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1. Surveillance programs are essential for detecting emerging pathogens and often rely on molecular methods to make inference about the presence of a target disease agent. However, molecular methods rarely detect target DNA perfectly. For example, molecular pathogen detection methods can result in misclassification (i.e., false positives and false negatives) or partial detection errors (i.e., detections with ‘ambiguous’, ‘uncertain’, or ‘equivocal’ results). Then, when data are to be analyzed, these?partial observations?are?either?discarded?or censored;?this, however, disregards information that could be used to make inference about the true state of the system. There is a critical need for more direction and guidance related to how many samples is enough to declare a unit of interest ‘pathogen-free’.
2. Here, we develop a Bayesian hierarchal framework that accommodates false negative, false positive, and uncertain detections to improve inference related to the occupancy of a pathogen. We apply our modeling framework to a case study of the fungal pathogen Pseudogymnoascus destructans (Pd) identified in Texas bats at the invasion front of white-nose syndrome. To improve future surveillance programs, we provide guidance on sample sizes required to be 95% certain a target organism is absent from a site.
3. We found that the presence of uncertain detections increased the variability of resulting posterior probability distributions of pathogen occurrence, and that our estimates of required sample size were very sensitive to prior information about pathogen occupancy, pathogen prevalence, and diagnostic test specificity. In the Pd case study, we found that the posterior probability of occupancy was very low in 2018, but occupancy probability approached 1 in 2020, reflecting increasing prior probabilities of occupancy and prevalence elicited from the site manager.
4. Our modeling framework provides the user a posterior probability distribution of pathogen occurrence, which allows for subjective interpretation by the decision-maker. To help readers apply and use the methods we developed, we provide an interactive?RShiny?app?that generates target species?occupancy estimation and sample size estimates to make these methods more accessible?to the scientific community (https://rmummah.shinyapps.io/ambigDetect_sampleSize).?This modeling framework and sample size guide may be useful for improving inferences from molecular surveillance data about emerging pathogens, non-native invasive species, and endangered species where misclassifications and ambiguous detections occur.

Countless species of animals—big game, birds, bats, insects, amphibians, reptiles, and fish—migrate to reach suitable habitats to feed, reproduce, and raise their young. Animal migrations developed over millennia commonly follow migration corridors—unique routes for each species—to move among seasonal habitats. Changes along those corridors, whether from human development (buildings, roads, dams) or from natural disturbances (for example, climate change, drought, fire, flooding, or invasive species), can make them harder to navigate. The U.S. Geological Survey’s Ecosystems Mission Area provides science that assists land managers in mapping, enhancing, protecting, and reconnecting migration corridors critical for diverse fish and wildlife populations that migrate, such as Odocoileus hemionus (mule deer) and Antilocapra americana (pronghorn), trout and salmon, salamanders, tortoises, bats, and Danaus plexippus (monarch butterflies).

Protected areas like national parks are essential elements of conservation because they limit human influence on the landscape, which protects biodiversity and ecosystem function. The role of national parks in conservation, however, often goes far beyond limiting human influence. The U.S. National Park Service and its system of land units contribute substantively to conservation by providing protected lands where researchers can document trends in species distributions and abundances, examine characteristics important for generating these trends, and identify and implement conservation strategies to preserve biodiversity. We reviewed the contribution of U.S. national parks to amphibian research and conservation and highlight important challenges and findings in several key areas. First, U.S. national parks were instrumental in providing strong support that amphibian declines were real and unlikely to be simply a consequence of habitat loss. Second, research in U.S. national parks provided evidence against certain hypothesized causes of decline, like UV-B radiation, and evidence for others, such as introduced species and disease. However, describing declines and identifying causes contributes to conservation only if it leads to management; importantly, U.S. national parks have implemented many conservation strategies and evaluated their effectiveness in recovering robust amphibian populations. Among these, removal of invasive species, especially fishes; conservation translocations; and habitat creation and enhancement stand out as examples of successful conservation strategies with broad applicability. Successful management for amphibians is additionally complicated by competing mandates and stakeholder interests; for example, past emphasis on increasing visitor enjoyment by introducing fish to formerly fishless lakes had devastating consequences for many amphibians. Other potential conflicts with amphibian conservation include increasing development, increased risk of introductions of disease and exotic species with increased visitation, and road mortality. Decision science and leveraging partnerships have proven to be key components of effective conservation under conflicting mandates in national parks. As resource managers grapple with large-scale drivers that are outside local control, public-private partnerships and adaptive strategies are increasing in importance. U.S. national parks have played an important role in many aspects of identifying and ameliorating the amphibian decline crisis and will continue to be essential for the conservation of amphibians in the future.

