White-tailed deer (Odocoileus virginianus) positively affect the growth of mature northern red oak (Quercus rubra) trees

Understanding and predicting the effects of deer (Cervidae) on forest ecosystems present significant challenges in ecosystem ecology. Deer herbivory can cause large changes in the biomass and species composition of forest understory plant communities, including early life-cycle trees (i.e., seedlings and saplings). Such changes can impact juvenile to adult transitions and the future age structure and species composition of mature forests. Changes to understory vegetation also impact flow of energy and nutrients in forest ecosystems. Studies examining the influence of deer on mature trees, however, are rare and rely on extrapolating effects from early life cycle stages of trees. We tested the hypothesis that the absence of deer would result in an increase in the growth rate of mature trees by examining the impact of white-tailed deer (Odocoileus virginianus) on mature canopy trees. We examined incremental growth in individuals of Quercus rubra, an important component of temperate deciduous forests in North America, inside and outside 16-year deer exclosures in eastern U.S. deciduous forests. We found that adult trees inside exclosures grew less than those directly exposed to deer. Our findings highlight the indirect effects of white-tailed deer on the growth of adult individuals of Q. rubra in a way opposite of what would be expected from previous studies based on immature or understory tree populations. We suggest the increased growth of adult trees in the presence of deer may be explained by increased nutrient inputs through deer fecal and urine deposits and the alteration of the competitive environment belowground through the reduction of understory vegetation by browsing. Underscoring the ecological and demographic importance of adult trees in forest ecosystems, results from this study suggest the direct and indirect effects of deer on mature trees should not be overlooked

Mammal species composition reveals new insights into Earth’s remaining wilderness

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/8/fee2192-sup-0004-FigS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/7/fee2192-sup-0005-FigS5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/6/fee2192-sup-0006-FigS6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/5/fee2192.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/4/fee2192-sup-0003-FigS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/3/fee2192-sup-0002-FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/2/fee2192-sup-0001-FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156493/1/fee2192_am.pd

Mammal communities are larger and more diverse in moderately developed areas

Developed areas are thought to have low species diversity, low animal abundance, few native predators, and thus low resilience and ecological function. Working with citizen scientist volunteers to survey mammals at 1427 sites across two development gradients (wild-rural-exurban- suburban-urban) and four plot types (large forests, small forest fragments, open areas and residential yards) in the eastern US, we show that developed areas actually had significantly higher or statistically similar mammalian occupancy, relative abundance, richness and diversity compared to wild areas. However, although some animals can thrive in suburbia, conservation of wild areas and preservation of green space within cities are needed to protect sensitive species and to give all species the chance to adapt and persist in the Anthropocene. DOI: https://doi.org/10.7554/eLife.38012.00

Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

Mapping the landscape of possible macromolecular polymer sequences to their fitness in performing biological functions is a challenge across the biosciences. A paradigm is the case of aptamers, nucleic acids that can be selected to bind particular target molecules. We have characterized the sequence-fitness landscape for aptamers binding allophycocyanin (APC) protein via a novel Closed Loop Aptameric Directed Evolution (CLADE) approach. In contrast to the conventional SELEX methodology, selection and mutation of aptamer sequences was carried out in silico, with explicit fitness assays for 44 131 aptamers of known sequence using DNA microarrays in vitro. We capture the landscape using a predictive machine learning model linking sequence features and function and validate this model using 5500 entirely separate test sequences, which give a very high observed versus predicted correlation of 0.87. This approach reveals a complex sequence-fitness mapping, and hypotheses for the physical basis of aptameric binding; it also enables rapid design of novel aptamers with desired binding properties. We demonstrate an extension to the approach by incorporating prior knowledge into CLADE, resulting in some of the tightest binding sequences

Increased stress in Asiatic black bears relates to food limitation, crop raiding, and foraging beyond nature reserve boundaries in China

AbstractAsiatic black bears (Ursus thibetanus) are declining throughout much of their range. In China they are partially protected by a nature reserve system and rely heavily on hard mast as a food source prior to winter denning. Bears may compensate for mast shortages by raiding agricultural crops and killing livestock, mainly outside reserves where they are exposed to increased threats of poaching. We hypothesized that stress would vary with availability of high-quality refugia and fluctuations in mast abundance. We collected fecal samples from free-ranging bears in and around nature reserves in southwestern China, recorded habitat characteristics at each fecal sample location, and quantified abundance of hard mast. We used feces for genetic and endocrine analysis and identified 106 individuals. Feces collected outside reserves, or in agricultural fields within reserves, contained elevated concentrations of glucocorticoid metabolites compared to samples collected in intact, mast-producing forests within reserves. Relationships with habitat variables indicated that the hypothalamic–pituitary–adrenal (HPA) axis of the Asiatic black bear is responsive to human activity, abundance of hard mast, extent of forest cover, and quality of diet. Our findings demonstrate biological reactions of a large mammal to variable forest quality, human threats, and foraging relative to boundaries of protected areas

An empirical evaluation of camera trap study design: How many, how long and when?

Abstract Camera traps deployed in grids or stratified random designs are a well‐established survey tool for wildlife but there has been little evaluation of study design parameters. We used an empirical subsampling approach involving 2,225 camera deployments run at 41 study areas around the world to evaluate three aspects of camera trap study design (number of sites, duration and season of sampling) and their influence on the estimation of three ecological metrics (species richness, occupancy and detection rate) for mammals. We found that 25–35 camera sites were needed for precise estimates of species richness, depending on scale of the study. The precision of species‐level estimates of occupancy (ψ) was highly sensitive to occupancy level, with 0.75) species, but more than 150 camera sites likely needed for rare (ψ < 0.25) species. Species detection rates were more difficult to estimate precisely at the grid level due to spatial heterogeneity, presumably driven by unaccounted habitat variability factors within the study area. Running a camera at a site for 2 weeks was most efficient for detecting new species, but 3–4 weeks were needed for precise estimates of local detection rate, with no gains in precision observed after 1 month. Metrics for all mammal communities were sensitive to seasonality, with 37%–50% of the species at the sites we examined fluctuating significantly in their occupancy or detection rates over the year. This effect was more pronounced in temperate sites, where seasonally sensitive species varied in relative abundance by an average factor of 4–5, and some species were completely absent in one season due to hibernation or migration. We recommend the following guidelines to efficiently obtain precise estimates of species richness, occupancy and detection rates with camera trap arrays: run each camera for 3–5 weeks across 40–60 sites per array. We recommend comparisons of detection rates be model based and include local covariates to help account for small‐scale variation. Furthermore, comparisons across study areas or times must account for seasonality, which could have strong impacts on mammal communities in both tropical and temperate sites

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions