Geology topics

M. J. Adams

Publications and source records attributed to M. J. Adams.

At least 19 recordsLinked to original sources

USGS2018

Batrachochytrium salamandriovrans (Bsal) in Appalachia—Using scenario building to proactively prepare for a wildlife disease outbreak caused by an invasive amphibian chytrid fungus

Batrachochytrium salamandrivorans ( Bsal ), a pathogenic chytrid fungus, is nonnative to the United States and poses a disease threat to vulnerable amphibian hosts. The Bsal fungus may lead to increases in threatened, endangered, and sensitive status listings at State, Tribal, and Federal levels, resulting in financial costs associated with implementing the Endangered Species Act of 1973. The United States is a global biodiversity hotspot for salamanders, an order of amphibians that is particularly vulnerable to developing a disease called chytridiomycosis when exposed to Bsal . Published Bsal risk assessments for North America have suggested that salamanders within the Appalachian region of the United States are at a high risk. In May 2017, a workshop was facilitated by the Department of the Interior’s Strategic Sciences Group. During the workshop, a discussion-based incident-response exercise focused on a hypothetical Bsal disease outbreak in Appalachia was led by U.S. Geological Survey staff members. Participants included representatives of the Eastern Band of the Cherokee Indians, U.S. Fish and Wildlife Service, National Park Service, Appalachian Landscape Conservation Cooperative, Tennessee Wildlife Resources Agency, and U.S. Department of Agriculture’s U.S. Forest Service. Scenario building was used to brainstorm cascading consequences (social, economic, and ecological) of a Bsal disease outbreak in the Appalachian region. This report highlights the management and science actions that could be undertaken to ensure an effective, rapid response to a Bsal introduction into the United States.

Open-File Report↗

USGS2018

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.

Nature Communications↗

USGS2018

Prepublication communication of research results

Publishing of scientific findings is central to the scientific process, and it is traditional to consider findings “provisional” until accepted by a peer-reviewed journal. Until publication, communication of provisional findings beyond participants in the study is typically limited. This practice helps assure scientific integrity. However, a dilemma arises when a provisional finding has urgent societal consequences that may be exacerbated by delay. This dilemma may be particularly pronounced when a discovery concerns wildlife health, which could have implications for conservation, public health (i.e., zoonoses), or domestic animal health (e.g., avian influenza). A scientist may see a need for prepublication communication but consider such communication to be problematic. We suggest that common concerns about directed prepublication communication are generally misplaced. Our perspective comes from natural resources science and management, but we suspect that this situation could arise in any branch of science and that discussing these issues will help scientists who may not routinely work with public officials navigate an unfamiliar situation.

EcoHealth↗

USGS2018

Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest

Comparative landscape genetics has uncovered high levels of variability in which landscape factors affect connectivity among species and regions. However, the relative importance of species traits versus environmental variation for predicting landscape patterns of connectivity is unresolved. We provide evidence from a landscape genetics study of two sister taxa of frogs, the Oregon spotted frog ( Rana pretiosa ) and the Columbia spotted frog ( Rana luteiventris ) in Oregon and Idaho, USA. Rana pretiosa is relatively more dependent on moisture for dispersal than R. luteiventris , so if species traits influence connectivity, we predicted that connectivity among R. pretiosa populations would be more positively associated with moisture than R. luteiventris . However, if environmental differences are important drivers of gene flow, we predicted that connectivity would be more positively related to moisture in arid regions. We tested these predictions using eight microsatellite loci and gravity models in two R. pretiosa regions and four R. luteiventris regions ( n = 1,168 frogs). In R. pretiosa , but not R. luteiventris , connectivity was positively related to mean annual precipitation, supporting our first prediction. In contrast, connectivity was not more positively related to moisture in more arid regions. Various temperature metrics were important predictors for both species and in all regions, but the directionality of their effects varied. Therefore, the pattern of variation in drivers of connectivity was consistent with predictions based on species traits rather than on environmental variation.

Molecular Ecology↗

USGS2018

Effect of cattle exclosures on Columbia Spotted Frog abundance

Livestock grazing is an important land use in the western USA and can have positive or negative effects on amphibians. Columbia Spotted Frog ( Rana luteiventris ) often use ponds that provide water for cattle. We conducted a long-term manipulative study on US Forest Service land in northeastern Oregon to determine the effects of full and partial exclosures that limited cattle access to ponds used by frogs. We found weak evidence of a short-term increase in abundance that did not differ between full and partial exclosures and that diminished with continuing exclusion of cattle. The benefit of exclosures was small relative to the overall decline in breeding numbers that we documented. This suggests that some protection can provide a short-term boost to populations.

