The Asperian Design

Reality is two-fold, composed of the lighted world as revealed in Genesis, and the darker primordiality which preceded it. The illuminated represents that which the human mind can comprehend, manipulate and re-order to its will: a “designed” and mechanical universe of parts. But behind it, in the backspace of reality, remains the darkness. A formless state of pre-creation, the darkness exists as an endless series of intertwining “signatures” – single possibilities waiting to be created in the illuminated forefront of reality. Permitting each and every part of the lighted world to be connected to the rest, it possesses a “design” all of its own. The question is, if we are blind in the dark, how could we ever come to know it

The Field

Life is a battlefield onto which we are thrown at birth, with only fate and fortune settling upon where we land. Wherever we land, whether it's on the front lines or surrounded by a network of defenses, we are all asking the same question: why are we here? The problem with this question, however, is that we tend to answer it from our own relative positions, and so we all arrive at different conclusions. The many answers we've created have filled the field. They have become banners that are raised high so that we can see and follow them. These banners are always at risk of being toppled though; always at risk of losing their capacity for belief. But then, what if belief is more than a mere by-product of our universal search? What if belief can change the very fabric of this field? That is, what if truth is actually irrelevant, and the only real thing that makes up this battlefield is the belief, and consequently the collective will, which we invest in our answers

Quantitative analysis of the links between forest structure and land surface albedo on a global scale

Forests are critical in regulating climate by altering the Earth's surface albedo. Therefore, there is an urgent need to enhance our knowledge about the effects of forest structure on albedo. Here, we present a global assessment of the links between forest structure and albedo at a 1-km spatial resolution using generalized additive models (GAMs). We used remotely sensed data to obtain variables representing forest structure, including forest density, leaf area index, and tree cover, during the peak growing season in 2005 with pure forest pixels that cover similar to 7% of the Earth's surface. Furthermore, we estimated black-sky albedo at a solar zenith angle of 38 degrees using the most recent collection of the moderate resolution imaging spectroradiometer (MODIS; version 6) at shortwave, near-infrared, and visible spectral regions. In addition, for the first time, we mapped the magnitude of the relationship between forest structure and albedo at each pixel with a 0.5-degree spatial resolution. Our results suggested that forest structure may modulate albedo in most of the sub-biomes. The response of shortwave albedo was always positive to the leaf area index and negative to the tree cover (except for deciduous broadleaf forests in mediterranean and temperate regions), while the response to forest density varied across space in 2005. The spatial map affirmed that the links between forest structure and albedo vary over geographical locations. In sum, our study emphasized the importance of forest structure in the surface albedo regulation. This paper provides the first spatially explicit evidence of the magnitude of relationships between forest structure and albedo on a global scale.Peer reviewe

A global database of soil nematode abundance and functional group composition

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns

The use of artificial media in fungal ecology

Can experiments conducted in agar really help us to understand the complexity of fungal systems? This question has been the focus of persistent and ongoing debate between fungal ecologists that favor reductionist versus holistic approaches. On one hand, artificial media are unrealistic and fail to reflect the heterogeneity and complexity of natural systems. But on the other hand, they offer simplified model systems that allow us to isolate mechanisms that would otherwise be obscured in natural systems. Following various technological advances that enable us to describe various aspects of complex fungal communities in situ, the dial appears to be tipping in favor of observational field studies, and the use of artificial media has declined. However, we argue that the loss of artificial media from experimental studies would impair our capacity to disentangle the complexities of fungal communities. Here, we discuss the pros and cons of artificial media in fungal ecology and outline the types of questions that are best addressed using fungi growing in artificial media. We conclude that renewed emphasis on the value of artificial media could help us to generate the mechanistic understanding that might be critical to explaining the exciting patterns that are emerging from real-world fungal ecology studies

Nitrogen-fixing symbiotic bacteria act as a global filter for plant establishment on islands

Island biogeography has classically focused on abiotic drivers of species distributions. However, recent work has highlighted the importance of mutualistic biotic interactions in structuring island floras. The limited occurrence of specialist pollinators and mycorrhizal fungi have been found to restrict plant colonization on oceanic islands. Another important mutualistic association occurs between nearly 15,000 plant species and nitrogen-fixing (N-fixing) bacteria. Here, we look for evidence that N-fixing bacteria limit establishment of plants that associate with them. Globally, we find that plants associating with N-fixing bacteria are disproportionately underrepresented on islands, with a 22% decline. Further, the probability of N-fixing plants occurring on islands decreases with island isolation and, where present, the proportion of N-fixing plant species decreases with distance for large, but not small islands. These findings suggest that N-fixing bacteria serve as a filter to plant establishment on islands, altering global plant biogeography, with implications for ecosystem development and introduction risks

