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1. Conservation science can be most effective in its decision-support role when seeking answers to clearly formulated questions of direct management relevance. Emerging wildlife diseases, a driver of global biodiversity loss, illustrate the challenges of performing this role: in spite of considerable research, successful mitigation remains uncommon. Decision analysis is increasingly advocated to guide mitigation planning, but its application remains uncommon.
2. Using an integral projection model, we explored potential mitigation actions for avoiding population declines and the ongoing spatial spread of the fungus Batrachochytrium salamandrivorans (Bsal). This fungus has recently caused severe amphibian declines in north-western Europe and threatens Palearctic salamander diversity.
3. Available evidence suggests that a Bsal outbreak in a fire salamander (Salamandra salamandra) population will lead to its rapid extirpation. Treatments such as antifungals or probiotics would need to almost entirely interrupt transmission (reduce probability of infection by more than 90%) to avert host extirpation and successfully eradicate the pathogen.
4. Improving the survival of infected hosts is most likely to be detrimental as it increases the potential for pathogen transmission and dispersal. Active removal of host species has some potential to reduce the spread of Bsal, but its effectiveness depends on the presence of Bsal reservoirs and on the host?s spatial dynamics, which should therefore represent research priorities.
5. Synthesis and applications. Mitigation of Bsal epidemics in susceptible host species is highly unlikely, requiring highly efficient interruption of transmission and substantial removal of host individuals. More in general, our study illustrates the advantages of framing conservation science directly in the management decision context, rather than adapting to it a posteriori.

Here, we report the first instances of Pacific boas (Candoia bibroni) eating amphibians in the wild. Specifically, we documented Cornufer vitianus (Fiji Ground Frog) and C. vitiensis (Fiji Tree Frog), both formerly in the genus Platymantis (for taxonomic discussion see Brown et al. 2015. Zool. J. Linn. Soc-Lond. 174:130?168), as prey for the first time.

From 2002-2006, we used a variety of sampling techniques to survey the amphibians and water chemistry of Lower Suwannee National Wildlife Refuge in Florida?s Big Bend region. We recorded 23 amphibian species, 19 frogs and 4 salamanders. Species richness was lower than in areas of the coastal Big Bend region to the north, perhaps due to a combination of variation in the geographic range of different amphibian species? ranges, sampling techniques, times of year when sampling occurred, and variation in detection probabilities among years and regions. Amphibians occupied a wide variety of habitats and appeared tolerant of the generally acidic conditions of many of the wetlands. Small streams and the Suwannee River were less acidic and had greater conductivities and mineral concentrations than isolated ponds; concentrations of heavy metals varied and mercury was not detected. Although additional species may yet be found in LSNWR, this survey provides a historic baseline for assessing future status and trends of amphibian populations as areas adjacent to the refuge are disturbed and as restoration and multi-use management continue within its boundaries.

Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors
affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A
major impediment to the estimation of demographic rates often used to parameterize and refine decision-support models is that life-stage-specific
monitoring data are frequently sparse for amphibians. We developed a new parameterization for integrated population models to match the ecology of amphibians and capitalize on relatively inexpensive monitoring data to document amphibian reintroductions. We evaluate the capability of this
model by fitting it to Oregon spotted frog (Rana pretiosa) monitoring data collected from 2007 to 2014 following their reintroduction within the Klamath Basin, Oregon, USA. The number of egg masses encountered and the estimated adult and metamorph abundances generally increased following reintroduction. We found that survival probability from egg to metamorph ranged from https://0.01 in 2008 to https://0.09 in 2009 and was not related to minimum spring temperatures, metamorph survival probability ranged from https://0.13 in 2010-2011 to https://0.86 in 2012-2013 and was positively related
to mean monthly temperatures (logit-scale slope = 2.37), adult survival probability was lower for founders (0.40) than individuals recruited after
reintroduction (0.56), and the mean number of egg masses per adult female was https://0.74. Our study represents the first to test hypotheses concerning Oregon spotted frog egg-to-metamorph and metamorph-to adult transition probabilities in the wild and document their response at multiple life stages following reintroduction. Furthermore, we provide an example to illustrate how the structure of our integrated population model serves as a useful foundation for amphibian decision-support models within adaptive management programs. The integration of multiple, but related, datasets has an advantage of being able to estimate complex ecological relationships across multiple life stages, offering a modeling framework that accommodates uncertainty, enforces parsimony, and ensures all model parameters can be confronted with monitoring data.

