Geology topics

Therese Donovan

Publications and source records attributed to Therese Donovan.

11 recordsLinked to original sources

USGS2016

A comparison of acoustic montoring methods for common anurans of the northeastern United States

Many anuran monitoring programs now include autonomous recording units (ARUs). These devices collect audio data for extended periods of time with little maintenance and at sites where traditional call surveys might be difficult. Additionally, computer software programs have grown increasingly accurate at automatically identifying the calls of species. However, increased automation may cause increased error. We collected 435 min of audio data with 2 types of ARUs at 10 wetland sites in Vermont and New York, USA, from 1 May to 1 July 2010. For each minute, we determined presence or absence of 4 anuran species ( Hyla versicolor , Pseudacris crucifer , Anaxyrus americanus , and Lithobates clamitans ) using 1) traditional human identification versus 2) computer-mediated identification with software package, Song Scope® (Wildlife Acoustics, Concord, MA). Detections were compared with a data set consisting of verified calls in order to quantify false positive, false negative, true positive, and true negative rates. Multinomial logistic regression analysis revealed a strong ( P  < 0.001) 3-way interaction between the ARU recorder type, identification method, and focal species, as well as a trend in the main effect of rain ( P  = 0.059). Overall, human surveyors had the lowest total error rate (<2%) compared with 18–31% total errors with automated methods. Total error rates varied by species, ranging from 4% for A. americanus to 26% for L. clamitans . The presence of rain may reduce false negative rates. For survey minutes where anurans were known to be calling, the odds of a false negative were increased when fewer individuals of the same species were calling.

Wildlife Society Bulletin↗

USGS2016

Tools for automated acoustic monitoring within the R package monitoR

The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.

Bioacoustics: The International Journal of Animal ↗

USGS2016

Assessment of error rates in acoustic monitoring with the R package monitoR

Detecting population-scale reactions to climate change and land-use change may require monitoring many sites for many years, a process that is suited for an automated system. We developed and tested monitoR, an R package for long-term, multi-taxa acoustic monitoring programs. We tested monitoR with two northeastern songbird species: black-throated green warbler ( Setophaga virens ) and ovenbird ( Seiurus aurocapilla ). We compared detection results from monitoR in 52 10-minute surveys recorded at 10 sites in Vermont and New York, USA to a subset of songs identified by a human that were of a single song type and had visually identifiable spectrograms (e.g. a signal:noise ratio of at least 10 dB: 166 out of 439 total songs for black-throated green warbler, 502 out of 990 total songs for ovenbird). monitoR’s automated detection process uses a ‘score cutoff’, which is the minimum match needed for an unknown event to be considered a detection and results in a true positive, true negative, false positive or false negative detection. At the chosen score cut-offs, monitoR correctly identified presence for black-throated green warbler and ovenbird in 64% and 72% of the 52 surveys using binary point matching, respectively, and 73% and 72% of the 52 surveys using spectrogram cross-correlation, respectively. Of individual songs, 72% of black-throated green warbler songs and 62% of ovenbird songs were identified by binary point matching. Spectrogram cross-correlation identified 83% of black-throated green warbler songs and 66% of ovenbird songs. False positive rates were for song event detection.

Bioacoustics: The International Journal of Animal ↗

USGS2015

R for fledglings

We’ve been asked to provide a short introduction to R and its utility in natural resource management. In this short introduction, we can guarantee one thing: you won’t learn R in a few days. That would be like learning to speak French in a few days. To actually learn R, you need to practice….Bode Miller didn’t win his Olympic medals without hours and hours of practice. However, in this short introduction, you can gain an appreciation for what R can do, be introduced to some key functions that you will likely use over and over again, and learn some strategies for creating scripts for automating your work. There are several excellent R books that provide much more information than this short introduction….. R has a steep learning curve, and our hope is to cover some basics to get you over the initial hump.

Book↗

USGS2014

Acceptability of residential development in a regional landscape: Potential effects on wildlife occupancy patterns

The conversion of natural lands to developed uses may pose the single greatest human threat to global terrestrial biodiversity. Continued human growth and development over the next century will further exacerbate these effects of habitat loss and fragmentation. Natural resource managers are tasked with managing wildlife as a public trust, yet often have little say in land use decisions. Generally speaking, decision makers could benefit from an understanding of what different regulations mean in terms of wildlife distribution. In a previous paper ( Bettigole et al., 2013 ), we surveyed town residents throughout Vermont to measure how respondents feel about a range of development levels within their town boundaries. We estimated the “social carrying capacity for development” – or SK d – for 251 towns in Vermont. SK d provides an estimate of the level of developed land cover classes that town residents deem “acceptable” within their town boundaries. In this paper, we design a framework for linking the town-specific SK d estimates with the wildlife distribution patterns for three wide-ranging mammalian species: American black bear ( Ursus americanus ), fisher ( Martes pennanti ), and bobcat ( Lynx rufus ). We simulated landscape conditions at SK d for each town in Vermont, and then used existing occupancy models for the three target species to spatially map and compare occupancy rates in the baseline year 2000 with occupancy rates at SK d . With nearly 90% of Vermont towns willing to increase developed landcover classes within town boundaries compared to baseline levels, significant state-wide changes in occupancy rates were predicted for all three focal species. Average occupancy rates declined by −15.9% and −3.1% for black bear and bobcats, respectively. Average occupancy rates for fisher increased by 9.0%. This study provides a method for linking development standards within a town with wildlife occurrence. Across towns, the methodology spatially identifies areas that may be at risk of future development, as well as identifying areas where wildlife distribution patterns may face future change as a result of increased human population growth and development.

