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 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

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

A Functional Naturalism

I provide two arguments against value-free naturalism. Both are based on considerations concerning biological teleology. Value-free naturalism is the thesis that both (1) everything is, at least in principle, under the purview of the sciences and (2) all scientific facts are purely non-evaluative. First, I advance a counterexample to any analysis on which natural selection is necessary to biological teleology. This should concern the value-free naturalist, since most value-free analyses of biological teleology appeal to natural selection. My counterexample is unique in that it is likely to actually occur. It concerns the creation of synthetic life. Recent developments in synthetic biology suggest scientists will eventually be able to develop synthetic life. Such life, however, would not have any of its traits naturally selected for. Second, I develop a simple argument that biological teleology is a scientific but value-laden notion. Consequently, value-free naturalism is false. I end with some concluding remarks on the implications for naturalism, the thesis that (1). Naturalism may be salvaged only if we reject (2). (2) is a dogma that unnecessarily constrains our conception of the sciences. Only a naturalism that recognizes value-laden notions as scientifically respectable can be true. Such a naturalism is a functional naturalism

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

Neuronal cell cycle re-entry mediates Alzheimer disease-type changes

AbstractEvidence showing the ectopic re-expression of cell cycle-related proteins in specific vulnerable neuronal populations in Alzheimer disease led us to formulate the hypothesis that neurodegeneration, like cancer, is a disease of inappropriate cell cycle control. To test this notion, we used adenoviral-mediated expression of c-myc and ras oncogenes to drive postmitotic primary cortical neurons into the cell cycle. Cell cycle re-entry in neurons was associated with increased DNA content, as determined using BrdU and DAPI, and the re-expression of cyclin B1, a marker for the G2/M phase of the cell cycle. Importantly, we also found that cell cycle re-entry in primary neurons leads to tau phosphorylation and conformational changes similar to that seen in Alzheimer disease. This study establishes that the cell cycle can be instigated in normally quiescent neuronal cells and results in a phenotype that shares features of degenerative neurons in Alzheimer disease. As such, our neuronal cell model may be extremely valuable for the development of novel therapeutic strategies

How large should whales be?

The evolution and distribution of species body sizes for terrestrial mammals is well-explained by a macroevolutionary tradeoff between short-term selective advantages and long-term extinction risks from increased species body size, unfolding above the 2g minimum size induced by thermoregulation in air. Here, we consider whether this same tradeoff, formalized as a constrained convection-reaction-diffusion system, can also explain the sizes of fully aquatic mammals, which have not previously been considered. By replacing the terrestrial minimum with a pelagic one, at roughly 7000g, the terrestrial mammal tradeoff model accurately predicts, with no tunable parameters, the observed body masses of all extant cetacean species, including the 175,000,000g Blue Whale. This strong agreement between theory and data suggests that a universal macroevolutionary tradeoff governs body size evolution for all mammals, regardless of their habitat. The dramatic sizes of cetaceans can thus be attributed mainly to the increased convective heat loss is water, which shifts the species size distribution upward and pushes its right tail into ranges inaccessible to terrestrial mammals. Under this macroevolutionary tradeoff, the largest expected species occurs where the rate at which smaller-bodied species move up into large-bodied niches approximately equals the rate at which extinction removes them.Comment: 7 pages, 3 figures, 2 data table

The Minimal Complexity of Adapting Agents Increases with Fitness

What is the relationship between the complexity and the fitness of evolved organisms, whether natural or artificial? It has been asserted, primarily based on empirical data, that the complexity of plants and animals increases as their fitness within a particular environment increases via evolution by natural selection. We simulate the evolution of the brains of simple organisms living in a planar maze that they have to traverse as rapidly as possible. Their connectome evolves over 10,000s of generations. We evaluate their circuit complexity, using four information-theoretical measures, including one that emphasizes the extent to which any network is an irreducible entity. We find that their minimal complexity increases with their fitness