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Article ; Online: Building Intuition Regarding the Statistical Behavior of Mass Medical Testing Programs

Lance Waller / Taal Levi

Harvard Data Science Review, Vol Special Issue

2021 Volume 1

Keywords	Electronic computers. Computer science ; QA75.5-76.95
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	The MIT Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mesocarnivore landscape use along a gradient of urban, rural, and forest cover

Jordan T. Rodriguez / Damon B. Lesmeister / Taal Levi

PeerJ, Vol 9, p e

2021 Volume 11083

Abstract: Mesocarnivores fill a vital role in ecosystems through effects on community health and structure. Anthropogenic-altered landscapes can benefit some species and adversely affect others. For some carnivores, prey availability increases with urbanization, ... ...

Abstract	Mesocarnivores fill a vital role in ecosystems through effects on community health and structure. Anthropogenic-altered landscapes can benefit some species and adversely affect others. For some carnivores, prey availability increases with urbanization, but landscape use can be complicated by interactions among carnivores as well as differing human tolerance of some species. We used camera traps to survey along a gradient of urban, rural, and forest cover to quantify how carnivore landscape use varies among guild members and determine if a species was a human exploiter, adapter, or avoider. Our study was conducted in and around Corvallis, Oregon from April 2018 to February 2019 (11,914 trap nights) using 47 camera trap locations on a gradient from urban to rural. Our focal species were bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), opossum (Didelphis virginiana), raccoon (Procyon lotor), and striped skunk (Mephitis mephitis). Raccoon and opossum were human exploiters with low use of forest cover and positive association with urban and rural developed areas likely due to human-derived resources as well as some refugia from larger predators. Coyote and gray fox were human adapters with high use of natural habitats while the effects of urbanization ranged from weak to indiscernible. Bobcat and striped skunk appeared to be human avoiders with negative relationship with urban cover and higher landscape use of forest cover. We conducted a diel temporal activity analysis and found mostly nocturnal activity within the guild, but more diurnal activity by larger-bodied predators compared to the smaller species. Although these species coexist as a community in human-dominated landscapes throughout much of North America, the effects of urbanization were not equal across species. Our results, especially for gray fox and striped skunk, are counter to research in other regions, suggesting that mesopredator use of urbanized landscapes can vary depending on the environmental conditions of the ...
Keywords	Bobcat (Lynx rufus) ; Coyote (Canis latrans) ; Gray fox (Urocyon cinereoargenteus) ; Raccoon (Procyon lotor) ; Striped skunk (Mephitis mephitis) ; Virgina opossums (Didelphis virginiana) ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	910
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pseudogymnoascus destructans growth in wood, soil and guano substrates

Jenny Urbina / Tara Chestnut / Jennifer M. Allen / Taal Levi

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose ... ...

Abstract	Abstract Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear ...
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using passive acoustic monitoring to estimate northern spotted owl landscape use and pair occupancy

Cara L. Appel / Damon B. Lesmeister / Adam Duarte / Raymond J. Davis / Matthew J. Weldy / Taal Levi

Ecosphere, Vol 14, Iss 2, Pp n/a-n/a (2023)

2023

Abstract: Abstract Managing forests for biodiversity conservation while maintaining economic output is a major challenge globally and requires accurate and timely monitoring of imperiled species. In the Pacific Northwest, USA, forest management is heavily ... ...

Abstract	Abstract Managing forests for biodiversity conservation while maintaining economic output is a major challenge globally and requires accurate and timely monitoring of imperiled species. In the Pacific Northwest, USA, forest management is heavily influenced by the status of northern spotted owls (Strix occidentalis caurina), which have been in continued population decline for the past four decades. The monitoring program for northern spotted owls is transitioning from mark–resight surveys to a passive acoustic framework, requiring development of alternative analysis approaches. To maintain relevance for conservation and management, these analyses must accurately track underlying population changes, identify responses to disturbance, and estimate occupancy of owl pairs. We randomly selected and surveyed 5‐km2 hexagons for 6 weeks using passive acoustic monitoring in the Olympic Peninsula of Washington and the Oregon Coast Range during the 2018 spotted owl breeding season. We used a convolutional neural network to identify spotted owl calls, followed by logistic regression to determine the sex of vocalizing owls to assign pair status. We implemented multistate occupancy models to estimate probabilities of detection, species‐level landscape use, and pair occupancy of spotted owls. We also quantified detections of barred owls (Strix varia), a congeneric competitor and important driver of spotted owl population declines. The overall rate of hexagon use by spotted owls was estimated at 0.21 (SD 0.04) after adjusting for imperfect detection, and pair occupancy was 0.07 (SD 0.02). The probability of detecting a pair (i.e., both female and male) during a weekly occasion was relatively low (0.03, SD 0.01), indicating that true pair occupancy was between 1.3 and 4.1 times greater than the proportion of hexagons with observed pair detections. Barred owls were ubiquitous, with a naïve occupancy rate of 0.97. The intensity of calling by barred owls had a weak, negative effect on the probability of spotted owls being paired ...
Keywords	barred owl ; bioacoustics ; detection probability ; occupancy ; passive acoustic monitoring ; spotted owl ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano

Jenny Urbina / Tara Chestnut / Donelle Schwalm / Jenn Allen / Taal Levi

PeerJ, Vol 8, p e

2020 Volume 8141

Abstract: Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, ...

Abstract	Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer roosts as well as movement from maternity ...
Keywords	Disease surveillance ; White-nose syndrome ; Degradation ; Non-invasive techniques ; Pseudogymnoascus destructans ; Mount Rainier ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparison of mechanical sorting and DNA metabarcoding for diet analysis with fresh and degraded wolf scats

Aimee L. Massey / Gretchen H. Roffler / Tessa Vermeul / Jennifer M. Allen / Taal Levi

Ecosphere, Vol 12, Iss 6, Pp n/a-n/a (2021)

2021

Abstract: Abstract DNA metabarcoding has become a powerful technique for identifying the species present in a bulk environmental sample. The application of DNA metabarcoding to wildlife diet analysis is a particularly promising tool for exploring trophic ... ...

Abstract	Abstract DNA metabarcoding has become a powerful technique for identifying the species present in a bulk environmental sample. The application of DNA metabarcoding to wildlife diet analysis is a particularly promising tool for exploring trophic interactions. The extent to which molecular approaches agree with traditional approaches, and how this varies with the quality of field‐collected scats, is unknown. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were to (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear were the primary prey species, but metabarcoding revealed a more diverse diet with greater occurrence of rare species. However, there was a large discrepancy in the occurrence of beaver in scats (52% and 25% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. While the number of wolf sequence reads for fresh scats was nearly eight times higher than in degraded scats, neither the number of prey sequence reads nor the quantity of DNA to be sequenced varied between fresh and degraded scats suggesting that metabarcoding is sensitive enough to determine prey assemblages in degraded scats. Even using scats from extremely wet conditions hostile to DNA preservation, we found that metabarcoding was more effective than mechanical sorting in describing diet.
Keywords	Alaska ; Canis lupus ; diet analysis ; eDNA ; metabarcoding ; noninvasive sampling ; Ecology ; QH540-549.5
Subject code	590
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrating multi‐method surveys and recovery trajectories into occupancy models

Brent R. Barry / Katie Moriarty / David Green / Rebecca A. Hutchinson / Taal Levi

Ecosphere, Vol 12, Iss 12, Pp n/a-n/a (2021)

2021

Abstract: Abstract Conservation and management of animal populations requires knowledge of their occurrence and drivers that influence their distribution. Noninvasive survey methods and occupancy models to account for imperfect detection have become the standard ... ...