Biological Conservation↗

USGS2014

Predicting impacts of future human population growth and development on occupancy rates of forest-dependent birds

Forest loss and fragmentation are among the largest threats to forest-dwelling wildlife species today, and projected increases in human population growth are expected to increase these threats in the next century. We combined spatially-explicit growth models with wildlife distribution models to predict the effects of human development on 5 forest-dependent bird species in Vermont, New Hampshire, and Massachusetts, USA. We used single-species occupancy models to derive the probability of occupancy for each species across the study area in the years 2000 and 2050. Over half a million new housing units were predicted to be added to the landscape. The maximum change in housing density was nearly 30 houses per hectare; however, 30% of the towns in the study area were projected to add less than 1 housing unit per hectare. In the face of predicted human growth, the overall occupancy of each species decreased by as much as 38% (ranging from 19% to 38% declines in the worst-case scenario) in the year 2050. These declines were greater outside of protected areas than within protected lands. Ninety-seven percent of towns experienced some decline in species occupancy within their borders, highlighting the value of spatially-explicit models. The mean decrease in occupancy probability within towns ranged from 3% for hairy woodpecker to 8% for ovenbird and hermit thrush. Reductions in occupancy probability occurred on the perimeters of cities and towns where exurban development is predicted to increase in the study area. This spatial approach to wildlife planning provides data to evaluate trade-offs between development scenarios and forest-dependent wildlife species.

Biological Conservation↗

USGS2013

Phenology monitoring protocol: Northeast Temperate Network

Phenology is critical to many aspects of human life and nearly all ecological relationships and processes. Recent climate change has already led to widespread changes in phenological patterns across the globe, and more change is inevitable. This protocol has been developed to provide standardized methods for monitoring phenology within the National Park Service (NPS) Northeast Temperate Network (NETN), as part of the NPS Inventory and Monitoring Program (I&M). NETN encompasses the Appalachian National Scenic Trail (APPA), Acadia National Park (ACAD), the Boston Harbor Islands National Recreation Area (BOHA), and 10 national historical parks and national historic sites in the northeastern US. This protocol was developed in collaboration with and relies upon the procedures and infrastructure of the USA National Phenology Network (USA-NPN), including Nature’s Notebook , USA-NPN’s online plant and animal phenology observation program (www.nn.usanpn.org). Organized in 2007, USA-NPN is a nation-wide partnership among federal agencies, schools and universities, citizen volunteers, and others to monitor and understand the influence of seasonal cycles on the nation’s biological resources. The overall goal of NETN’s phenology monitoring program is to determine trends in the phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources. An additional programmatic goal is to interest and educate park visitors and staff, as well as a cadre of volunteer monitors.

National Park Service Natural Resource Report↗

USGS2012

Carbon storage, timber production, and biodiversity: comparing ecosystem services with multi-criteria decision analysis

Increasingly, land managers seek ways to manage forests for multiple ecosystem services and functions, yet considerable challenges exist in comparing disparate services and balancing trade-offs among them. We applied multi-criteria decision analysis (MCDA) and forest simulation models to simultaneously consider three objectives: (1) storing carbon, (2) producing timber and wood products, and (3) sustaining biodiversity. We used the Forest Vegetation Simulator (FVS) applied to 42 northern hardwood sites to simulate forest development over 100 years and to estimate carbon storage and timber production. We estimated biodiversity implications with occupancy models for 51 terrestrial bird species that were linked to FVS outputs. We simulated four alternative management prescriptions that spanned a range of harvesting intensities and forest structure retention. We found that silvicultural approaches emphasizing less frequent harvesting and greater structural retention could be expected to achieve the greatest net carbon storage but also produce less timber. More intensive prescriptions would enhance biodiversity because positive responses of early successional species exceeded negative responses of late successional species within the heavily forested study area. The combinations of weights assigned to objectives had a large influence on which prescriptions were scored as optimal. Overall, we found that a diversity of silvicultural approaches is likely to be preferable to any single approach, emphasizing the need for landscape-scale management to provide a full range of ecosystem goods and services. Our analytical framework that combined MCDA with forest simulation modeling was a powerful tool in understanding trade-offs among management objectives and how they can be simultaneously accommodated.