1. The amphibian skin microbiome is recognized for its role in defense against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments.
2. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease.
3. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (3571 P. cinereus, 17 P. glutinosus, 10 P. cylindraceus) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700 ? 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members.
4. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% (SD ? 8.5) per salamander. All salamanders tested negative for Bd.
5. We conclude that environment is more influential in shaping skin microbiome structure than host differences for these congeneric species, and suggest that environmental characteristics that co-vary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

The California red-legged frog Rana draytonii has been declining across its native range since the 1960s and was considered extirpated from most of southern California. In February 2017, a population of R. draytonii was re-discovered in the San Bernardino Mountains of Riverside County, California, where it has not been documented since 1959 (LACM 91074). This population belongs to a mtDNA lineage thought to be extinct from this species within the United States but still extant in Mexican populations. This discovery increases the potential for future, evolutionarily-informed translocations within the southern portion of this species range in California.

This paper summarizes the results of Bd and Bsal testing of 76 Gulf Coast Waterdogs captured from southeast Louisiana.

As the spatial and temporal scale of ecological research expands, there is increasing need for methods that integrate multiple data types into a single analytical framework. Current work on this topic primarily focuses on combining capture-recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection/nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count versus detection/nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection/nondetection data (1995-2014) with newly collected count data (2015-2016) from a growing population of barred owls (Strix varia) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.

Although not yet detected in the United States, the emergence of Bsal (a fungal pathogen) could threaten the salamander population, which is the most diverse in the world. The spread of Bsal likely will lead to more State and federally listed threatened or endangered amphibian species, and associated economic effects. Because of concern expressed by resource management agencies, the U. S. Geological Survey has made Bsal and similar pathogens a priority for research.

Diverse bacteria inhabit amphibian skin, some of which inhibit growth of the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Yet, there has been no systematic survey of anti-Bd bacteria across localities, species and elevations. This is important given geographic and taxonomic variation in amphibian susceptibility to Bd. Our sites were within the Appalachian Mountains where previous sampling indicated low Bd prevalence. We determined the number and identity of anti-Bd bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) using culturing methods and 16S rDNA sequencing. We sampled co-occurring species at three localities, and P. cinereus along an elevational gradient (700 ? 1000 masl) at one locality. We identified 50 anti-Bd bacterial OTUs and found that the degree of Bd inhibition was not correlated with relatedness. Five anti-Bd bacteria occurred on multiple species at multiple localities, but none were shared among all species and localities. Prevalence of
36 anti-Bd bacteria was higher at Shenandoah NP, VA, with 96% (25/26) of salamanders hosting at least one anti-Bd bacteria compared to 50% (7/14) at Catoctin MP, MD and 38% (8/21) at Mt. Rogers NRA, VA. At the individual level, salamanders at Shenandoah NP had more anti-Bd bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for Bd. Anti-Bd bacteria are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacteria we identified may play a protective role for these salamanders.

Our work is motivated by the impacts of the emerging infectious disease chytridiomycosis, a disease of amphibians that associated with declines of many species worldwide. Using this host-pathogen system as a general example, we first illustrate how misleading inferences can result from failing to incorporate pathogen dynamics into the modeling process, especially when the pathogen is difficult or impossible to survey in the absence of a host species. We found that traditional modeling techniques can underestimate the effect of a pathogen on host species occurrence and dynamics when the pathogen can only be detected in the host, and pathogen information is treated as a covariate. We propose a dynamic multistate modeling approach that is flexible enough to account for the detection structures that may be present in complex multistate systems, especially when the sampling design is limited by a species’ natural history or sampling technology.