Wetlands Ecology and Management↗

USGS2018

Fitting N-mixture models to count data with unmodeled heterogeneity: Bias, diagnostics, and alternative approaches

Monitoring animal populations is central to wildlife and fisheries management, and the use of N-mixture models toward these efforts has markedly increased in recent years. Nevertheless, relatively little work has evaluated estimator performance when basic assumptions are violated. Moreover, diagnostics to identify when bias in parameter estimates from N-mixture models is likely is largely unexplored. We simulated count data sets using 837 combinations of detection probability, number of sample units, number of survey occasions, and type and extent of heterogeneity in abundance or detectability. We fit Poisson N-mixture models to these data, quantified the bias associated with each combination, and evaluated if the parametric bootstrap goodness-of-fit (GOF) test can be used to indicate bias in parameter estimates. We also explored if assumption violations can be diagnosed prior to fitting N-mixture models. In doing so, we propose a new model diagnostic, which we term the quasi-coefficient of variation (QCV). N-mixture models performed well when assumptions were met and detection probabilities were moderate (i.e., ≥0.3), and the performance of the estimator improved with increasing survey occasions and sample units. However, the magnitude of bias in estimated mean abundance with even slight amounts of unmodeled heterogeneity was substantial. The parametric bootstrap GOF test did not perform well as a diagnostic for bias in parameter estimates when detectability and sample sizes were low. The results indicate the QCV is useful to diagnose potential bias and that potential bias associated with unidirectional trends in abundance or detectability can be diagnosed using Poisson regression. This study represents the most thorough assessment to date of assumption violations and diagnostics when fitting N-mixture models using the most commonly implemented error distribution. Unbiased estimates of population state variables are needed to properly inform management decision making. Therefore, we also discuss alternative approaches to yield unbiased estimates of population state variables using similar data types, and we stress that there is no substitute for an effective sample design that is grounded upon well-defined management objectives.

Ecological Modelling↗

USGS2018

Identifying management-relevant research priorities for responding to disease-associated amphibian declines

A research priority can be defined as a knowledge gap that, if resolved, identifies the optimal course of conservation action. We (a group of geographically distributed and multidisciplinary research scientists) used tools from nominal group theory and decision analysis to collaboratively identify and prioritize information needs within the context of disease-associated amphibian decline , in order to develop a strategy that would support US management agency needs. We developed iterated influence diagrams to create and assess a unified research strategy. We illustrated a transparent process for identifying specific knowledge gaps in amphibian disease ecology relevant to environmental management, and then constructed a research plan to address these uncertainties. The resulting priorities include a need to: (1) understand the drivers of the community-disease relationship, (2) determine the mechanisms by which exposure to contaminants influence disease outcomes, (3) identify elements of terrestrial and aquatic habitats that stabilize host-pathogen dynamics, (4) discuss how metapopulations may be managed to reduce the speed and intensity of disease outbreaks, and (5) define the relationship between habitat management and the environmental and host microbiomes. Along with identifying research priorities for disease management, we present the details of the process used to develop a consensus plan for addressing disease-related declines in amphibians on federally managed lands of the United States.

Global Ecology and Conservation↗

USGS2018

Late-season movement and habitat use by Oregon spotted frogs (Rana pretiosa) in Oregon, USA

Many amphibians use multiple habitats across seasons. Information on seasonal habitat use, movement between seasonal habitat types, and habitats that may be particularly valuable is important to conservation and management. We used radio-telemetry to study late-season movement and habitat use by Oregon Spotted Frog ( Rana pretiosa ) at nine sites from four populations along the Cascade Mountains in Oregon. Movement rates declined with date and were the lowest at the end of tracking in December and January. Frogs across our sites used vegetated shallows in late summer and early fall. In fall, frogs used a range of habitat types, and at several sites moved to distinctive habitats such as springs, interstices in lava rock, and semi-terrestrial beaver channels. Distance between first and last tracking location was <250 m for 84.5% (49/58) of frogs, ranged up to 1145 m, and was greater for frogs in ditch habitats than those not in ditches. Distinctive features like springs or semi-terrestrial retreats can host multiple frogs and may represent particularly valuable wintering habitat for R. pretiosa in some sites in their Oregon range.

Oregon↗

USGS2017

Heterogeneous responses of temperate-zone amphibian populations to climate change complicates conservation planning

The pervasive and unabated nature of global amphibian declines suggests common demographic responses to a given driver, and quantification of major drivers and responses could inform broad-scale conservation actions. We explored the influence of climate on demographic parameters (i.e., changes in the probabilities of survival and recruitment) using 31 datasets from temperate zone amphibian populations (North America and Europe) with more than a decade of observations each. There was evidence for an influence of climate on population demographic rates, but the direction and magnitude of responses to climate drivers was highly variable among taxa and among populations within taxa. These results reveal that climate drivers interact with variation in life-history traits and population-specific attributes resulting in a diversity of responses. This heterogeneity complicates the identification of conservation ‘rules of thumb’ for these taxa, and supports the notion of local focus as the most effective approach to overcome global-scale conservation challenges.

