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The California Red-legged Frog (Rana draytonii) is a threatened species in the United States that has undergone population declines, especially in southern California. Due to the lack of information on the status of Mexican populations, we surveyed for the presence of R. draytonii in Baja California and assessed possible threats to population persistence. The two-year study (2013−2014) extended from the U.S.-Mexican border to the southern end of the species distribution in the Sierra San Pedro Mártir. We found R. draytonii at six of 15 historical sites, none of five proxy sites and four of 24 additional sites sites. All 10 occupied sites are confined to three watersheds within the Sierra San Pedro Mártir (two sites at Arroyo San Rafael, two sites at Arroyo San Telmo, and six sites at Arroyo Santo Domingo). Capture rates ranged from 1–11 individuals per visit, with the exception of La Grulla, where the average was 68. Rana draytonii was absent from 9 historical sites, including the highest elevation site at La Encantada and numerous drainages in low-lying coastal areas, suggesting the species is in decline in Baja California. The main threats identified across the study area include presence of exotic animal species, water diversion, and cattle grazing. Management of the remaining populations and local education is needed to prevent further declines.

eSummary(1) Biological monitoring programs are increasingly relying upon large volumes of citizenscience data to improve the scope and spatial coverage of information, ch a l l en g i n g thescientific commun i ty to develop design and model - b ase d approaches to improve inference.(2) Recent statistical models in ecology have be en develope d to accommodate false-negativeerrors, although recent work points to false positive errors as equally important sources ofbias. This is of particular concern for the success of any m o n i t or i n g program given rates assmall as 3% could lead to th e overestimation of the occurrence of rare events by as much as50%, and even small false positive r a t es can severely b i as estimates of occurrence dynamics.(3) We present an int eg ra t ed , comput at i o n al l y efficient Bayesian hierar chical model tocorrect for fal se positi ve and negative error s in detection/no n -d et ec ti o n data. Our modelcombines ind ependent, a u x i l i ar y data sources with field observations to i m p r ove t h eestimation of false positive rate s, when a subset of field observatio n s cannot be validated aposteriori or assumed as per fe ct . We evaluated the performance of the model across arange of occurren ce rates, false positive and negative errors, and quantity of auxil i ar y data.(4) Th e mode l perfor m ed well under all simulated scenario s, and we were able t o identifycritical auxiliary data characteristics which resul t ed in improved infer en ce. We applied ourfalse positive m odel to a large-scale, citizen -sci e n ce monitor i n g program for anurans in theNortheastern U.S., using auxiliary data from an experiment d esi g n ed to estimate falsepositive er r o r rates. Not correcting for false positive ra t es resulted in biased estimates ofoccupancy in 4 of the 10 anu r a n species we an a l y zed , leadin g to an overestima t i on of theaverage number of occupi ed survey routes by as much as 70%.Conclusions. The framework we present for da ta collecti o n and analysis is able toefficiently pr ovide reliable inference for occurrence patterns using data from acitizen-science monitorin g program . However, our approach is ap p l i ca b le to data generatedby any type of research and monit or i n g program , independent of skill level or scale, when effort i s placed on obtaining independent info rma t i on on false positive rates

A newly identified fungal pathogen, <i>Batrachochytrium salamandrivorans</i> (<i>Bsal</i>), is responsible for mass mortality events and severe population declines in European salamanders. The eastern USA has the highest diversity of salamanders in the world and the introduction of this pathogen is likely to be devastating. Although data is inevitably limited for new pathogens, disease risk assessments utilize best available data to inform management decisions. Using characteristics of <i>Bsal</i> ecology, spatial data on imports and pet trade establishments, and salamander species diversity, we identify high risk areas with both a high likelihood of introduction and severe consequences for local salamanders. We predict that the Pacific coast, southern Appalachian Mountains, and mid-Atlantic regions will have the highest relative risk from <i>Bsal</i>. Management of invasive pathogens becomes difficult once they are established in wildlife populations; therefore, import restrictions to limit pathogen introduction and early detection through surveillance of high risk areas are priorities for preventing the next crisis for North American salamanders

