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Larval Sonoran tiger salamander
B Sigafus  
This is an ARMI Product. ARMI 2014 Annual Update
Authors: Muths E, Grant EHC, Chestnut T, Sadinski W, Waddle H, Adams M | Date: 2015 | Format: .PDF
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.

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E Muths  
This is an ARMI Product. Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction
Authors: Chandler RB, Muths E, Sigafus BH, Schwalbe CR, Jarchow CJ, Hossack BH | Date: 2015 | Outlet: Journal of Applied Ecology | Format: .PDF
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.

Aerial imagery of sites modeled as suitable and not suitable for arroyo toads based on current
conditions.
USDA  
This is an ARMI Product. Integrating Multiple Distribution Models to Guide Conservation Efforts of an Endangered Toad
Authors: Treglia M, Fisher R, Fitzgerald L | Date: 2015-06-30 | Outlet: PloS ONE | Format: .PDF
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.

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E Muths  
This is an ARMI Product. Trends in Rocky Mountain Amphibians and the Role of Beaver as a Keystone Species
Authors: Hossack BR, Gould WR, Patla DA, Muths E, Daley R, Legg K, Corn PS | Date: 2015 | Outlet: Biological Conservation | Format: .PDF
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.

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E Muths  
This is an ARMI Product. Modeling habitat connectivity to inform reintroductions: a case study with the Chiricahua leopard frog
Authors: Jarchow CJ, Hossack BR, Sigafus BH, Schwalbe CR, Muths EL | Date: 2015 | Outlet: Journal of Herpetology | Format: .PDF
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.

This is an ARMI Product. Geographically Isolated Wetlands:
Authors: Mushet DM, Calhoun AJK, Alexander LC, Cohen MJ, DeKeyser ES, Fowler L, Lane CR, Lang MW, Rains MC, Walls SC
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.

[I]Hyla cinerea[/I]
H. Waddle  
This is an ARMI Product. Testing hypotheses on distribution shifts and changes in phenology of imperfectly detectable species
Authors: Chambert T, Kendall WL, Hines JE, Nichols JD, Pedrini P, Waddle JH, Tavecchia G, Walls SC, Tenan S | Outlet: Methods in Ecology and Evolution
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.

[I]Pseudacris regilla[/I] with hemimelia.
D. Cowman  
This is an ARMI Product. In situ effects of pesticides on amphibians in the Sierra Nevada
Authors: Sparling DW, Bickham J, Cowman D, Fellers GM, Lacher L, Matson CW, McConnell LL | Date: 2015-03 | Outlet: Ecotoxicology 24:262-278 | Format: URL
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.

This is an ARMI Product. Environmental DNA: Can it improve our understanding of biodiversity on NPS lands?
Authors: Ray A, Sepulveda A, Hossack BR, Patla D, Legg K | Date: 2014 | Outlet: Park Science 31:118 | Format: .PDF

[I]Pseudacris crucifer[/I]
C. Brown  
This is an ARMI Product. Modeling false positive detections in species occurrence data under different study designs
Authors: Chambert T, Miller DAW, Nichols JD | Outlet: Ecology | Format: URL
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.


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