Abstract	Abstract Conservation and management of animal populations requires knowledge of their occurrence and drivers that influence their distribution. Noninvasive survey methods and occupancy models to account for imperfect detection have become the standard tools for this purpose. Simultaneously addressing both occurrence and occurrence–environment relationships, however, presents multiple challenges, particularly for species with reduced ranges or those recovering from historical declines. Here, we present a comprehensive framework to satisfy the assumption of organism–environment equilibrium, map the range of a species, incorporate camera traps and detection dogs as complementary data sources, and make inference about wildlife space use at multiple scales. To meet these goals, we developed a Bayesian spatial occupancy model for Pacific fishers (Pekania pennanti) in Oregon using data from a large‐scale (64,280 km2) empirical effort combining 1240 camera traps (74,219 trap nights) and 196 detector dog surveys (3 × 3 km units, survey average = 17.3 km/unit). We deployed this model with and without a geoadditive term to improve predicted range map generation and covariate inference, respectively. We used reaction–diffusion models to project recovery trajectories to determine both plausible spatial extents for inclusion in our occupancy model and whether the current distribution can be explained by time‐limited population expansion from historical refugia. To assess nonstationary effects where species–habitat relationships vary spatially, we fit separate models within distinct ecological regions. We confirmed the presence of the native and introduced fisher populations, but populations occupy less area than previously believed. The spatial extent of the introduced population was less than expected except under our lowest growth model, suggesting limiting factors were preventing population expansion. The native population extent matched expectations under several growth scenarios, suggesting that the contemporary distribution is plausibly due to time‐limited expansion. The relationship of fisher occupancy to environmental covariates varied with scale, spatial extent, and ecological region, but fishers consistently selected for old forests at fine spatial scales in the detection model across spatial extents and detection modalities. Collectively, we provide an integration of camera traps and detection dogs into spatial occupancy models and demonstrate how to generate plausible spatial extents to improve inferences for species recovering from range contractions.
Keywords	camera traps ; detection dogs ; multi‐scale ; nonstationarity ; occupancy models ; Pekania pennanti ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The primacy of bears as seed dispersers in salmon‐bearing ecosystems

Laurie E. F. Harrer / Taal Levi

Ecosphere, Vol 9, Iss 1, Pp n/a-n/a (2018)

2018

Abstract: Abstract Salmon–bear ecosystems that historically existed throughout most of the northern temperate and boreal regions of planet earth now persist only in the North Pacific. Extensive research on salmon–bear interactions has focused on the role that ... ...

Abstract	Abstract Salmon–bear ecosystems that historically existed throughout most of the northern temperate and boreal regions of planet earth now persist only in the North Pacific. Extensive research on salmon–bear interactions has focused on the role that bears (Ursus arctos and U. americanus) play in provisioning terrestrial systems with marine‐derived nutrients, but little attention has been paid to how the much higher bear population densities in salmon‐bearing ecosystems then affect ecological communities. Salmon‐supported brown bears secondarily consume large quantities of fruit and may thus serve as important seed dispersers, but the relative seed dispersal services provided by bears and birds are unknown. We sought to (1) quantify the number of seeds dispersed by bears relative to birds, and (2) by brown bears relative to black bears, and to (3) assess whether the two sympatric bears temporally partition berry resources as a result of competitively dominant brown bears switching to feed on salmon, thus opening niche space for black bears. We used a combination of motion‐triggered camera traps and environmental DNA (eDNA) from residual saliva to quantify the roles of birds, black bears, and brown bears as seed dispersers of devil's club (Oplopanax horridus), the dominant understory shrub at our field site in northern southeast Alaska. Brown bears were the numerically dominant seed dispersers, particularly before salmon became widely available, after which black bears became common seed dispersers, likely due to alleviation of interference competition. Birds accounted for only a small fraction of seed dispersal. This is the first demonstration of a temperate plant being primarily dispersed by mammalian gut passage. Our results suggest that bears are uniquely important seed dispersers, which may influence plant community composition in salmon‐bearing ecosystems.
Keywords	Alaska ; devil's club ; interference competition ; mutualism ; seed dispersal ; Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The spatial overlap of small‐scale cannabis farms with aquatic and terrestrial biodiversity

Phoebe Parker‐Shames / Christopher Choi / Van Butsic / David Green / Brent Barry / Katie Moriarty / Taal Levi / Justin S. Brashares

Conservation Science and Practice, Vol 4, Iss 2, Pp n/a-n/a (2022)

2022

Abstract: Abstract The rapid expansion of cannabis agriculture in the Western United States provides a rare opportunity to study how an abrupt change in land‐use policy affects local biodiversity. There is broad speculation that cannabis production on private land ...

