than 48 d, while those in moderately heated aquaria (mean = 18°C) survived 115 d post-exposure and exhibited behavioral fever, selecting warmer sites across a temperature gradient. We also found benefits of prior Bd infection: previously exposed toads survived 3 times longer than Bd-naïve toads after re-exposure to 106 zoospores (89 vs. 30 d), but only when dry microenvironments were available. This study illustrates how the outcome of Bd infection in boreal toads is environmentally dependent: when continuously wet, high reinfection rates may overwhelm defenses, but periodic drying, moderate warming, and previous infection may allow infected toads to extend their survival.

1. Altered global climates in the 21st century pose serious threats for biological systems and practical actions are needed to mount a response for species at risk.<br />
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2. We identify management actions from across the world and from diverse disciplines that are applicable to minimizing loss of amphibian biodiversity under climate change. Actions were grouped under three thematic areas of intervention: (i) installation of microclimate and microhabitat refuges; (ii) enhancement and restoration of breeding sites; and (iii) manipulation of hydroperiod or water levels at breeding sites.<br />
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3. Synthesis and applications. There are currently few meaningful management actions that will tangibly impact the pervasive threat of climate change on amphibians. A host of potentially useful but poorly tested actions could be incorporated into local or regional management plans, programmes and activities for amphibians. Examples include: installation of irrigation sprayers to manipulate water potentials at breeding sites; retention or supplementation of natural and artificial shelters (e.g. logs, cover boards) to reduce desiccation and thermal stress; manipulation of canopy cover over ponds to reduce water temperature; and, creation of hydrologoically diverse wetland habitats capable of supporting larval development under variable rainfall regimes. We encourage researchers and managers to design, test and scale up new initiatives to respond to this emerging crisis.

The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000–2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probability, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from (1) field survey site data only, (2) field data combined with data from geospatial models, and (3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from https://0.70 to 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from https://0.30 to https://0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from https://0.60 to https://0.80. Combining results from the geospatial multiyear models yielded maps of ‘‘core’’ breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative areas that could be protected for each species, including 6828–10 764 ha for tiger salamanders, 971–3017 ha for western toads, 4732–16 696 ha for boreal chorus frogs, and 4940–19 690 ha for Columbia spotted frogs.

Variation in the occurrence and abundance of species across landscapes has traditionally been attributed to processes at fine spatial scales (i.e., local conditions), but processes that operate across larger spatial scales such as seasonal migration or dispersal are also important. Recognition of the importance of processes that operate at broad, as well as fine, scales is growing. We evaluated hypothesized relationships between the probability of occupancy in wetlands by wood frogs (Lithobates sylvaticus) and boreal chorus frogs (Pseudacris maculata) during the breeding season and attributes of the landscape measured at three spatial scales in Rocky Mountain National Park, Colorado. We also used cost-based buffers and least-cost distances to derive estimates of landscape attributes at the broader spatial scales represented by seasonal movement and dispersal. Occupancy by breeding wood frogs was associated positively with the amount of streamside habitat adjacent to a wetland and associated negatively with the cost-based distance to the nearest occupied wetland. Occupancy by boreal chorus frogs was associated positively with the number of neighboring, occupied wetlands. We found little evidence that occupancy was correlated with fine-scale attributes measured at the wetlands.