Climate can have a strong influence on species distributions, and amphibians with different life histories might be affected by annual variability in precipitation in different ways. The Sierra Nevada of California, United States, experienced some of the driest and wettest years on record in the early 21st Century, with variability in annual precipitation predicted to increase with climate change. We  examined the relationship between adult occupancy dynamics of three high elevation anurans and site and annual variation in measures of winter severity, summer wetness, and cumulative drought. We further evaluated how these weather conditions affected the probability that each species would reproduce, conditional on their occurrence at a site. We found that although different aspects of weather affected the occupancy dynamics of each species differently, adult occupancy probabilities were generally stable throughout our 15-year study period. The probability of reproduction, although slightly more variable than adult occupancy, was similarly stable throughout the study. Although occurrence of the three species was resilient to recent extremes in precipitation, more detailed demographic study would inform the extent to which amphibian populations will remain resilient to increasing severity, duration, and frequency of drought and flood cycles.

Quantifying how contaminants change across life cycles of species who undergo metamorphosis is critical to assessing risk to organisms and their consumers. Pond-breeding amphibians can dominate aquatic animal biomass as larvae and are terrestrial prey as metamorphs and adults. Thus, amphibians can be vectors of mercury accumulation in both aquatic and terrestrial food webs. However, it is still unclear how mercury concentrations are affected by exogenous (e.g., habitat or diet) vs. endogenous factors (e.g., catabolism during hibernation) as amphibians undergo large diet shifts and periods of fasting during ontogeny. We measured total mercury (THg), methylmercury (MeHg), and isotopic compositions (?13C, ?15N) in boreal chorus frogs (Pseudacris maculata) across five life stages in two metapopulations in Colorado, USA. We found large differences in MeHg concentrations and percent of THg as MeHg among life stages. Frog MeHg concentrations spiked after metamorphosis and hibernation coinciding with the most energetically demanding stages of their life cycle. Transitions among life stages led to large step changes in mercury concentrations – the endogenous processes of metamorphosis and hibernation biomagnified MeHg, decoupling isotopic compositions and MeHg concentrations. These step changes are not often considered in conventional expectations of how food web processes predict trophic transfer, accumulation, and transport of contaminants. ?

Climate change is an increasingly important driver of biodiversity loss. The ectothermic nature of amphibians may make them particularly sensitive to changes in normal temperature and precipitation regimes, exacerbating global declines from other threats. In this study, we used large-scale citizen science data from the eastern half of the United States to assess how variation in winter severity influenced occupancy dynamics of 11 anuran species. We found that most species had increased occupancy in years with greater than average snow cover and warmer than average mean winter temperatures. Surprisingly, we found that climatic conditions in winter affected occupancy dynamics of both spring and summer breeding species, indicating that changing winter conditions may have consequences for anuran species with varying life history characteristics. As the climate continues to change, expected reductions in snowpack may act as an additional stressor on already declining anuran populations, while milder winters may improve overwinter survival for some species.

Increasing temperatures and climate-driven disturbances like wildfire are a growing threat to many species,
including cold-water specialists. Montane areas and cold streams are often considered climate refugia that buffer
communities against change. However, climate refugia are often species-specific, and despite growing awareness
that life histories and habitat requirements shape responses to change, small or non-game species are often
under-represented in monitoring and planning programs. A recent study in Montana, USA, revealed much larger
warming-related declines in occupancy for small, non-game slimy sculpin (Cottus cognatus) between 1993 and
1995 and 2011–2013 than for two socially valued salmonid fishes that shape regional conservation efforts. To
broaden insight into climate change vulnerabilities of headwater stream communities, we analyzed data for
Rocky Mountain tailed frogs (Ascaphus montanus) that were collected during those same electrofishing surveys
for fishes from 241 stream reaches. Tailed frogs occupy small, cold streams and have several life-history traits
that make them sensitive to environmental change. We used a Bayesian framework to estimate occupancy,
colonization, and extinction dynamics relative to forest canopy, estimated stream temperature, and wildfire
effects. Tailed frog occupancy decreased by 19 % from 1993 to 1995 to 2011–2013. Changes in occupancy were
linked with increased extinction and reduced colonization where there were fire-driven reductions in canopy
cover, and reduced colonization of stream reaches that warmed on average 0.8 ?C during the study. Our results
highlight extensive extirpations for oft-overlooked species and emphasize the importance of including species
with diverse habitat requirements and life histories in conservation planning.

