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Type:Article
Subject:Computer vision
Deep convolutional neural networks
Image classification
Machine learning
Motion-activated camera
R package
Remote sensing
Species identification
Description:Motion-activated wildlife cameras (or “camera traps”) are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the “species model,” and one that determines if an image is empty or if it contains an animal, the “empty-animal model.” Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%–91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%–94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths. [show more]
Type:Article
Subject:Colorado
Demography
Fawn ratios
Land-use change
Odocoileus hemionus
Residential development
Weather
Winter range
Description:Land-use change due to anthropogenic development is pervasive across the globe and commonly associated with negative consequences for biodiversity. While land-use change has been linked to shifts in the behavior and habitat-use patterns of wildlife species, little is known about its influence on animal population dynamics, despite the relevance of such information for conservation. We conducted the first broad-scale investigation correlating temporal patterns of land-use change with the demographic rates of mule deer, an iconic species in the western United States experiencing wide-scale population declines. We employed a unique combination of long-term (1980–2010) data on residential and energy development across western Colorado, in conjunction with congruent data on deer recruitment, to quantify annual changes in land-use and correlate those changes with annual indices of demographic performance. We also examined annual variation in weather conditions, which are well recognized to influence ungulate productivity, and provided a basis for comparing the relative strength of different covariates in their association with deer recruitment. Using linear mixed models, we found that increasing residential and energy development within deer habitat were correlated with declining recruitment rates, particularly within seasonal winter ranges. Residential housing had two times the magnitude of effect of any other factor we investigated, and energy development had an effect size similar to key weather variables known to be important to ungulate dynamics. This analysis is the first to correlate a demographic response in mule deer with residential and energy development at large spatial extents relevant to population performance, suggesting that further increases in these development types on deer ranges are not compatible with the goal of maintaining highly productive deer populations. Our results underscore the significance of expanding residential development on mule deer populations, a factor that has received little research attention in recent years, despite its rapidly increasing footprint across the landscape. [show more]
Type:Article
Subject:Behavioral plasticity
Black bear
Ecological trap
Human-caused mortality
Description:Large carnivores are negotiating increasingly developed landscapes, but little is known about how such behavioral plasticity influences their demographic rates and population trends. Some investigators have suggested that the ability of carnivores to behaviorally adapt to human development will enable their persistence, and yet, others have suggested that such landscapes are likely to serve as population sinks or ecological traps. To understand how plasticity in black bear (Ursus americanus) use of residential development influences their population dynamics, we conducted a 6-yr study near Durango, Colorado, USA. Using space-use data on individual bears, we examined the influence of use of residential development on annual measures of bear body fat, cub productivity, cub survival, and adult female survival, after accounting for variation in natural food availability and individual attributes (e.g., age). We then used our field-based vital rate estimates to parameterize a matrix model that simulated asymptotic population growth for bears using residential development to different degrees. We found that bear use of residential development was highly variable within and across years, with bears increasing their foraging within development when natural foods were scarce. Increased bear use of development was associated with increased body fat and cub productivity, but reduced cub and adult survival. When these effects were simultaneously incorporated into a matrix model, we found that the population was projected to decline as bear use of development increased, given that the costs of reduced survival outweighed the benefits of enhanced productivity. Our results provide a mechanistic understanding of how black bear use of residential development exerts opposing effects on different bear fitness traits and a negative effect on population growth, with the magnitude of those effects mediated by variation in environmental conditions. They also highlight the importance of monitoring bear population dynamics, particularly as shifts in bear behavior are likely to drive increases in human–bear conflicts and the perception of growing bear populations. Finally, our work emphasizes the need to consider the demographic viability of large carnivore populations when promoting the coexistence of people and carnivores on shared landscapes. [show more]
