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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.

Volumes of data illustrate the severity of the crisis affecting amphibians, where >32% of amphibians worldwide are threatened with declining populations. Although there have been isolated victories, the current approach to the issue is unsuccessful. 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 inertia and lack of cohesion in responding to amphibian issues. We acknowledge existing efforts and the useful research that has been conducted, but we suggest that a change is warranted and that the identification of a new amphibian chytrid provides the impetus for such a change. Our goal is to recognize that without a centralized effort we (collectively) are likely to fail in responding to this challenge.

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 https://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 https://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.

The salamander chytrid fungus (Batrachochytrium salamandrivorans; Bsal) was described in 2014, when die-offs in fire salamander (Salamandra salamandra) populations were reported in Europe. Susceptibility to this pathogen varies, but lethality is indicated in the families Salamandridae and Plethodontidae and members of both families occur in the US. Based on this endemicity, the discontinuity of the global incidence of Bsal, and the popularity of salamanders as pets, the emergence of this pathogen in Europe is presumed to have originated via the pet trade.

Over 28 million amphibians were imported in the US over a 6 year period during the last decade and that importation rate has not declined. Thus, there is serious concern that the disease may be introduced into the US in the near future, if it is not already present. This is particularly alarming because the eastern US is home to the highest diversity of salamanders in the world, including 141 species in the known susceptible family, Plethodontidae. Bsal is also known to be lethal to other US genera in the family Salamandridae (the rough skinned newt, Taricha granulosa, in the Pacific Northwest, and the Eastern newt Notophthalmus viridescens). This pathogen has the potential to have devastating consequences for native US salamanders, similar to extirpations observed in frog species in South America and Australia.

Therefore, a primary objective is to design a sampling strategy to detect the occurrence of the disease in the US (i.e., surveillance). Regardless of whether the disease already occurs in the US, a monitoring design must be developed to identify, with sufficient power, the probability the disease occurs in amphibian populations throughout the US, which must be assessed annually along with population estimates to understand the spread of Bsal and the fate of infected populations. A monitoring program in absence of a management plan is of limited use, and the design of a surveillance and monitoring program must consider possible management responses to monitoring results.

The threat of Bsal to US species provides a unique opportunity to address the introduction, spread, population effects, and control strategies for a novel infectious disease before we are dealing with widespread declines in native populations. By framing this crisis as an opportunity for learning and approaching the problem in a formal decision making context, we will increase the probabilities of early detection, containment, and successful mitigation of the Bsal pathogen. This working group will also provide a template for planning actions for future novel infectious diseases.

There is no coordinated effort to bring together scientists, managers, and policy makers to confront this crisis. In fact, such an approach to emerging infectious diseases is unprecedented, though this conceptual approach has been suggested in other disease outbreak contexts. We propose to bring together scientists, managers, and policy makers to develop an optimal surveillance and monitoring plan based on an adaptive management framework. The plan will also prescribe potential actions based on theoretical but likely scenarios develop from our experience with the amphibian chytrid fungus (Bd) in the US and other countries and the recent experience of our colleagues in Europe with Bsal. We will use a formal, structured working group with participation from scientists and managers from the US and Europe to frame an adaptive management and monitoring plan for this disease.

A formal working group, led by Amphibian Research and Monitoring Initiative (ARMI) scientists at the Patuxent Wildlife Research Center (Evan Grant), Fort Collins Science Center (Erin Muths) and Forest and Rangeland Ecosystem Science Center (Mike Adams) is scheduled to be held at the Powell Center for Analysis and Synthesis in Fort Collins, CO in June.

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.

This project provides an example of how spatio-temporal statistical models based on ecological theory can be applied to forecast the outcomes of conservation actions such as reintroduction. illustrates how spatial occupancy models overcome many of the obstacles hindering the application of metapopulation theory for informing reintroduction efforts.Our spatial occupancy model should be particularly useful when management agencies lack the funds to collect intensive individual-level data.

