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Efficient 3D movement-based kernel density estimator and application to wildlife ecology
We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.
Microrefuges and the occurrence of thermal specialists: implications for wildlife persistence amidst changing temperatures
Background Contemporary climate change is affecting nearly all biomes, causing shifts in animal distributions, phenology, and persistence. Favorable microclimates may buffer organisms against rapid changes in climate, thereby allowing time for populations to adapt. The degree to which microclimates facilitate the local persistence of climate-sensitive species, however, is largely an open question. We addressed the importance of microrefuges in mammalian thermal specialists, using the American pika ( Ochotona princeps ) as a model organism. Pikas are sensitive to ambient temperatures, and are active year-round in the alpine where conditions are highly variable. We tested four hypotheses about the relationship between microrefuges and pika occurrence: 1) Local-habitat Hypothesis (local-habitat conditions are paramount, regardless of microrefuge); 2) Surface-temperature Hypothesis (surrounding temperatures, unmoderated by microrefuge, best predict occurrence); 3) Interstitial-temperature Hypothesis (temperatures within microrefuges best predict occurrence), and 4) Microrefuge Hypothesis (the degree to which microrefuges moderate the surrounding temperature facilitates occurrence, regardless of other habitat characteristics). We examined pika occurrence at 146 sites across an elevational gradient. We quantified pika presence, physiographic habitat characteristics and forage availability at each site, and deployed paired temperature loggers at a subset of sites to measure surface and subterranean temperatures. Results We found strong support for the Microrefuge Hypothesis. Pikas were more likely to occur at sites where the subsurface environment substantially moderated surface temperatures, especially during the warm season. Microrefugium was the strongest predictor of pika occurrence, independent of other critical habitat characteristics, such as forage availability. Conclusions By modulating surface temperatures, microrefuges may strongly influence where temperature-limited animals persist in rapidly warming environments. As climate change continues to manifest, efforts to understand the changing dynamics of animal-habitat relationships will be enhanced by considering the quality of microrefuges.
Trace elements and nutrition interactions in fish and wildlife
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California's Yolo Bypass: Evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture
Unlike conventional flood control systems that frequently isolate rivers from ecologically-essential floodplain habitat, California's Yolo Bypass has been engineered to allow Sacramento Valley floodwaters to inundate a broad floodplain. From a flood control standpoint, the 24,000 ha leveed floodplain has been exceptionally successful based on its ability to convey up to 80% of the flow of the Sacramento River basin during high water events. Agricultural lands and seasonal and permanent wetlands within the bypass provide key habitat for waterfowl migrating through the Pacific Flyway. Our field studies demonstrate that the bypass seasonally supports 42 fish species, 15 of which are native. The floodplain appears to be particularly valuable spawning and rearing habitat for the splittail (Pogonichthys macrolepidotus), a federally-listed cyprinid, and for young chinook salmon (Oncorhynchus tshawytscha), which use the Yolo Bypass as a nursery area. The system may also be an important source to the downstream food web of the San Francisco Estuary as a result of enhanced production of phytoplankton and detrital material. These results suggest that alternative flood control systems can be designed without eliminating floodplain function and processes, key goals of the 1996 Draft AFS Floodplain Management Position Statement.
Red imported fire ant impacts on wildlife: A decade of research
The negative impacts of biological invasion are economically and ecologically significant and, while incompletely quantified, they are clearly substantial. Ants (family Formicidae) are an important, although often overlooked, component of many terrestrial ecosystems. Six species of ants are especially striking in their global ability to invade, and their impacts. This paper focuses on the impacts of the most destructive of those species, the red imported fire ant ( Solenopsis invicta ), and focuses on impacts on native vertebrates. Red imported fire ants often become the dominant ant species in infested areas outside of their native range due to their aggressive foraging behavior, high reproductive capability and lack of predators and/or other strong competitors. The evidence suggests that mammals, birds and herpetofauna are vulnerable to negative impacts from fire ants, and some species are more likely to experience negative population-level impacts than other species. Assessing the ecological impacts of fire ants on wild animal populations is logistically difficult, and very few studies have combined replicated experimental manipulation with adequate spatial (>10 ha) and temporal (>1 y) scale. Thus, most studies have been observational, opportunistic, small-scale or 'natural' experiments. However, significant research, including an increase in experimental and mechanistic investigations, has occurred during the past decade, and this has led to information that can lead to better management of potentially affected species.
Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance
Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientific questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mechanisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unified modeling interface. The R package unmarked provides such a unified modeling framework, including tools for data exploration, model fitting, model criticism, post-hoc analysis, and model comparison.