Habitat disturbance from stream culverts can affect aquatic organisms by increasing sedimentation or forming barriers to movement. Land managers are replacing many culverts to reduce these negative effects, primarily for stream fishes. However, these management actions are likely to have broad implications for many organisms, including amphibians in small streams. To assess the effects of culverts on movement and survival of Dicamptodon aterrimus, the Idaho giant salamander, we used capture-mark-recapture surveys and measured sediment in 9 streams with 3 culvert types: unimproved culverts, improved culverts, and no culverts. We predicted culverts would increase stream sediment levels, limit movement, and reduce survival of D. aterrimus. We also determined the effect of sediment levels on survival of salamanders, because although sediment is often associated with distribution and abundance of stream amphibians, links with vital rates remain unclear. To estimate survival, we used a spatial Cormack-Jolly-Seber (CJS) model that explicitly incorporated information on movement, eliminating bias in apparent survival estimated from traditional (i.e., non-spatial) CJS models caused by permanent emigration beyond the study area. To demonstrate the importance of using spatial data in studies of wildlife populations, we compared estimates from the spatial CJS to estimates of apparent survival from a traditional CJS model. Although high levels of sediment reduced survival of salamanders, culvert type was unrelated to sediment levels or true survival of salamanders. Across all streams, we documented only 15 movement events between study reaches. All movement events were downstream, and they occurred disproportionately in 1 stream, which precluded measuring the effect of culvert design on movement. Interestingly, although movement was low overall, the variance among streams was high enough to bias estimates of apparent survival compared to true survival. Our results suggest that where sedimentation occurs from roads and culverts, survival of D. aterrimus could be reduced. Though culverts clearly do not completely block downstream movements of D. aterrimus, the degree to which culvert improvements affect movements under roads in comparison to unimproved culverts remains unclear, especially for rare, but potentially important, upstream movements.

Conservation of imperiled species often requires knowledge of vital rates and population dynamics. However, these can be difficult to estimate for rare species and small populations. This problem is further exacerbated when individuals are not available for detection during some surveys due to limited access, delaying surveys and creating mismatches between the breeding behavior and survey timing. Here we use simulations to explore the impacts of this issue using four separate boreal toad (Anaxyrus boreas boreas) populations, representing combinations of logistical access (accessible, inaccessible) and breeding behavior (synchronous, asynchronous). We examine the bias and precision of survival and breeding probability estimates generated by survey designs that differ in effort and timing for these populations.

Decision-analytic models provide forecasts of how systems of interest will respond to management. These models can be parameterized using empirical data, but sometimes require information elicited from experts. When evaluating the effects of disease in species translocation programs, expert judgment is likely to play a role because complete empirical information will rarely be available. We illustrate development of a decision-analytic model built to inform decision-making regarding translocations and other management actions for the boreal toad (Anaxyrus boreas boreas), a species with declines linked to chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd).

Adaptive management provides a useful framework for managing natural resources in the
face of uncertainty. An important component of adaptive management is identifying clear,
measurable conservation objectives that reflect the desired outcomes of stakeholders. A common
objective is to have a sustainable population, or metapopulation, but it can be difficult to quantify
a threshold above which such a population is likely to persist. We performed a Bayesian
metapopulation viability analysis (BMPVA) using a dynamic occupancy model to quantify the
characteristics of two wood frog (Lithobates sylvatica) metapopulations resulting in sustainable
populations, and we demonstrate how the results could be used to define meaningful objectives
that serve as the basis of adaptive management. We explored scenarios involving
metapopulations with different numbers of patches (pools) using estimates of breeding
occurrence and successful metamorphosis from two study areas to estimate the probability of
quasi-extinction and calculate the proportion of vernal pools producing metamorphs. Our results
suggest that >50 pools are required to ensure long-term persistence with approximately 16% of
pools producing metamorphs in stable metapopulations. We demonstrate one way to incorporate
the BMPVA results into a utility function that balances the trade-offs between ecological and
financial objectives, which can be used in an adaptive management framework to make optimal,
transparent decisions. Our approach provides a framework for using a standard method (i.e.,
PVA) and available information to inform a formal decision process to determine optimal and
timely management policies.

Cold environments at high elevation and high latitude are often viewed as resistant to biological invasions. However, climate warming, land use change and associated increased connectivity all increase the risk of biological invasions in these environments. Here we present a summary of the key discussions of the workshop ‘Biosecurity in Mountains and Northern Ecosystems: Current Status and Future Challenges’ (Flen, Sweden, 1-3 June 2015). The aims of the workshop were to (i) increase awareness about the growing importance of species expansion – both non-native and native – at high elevation and high latitude with climate change, (ii) review existing knowledge about invasion risks in these areas, and (iii) encourage more research on how species will move and interact in cold environments, and the consequences for animal and human health and wellbeing. The diversity of potential and actual invaders reported at the workshop and the likely interactions between them create major challenges for managers of cold environments. However, since these cold environments have experienced fewer invasions when compared with many warmer, more populated environments, prevention has a real chance of success, especially if it is coupled with prioritisation schemes for targeting invaders likely to have greatest impact. Communication and co-operation between cold environment regions will facilitate rapid response and maximise use of limited research and management resources.