Scientific Reports↗

USGS2017

A new parameterization for integrated population models to document amphibian reintroductions

Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A major impediment to the estimation of demographic rates often used to parameterize and refine decision-support models is that life-stage-specific monitoring data are frequently sparse for amphibians. We developed a new parameterization for integrated population models to match the ecology of amphibians and capitalize on relatively inexpensive monitoring data to document amphibian reintroductions. We evaluate the capability of this model by fitting it to Oregon spotted frog ( Rana pretiosa ) monitoring data collected from 2007 to 2014 following their reintroduction within the Klamath Basin, Oregon, USA. The number of egg masses encountered and the estimated adult and metamorph abundances generally increased following reintroduction. We found that survival probability from egg to metamorph ranged from 0.01 in 2008 to 0.09 in 2009 and was not related to minimum spring temperatures, metamorph survival probability ranged from 0.13 in 2010–2011 to 0.86 in 2012–2013 and was positively related to mean monthly temperatures (logit-scale slope = 2.37), adult survival probability was lower for founders (0.40) than individuals recruited after reintroduction (0.56), and the mean number of egg masses per adult female was 0.74. Our study is the first to test hypotheses concerning Oregon spotted frog egg-to-metamorph and metamorph-to-adult transition probabilities in the wild and document their response at multiple life stages following reintroduction. Furthermore, we provide an example to illustrate how the structure of our integrated population model serves as a useful foundation for amphibian decision-support models within adaptive management programs. The integration of multiple, but related, data sets has an advantage of being able to estimate complex ecological relationships across multiple life stages, offering a modeling framework that accommodates uncertainty, enforces parsimony, and ensures all model parameters can be confronted with monitoring data.

Ecological Applications↗

USGS2017

Using decision analysis to support proactive management of emerging infectious wildlife diseases

Despite calls for improved responses to emerging infectious diseases in wildlife, management is seldom considered until a disease has been detected in affected populations. Reactive approaches may limit the potential for control and increase total response costs. An alternative, proactive management framework can identify immediate actions that reduce future impacts even before a disease is detected, and plan subsequent actions that are conditional on disease emergence. We identify four main obstacles to developing proactive management strategies for the newly discovered salamander pathogen Batrachochytrium salamandrivorans ( Bsal ). Given that uncertainty is a hallmark of wildlife disease management and that associated decisions are often complicated by multiple competing objectives, we advocate using decision analysis to create and evaluate trade-offs between proactive (pre-emergence) and reactive (post-emergence) management options. Policy makers and natural resource agency personnel can apply principles from decision analysis to improve strategies for countering emerging infectious diseases.

Frontiers in Ecology and the Environment↗

USGS2017

Early action to address an emerging wildlife disease

A deadly fungal pathogen, Batrachochytrium salamandrivorans ( Bsal ) that affects amphibian skin was discovered during a die-off of European fire salamanders ( Salamandra salamandra ) in 2014. This pathogen has the potential to worsen already severe worldwide amphibian declines. Bsal is a close relative to another fungal disease known as Batrachochytrium dendrobatidis ( Bd ). Many scientists consider Bd to be the greatest threat to amphibian biodiversity of any disease because it affects a large number of species and has the unusual ability to drive species and populations to extinction. Although not yet detected in the United States, the emergence of Bsal could threaten the salamander population, which is the most diverse in the world. The spread of Bsal likely will lead to more State and federally listed threatened or endangered amphibian species, and associated economic effects. Because of the concern expressed by resource management agencies, the U.S. Geological Survey (USGS) has made Bsal and similar pathogens a priority for research.

Fact Sheet↗

USGS2017

Inference of timber harvest effects on survival of stream amphibians is complicated by movement

The effects of contemporary logging practices on headwater stream amphibians have received considerable study but with conflicting or ambiguous results. We posit that focusing inference on demographic rates of aquatic life stages may help refine understanding, as aquatic and terrestrial impacts may differ considerably. We investigated in-stream survival and movement of two stream-breeding amphibian species within a before-after timber harvest experiment in the Oregon Coast Range. We used recaptures of marked individuals and a joint probability model of survival, movement, and capture probability, to measure variation in these rates attributed to stream reach, stream gradient, pre- and post-harvest periods, and the timber harvest intensity. Downstream biased movement occurred in both species but was greater for Coastal Tailed Frog ( Ascaphus truei ) larvae than aquatic Coastal Giant Salamanders ( Dicamptodon tenebrosus ). For D. tenebrosus , downstream biased movement occurred early in life, soon after an individual's first summer. Increasing timber harvest intensity reduced downstream movement bias and reduced survival of D. tenebrosus , but neither of these effects were detected for larvae of A. truei . Our findings provide insight into the demographic mechanisms underlying previous nuanced studies of amphibian responses to timber harvest based on biomass or counts of larvae.