Interfacing models of wildlife habitat and human development to predict the future distribution of puma habitat
The impact of human land uses on ecological systems typically differ relative to how extensively natural conditions are modified. Exurban development is intermediate-intensity residential development that often occurs in natural landscapes. Most species-habitat models do not evaluate the effects of such intermediate levels of human development and even fewer predict how future development patterns might affect the amount and configuration of habitat. We addressed these deficiencies by interfacing a habitat model with a spatially-explicit housing-density model to study the effect of human land uses on the habitat of pumas ( Puma concolor ) in southern California. We studied the response of pumas to natural and anthropogenic features within their home ranges and how mortality risk varied across a gradient of human development. We also used our housing-density model to estimate past and future housing densities and model the distribution of puma habitat in 1970, 2000, and 2030. The natural landscape for pumas in our study area consisted of riparian areas, oak woodlands, and open, conifer forests embedded in a chaparral matrix. Pumas rarely incorporated suburban or urban development into their home ranges, which is consistent with the hypothesis that the behavioral decisions of individuals can be collectively manifested as population-limiting factors at broader spatial scales. Pumas incorporated rural and exurban development into their home ranges, apparently perceiving these areas as modified, rather than non-habitat. Overall, pumas used exurban areas less than expected and showed a neutral response to rural areas. However, individual pumas that selected for or showed a neutral response to exurban areas had a higher risk of mortality than pumas that selected against exurban habitat. Exurban areas are likely hotspots for puma-human conflict in southern California. Approximately 10% of our study area will transform from exurban, rural, or undeveloped areas to suburban or urban by 2030, and 35% of suitable puma habitat on private land in 1970 will have been lost by 2030. These land-use changes will further isolate puma populations in southern California, but the ability to visualize these changes had provided a new tool for developing proactive conservation solutions.
Evaluation of road expansion and connectivity mitigation for wildlife in southern California
We designed a remote-camera survey to study how the expansion of California State Route 71 (CA-71) and implementation of connectivity mitigation affected the use of underpasses by large mammals in southern California. Based on detections by cameras, the use of underpasses by bobcats ( Lynx rufus ) was higher within the area of expansion and mitigation after construction than before, but there was no difference in use of underpasses in the impact zone compared to the control zone before or after construction. Use of underpasses by coyotes ( Canis latrans ) was higher in the control zone than in the impact zone, but there was no difference in use before and after construction. Small numbers of detections of mule deer ( Odocoileus hemionus ) at only a few underpasses precluded comparison between control and impact zones. However, a comparison of use before and after construction revealed that use of underpasses by mule deer was slightly higher post-construction. We cannot fully attribute increased detections post-construction to mitigative efforts, because other factors, such as availability of habitat, urbanization, or demography, also may have influenced use of underpasses along CA-71. Nonetheless, even with the expansion of the freeway and subsequent increase in volume of traffic, mitigative structures along CA-71 did allow for continued movement and, hence, connectivity across the roadway for large mammals.
The impact of disease on wildlife populations
It is postulated that disease is a product of adverse habitats. Overpopulation causes overutilization of food supplies, which results in malnutrition and a decrease in resistance to diseases. Examples of such ecological relationships in populations of Canada geese, California quail, red grouse, deer, rabbits, voles, mice and lemmings are presented.
The disappearance of Guam's wildlife: New insights for herpetology, evolutionary ecology, and conservation
The wealth of data generated from intensive study of the brown tree snake as a result of the need to control introduced populations of this pest species allow several important conclusions. First, that the snakes on Guam are extraordinary in terms of their absolute abundance and in terms of their ability to exploit a broad prey base. Our data suggest an exceptionally high reproductive success on Guam for a snake with an otherwise unnoteworthy reproductive capability and life history (i.e. small clutch size, typical ontogenetic shift from small heterothermic prey to larger homeotherms). Especially important was the snakes versatility in taking advantage of extremely common prey on islands; population expansion was slow but survival was maximal, ultimately leading to high population levels. The brown tree snake shares many attributes with other snakes that could cause similar biodiversity crises in a wide variety of contexts in which they lack coevolutionary histories (especially formerly snake-free island environments). As opposed to their relatively poor history as over-water dispersers, snakes may be especially problematic as travelers in increasing ship and air traffic between widely separated geographic regions of the world.
[Book review] Techniques for Wildlife Investigations: Design and Analysis of Capture Data, by J. R. Skalski and D. S. Robson
No abstract available.
Within-site variability in surveys of wildlife populations
Most large-scale surveys of animal populations are based on counts of individuals observed during a sampling period, which are used as indexes to the population. The variability in these indexes not only reflects variability in population sizes among sites but also variability due to the inexactness of the counts. Repeated counts at survey sites can be used to document this additional source of variability and, in some applications, to mitigate its effects. We present models for evaluating the proportion of total variability in counts that is attributable to this within-site variability and apply them in the analysis of data from repeated counts on routes from the North American Breeding Bird Survey. We analyzed data on 98 species, obtaining estimates of these percentages, which ranged from 3.5 to 100% with a mean of 36.25%. For at least 14 of the species, more than half of the variation in counts was attributable to within-site sources. Counts for species with lower average counts had a higher percentage of within-site variability. We discuss the relative cost efficiency of replicating sites or initiating new sites for several objectives, concluding that it is frequently better to initiate new sites than to attempt to replicate existing sites.
Alaska: Alaska National Interest Lands Conservation Act, December 2, 1980, P.L. 96-487: Yukon Delta National Wildlife Refuge, Alaska
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