Mortality events in wild amphibians go largely undocumented, and where events are detected, the numbers of dead amphibians observed are probably a small fraction of actual mortality. Incidental observations from field surveys can, despite limitations, provide valuable information on the presence, host species, and spatial distribution of diseases. Here we summarize amphibian mortality events and diagnoses recorded from 2000 to 2014 in four management areas: Yellowstone National Park; Grand Teton National Park; the John D. Rockefeller, Jr. Memorial Parkway; and the National Elk Refuge, which together span a large portion of protected areas within the Greater Yellowstone Ecosystem.

The recently identified pathogenic chytrid fungus, Batrachochytrium salamandrivorans (Bsal), poses a severe threat to the distribution and abundance of salamanders within the United States and Europe. Development of a response strategy for the potential, and likely, invasion of Bsal into the United States is critical to protect global salamander biodiversity. A formal working group, led by Amphibian Research and Monitoring Initiative (ARMI) scientists from the U.S. Geological Survey (USGS) Patuxent Wildlife Research Center, Fort Collins Science Center, and Forest and Rangeland Ecosystem Science Center, was held at the USGS Powell Center for Analysis and Synthesis in Fort Collins, Colorado, USA from June 23 to June 25, 2015, to identify critical Bsal research and monitoring needs that could inform conservation and management strategies for salamanders in the United States. Key findings of the workshop included the following: (1) the introduction of Bsal into the United States is highly probable, if not inevitable, thus requiring development of immediate short-term and long-term intervention strategies to prevent Bsal establishment and biodiversity decline; (2) management actions targeted towards pathogen containment may be ineffective in reducing the long-term spread of Bsal throughout the United States; and (3) early detection of Bsal through surveillance at key amphibian import locations, among high-risk wild populations, and through analysis of archived samples is necessary for developing management responses. Top research priorities during the pre-invasion stage included the following: (1) deployment of qualified diagnostic methods for Bsal and establishment of standardized laboratory practices, (2) assessment of susceptibility for amphibian hosts (including anurans), and (3) development and evaluation of short- and long-term pathogen intervention and management strategies. Several outcomes were achieved during the workshop, including development of an organizational structure with working groups for a Bsal Task Force, creation of an initial influence diagram to aid in identifying effective management actions in the face of uncertainty, and production of a list of potential management actions and key research uncertainties. Additional products under development include a Bsal Strategic Action plan, an emergency response plan, a monitoring and surveillance program, a standardized diagnostic approach, decision-models for natural resource agencies, and a reporting database for salamander mortalities. This workshop was the first international meeting to address the threat of Bsal to salamander populations in the United States, with more than 30 participants from U.S. conservation and resource management agencies (USFWS, USFS, DoD, NPS, and AFWA) and academic research institutions from Australia, the Netherlands, Switzerland, the United Kingdom, and the United States.

The primary goal of the Trinity River Restoration Program (TRRP) is to rehabilitate the fisheries on the dam-controlled Trinity River; however, maintaining and enhancing other wildlife populations through the restoration initiatives is also a key objective. For herpetological species, foothill yellow-legged frogs and western pond turtles have been identified as important species on which to focus monitoring efforts due to their status as California state-listed Species of Concern and potential listing on the U.S. Endangered Species List. We have developed and implemented a monitoring strategy for these species specific to the Trinity River with the objective of establishing baseline values for probabilities of site occupancy, colonization and local extinction; identify site characteristics that correlate with the probability of extinction; and to estimate overall trends in abundance. Our three-year study suggests that foothill yellow-legged frogs declined in the probability of site occupancy. Conversely, our results suggest that western pond turtle increased in both abundance and the probability of site occupancy. The short length of our study period makes it difficult to draw firm conclusions, however these result provide needed baseline data. Further monitoring and directed studies are required to assess how habitat changes and management decisions relate to the status and trend of these species.

Book chapter: All wild animal populations harbor a range of parasitic organisms, ranging from viruses and bacteria to multicellular parasites such as helminths and arthropods. While some of these are mutualists and some are commensal, others cause infectious disease in at least some members of the population and some may have substantial population-level impacts. The reintroduction of animals requires an immense amount of effort, and considering known and potential diseases is crucial to all phases of a well-formulated reintroduction plan (site and donor selection, implementation and monitoring). While disease has been recognized as a potential factor in reintroductions for decades (e.g. Griffith et al. 1993), heightened conservation concerns and increasing numbers of emerging pathogens bring a consideration of disease to the forefront of many projects.