Information on interactions between pesticide exposure and disease prevalence in amphibian populations is limited, especially from field data.Exposure to certain herbicides and insecticides has the potential to decrease immune response in frogs which can potentially lead to an increased abundance of Batrachochytrium dendrobatidis (Bd) zoospores on individuals and in the https://wetlands.In contrast, exposure to certain fungicides can decrease Bd abundance on frog skin. We examined the relationships between the abundance of Bd on the skin of individual Boreal Chorus Frogs(Pseudacris maculata) and the concentrations of pesticides in the water and in frog tissue at six agriculturally dominated wetlands in Iowa, USA

Many coastal dune ecosystems have been degraded by non-native dune vegetation, but these systems might still provide valuable habitat for some taxa, including amphibians. Because restoration of degraded dune systems is occurring and likely to continue, we examined the occurrence of amphibians in drainages associated with a coastal dune ecosystem degraded by invasive plants (European Beachgrass, Ammophila arenaria, and Iceplant, Carpobrotus edulis). We found that occupancy of 3 amphibian species (California Red-legged Frog, Rana draytonii; Sierran Treefrog, Hyliola sierra; and Rough-skinned Newt, Taricha granulosa) among 21 coastal dune drainages was high, with most coastal dune drainages occupied by all 3 species. Furthermore, reproduction of Sierran Treefrogs and California Red-legged Frogs was estimated to occur in approximately 1/2 and 1/3; of the drainages, respectively. The probability of occurrence of Rough-skinned Newts and pre-metamorphic life stages of both anurans decreased during the study, perhaps because of ongoing drought in California or precipitation-induced changes in phenology during the final year of the study. Maintaining structural cover and moist features during dune restoration will likely benefit native amphibian populations inhabiting coastal dune ecosystems.

Understanding the additive or interactive threats of habitat transformation and invasive species is critical for conservation, especially where climate change is expected to increase the severity or frequency of drought. In the arid southwestern USA, this combination of stressors has caused widespread declines of native aquatic and semi-aquatic species. Achieving resilience to drought and other effects of climate change may depend upon continued management, so understanding the combined effects of stressors is important. We used Bayesian hierarchical models fitted with 10-yrs of pond-based monitoring surveys for the federally-endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi) and invasive predators (fishes and American Bullfrogs, Lithobates catesbeianus) that threaten native species. We estimated trends in occupancy of salamanders and invasive predators while accounting for hydrological dynamics of ponds, then used a two-species interaction model to directly estimate how invasive predators affected salamander occupancy. We also tested a conceptual model that predicted that drought, by limiting the distribution of invasive predators, could ultimately benefit native species. Even though occupancy of invasive predators was stationary and their presence in a pond reduced the probability of salamander presence by 23%, occupancy of Sonoran Tiger Salamanders increased, annually, by 2.2%. Occupancy of salamanders and invasive predators both declined dramatically following the 5th consecutive year of drought. Salamander occupancy recovered quickly after return to non-drought conditions, while occupancy of invasive predators remained suppressed. Models that incorporated three time-lagged periods (1 to 4 yrs) of local moisture conditions confirmed that salamanders and invasive predators responded differently to drought, reflecting how life-history strategies shape responses to disturbances. The positive 10-yr trend in salamander occupancy and their rapid recovery after drought provided partial support for the hypothesis of drought-mediated coexistence with invasive predators. These results also suggest management opportunities for conservation of the Sonoran Tiger Salamander and other imperiled organisms in human-transformed landscapes.

California Red-legged Frogs (Rana draytonii) are typically regarded as inhabitants of permanent ponds, marshes, and slow-moving streams, but their ecology in other habitats, such as drainages among coastal dunes, remains obscure. Because coastal dune ecosystems have been degraded by development, off-highway vehicle use, stabilization, and invasive species, these unique ecosystems are the focus of restoration efforts. To better understand the ecology of California Red-legged Frogs in coastal dune ecosystems and to avoid and minimize potential negative effects of dune restoration activities on these rare frogs, we studied their spatial ecology, habitat selection, and survival in coastal dune drainages at Point Reyes National Seashore, California, USA. All 22 radio-marked frogs remained in their home drainages throughout the spring and summer of 2015 and, with some notable exceptions, most remained close to water. Local convex hull home ranges of four out of five California Red-legged Frogs with > 20 observations in dunes were < 1,600 m2. At the population level, frogs were 1.7 (1.2-4.4) times more likely to select sites 1 m closer to water, and were 83 (2.0-17,000) times more likely to select sites with 10% greater percent cover of logs that served as refuges from environmental extremes and predators. On average, California Red-legged Frogs avoided the invasive plants Iceplant (Carpobrotus edulis) and European Beachgrass (Ammophila arenaria). Frogs were https://0.68 (0.32-0.89) and https://0.55 (0.24-0.75) times as likely to select areas that had 10% greater cover of these plants, respectively. Assuming constant risk of mortality, California Red-legged Frogs had an annual survival rate of https://0.70 (range, 0.27-0.96) in coastal dune drainages. This relatively high survival rate suggests that coastal dune drainages provide a locally important habitat for California Red-legged Frogs. Restoration practices that maintain wetted drainages with logjams are likely to benefit California Red-legged Frogs.