Invasive species and emerging infectious diseases are two of the greatest
threats to biodiversity. American Bullfrogs (Rana [Lithobates] catesbeiana),
which have been introduced to many parts of the world, are often linked with
declines in native amphibians via predation and the spread of emerging pathogens
such as amphibian chytrid fungus (Batrachochytrium dendrobatidis [Bd])
and ranaviruses. Although many studies have investigated the potential role of
bullfrogs in the decline of native amphibians, analyses that account for shared
habitat affinities and imperfect detection have found limited support for
clear effects. Similarly, the role of bullfrogs in shaping the patch-level distribution
of pathogens is unclear. We used eDNA methods to sample 233 sites in the southwestern USA and Sonora, Mexico (2016–2018) to estimate how
the presence of bullfrogs affects the occurrence of four native amphibians,
Bd, and ranaviruses. Based on two-species, dominant-subordinate occupancy
models fitted in a Bayesian context, federally threatened Chiricahua Leopard
Frogs (Rana chiricahuensis) and Western Tiger Salamanders (Ambystoma
mavortium) were eight times (32% vs. 4%) and two times (36% vs. 18%), respectively,
less likely to occur at sites where bullfrogs occurred. Evidence for the
negative effects of bullfrogs on Lowland Leopard Frogs (Rana yavapaiensis)
and Northern Leopard Frogs (Rana pipiens) was less clear, possibly because of
smaller numbers of sites where these native species still occurred and because
bullfrogs often occur at lower densities in streams, the primary habitat for
Lowland Leopard Frogs. At the community level, Bd was most likely to occur
where bullfrogs co-occurred with native amphibians, which could increase the
risk to native species. Ranaviruses were estimated to occur at 33% of bullfrogonly
sites, 10% of sites where bullfrogs and native amphibians co-occurred,
and only 3% of sites where only native amphibians occurred. Of the 85 sites
where we did not detect any of the five target amphibian species, we also did
not detect Bd or ranaviruses; this suggests other hosts do not drive the distribution
of these pathogens in our study area. Our results provide landscape-scale
evidence that bullfrogs reduce the occurrence of native amphibians and
increase the occurrence of pathogens, information that can clarify risks and
aid the prioritization of conservation actions.

Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. Aims. We sought to model the occupancy dynamics of the Dixie Valley toad (Anaxyrus williamsi), a recently described species endemic to a small desert spring wetland complex in Nevada, USA. Methods. We divided the species’ range into 20 m × 20 m cells and surveyed for Dixie Valley toads at 60 cells during six primary periods from 2018 to 2021, following an occupancy study design. We analysed our survey data by using a multi-state dynamic occupancy model to estimate the probability of adult occurrence, colonisation, site survival, and larval occurrence and the relationship of each to environmental covariates. Key results. The detection probabilities of adult and larval toads were affected by survey length and time of day. Adult Dixie Valley toads were widely distributed, with detections in 75% of surveyed cells at some point during the 3-year study, whereas larvae were observed only in 20% of cells during the study. Dixie Valley toad larvae were more likely to occur in cells far from spring heads with a high coverage of surface water, low emergent vegetation cover, and water temperatures between 20°C and 28°C. Adult toads were more likely to occur in cells with a greater coverage of surface water and water depth >10 cm. Cells with more emergent vegetation cover and surface water were more likely to be colonised by adult toads. Conclusions. Our results showed that Dixie Valley toads are highly dependent on surface water in both spring and autumn. Adults and larvae require different environmental conditions, with larvae occurring farther from spring heads and in fewer cells. Implications. Disturbances to the hydrology of the desert spring wetlands in Dixie Valley could threaten the persistence of this narrowly distributed toad.

Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across the invasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.