Amphibians are declining throughout the United States and worldwide due, partly, to habitat loss. The Iowa Conservation Reserve Enhancement Program (CREP) strategically restores wetlands to denitrify tile drainage effluent and restore ecosystem services. Understanding how eutrophication , hydroperiod, predation, and disease affect amphibians in restored wetlands is central to maintaining healthy amphibian populations in the region. We examined the quality of amphibian habitat in restored CREP wetlands relative to reference wetlands by comparing species richness, developmental stress, and adult leopard frog (Lithobates pipiens) survival probabilities to a suite of environmental metrics. Although measured habitat variables differed between restored and reference wetlands, differences appeared to have sub-lethal rather than lethal effects on resident populations . There were few differences in amphibian species richness and no difference in estimated survival probabilities between wetland types. Restored wetlands had more nitrate and alkaline pH, longer hydroperiods, and were deeper, whereas reference wetlands had more amphibian chytrid fungus zoospores and resident amphibians exhibited increased developmental stress. Restored and reference wetlands are both important components of the landscape in central Iowa and maintaining a complex of fish-free wetlands with a variety of hydroperiods will likely contribute to the persistence of amphibians in this landscape.

We suggest that a radically different approach, something akin to human emergency response management (i.e., the Incident Command System) is one alternative to addressing the lack of cohesion and inertia in responding to amphibian issues. While we acknowledge existing efforts and the prodigious amount of useful research, we suggest that a change is warranted and that the identification of a new amphibian chytrid provides the impetus for such a change.

ABSTRACT: Spatial capture-recapture (SCR) is a relatively recent development in ecological statistics that provides a spatial context for estimating abundance and space use patterns, and as a result improves inference about absolute population density. SCR has been applied to individual encounter data collected non-invasively using methods such as camera traps, hair snares and scat surveys. Despite the wide-spread use of capture based surveys to monitor amphibians and reptiles, there are few applications of SCR in the herpetological literature. We demonstrate the utility and promise of the application of SCR in studies of reptiles and amphibians by analyzing capture recapture data from red-backed salamanders, Plethodon cinereus, collected using artificial cover boards. Using SCR to analyze spatial encounter histories of marked individuals, we found evidence that density differed little among 4 sites within the same forest (on average 1.59 salamanders per m2) and that salamander detection probability peaked in early October (Julian day 278) reflecting expected surface activity patterns of the species. The spatial scale of detectability, a measure of space use, suggests that the 95% fall home range size for this population of red-backed salamanders was 16.89 m2. Surveying reptiles and amphibians using artificial cover boards regularly generates spatial encounter history data of known individuals which can readily be analyzed using SCR methods, providing estimates of absolute density and inference about the spatial scale of habitat use.

Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history, and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation—as would be expected if incipient speciation were occurring—and if so, whether behavioral isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number, and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioral isolation: in phonotaxis experiments, low elevation females tended to prefer an average low elevation call over a high elevation call, and vice versa for high elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.

Heterogeneous landscapes and fluctuating environmental conditions can affect species’ dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

Regional monitoring strategies frequently employ a nested sampling design where a finite set of study areas from throughout a region are selected within which intensive sub-sampling occurs. This sampling protocol naturally lends itself to a hierarchical analysis to account for dependence among sub-samples. Implementing such an analysis within a classic likelihood framework is computationally prohibitive with species occurrence data when accounting for detection probabilities. Bayesian methods offer an alternative framework to make this analysis feasible. We demonstrate a general approach for estimating occupancy when data come from a nested sampling design. Using data from a regional monitoring program of wood frogs (Lithobates sylvaticus) and spotted salamanders (Ambystoma maculatum) in vernal pools, we analyzed data using static and dynamic occupancy frameworks. We analyzed observations from 2004-2013collected within 14 protected areas located throughout the northeast United States. We use the data set to estimate trends in occupancy at both the regional and individual protected area level. We show that occupancy at the regional level was relatively stable for both species. Much more variation occurred within individual study areas, with some populations declining and some increasing for both species. We found some evidence for a latitudinal gradient in trends among protected areas. However, support for this pattern is overestimated when the hierarchical nature of the data collection is not controlled for in the analysis. For both species, occupancy appeared to be declining in the most southern areas, while occupancy was stable or increasing in more northern areas. These results shed light on the range-level population status of these pond-breeding amphibians and our approach provides a framework that can be used to examine drivers of change including among-year and among-site variation in occurrence dynamics, while properly accounting for nested structure of data collection.

ARMI is uniquely qualified to provide information that is scalable from local to national levels and is useful to resource managers. Here we provide highlights and significant milestones of this innovative program. ARMI has now produced over 500 publications. We feature several in this fact sheet, but please visit our website (http://armi.usgs. gov) for additional information on ARMI products, to find summaries of research topics, or to search for ARMI activities in your area.