Abstract	Abstract The rapid expansion of cannabis agriculture in the Western United States provides a rare opportunity to study how an abrupt change in land‐use policy affects local biodiversity. There is broad speculation that cannabis production on private land is expanding and having negative effects on aquatic and terrestrial ecosystems, yet there exist little empirical data to evaluate this concern. In this study, we mapped and characterized outdoor cannabis production during the first season of legal recreational production (2016) in a large legacy cannabis‐producing region of Southern Oregon, Josephine County. We descriptively compared cannabis farms to all available private parcels based on proximity to rivers/streams and undeveloped land and their overlap with carnivore richness. Using publicly available satellite imagery, we found approximately 1.34 km2 (331 acres) of cannabis cultivation within Josephine County during the first season of legal recreational production. Most cannabis production areas were small (median size 414 m2), spatially clustered at all observed scales, and recently established (67% were not visible in 2013–2014 pre‐legalization). When compared with all available private parcels, cannabis was preferentially located in forested areas, undeveloped land and slightly closer to rivers. Within riparian areas, farms were slightly closer to rivers with predicted occurrence of coho salmon (Oncorhynchus kisutch). While projected carnivore richness was similar between cannabis and all private parcels, projected fisher (Pekania pennanti) occupancy was more than five times higher on cannabis farms, with a median occupancy of 0.69 (interquartile range: 0.24–0.87). Our results establish a baseline for cannabis land cover at the time of early recreational legalization and rapid expansion and can be used to predict future patterns or ecological consequences of cannabis development in other production areas. Understanding the potential ecological impact of cannabis is increasingly important as legalization ...
Keywords	agricultural frontier ; carnivore richness ; coho salmon (Onchorhynus kisutch) ; fisher (Pekania pennanti) ; land‐use change ; marijuana ; Ecology ; QH540-549.5 ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	333
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Projecting the future of an alpine ungulate under climate change scenarios

White, Kevin S / David P. Gregovich / Taal Levi

Global change biology. 2018 Mar., v. 24, no. 3

2018

Abstract: Climate change represents a primary threat to species persistence and biodiversity at a global scale. Cold adapted alpine species are especially sensitive to climate change and can offer key âearly warning signsâ about deleterious effects of ... ...

Abstract	Climate change represents a primary threat to species persistence and biodiversity at a global scale. Cold adapted alpine species are especially sensitive to climate change and can offer key âearly warning signsâ about deleterious effects of predicted change. Among mountain ungulates, survival, a key determinant of demographic performance, may be influenced by future climate in complex, and possibly opposing ways. Demographic data collected from 447 mountain goats in 10 coastal Alaska, USA, populations over a 37âyear time span indicated that survival is highest during low snowfall winters and cool summers. However, general circulation models (GCMs) predict future increase in summer temperature and decline in winter snowfall. To disentangle how these opposing climateâdriven effects influence mountain goat populations, we developed an ageâstructured population model to project mountain goat population trajectories for 10 different GCM/emissions scenarios relevant for coastal Alaska. Projected increases in summer temperature had stronger negative effects on population trajectories than the positive demographic effects of reduced winter snowfall. In 5 of the 10 GCM/representative concentration pathway (RCP) scenarios, the net effect of projected climate change was extinction over a 70âyear time window (2015â2085); smaller initial populations were more likely to go extinct faster than larger populations. Using a resource selection modeling approach, we determined that distributional shifts to higher elevation (i.e., âthermoneutralâ) summer range was unlikely to be a viable behavioral adaptation strategy; due to the conical shape of mountains, summer range was expected to decline by 17%â86% for 7 of the 10 GCM/RCP scenarios. Projected declines of mountain goat populations are driven by climateâlinked bottomâup mechanisms and may have wide ranging implications for alpine ecosystems. These analyses elucidate how projected climate change can negatively alter population dynamics of a sentinel alpine species and provide insight into how demographic modeling can be used to assess risk to species persistence.
Keywords	age structure ; altitude ; biodiversity ; climate ; climate change ; data collection ; ecosystems ; emissions ; extinction ; General Circulation Models ; mountains ; Oreamnos americanus ; population dynamics ; snow ; summer ; temperature ; ungulates ; winter ; Alaska
Language	English
Dates of publication	2018-03
Size	p. 1136-1149.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1281439-8
ISSN	1365-2486 ; 1354-1013
ISSN (online)	1365-2486
ISSN	1354-1013
DOI	10.1111/gcb.13919
Database	NAL-Catalogue (AGRICOLA)

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