Copeia↗

USGS2017

Potential concerns with analytical Methods Used for the detection of Batrachochytrium salamandrivorans from archived DNA of amphibian swab samples, Oregon, USA

Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.

Oregon↗

USGS2016

Herpetological monitoring and assessment on the Trinity River, Trinity County, California—Final report

The primary goal of the Trinity River Restoration Program is to rehabilitate the fisheries on the dam-controlled Trinity River. However, maintaining and enhancing other wildlife populations through the restoration initiative is also a key objective. Foothill yellow-legged frogs ( Rana boylii ) and western pond turtles ( Actinemys marmorata ) have been identified as important herpetological 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 developed and implemented a monitoring strategy for these species specific to the Trinity River with the objectives of establishing baseline values for probabilities of site occupancy, colonization, and local extinction; identifying site characteristics that correlate with the probability of extinction; and estimating overall trends in abundance. Our 3-year study suggests that foothill yellow-legged frogs declined in the probability of site occupancy. Conversely, our results suggest that western pond turtles increased in both abundance and the probability of site occupancy. The short length of our study period makes it difficult to draw firm conclusions, but these results provide much-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 over the long term.

California↗

USGS2016

Quantitative evidence for the effects of multiple drivers on continental-scale amphibian declines

Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a “smoking gun” was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extinction risk, evidence for effects of these drivers is lacking at large spatial scales. Here, we use observations of 389 time-series of 83 species and complexes from 61 study areas across North America to test the effects of 4 of the major hypothesized drivers of declines. While we find that local amphibian populations are being lost from metapopulations at an average rate of 3.79% per year, these declines are not related to any particular threat at the continental scale; likewise the effect of each stressor is variable at regional scales. This result - that exposure to threats varies spatially, and populations vary in their response - provides little generality in the development of conservation strategies. Greater emphasis on local solutions to this globally shared phenomenon is needed.

Scientific Reports↗

USGS2016

Salamander chytrid fungus ( Batrachochytrium salamandrivorans ) in the United States—Developing research, monitoring, and management strategies

The recently (2013) identified pathogenic chytrid fungus, Batrachochytrium salamandrivoran s ( Bsal ), poses a severe threat to the distribution and abundance of salamanders within the United States and Europe. Development of a response strategy for the potential, and likely, invasion of Bsal into the United States is crucial to protect global salamander biodiversity. A formal working group, led by Amphibian Research and Monitoring Initiative (ARMI) scientists from the U.S. Geological Survey (USGS) Patuxent Wildlife Research Center, Fort Collins Science Center, and Forest and Rangeland Ecosystem Science Center, was held at the USGS Powell Center for Analysis and Synthesis in Fort Collins, Colorado, United States from June 23 to June 25, 2015, to identify crucial Bsal research and monitoring needs that could inform conservation and management strategies for salamanders in the United States. Key findings of the workshop included the following: (1) the introduction of Bsal into the United States is highly probable, if not inevitable, thus requiring development of immediate short-term and long-term intervention strategies to prevent Bsal establishment and biodiversity decline; (2) management actions targeted towards pathogen containment may be ineffective in reducing the long-term spread of Bsal throughout the United States; and (3) early detection of Bsal through surveillance at key amphibian import locations, among high-risk wild populations, and through analysis of archived samples is necessary for developing management responses. Top research priorities during the preinvasion stage included the following: (1) deployment of qualified diagnostic methods for Bsal and establishment of standardized laboratory practices, (2) assessment of susceptibility for amphibian hosts (including anurans), and (3) development and evaluation of short- and long-term pathogen intervention and management strategies. Several outcomes were achieved during the workshop, including development of an organizational structure with working groups for a Bsal Task Force, creation of an initial influence diagram to aid in identifying effective management actions in the face of uncertainty, and production of a list of potential management actions and key research uncertainties. Additional products under development include a Bsal Strategic Action plan, an emergency response plan, a monitoring and surveillance program, a standardized diagnostic approach, decision models for natural resource agencies, and a reporting database for salamander mortalities. This workshop was the first international meeting to address the threat of Bsal to salamander populations in the United States, with more than 30 participants from U.S. conservation and resource management agencies (U.S. Fish and Wildlife Service, U.S. Forest Service, U.S. Department of Defense, U.S. National Park Service, and Association of Fish and Wildlife Agencies) and academic research institutions in Australia, the Netherlands, Switzerland, the United Kingdom, and the United States.

Open-File Report↗

USGS2016

Spatial variation in risk and consequence of Batrachochytrium salamandrivorans introduction in the USA

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

Royal Society Open Science↗