Ecological Applications↗

USGS2012

Estimating landscape carrying capacity through maximum clique analysis

Habitat suitability (HS) maps are widely used tools in wildlife science and establish a link between wildlife populations and landscape pattern. Although HS maps spatially depict the distribution of optimal resources for a species, they do not reveal the population size a landscape is capable of supporting--information that is often crucial for decision makers and managers. We used a new approach, "maximum clique analysis," to demonstrate how HS maps for territorial species can be used to estimate the carrying capacity, N(k), of a given landscape. We estimated the N(k) of Ovenbirds (Seiurus aurocapillus) and bobcats (Lynx rufus) in an 1153-km2 study area in Vermont, USA. These two species were selected to highlight different approaches in building an HS map as well as computational challenges that can arise in a maximum clique analysis. We derived 30-m2 HS maps for each species via occupancy modeling (Ovenbird) and by resource utilization modeling (bobcats). For each species, we then identified all pixel locations on the map (points) that had sufficient resources in the surrounding area to maintain a home range (termed a "pseudo-home range"). These locations were converted to a mathematical graph, where any two points were linked if two pseudo-home ranges could exist on the landscape without violating territory boundaries. We used the program Cliquer to find the maximum clique of each graph. The resulting estimates of N(k) = 236 Ovenbirds and N(k) = 42 female bobcats were sensitive to different assumptions and model inputs. Estimates of N(k) via alternative, ad hoc methods were 1.4 to > 30 times greater than the maximum clique estimate, suggesting that the alternative results may be upwardly biased. The maximum clique analysis was computationally intensive but could handle problems with < 1500 total pseudo-home ranges (points). Given present computational constraints, it is best suited for species that occur in clustered distributions (where the problem can be broken into several, smaller problems), or for species with large home ranges relative to grid scale where resampling the points to a coarser resolution can reduce the problem to manageable proportions.

Ecological Applications↗

USGS2011

A multi-species framework for landscape conservation planning

&ensp;Rapidly changing landscapes have spurred the need for quantitative methods for conservation assessment and planning that encompass large spatial extents. We devised and tested a multispecies framework for conservation planning to complement single-species assessments and ecosystem-level approaches. Our framework consisted of 4 elements: sampling to effectively estimate population parameters, measuring how human activity affects landscapes at multiple scales, analyzing the relation between landscape characteristics and individual species occurrences, and evaluating and comparing the responses of multiple species to landscape modification. We applied the approach to a community of terrestrial birds across 25,000 km 2 with a range of intensities of human development. Human modification of land cover, road density, and other elements of the landscape, measured at multiple spatial extents, had large effects on occupancy of the 67 species studied. Forest composition within 1 km of points had a strong effect on occupancy of many species and a range of negative, intermediate, and positive associations. Road density within 1 km of points, percent evergreen forest within 300 m, and distance from patch edge were also strongly associated with occupancy for many species. We used the occupancy results to group species into 11 guilds that shared patterns of association with landscape characteristics. Our multispecies approach to conservation planning allowed us to quantify the trade-offs of different scenarios of land-cover change in terms of species occupancy.

Conservation Biology↗

USGS2011

Quantifying home range habitat requirements for bobcats (Lynx rufus) in Vermont, USA

We demonstrate how home range and habitat use analysis can inform landscape-scale conservation planning for the bobcat, Lynx rufus , in Vermont USA. From 2005 to 2008, we outfitted fourteen bobcats with GPS collars that collected spatially explicit locations from individuals every 4 h for 3–4 months. Kernel home range techniques were used to estimate home range size and boundaries, and to quantify the utilization distribution (UD), which is a spatially explicit, topographic mapping of how different areas within the home range are used. We then used GIS methods to quantify both biotic (e.g. habitat types, stream density) and abiotic (e.g. slope) resources within each bobcat’s home range. Across bobcats, upper 20th UD percentiles (core areas) had 18% less agriculture, 42% less development, 26% more bobcat habitat (shrub, deciduous, coniferous forest, and wetland cover types), and 33% lower road density than lower UD percentiles (UD valleys). For each bobcat, we used Akaike’s Information Criterion (AIC) to evaluate and compare 24 alternative Resource Utilization Functions (hypotheses) that could explain the topology of the individual’s UD. A model-averaged population-level Resource Utilization Function suggested positive responses to shrub, deciduous, coniferous forest, and wetland cover types within 1 km of a location, and negative responses to roads and mixed forest cover types within 1 km of a location. Applying this model-averaged function to each pixel in the study area revealed habitat suitability for bobcats across the entire study area, with suitability scores ranging between −1.69 and 1.44, where higher values were assumed to represent higher quality habitat. The southern Champlain Valley, which contained ample wetland and shrub habitat, was a concentrated area of highly suitable habitat, while areas at higher elevation areas were less suitable. Female bobcat home ranges, on average, had an average habitat suitability score of near 0, indicating that home ranges consisted of both beneficial and detrimental habitat types. We discuss the application of habitat suitability mapping and home range requirements for bobcat conservation and landscape scale management.

Vermont↗