Species distribution models are used for numerous purposes such as predicting changes in species’ ranges and identifying biodiversity hotspots. Although implications of distribution models for conservation are often implicit, few studies use these tools explicitly to inform conservation efforts. Herein, we illustrate how multiple distribution models developed using distinct sets of environmental variables can be integrated to aid in identification sites for use in conservation. We focus on the endangered arroyo toad (Anaxyrus californicus), which relies on open, sandy streams and surrounding floodplains in southern California, USA, and northern Baja California, Mexico. Declines of the species are largely attributed to habitat degradation associated with vegetation encroachment, invasive predators, and altered hydrologic regimes. We had three main goals: 1) develop a model of potential habitat for arroyo toads, based on long-term environmental variables and all available locality data; 2) develop a model of the species’ current habitat by incorporating recent remotely-sensed variables and only using recent locality data; and 3) integrate results of both models to identify sites that may be employed in conservation efforts. We used Random Forests to develop the models, focused on riparian zones in southern California. We identified 14.37% and 10.50% of our study area as potential and current habitat for the arroyo toad, respectively. Generally, inclusion of remotely-sensed variables reduced modeled suitability of sites, thus many areas modeled as potential habitat were not modeled as current habitat. We propose such sites could be made suitable for arroyo toads through active management, increasing current habitat by up to 67.02%. Our general approach can be employed to guide conservation efforts of virtually any species with sufficient data necessary to develop appropriate distribution models.

Despite prevalent awareness of global amphibian declines, there is still little information on trends for many widespread species. To inform land managers of trends on protected landscapes and identify potential conservation strategies, we collected occurrence data for five wetland-breeding amphibian species in four national parks in the U.S. Rocky Mountains during 2002–2011. We used explicit dynamics models to estimate variation in annual occupancy, extinction, and colonization of wetlands according to summer drought and several biophysical characteristics (e.g., wetland size, elevation), including the influence of North American beaver (Castor canadensis). We found more declines in occupancy than increases, especially in Yellowstone and Grand Teton national parks (NP), where three of four species declined since 2002. However, most species in Rocky Mountain NP were too rare to include in our analysis, which likely reflects significant historical declines. Although beaver were uncommon, their creation or modification of wetlands was associated with higher colonization rates for 4 of 5 amphibian species, producing a 34% increase in occupancy in beaver-influenced wetlands compared to wetlands without beaver influence. Also, colonization rates and occupancy of boreal toads (Anxyrus boreas) and Columbia spotted frogs (Rana luteiventris) were ≥2 times higher in beaver-influenced wetlands. These strong relationships suggest management for beaver that fosters amphibian recovery could counter declines in some areas. Our data reinforce reports of widespread declines of formerly and currently common species, even in areas assumed to be protected from most forms of human disturbance, and demonstrate the close ecological association between beaver and wetland-dependent species.

This publication is meant to serve as a how-to guide for collection, concentration, and preservation of eDNA samples from lentic and lotic systems and provides three sampling protocols and a list of necessary supplies similar to those used by Goldberg and others (2011), Goldberg and others (2013), Pilliod and others (2013a), and Laramie and others (2015). These protocols have been used to reliably and consistently collect and concentrate eDNA from stream samples. However, adaptations to these protocols may be necessary, depending on target taxa or environmental conditions of the system being sampled. The protocols included in this document utilize cellulose nitrate filter membranes with a 0.45μm pore diameter (see Appendix A for supplies list) for water samples ideally ranging from 250ml to 1000ml. Samples collected from streams or ponds with an abundance of impurities such as tannins and organic materials will likely be limited to 500ml or less, using the described filter type. Alternative filter materials, with lower protein binding affinities, such as cellulose acetate have been successfully substituted to increase water sample volume and reduce clogging of the filter membrane (Takahara and others 2013). Additionally, filters with a greater pore diameter (0.45μm-3.0μm+) could also reduce clogging of the filter, increasing the sample volume, when desired. Turner and others (2013) provides an isocline equation to predict eDNA collection equivalents for various pore size and sample volumes using carp as a model organism. Essentially, with greater pore size, you risk eDNA molecules passing through the filter without being collected but are able to filter a greater volume of water. Examination of literature or empirical testing may be necessary to determine the most suitable materials for your desired application. Additionally, researchers must also consider the ecology of the target organism and the characteristics of the water body being sampled to determine the most suitable locations within a body of water to collect water samples (e.g. stream margins, thalweg). When possible, it is advised that samples be collected without entering a stream or pond, simply to reduce the probability of contaminating the site, boots and clothing, and/or sampling equipment.

