Uncertainty in biological monitoring: a framework fordata collection and analysis to account for multiplesources of sampling bias
Authors: Ruiz-Gutierrez V, Hooten MB, Grant EHC | Outlet: Methods in Ecology and Evolution doi/10.1111/2041-210X.12542
eSummary(1) Biological monitoring programs are increasingly relying upon large volumes of citizenscience data to improve the scope and spatial coverage of information, ch a l l en g i n g thescienti&#64257;c commun i ty to develop design and model - b ase d approaches to improve inference.(2) Recent statistical models in ecology have be en develope d to accommodate false-negativeerrors, although recent work points to false positive errors as equally important sources ofbias. This is of particular concern for the success of any m o n i t or i n g program given rates assmall as 3% could lead to th e overestimation of the occurrence of rare events by as much as50%, and even small false positive r a t es can severely b i as estimates of occurrence dynamics.(3) We present an int eg ra t ed , comput at i o n al l y e&#64259;cient Bayesian hierar chical model tocorrect for fal se positi ve and negative error s in detection/no n -d et ec ti o n data. Our modelcombines ind ependent, a u x i l i ar y data sources with &#64257;eld observations to i m p r ove t h eestimation of false positive rate s, when a subset of &#64257;eld observatio n s cannot be validated aposteriori or assumed as per fe ct . We evaluated the performance of the model across arange of occurren ce rates, false positive and negative errors, and quantity of auxil i ar y data.(4) Th e mode l perfor m ed well under all simulated scenario s, and we were able t o identifycritical auxiliary data characteristics which resul t ed in improved infer en ce. We applied ourfalse positive m odel to a large-scale, citizen -sci e n ce monitor i n g program for anurans in theNortheastern U.S., using auxiliary data from an experiment d esi g n ed to estimate falsepositive er r o r rates. Not correcting for false positive ra t es resulted in biased estimates ofoccupancy in 4 of the 10 anu r a n species we an a l y zed , leadin g to an overestima t i on of theaverage number of occupi ed survey routes by as much as 70%.Conclusions. The framework we present for da ta collecti o n and analysis is able toe&#64259;ciently pr ovide reliable inference for occurrence patterns using data from acitizen-science monitorin g program . However, our approach is ap p l i ca b le to data generatedby any type of research and monit or i n g program , independent of skill level or scale, when e&#64256;ort i s placed on obtaining independent info rma t i on on false positive rates
A Model to Inform Management Actions as a Response to Chytridiomycosis-Associated Decline
Authors: Converse SJ, Bailey LL, Mosher BA, Funk WC, Gerber BD, Muths E | Date: 2016-02-15 | Outlet: Ecohealth | Format: .PDF
Decision-analytic models provide forecasts of how systems of interest will respond to management. These models can be parameterized using empirical data, but sometimes require information elicited from experts. When evaluating the effects of disease in species translocation programs, expert judgment is likely to play a role because complete empirical information will rarely be available. We illustrate development of a decision-analytic model built to inform decision-making regarding translocations and other management actions for the boreal toad (Anaxyrus boreas boreas), a species with declines linked to chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd).
Non-native and native organisms moving into high elevation and high latitude ecosystems in an era of climate change: new challenges for ecology and conservation
Authors: Albihn A, Alexander J, Burgess T, Daehler C, Englund G, Essl F, Evengård B, Greenwood G, Haider S, Lenoir J, McDougall K, Muths E, Nuñez M, Olofsson J, Pellissier L, Rabitsch W, Rew L, Robertson M, Sanders N, Kueffer C, Milbau A, Pauchard A | Date: 2016 | Outlet: Biological Invasions | Format: .PDF
Cold environments at high elevation and high latitude are often viewed as resistant to biological invasions. However, climate warming, land use change and associated increased connectivity all increase the risk of biological invasions in these environments. Here we present a summary of the key discussions of the workshop ‘Biosecurity in Mountains and Northern Ecosystems: Current Status and Future Challenges’ (Flen, Sweden, 1-3 June 2015). The aims of the workshop were to (i) increase awareness about the growing importance of species expansion – both non-native and native – at high elevation and high latitude with climate change, (ii) review existing knowledge about invasion risks in these areas, and (iii) encourage more research on how species will move and interact in cold environments, and the consequences for animal and human health and wellbeing. The diversity of potential and actual invaders reported at the workshop and the likely interactions between them create major challenges for managers of cold environments. However, since these cold environments have experienced fewer invasions when compared with many warmer, more populated environments, prevention has a real chance of success, especially if it is coupled with prioritisation schemes for targeting invaders likely to have greatest impact. Communication and co-operation between cold environment regions will facilitate rapid response and maximise use of limited research and management resources.
Restored agricultural wetlands in central Iowa: habitat quality and amphibian response
Authors: Reeves RA, Pierce CL, Smalling KL, Klaver RW, Vandever MW, Battaglin WA, Muths E | Date: 2016-02 | Outlet: Wetlands | Format: .PDF
Amphibians are declining throughout the United States and worldwide due, partly, to habitat loss. The Iowa Conservation Reserve Enhancement Program (CREP) strategically restores wetlands to denitrify tile drainage effluent and restore ecosystem services. Understanding how eutrophication , hydroperiod, predation, and disease affect amphibians in restored wetlands is central to maintaining healthy amphibian populations in the region. We examined the quality of amphibian habitat in restored CREP wetlands relative to reference wetlands by comparing species richness, developmental stress, and adult leopard frog (Lithobates pipiens) survival probabilities to a suite of environmental metrics. Although measured habitat variables differed between restored and reference wetlands, differences appeared to have sub-lethal rather than lethal effects on resident populations . There were few differences in amphibian species richness and no difference in estimated survival probabilities between wetland types. Restored wetlands had more nitrate and alkaline pH, longer hydroperiods, and were deeper, whereas reference wetlands had more amphibian chytrid fungus zoospores and resident amphibians exhibited increased developmental stress. Restored and reference wetlands are both important components of the landscape in central Iowa and maintaining a complex of fish-free wetlands with a variety of hydroperiods will likely contribute to the persistence of amphibians in this landscape.
An alternative framework for responding to the amphibian crisis
Authors: Muths E, Fisher RN | Outlet: Oryx | Format: .PDF
We suggest that a radically different approach, something akin to human emergency response management (i.e., the Incident Command System) is one alternative to addressing the lack of cohesion and inertia in responding to amphibian issues. While we acknowledge existing efforts and the prodigious amount of useful research, we suggest that a change is warranted and that the identification of a new amphibian chytrid provides the impetus for such a change.
Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient
Authors: Funk WC, Murphy MA, Hoke KL, Muths E, Amburgey SA, Moriarty Lemmon E, Lemmon AR | Date: 2015 | Outlet: Journal of Evolutionary Biology | Format: .PDF
Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history, and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation—as would be expected if incipient speciation were occurring—and if so, whether behavioral isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number, and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioral isolation: in phonotaxis experiments, low elevation females tended to prefer an average low elevation call over a high elevation call, and vice versa for high elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.
How spatio-temporal habitat connectivity affects amphibian genetic structure
Authors: Watts AG, Schlichting P, Billerman SM, Jesmer B, Micheletti S, Fortin M, Funk WC, Hapeman P, Muths E, Murphy MA | Date: 2015 | Outlet: Frontiers in Genetics | Format: .PDF
Heterogeneous landscapes and fluctuating environmental conditions can affect species’ dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.
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.
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.
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.