Type: Article
Subjects: Mercury bioaccumulation
Triploid walleye
Diploid walleye
<em>Sander vitreus</em>
Narraguinnep Reservoir, Colorado
Type:Article
Subject:Mercury bioaccumulation
Triploid walleye
Diploid walleye
<em>Sander vitreus</em>
Narraguinnep Reservoir, Colorado
Description:
We compared mercury bioaccumulation in triploid and diploid walleye (Sander vitreus) in Narraguinnep Reservoir, Colorado, USA, and made several hypotheses that sex- and ploidy-specific differences in the allocation of energy towards reproductive development would affect mercury bioaccumulation. We tested our hypotheses with linear regression and a bioenergetics model informed by field data. We found diploid walleye had 28%–31% higher mercury concentrations on average than triploids, but there were no differences between sexes of the same ploidy. Triploids of mature age exhibited minimal gonadal development when compared to diploids. After accounting for reproductive investment, the bioenergetics model accounted for most of the observed difference in average mercury concentration between ploidies for females. Conversely, the energetic cost of producing testes was low, and gonadal development could not explain observed patterns for males. Costs associated with elevated swimming activity and metabolism by diploid males relative to other groups could explain the difference but requires further investigation. The use of triploid fish in stocking programs could prove useful for reducing mercury in fish destined for human consumption.
Nous comparons la bioaccumulation de mercure dans des dorés jaunes (Sander vitreus) triploïdes et diploïdes dans le réservoir Narraguinnep (Colorado, États-Unis) et formulons plusieurs hypothèses à l’effet que des différences selon le sexe et la ploïdie sur le plan de l’affectation de ressources énergétiques au développement des organes reproducteurs auraient une incidence sur la bioaccumulation de mercure. Nous validons ces hypothèses à l’aide de la régression linéaire et d’un modèle bioénergétique alimenté de données de terrain. Nous constatons que les dorés diploïdes présentent des concentrations de mercure de 28 % à 31 % plus importantes, en moyenne, que les triploïdes, mais aucune différence n’est relevée entre les sexes de même ploïdie. Les triploïdes d’âge mature présentent un développement gonadique minimal comparativement aux diploïdes. Une fois pris en compte l’investissement dans le système reproducteur, le modèle bioénergétique explique la majeure partie des différences observées des concentrations de mercure moyennes entre femelles de ploïdies différentes. À l’inverse, le coût énergétique de la production de testicules est faible, et le développement des gonades ne peut expliquer les motifs observés chez les mâles. Les coûts associés à une activité de nage et un métabolisme plus élevés chez les mâles diploïdes par rapport aux autres groupes pourraient expliquer la différence, mais cela nécessite un examen plus approfondi. L’utilisation de poissons triploïdes dans les programmes d’empoissonnement pourrait s’avérer utile pour réduire les concentrations de mercure dans les poissons destinés à la consommation humaine. [Traduit par la Rédaction]
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Type:Article
Subject:Bilateral images
Camera trapping
Sampling bias
Spatial alignment
Paired camera station
Description:The probability of obtaining images of target species may vary across camera models or relative position of cameras at survey locations. Alignment of cameras within paired camera stations (hereafter, stations) could affect species detection due to issues with image exposure. We quantified effects of 3 camera models and alignment (staggered, offset by a perpendicular distance of 4.6 m, and aligned, directly facing one another) on camera performance in a station design. Mean exposure events (flash from one camera overexposes or underexposes pictures) at aligned stations was 3.93 (SE = 1.01; n = 40), whereas no exposure events were documented at staggered (n = 36) stations. Overall frequency of exposure events of mammal images at aligned cameras was 44% (68 exposure events/153 images). On average, 8% (range 0−35%) of mammal images from aligned stations were exposure events. We detected no difference (P = 0.88) in exposure events among paired camera models. Further, we detected no overall differences (P ≥ 0.07) in paired camera performance (i.e., number of mammal images over survey interval) between aligned or staggered stations, though reliability (i.e., percentage of camera stations that lasted entire survey interval) varied (P ≤ 0.001) between model types. Research deploying 2 cameras within a camera station framework can eliminate exposure events by using a staggered camera alignment without affecting the number of usable mammal photos. Rigorous field testing prior to deployment of stations is warranted to optimize reliability. One of our low-cost models performed as well as a more expensive model within our paired camera stations at collecting mammal images, and thus could be incorporated into study designs without compromising quality of camera photo data. We suggest a pilot study before large-scale deployment to evaluate reliability and performance of cameras, particularly when deploying multiple models. [show more]
Description:

Led ByJake Ivan

Study AreaUSFS land in Colorado

Project StatusOngoing

Research Objectives

To assess impacts of common forest management techniques on snowshoe hare density in both lodgepole pine and spruce-fir systems in Colorado.

Project Description­­

Understanding and monitoring snowshoe hare density in Colorado is important because hares comprise 70% of the diet of the state-endangered, federally threatened Canada lynx. Forest management is an important driver of snowshoe hare density, and all National Forests in Colorado are required to include management direction aimed at conservation of Canada lynx and snowshoe hare. At the same time, Forests in the Region are compelled to meet timber production and management response obligations. Such activities may depress snowshoe hare density, improve it, or have mixed effects dependent on the specific activity and the time elapsed since that activity was initiated. 

Associated Publications

Ivan, J. S. and E. Newkirk. 2019. Influence of forest management on snowshoe hare density in lodgepole and spruce-fir systems in Colorado. Pages 2-4 in Wildlife Research Report, Mammals Research Program, Colorado Division of Parks and Wildlife, Fort Collins, CO. 48 pages.

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Description:

Led By

Zachary Hooley-Underwood​, CPW; Kevin Thompson, CPW - retired

Study Area

Gunnison River Basin

Project Status

Ongoing

Research Objectives

  • Determine whether CPW biologists can effectively use exclusion devices such as weirs to prevent non-native and hybridized suckers from participating in native sucker spawning events in intermittent tributary streams.​

Project Description

Flannelmouth Sucker (Catostomus latipinnis), Bluehead Sucker (Catostomus discobolus), and Roundtail Chub (Gila robusta) are often referred to as the “three species” because the typically coexist with each other, and have similar life cycles.  Natives of the Colorado River basin, they each occupy only 45 – 55% of their historic native range in the upper Colorado River basin. All three have experienced declines due to habitat loss and invasions of non-native predatory and competitory fishes. In addition, Bluehead and Flannelmouth suckers are prone to hybridization with non-native sucker species (primarily white sucker and longnose sucker) that were unintentionally introduced to the Western Slope. The range and relative numbers of these non-native suckers have expanded in western Colorado over the last 30 years, in some areas dramatically. Continued hybridization and introgression could result in the eventual extinction of the native suckers.

Unlike native Cutthroat Trout or other coldwater species, these native suckers rely on big rivers and low elevation tributaries for much of the year. Therefore, CPW can’t effectively conserve the genetics of these species by creating isolated populations of these suckers above barriers in small streams as they do with Cutthroat Trout. Instead, CPW initiated a study to investigate the effects of excluding non-native suckers and their hybrids from an important spawning tributary of the Gunnison River.  CPW conducted a three-year study of excluding non-native and hybridized suckers from the spawning run using a picket weir and fish trap to answer this question, comparing the selected stream to another in which no fish control was attempted. To test the effectiveness of the exclusion, larval suckers were collected in both streams, and were genetically analyzed to identify the species, or hybrid composition, of each larvae. We found that picket weirs cannot always accommodate the volume of water and debris associated with spring runoff in the streams these fish spawn in, and unfortunately, there were periods of time when the weir was compromised during each year of the study. This resulted in the entry of at least some non-native suckers every year, and many of the resulting larvae had non-native genetics. Additionally, we found that the ratio of non-native to native larvae was much higher than the ratio of non-native to native adults in the exclusion stream, but these ratios matched up in the unmanipulated stream. The unmanipulated stream hosted a greater proportion of just the two native sucker species compared to the manipulated stream. This finding was concerning as it indicated that a few non-natives participating in the spawning run can have a large, disproportional effect on the population.

A new study is underway to use a better weir design – a resistance board weir – in a larger stream to exclude greater numbers of White Suckers and hybrids. Resistance board weirs can be more easily kept clean, and if overwhelmed they submerge, allowing debris to pass over. The new weir was deployed in March 2020, but precautions surrounding the Covid-19 pandemic resulted in an early termination of the work. The study resumed in 2021 and was replicated in 2022. The weir was operated during the full spawning period in 2021, and we expect that non-native suckers were unable to gain entry to the stream that year. A heavy snowpack and cool spring followed by a week of rapid warming in 2022 resulted in far-above-average flows in the creek that overwhelmed the abilities of the weir. Non-native suckers were able to access the creek for approximately half of the spawning season. Larvae collected in 2019-2023 will be genetically analyzed to determine the effectiveness of the weir.

