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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.

Amphibians have been selected as a “vital sign” by several
National Park Service (NPS) Inventory and Monitoring (I&M)
networks. An eight-year amphibian monitoring data set provided
opportunities to examine spatial and temporal patterns in
amphibian breeding richness and wetland desiccation across
Yellowstone and Grand Teton National Parks. Amphibian
breeding richness was variable across both parks, and only 4 of
31 permanent monitoring catchments contained all four widely
distributed species. Annual breeding richness was also variable
through time and fl uctuated by as much as 75% in some years and
catchments. Wetland desiccation was also documented across the
region, but alone did not explain variations in amphibian richness.
High annual variability across the region emphasizes the need for
multiple years of monitoring to accurately describe amphibian
richness and wetland desiccation dynamics.

Extensive corn production in the midwestern United States has physically eliminated or fragmented vast areas of historical amphibian habitat. Midwestern corn farmers also apply large quantities of fertilizers and herbicides, which can cause direct and indirect effects on amphibians. Limited field research regarding the statuses of midwestern amphibian populations near areas of corn production has left resource managers, conservation planners, and other stakeholders needing more information to improve conservation strategies and management plans. We repeatedly sampled amphibians in wetlands in four conservation areas along a gradient of proximity to corn production in Illinois, Iowa, Minnesota, and Wisconsin from 2002 to 2005 and estimated site occupancy. We measured frequencies of gross physical deformities in recent metamorphs and triazine concentrations in the water at breeding sites. We also measured trematode infection rates in kidneys of recently metamorphosed Lithobates pipiens collected from nine wetlands in 2003 and 2004. We detected all possible amphibian species in each study area. The amount of nearby row crops was limited in importance as a covariate for estimating site occupancy. We observed deformities in <5% of metamorphs sampled and proportions were not associated with triazine concentrations. Trematode infections were high in metamorphs from all sites we sampled, but not associated with site triazine concentrations, except perhaps for a subset of sites sampled in both years. We detected triazines more often and in higher concentrations in breeding wetlands closer to corn production. Triazine concentrations increased in floodplain wetlands as water levels rose after rainfall and were similar among lotic and lentic sites. Overall, our results suggest amphibian populations were not faring differently among these four conservation areas, regardless of their proximity to corn production, and that the ecological dynamics of atrazine exposure were complex.

Wetlands provide ecosystem goods and services vitally important to humans. Land managers and policymakers working to conserve wetlands require regularly updated information on the statuses of wetlands across the landscape. However, wetlands are challenging to map remotely with high accuracy and consistency. We investigated the use of multitemporal polarimetric synthetic aperture radar (SAR) data acquired with Canada’s Radarsat-2 system to track within-season changes in wetland vegetation and surface water. We speculated, a priori, how temporal and morphological traits of different types of wetland vegetation should respond over a growing season with respect to four energy-scattering mechanisms. We used ground-based monitoring data and other ancillary information to assess the limits and consistency of the SAR data for tracking seasonal changes in wetlands. We found the traits of different types of vertical emergent wetland vegetation were detected well with the SAR data and corresponded with our anticipated backscatter responses. We also found using data from Landsat’s optical/infrared sensors in conjunction with SAR data helped remove confusion of wetland features with upland grasslands. These results suggest SAR data can provide useful monitoring information on the statuses of wetlands over time.

We estimated wetland occupancy and population trends for three species of pond-breeding anurans in Yosemite National Park from 2007 – 2011. We used a double survey technique in which two observers independently surveyed each site on the same day. Double surveys allowed us to calculate detectability for the three most common anurans within the park: Rana sierrae, Anaxyrus canorus, and Pseudacris regilla. Annual estimates of detectability were generally high; mean detectability ranged from 73.7% + 0.6 (SE) for any life history stage of A. canorus to 86.7% + 0.7 for sites with P. regilla reproduction (eggs or larvae present). Detectability was most variable for Anaxyrus canorus, which ranged from 45.9% to 99.7%. The probability of occupancy for R. sierrae was highest in larger, low-elevation wetlands that lacked fish. Anaxyrus canorus were more common in shallow high-elevation ponds; their occurrence was minimally impacted by the presence of fish. Finally, occurrence of P. regilla was largely unrelated to wetland size and elevation, but like R. sierrae, they were less likely to occupy sites with fi sh. Occupancy showed no trend over the five years of our study for R. sierrae or A. canorus when considering either sites with any life stage or only sites with reproduction. However, P. regilla showed a modest downward trend for sites with any life stage and sites with reproduction. Our results for R. sierrae run counter to expectations given recent concern about the decline of this species, while our findings for P. regilla raise concerns for this widespread and generally common species.