SUMMARY
1. While Tthere is an increasing emphasis in terrestrial ecology on determining the influence of the area habitat that surroundsing habitat patches (the landscape ‘matrix’) relative to the focal habitat patch characteristics of the patches themselvesin terrestrial landscapes, research on these aspects in running-water ecosystems is still rather have been under-represented or at least, terrestrial ecologists did not really recognized parallel studies by stream ecologists. While stream ecologists have long considered the patchiness inherent in running-waters, their work has not been recognized in terrestrial landscape ecology. This is unfortunate, as it does not take full advantage of learning in these two systems, which are characterized by differences in e.g., geometric complexity, and offer opportunities to advance our understanding of conservation decisions in fragmented systems.
2. Here we outline conceptual foundations of matrix ecology for stream and river ecosystems (‘riverscapes’). We discuss how a hierarchical, patch-based perspective is necessarymay be useful for the explicit delineation of habitat patches and the surrounding matrix, through which we may identify two classes of habitat edges in riverscapes (i.e. edges between the terrestrial-aquatic interface and within-stream edges within streams).
3. Under this conceptual framework, we review discuss the role of the matrix in influencing between-patch movement, and resource quality y, and resource quantity within and among habitat patches in riverscapes. We also review identify types of empirical and modelling approaches which may advance our understanding of fragmentation effects in these systems.
4. We identify five key challenges for better improved understanding of fragmentation and matrix effects: (i) defining populations and the ir population status (i.e. quantifying the demographic contribution of habitat patches to metapopulation dynamics), (ii) scaling from metapopulations to metacommunites, (i.e. searching for generalities in species responses to landscape heterogeneity), (iii) scaling from metacommunities to metaecosystems, (i.e. exploring the interactive role of the terrestrial-aquatic and within-stream matrix effects on the flow of material and energy at the network scale), (iv) understanding temporal dynamics in matrix permeability, and (v) revealing the utility of different patch and matrix representations for modelling connectivity relationships.
5. Fragmentation of habitats is a critical issue in the conservation and management of stream networks acrossat multiple spatial scales. Although the effects of individual barriers (e.g. reservoir dams) are well documented, wWe argue suggest that a more comprehensive patch-matrix landscape model will improve our understanding of fragmentation effects, and improve management in riverscapes.

Managing a species with intensive tools like reintroduction may focus on single sites or entire landscapes. For vagile species, long-term persistence will require colonization and establishment in neighboring habitats. Thus, both suitable colonization sites and suitable dispersal corridors between sites are required. Assessment of landscapes for both requirements can contribute to ranking and selection of reintroduction areas, thereby improving management success. Following eradication of invasive American bullfrogs (Lithobates catesbeianus) from most of Buenos Aires National Wildlife Refuge (BANWR; Arizona, USA), larval Chiricahua leopard frogs (L. chiricahuensis) from a private pond were reintroduced into three stock ponds. Populations became established at all three reintroduction sites, followed by colonization of neighboring ponds in subsequent years. Our aim was to better understand colonization patterns by the federally-threatened L. chiricahuensis, which could help inform other reintroduction efforts in the region. We assessed the influence of five landscape features on colonization. Using surveys from 2007 and information about the landscape, we developed a habitat connectivity model based on electrical circuit theory that identified potential dispersal corridors, after explicitly accounting for imperfect detection of frogs. Landscape features provided little insight into why some sites were colonized and others were not, results that are likely due to the uniformity of the landscape at BANWR. While corridor modeling may be effective in more complex landscapes, an approach more focused on local habitat is required at BANWR. We also illustrate that existing data, even when limited in spatial or temporal resolution, can provide information useful in formulating management actions.