If this study determines that non-natives can be successfully repressed to the advantage of native suckers, progeny produced in a manipulated stream would result in more pure fish in the Gunnison River. While this approach would not result in the disappearance of non-native suckers from the entire Gunnison basin, it may provide an avenue toward ensuring that the native species persist in the Gunnison Basin. If successful, this strategy could be implemented in other river basins on appropriate tributaries as well.

Video (1:55):Western Slope Native Suckers Leaving Spawning Grounds

These Colorado River basin native Bluehead Suckers and Flannelmouth Suckers are leaving a spawning tributary in the Roubideau Creek drainage near Delta, Colorado. This video was captured in late May 2016, and PIT tag antenna data indicate that this type of scene was common for about 4 days as the tremendous numbers of fish that had ascended the stream to spawn made their exit as the water began to drop and clear up.Video (12:09): The Native ThreeColorado Parks and Wildlife's aquatic research scientists have embarked on multiple projects to protect the three fish species native to the Upper Colorado River Basin (Flannelmouth Sucker, Bluehead Sucker and Roundtail Chub). This video, ‘The Native Three’ helps tell that story. Produced by Sean Ender, Peak to Creek Films, featuring Zachary Hooley-Underwood, CPW Aquatic Research Scientist.

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Type: Article
Subjects: Social science
Conservation planning
Wolf reintroduction
Adaptive management
Type:Article
Subject:Social science
Conservation planning
Wolf reintroduction
Adaptive management
Description:A growing body of literature has highlighted the value of social science for conservation, yet the diverse approaches of the social sciences are still inconsistently incorporated in conservation initiatives. Building greater capacity for social science integration in conservation requires frameworks and case studies that provide concrete guidance and specific examples. To address this need, we have developed a framework aimed at expanding the role for social science in formal conservation planning processes. Our framework illustrates multiple ways in which social science research can contribute to four stages of such processes: 1) defining the problem and project team; 2) defining goals; 3) identifying impact pathways and designing interventions; and 4) developing and evaluating indicators of success (or failure). We then present a timely case study of wolf reintroduction in Colorado, U.S.A., to demonstrate the opportunities, challenges, and complexities of applying our framework in practice. [show more]
Type:Article
Subject:Mysis relicta
Kokanee
Colorado
Habitat management
Description:Abstract. In studies of zooplankton and kokanees Oncorhynchus nerka in Lake Granby, Colorado, conducted from 1981 to 1983, we investigated the suspected role of introduced Mysis relicta in the decline of the kokanee sport fishery and egg take. Mysis relicta entered surface watersat night and preyed on zooplankton, except when summer temperatures above 14°C excluded it from the epilimnion and created a temporary refuge for cladocerans. We attributed the disappearance of hypolimnetic Daphnia longiremis to predation by mysids, and the virtual elimination of Daphnia pulex (once the preferred item in the kokanee diet) to the effects of intense selective predation by abundant M. relicta and to kokanee overstocking. Daphnia galeata mendotae, historically the most abundant daphnid, has replaced D. pulex as the principal item in the kokanee diet. Premysid populations of Daphnia spp. appeared by late May and peaked by late July, whereas postmysid populations appeared in late June and peaked in late August or early September. Mysis relicta appeared more frequently in stomachs of large  kokanees ( 21)0 mm in total length) and sometimes contributed substantially to the biomass of the kokanee diet. However, actual numbers of mysids and their frequency of occurrence in individual kokanee stomachs remained low. The disappearance or persistence of Daphnia spp. in other Colorado waters containing mysids appears to be explained by thermal conditions. It is clear that the introduced M. relicta has not adequately substituted for the diminished daphnid populations that were used heavily by planktivorous fishes. [show more]
Type:Moving Image
Description:Video Tutorial demonstrating the features of the new EBSCO Discovery Service user interface.