At least one-third of all amphibian species face the threat of extinction, and current amphibian extinction rates are four orders of magnitude greater than background rates. Preventing extirpation often requires both ex situ (i.e., conservation breeding programs) and in situ strategies (i.e., protecting natural habitats). Flatwoods salamanders (Ambystoma bishopi and A. cingulatum) are protected under the U.S. Endangered Species Act. The two species have decreased from 476 historical locations to 63 recently extant locations (86.8% loss). Recovery efforts are needed to increase populations and prevent extinction, but uncertainty regarding optimal actions in both ex situ and in situ realms hinders recovery planning. We used structured decision making (SDM) to address key uncertainties regarding captive breeding and habitat restoration, and developed short-, medium-, and long-term goals to achieve recovery objectives. In promoting a transparent, logical approach, SDM has proven vital for developing recovery plans for flatwoods salamanders. The SDM approach has clear advantages over other previous approaches to recovery efforts, and should be considered for other complex decisions regarding endangered species.

We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in severity. Recent declines and local extinctions of California newt populations in Santa Monica Mountain streams motivate our study of the impact of drought on newt population sizes. Although newts are terrestrial salamanders, they migrate to streams each spring to breed and lay eggs. Since egg and larval stages occur in water, a precipitation deficit due to drought conditions reduces the space for newt egg-laying and the necessary habitat for larval development. To mathematically forecast newt population dynamics, we develop a nonlinear system of discrete equations that includes demographic parameters such as survival rates for newt life stages and egg production, which depend on habitat availability and rainfall. We estimate these demographic parameters using 15 years of stream survey data collected from Cold Creek in Los Angeles County, California, and our model captures the observed decline of the parameterized Cold Creek newt population. Based upon data analysis, we predict how the number of available newt egg-laying sites varies with annual precipitation. Our model allows us to make predictions about how the length and severity of drought can affect the likelihood of persistence and the time to critical endangerment of a local newt population. We predict that sustained severe drought will critically endanger the newt population but that the newt population can rebound if a drought is sufficiently short.

Small, seasonal pools and temporary ponds (<4.0ha) are the most numerous and biologically diverse wetlands in many natural landscapes. Thus, accurate determination of their numbers and spatial characteristics is beneficial for conservation and management of biodiversity associated with these freshwater systems. We examined the utility of a topographic position index (TPI) landscape classification to identify and classify depressional wetlands. We also assessed relationships between topographic characteristics and ponded duration of known wetlands to allow hydrological characteristics to be extended to non-monitored locations. Our results indicate that this approach was successful at identifying wetlands, but did have higher errors of commission (10%) than omission (5%). Additionally, the TPI procedure provided a reasonable means to correlate general ponded duration characteristics (long/short) with wetland topography. Although results varied by hydrologic class, permanent/long ponded duration wetlands were more often classified correctly (80%) than were short ponded duration wetlands (67%). However, classification results were improved to 100% and 75% for permanent/long and short ponded duration wetlands, respectively, by removing wetlands occurring on an abrupt marine terrace that erroneously inflated pond topographic characteristics. Our study presents an approach for evaluating wetland suitability for species or guilds that are associated with key habitat characteristics, such as hydroperiod.

The rapid emergence and reemergence of zoonotic diseases requires the ability to rapidly evaluate and implement optimal management decisions. Actions to control or mitigate the effects of emerging pathogens are commonly delayed because of uncertainty in the estimates and the predicted outcomes of the control tactics. The development of models that describe the best known information regarding the disease system at the early stages of disease emergence is an essential step for optimal decision-making. Models can predict the potential effects of the pathogen, provide guidance for assessing the likelihood of success of different proposed management actions, quantify the uncertainty surrounding the choice of the optimal decision, and highlight critical areas for immediate research. We demonstrate how to develop models that can be used as a part of a decision-making framework to determine the likelihood of success of different management actions given current knowledge.