Among the multiple stressors potentially affecting the presence of amphibians across agricultural landscapes, habitat loss and exposure to pesticides are likely primary factors contributing to amphibian decline. Conservation efforts have attempted to restore wetlands lost through landscape modifications with the aim of reducing contaminant loads in surface waters and providing quality habitat to wildlife. However, the benefits of this increased wetland area, perhaps especially for amphibians, may be negated if habitat quality is insufficient to support persistent populations. We examined the presence of pesticides and nutrients in water and sediment as indicators of habitat quality and assessed the accumulation of pesticides in tissue of two native amphibian species Pseudacris maculata (chorus frogs) and Lithobates pipiens (leopard frogs) at six wetlands (3 restored and 3 reference) in Iowa, USA. Restored wetlands are positioned on the landscape to receive subsurface tile drainage water while reference wetlands receive water from overland run-off and shallow groundwater sources. Concentrations of the pesticides frequently detected in water and sediment samples were not different between wetland types. The herbicide atrazine was detected in 100% of the water samples and in some instances at concentrations high enough to potentially cause reproductive effects in leopard frogs. Nutrient concentrations were higher in the restored wetlands but lower than concentrations thought to cause lethality in frogs. Seventeen pesticides were detected in tissue samples with concentrations ranging from https://0.08 to 1,500 µg/kg wet weight. No significant differences in pesticide concentrations were observed between species, although concentrations tended to be higher in leopard frogs compared to chorus frogs, possibly because of differences in life histories. Our results provide information on habitat quality in restored wetlands that will assist state and federal agencies, landowners, and resource managers in identifying and implementing conservation and management actions for these and similar wetlands in agriculturally dominated landscapes.

Reproductive aspects of Ambystoma salamanders were investigated at a site in Louisiana (2010–2012) and a site in Mississippi (2013). Three species occurred at the Louisiana site, Spotted Salamander (A. maculatum), Marbled Salamander (A. opacum), and Mole Salamander (A. talpoideum), whereas only Spotted Salamanders were studied at the Mississippi site. A total of 162 and 71 egg masses of Spotted Salamanders were examined at the Louisiana and Mississippi sites, respectively. Significantly more Spotted Salamander eggs per mass were observed at the Mississippi site (78.2) than the Louisiana site (53.8; p<0.001). The mean snout-vent length of female Spotted Salamanders at the Mississippi site (82.9 mm) was significantly larger than the Louisiana site (76.1 mm; p<0.001). Opaque Spotted Salamander egg masses were not found at the Mississippi site, but accounted for 11% of examined egg masses at the Louisiana site. The mean number of eggs per mass at the Louisiana site did not differ between opaque (47.3) and clear (54.6) egg masses (p=0.21). A total of 47 egg masses of the Mole Salamander were examined, with a mean number of 6.7 embryos per mass. Twenty-three individual nests of the Marbled Salamander were found either under or in decaying logs in the dry pond basins. There was no difference between the mean numbers of eggs per mass of attended nests (93.0) versus those that were discovered unattended (86.6; p=0.67). Females tended to place their nests at intermediate heights within the pond basin.

I review the primary literature to ascertain the status of amphibian monitoring efforts in the southeastern USA, a “hotspot” for biodiversity in North America. This effort revealed taxonomic, geographic and ecological disparities in studies of amphibian populations in this region. Of the species of anurans and caudates known to occur in the Southeast, 73.8% and 33.3%, respectively, have been monitored continuously for at least 4 years. Anurans are generally shorter-lived than are caudates and, thus, have been studied for the equivalent of at least one population turnover more than have caudates. The percentage of species (of those occurring in a given state) monitored continuously for at least 4 years was lowest for Alabama and Mississippi and highest for Florida for both taxa. The vast majority of studies (69.6%) were conducted on species that inhabit natural freshwater wetlands, in contrast to other aquatic and terrestrial habitats. Species considered threatened by the International Union for Conservation of Nature (IUCN) comprised only 7.7% of 65 species that have been studied consistently. The majority of comparative studies of contemporary vs. historical occurrences were potentially biased by the use of “presence-only” historical data and resurveys of short duration. Other issues, such as inadequate temporal and spatial scale and neglect of different sources of error, were common. Awareness of these data gaps and sampling and statistical issues may help facilitate informed decisions in setting future monitoring priorities, particularly with respect to species, habitats and locations that have been largely overlooked in past and ongoing studies.