Using ecological networks to answer questions in global biogeography and ecology

Ecological networks have classically been studied at site and landscape scales, yet recent efforts have been made to collate these data into global repositories. This offers an opportunity to integrate and upscale knowledge about ecological interactions from local to global scales to gain enhanced insights from the mechanistic information provided by these data. By drawing on existing research investigating patterns in ecological interactions at continental to global scales, we show how data on ecological networks, collected at appropriate scales, can be used to generate an improved understanding of many aspects of ecology and biogeography—for example, species distribution modelling, restoration ecology and conservation. We argue that by understanding the patterns in the structure and function of ecological networks across scales, it is possible to enhance our understanding of the natural world

Native diversity buffers against severity of non-native tree invasions

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5,6,7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.EEA Santa CruzFil: Delavaux, Camille S. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Crowther, Thomas W. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Zohner, Constantin M. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Robmann, Niamh M. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Lauber, Thomas. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: van den Hoogen, Johan. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Kuebbing, Sara. Yale University. The Forest School at The Yale School of the Environment; Estados UnidosFil: Liang, Jingjing. Purdue University. Department of Forestry and Natural Resources; Estados UnidosFil: de-Miguel, Sergio. University of Lleida. Department of Crop and Forest Sciences; EspañaFil: de-Miguel, Sergio. Joint Research Unit CTFC–AGROTECNIO–CERCA; EspañaFil: Nabuurs, Gert-Jan. Wageningen University and Research; Países BajosFil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Maynard, Daniel S. Swiss Federal Institute of Technology. Institute of Integrative Biology; SuizaFil: Maynard, Daniel S. University College London. Department of Genetics, Evolution, and Environment; Reino Unid

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics, but the prediction of viral cross-protection remains an important unsolved problem. For foot-and-mouth disease virus (FMDV) research in particular, improved methods for predicting this cross-protection are critical for predicting the severity of outbreaks within endemic settings where multiple serotypes and subtypes commonly co-circulate, as well as for deciding whether appropriate vaccine(s) exist and how much they could mitigate the effects of any outbreak. To identify antigenic relationships and their predictors, we used linear mixed effects models to account for variation in pairwise cross-neutralization titres using only viral sequences and structural data. We identified those substitutions in surface-exposed structural proteins that are correlates of loss of cross-reactivity. These allowed prediction of both the best vaccine match for any single virus and the breadth of coverage of new vaccine candidates from their capsid sequences as effectively as or better than serology. Sub-sequences chosen by the model-building process all contained sites that are known epitopes on other serotypes. Furthermore, for the SAT1 serotype, for which epitopes have never previously been identified, we provide strong evidence - by controlling for phylogenetic structure - for the presence of three epitopes across a panel of viruses and quantify the relative significance of some individual residues in determining cross-neutralization. Identifying and quantifying the importance of sites that predict viral strain cross-reactivity not just for single viruses but across entire serotypes can help in the design of vaccines with better targeting and broader coverage. These techniques can be generalized to any infectious agents where cross-reactivity assays have been carried out. As the parameterization uses pre-existing datasets, this approach quickly and cheaply increases both our understanding of antigenic relationships and our power to control disease

Soils in warmer and less developed countries have less micronutrients globally

Soil micronutrients are capital for the delivery of ecosystem functioning and food provision worldwide. Yet, despite their importance, the global biogeography and ecological drivers of soil micronutrients remain virtually unknown, limiting our capacity to anticipate abrupt unexpected changes in soil micronutrients in the face of climate change. Here, we analyzed >1300 topsoil samples to examine the global distribution of six metallic micronutrients (Cu, Fe, Mn, Zn, Co and Ni) across all continents, climates and vegetation types. We found that warmer arid and tropical ecosystems, present in the least developed countries, sustain the lowest contents of multiple soil micronutrients. We further provide evidence that temperature increases may potentially result in abrupt and simultaneous reductions in the content of multiple soil micronutrients when a temperature threshold of 12–14°C is crossed, which may be occurring on 3% of the planet over the next century. Altogether, our findings provide fundamental understanding of the global distribution of soil micronutrients, with direct implications for the maintenance of ecosystem functioning, rangeland management and food production in the warmest and poorest regions of the planet