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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.

Populations are rarely censused. Instead observations are affected by incomplete detection, misclassification, and detection heterogeneity that results from human and environmental constraints. Though numerous methods have been developed to deal with observational uncertainty, validation under field conditions are rare because truth is rarely known. We present the most comprehensive test of occupancy methods to date, using more than 33,000 auditory call observations collected under standard field conditions but where the true occupancy status of sites was known. Basic occupancy estimation approaches were biased when two key assumptions were not met: that no false positives occur and that no unexplained heterogeneity in detection parameters occurs. The greatest bias occurred for dynamic parameters (i.e., local colonization and extinction) and in many cases the degree of inaccuracy would render results largely useless. We examined three approaches to increase adherence or relax these assumptions: modifying the sampling design, employing estimators that account for false positive detections, and using covariates to account for site-level heterogeneity in both false negative and false positive detection probabilities. We demonstrate that bias can be substantially reduced by modifications to sampling methods and by using estimators that simultaneously account for false positive detections and site-level covariates to explain heterogeneity. Our results demonstrate that even small probabilities of misidentification and among-site detection heterogeneity can have severe effects on estimator reliability if ignored. We challenge researchers to place greater attention to both heterogeneity and false positives when designing and analyzing occupancy studies and provide 9 specific guidelines for design, implementation, and analysis of occupancy studies to meet this challenge.

Beavers (Castor canadensis) influence habitat for many species and pose challenges in developed landscapes. They are increasingly viewed as a cost?efficient means of riparian habitat restoration and water storage. Still, information on their status is rare, particularly in western North America. We used aerial photography to evaluate changes in beaver occupancy between 1942–1968 and 2009 in upper portions of 2 large watersheds in Oregon, USA. We used multiple observers and occupancy modeling to account for bias related to photo quality, observers, and imperfect detection of beaver impoundments. Our analysis suggested a slightly higher rate of beaver occupancy in the upper Deschutes than the upper Klamath basin. We found weak evidence for beaver increases in the west and declines in eastern parts of the study area. Our study presents a method for dealing with observer variation in photo interpretation and provides the first assessment of the extent of beaver influence in 2 basins with major water?use challenges. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Hydrological and biological investigations were done during 2005 and 2006 in cooperation with the U.S. National Park Service to investigate the source, discharge, and chemical characteristics of selected springs and the abundance and health of endemic anuran (frog and toad) species at Darwin Falls in Death Valley National Park, Piute Spring in Mojave National Preserve, and Fortynine Palms Oasis in Joshua Tree National Park. Discharge from the springs at these sites sustains isolated riparian habitats in the normally dry Mojave Desert. Data were collected on water quantity (discharge) and quality, air and water temperature, and abundance and health of endemic anuran species. In addition, a single survey of the abundance and health of endemic anuran species was completed at Rattlesnake Canyon in Joshua Tree National Park. Results from this study were compared to limited historical data, where they exist, and can provide a baseline for future hydrological and biological investigations to evaluate the health and sustainability of the resource and its response to changing climate and increasing human use.

Radiocarbon dating of the water yielded estimated ages of about 7,000 years at Piute Spring and about 3,000 years at Darwin Spring, and tritium-helium-3 dating indicated an age of less than 2 years at Fortynine Palms Oasis. Stable hydrogen-isotope ratios were used to interpret an average altitude of recharge of 2,348 meters for Darwin Spring (about 1,415 meters higher than the altitude of Darwin Spring), 1,668 meters for Piute Spring (about 766 meters higher than the altitude of Piute Spring), and 1,400 meters for the Upper Pool at Fortynine Palms Oasis (about 543 meters higher than the altitude of the Upper Pool). Water-quality data collected for this study did not appear to be sensitive to trends in precipitation or seasonality in the Darwin Falls and Piute Spring study areas; however, it was sensitive to trends in Fortynine Palms Oasis where salinity increased by more than 10 percent during the 2 years of this study. Such a rapid response is consistent with the comparatively short travel time of less than 2 years from recharge to discharge at Fortynine Palms Oasis. Of the 14 trace elements analyzed, only concentrations of uranium at Fortynine Palms Oasis and arsenic at Darwin Spring were above drinking water standards; both constituents are derived from natural sources in the drainage basin and, therefore, are likely to have accumulated as a result of natural processes.

Endemic anuran species were surveyed at Darwin Falls for the western toad [Anaxyrus boreas] and the red-spotted toad [Anaxyrus punctatus], at Piute Spring for the red-spotted toad, and at Fortynine Palms Oasis for the red-spotted toad and California treefrog [Pseudacris cadaverina]. Historically, red-spotted toads were at the edge of their range at Darwin Falls, but they were not detected during this study and have not been detected since the early 1980s. The 2006 western toad population at Darwin Falls was estimated at 381 adults (95-percent confidence interval [CI] of 314–482). The population of red-spotted toads at Piute Spring was estimated at 1,153 adults (95-percent CI of 935–1,503). However, an elevated rate of abnormalities (approximately 5 percent) was recorded in red-spotted toads as well as the presence of the chytrid fungus,[Bactrochochytrium dendrobatidis], at Piute Spring. In Joshua Tree National Park, the California treefrog now occupies only three of the seven historically occupied drainages. Populations of California treefrogs at Fortynine Palms Oasis have declined more than 50 percent from 288 in 1969–71 to 109 in 2006. A similar decline was observed in the populations of red-spotted toads at Fortynine Palms Oasis from 300 adults in 1969–71 to 155 adults (95-percent CI of 90–139) in 2006. The red-spotted toads at Fortynine Palms Oasis also exhibited the presence of [Bactrochochytrium dendrobatidis].