We explore the category geographically isolated
wetlands(GIWs; i.e., wetlands completely surrounded by
uplands at the local scale) as used in the wetland sciences.
As currently used, the GIW category (1) hampers scientific
efforts by obscuring important hydrological and ecological
differences among multiple wetland functional types, (2)
aggregates wetlands in a manner not reflective of regulatory
and management information needs, (3) implies wetlands so
described are in some way isolated, an often incorrect
implication, (4) is inconsistent with more broadly used and
accepted concepts of geographic isolation, and (5) has
injected unnecessary confusion into scientific investigations
and discussions. Instead, we suggest other wetland classification
systems offer more informative alternatives. For
example, hydrogeomorphic (HGM) classes based on wellestablished
scientific definitions account for wetland functional
diversity thereby facilitating explorations into
questions of connectivity without an a priori designation of
isolation. Additionally, an HGM-type approach could be
used in combination with terms reflective of current regulatory
or policymaking needs. For those rare cases in which
the condition of being surrounded by uplands is the relevant
distinguishing characteristic, use of terminology that does
not unnecessarily imply isolation (e.g., upland embedded
wetlands) would help alleviate much confusion caused by
the geographically isolated wetlands misonomer.

With ongoing climate change, many species are expected to shift their spatial and temporal distributions. To document changes in species distribution and phenology, detection/non-detection data have proven very useful. Occupancy models provide a robust way to analyze such data, but inference is usually focused on species spatial distribution, not phenology.
We present a multi-season extension of the staggered-entry occupancy model of Kendall et al. (2013), which permits inference about the within-season patterns of species arrival and departure at sampling sites. The new model presented here allows investigation of species phenology and spatial distribution across years, as well as site extinction/colonization dynamics.
We illustrate the model with two datasets on European migratory passerines and one dataset on North American tree frogs. We show how to derive several additional phenological parameters, such as annual mean arrival and departure dates, from estimated arrival and departure probabilities.
Given the extent of detection/non-detection data that are available, we believe that this modeling approach will prove very useful to further understand and predict species responses to climate change.

For more than 20 years, conservationists have agreed that amphibian populations around the world are declining. Results obtained through laboratory or mesocosm studies and measurement of contaminant concentrations in areas experiencing declines have supported a role of contaminants in these declines. The current study examines the effects of contaminant exposure to amphibians in situ in areas actually experiencing declines. Early larval Pseudacris regilla were translocated among Lassen Volcanic, Yosemite and Sequoia National Parks, California, USA and caged in wetlands in 2001 and 2002 until metamorphosis. Twenty contaminants were identified in tadpoles with an average of 1.3–5.9 (maximum = 10) contaminants per animal. Sequoia National Park, which had the greatest variety and concentrations of contaminants in 2001, also had tadpoles that experienced the greatest mortality, slowest developmental rates and lowest cholinesterase activities. Yosemite and Sequoia tadpoles and metamorphs had greater genotoxicity than those in Lassen during 2001, as determined by flow cytometry. In 2001 tadpoles at Yosemite had a significantly higher rate of malformations, characterized as hemimelia (shortened femurs), than those at the other two parks but no significant differences were observed in 2002. Fewer differences in contaminant types and concentrations existed among parks during 2002 compared to 2001. In 2002 Sequoia tadpoles had higher mortality and slower developmental rates but there was no difference among parks in cholinesterase activities. Although concentrations of most contaminants were below known lethal concentrations, simultaneous exposure to multiple chemicals and other stressors may have resulted in lethal and sublethal effects.

Agricultural activity, urban development and habitat alteration have caused the disappearance of the western spadefoot (Spea hammondii) from 80% of its range in southern California. Despite the western spadefoot’s continuing decline, little research has been conducted on its natural history. The home range of adult spadefoot is unknown, and their use of upland habitat is poorly understood. Both of these factors are important for the long-term conservation of the species because adult spadefoot spend the majority of their lives away from breeding pools. During the course of this study, radio transmitters were surgically implanted in 15 spadefoot and their movements and habitat use recorded for an average of 272 days. During that time, rain was the only significant predictor of spadefoot movement. The overall mean distance moved between burrow sites was https://17.56 m (SD ± https://23.96 m, N = 184). The mean distance moved away from the breeding pools was https://40.04 m (SD ± https://37.42, N = 200). The maximum distance moved away from the breeding pools was https://261.99 m. The amount of clay was the only predictor of spadefoot burrow locations, with spadefoot burrowing in friable soil with significantly less clay than random non-spadefoot sites. This study enhances our understanding of a little-studied species and will assist land managers in the formation of effective management plans for the spadefoot.