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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 °C, 20 °C, 25 °C, or 15 °C to 25 °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.

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.