The occurrence of false positive detections in presence-absence data, even when they occur infrequently, can lead to severe bias when estimating species occupancy patterns. Building upon previous efforts to account for this source of observational error (Royle & Link 2006; Miller et al. 2011, 2013), we establish a general framework to model false positives in occupancy studies and extend existing modeling approaches to encompass a broader range of sampling designs. Specifically, we identified three common sampling designs that are likely to cover most scenarios encountered by researchers. The different designs all include ambiguous detections, as well as some known-truth data, but their modeling differs in the level of the model hierarchy at which the known-truth information is incorporated (site-level or observation-level). For each model, we provide the likelihood, as well as R and BUGS code needed for implementation. We also establish a clear terminology and provide guidance to help choosing the most appropriate design and modeling approach.

Glyphosate use in the US increased from less than 5,000 to more than 80,000 metric tons per year between 1987 and 2007. Glyphosate is popular due to its ease of use on soybean, cotton and corn crops that are genetically modified to tolerate it, utility in no-till farming practices, utility in urban areas, and the perception that it has low toxicity and little mobility in the environment. This compilation is the largest and most comprehensive assessment of the environmental occurrence of glyphosate and AMPA in the US conducted to date, summarizing the results of 3,732 water and sediment and 1,018 quality-assurance samples collected between 2001 and 2010 from 38 States. Results indicate that glyphosate and AMPA are usually detected together, mobile, and occur widely in the environment. Glyphosate was detected without AMPA in only 2.3% of samples, whereas AMPA was detected without glyphosate in 17.9% of samples. Glyphosate and AMPA were detected frequently in soils and sediment, ditches and drains, precipitation, rivers, and streams; and less frequently in lakes, ponds, and wetlands; soil water; and groundwater. Concentrations of glyphosate were below levels of concern for humans or wildlife; however, pesticides are often detected in mixtures. Ecosystem effects of chronic low-level exposures to pesticide mixtures are uncertain. The environmental health risk of low-level detections of glyphosate, AMPA, and associated adjuvants and mixtures remain to be determined.

Complex, interactive ecological constraints regulate species distributions, and understanding these factors is crucial for predicting species persistence. We used occupancy analysis, which corrects for imperfect detection, to test the importance of abiotic and biotic habitat and landscape factors on probability of occupancy by boreal chorus frog (Pseudacris maculata; Agassiz 1850) tadpoles. We hypothesized that hydropattern and predators are primarily important as they affect desiccation and predation risk and can interact in ways difficult to predict. We surveyed 62 wetland sites across an elevational gradient in Colorado, USA and modeled patterns in P. maculata occupancy. Tadpoles were most frequently present in intermediate hydropattern systems with lower desiccation risk and no predatory fish due to occasional drying. P. maculata occupancy had a strong negative relationship with fish presence while tadpoles, odonate larvae and tiger salamanders (Ambystoma mavortium; Baird 1850) frequently co-occurred. Dry seasonal conditions will likely result in fewer intermediate hydropattern ponds available for amphibian breeding. We hypothesize that this will force P. maculata to breed in habitats with fish. As habitats shrink, predators that co-occur with P. maculata are expected to concentrate in the remaining habitat and increase predation risk for developing tadpoles (assuming predators are similarly constricted in their habitat use as amphibians are).

Natural gas production from the Marcellus shale is rapidly increasing in the northeastern United States. Most of the endemic terrestrial salamander species in the region are classified as ‘globally secure’ by the IUCN, primarily because much of their ranges include state- and federally protected lands, which have been presumed to be free from habitat loss. However, the proposed and ongoing development of the Marcellus gas resources may result in significant range restrictions for these and other terrestrial forest salamanders. To begin to address the gaps in our knowledge of the direct impacts of shale gas development, we developed occurrence models for five species of terrestrial plethodontid salamanders found largely within the Marcellus shale play. We predicted future Marcellus shale development under several scenarios. Under scenarios of 10000, 20000, and 50000 new gas wells, we predict 4%, 8%, and 20% forest loss, respectively, within the play. Predictions of habitat loss vary among species, but in general, Plethodon electromorphus and P. wehrlei are predicted to lose the greatest proportion of forested habitat within their ranges if future Marcellus predictions are based on characteristics of the shale play. If predictions are based on current well locations, P. richmondi is predicted to lose the greatest proportion of habitat. Models showed high uncertainty in species’ ranges and emphasize the need for distribution data collected by widespread and repeated, randomized surveys.

The Oregon spotted frog (Rana pretiosa) occupies only a fraction of its original range and is listed as Threatened under the Endangered Species Act. We surveyed 93 sites in a rotating panel frame design (2010–13) in the Klamath and Deschutes Basins, Oregon, which encompass most of the species’ core extant range. Oregon spotted frogs are decreasing in probability of both site occupancy and abundance. We did not find an association between the probability that Oregon spotted frogs disappear from a site (local extinction) and any of the variables hypothesized to affect Oregon spotted frog occupancy. This 4-year study provides baseline data, but the 4-year period was too short to draw firm conclusions about current (2014) trends. Further study is essential to understand how habitat changes and management practices relate to the status and trends of this species.