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"Botany - Europe"
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A review of evidence about use and performance of species distribution modelling ensembles like BIOMOD
Aim The idea of combining predictions from different models into an ensemble has gained considerable popularity in species distribution modelling, partly due to free and comprehensive software such as the R package BIOMOD. However, despite proliferation of ensemble models, we lack oversight of how and where they are used for modelling distributions, and how well they perform. Here, we present such an overview. Location Global. Methods Since BIOMOD is freely available and widely used by ensemble species distribution modellers, we focused on articles that apply BIOMOD, filtering the initial 852 papers identified in our structured literature search to a relevant final subset of 224 eligible peer‐reviewed journal articles. Results BIOMOD‐based ensembles are used across many taxa and locations, with terrestrial plants being the most represented group of species (n = 72) and Europe being the most represented continent (n = 106). These studies often focus on forecasting distributions in the future (n = 109), and commonly use presence‐only species data (n = 139) and climatic environmental predictors (n = 219). An average of six models are used in ensembles, and approximately half of ensembles weight contributions of models by their cross‐validation performance. However, discussion about choices made in the modelling process and unambiguous information on the performance of ensemble models versus individual models are limited. The use of independent data to validate model performance is particularly uncommon. Main conclusions We document the breadth of ensemble applications, but could not draw strong quantitative conclusions about the predictive performance of ensemble models, due to lack of unambiguous information reported. Understanding how and where ensembles are best used when modelling species distributions is important for enabling best choices for different applications. To enable this objective to be achieved, we provide recommendations for thorough reporting practices in a BIOMOD‐based ensemble workflow.
Journal Article
Neolithic Farming in Central Europe
Neolithic Farming in Central Europe examines the nature of the earliest crop cultivation, a subject that illuminates the lives of Neolithic farming families and the day-to-day reality of the transition from hunting and gathering to farming.
Debate surrounding the nature of crop husbandry in Neolithic central Europe has focussed on the permanence of cultivation, its intensity and its seasonality: variables that carry different implications for Neolithic society.
Amy Bogaard reviews the archaeological evidence for four major competing models of Neolithic crop husbandry - shifting cultivation, extensive plough cultivation, floodplain cultivation and intensive garden cultivation - and evaluates charred crop and weed assemblages.
Her conclusions identify the most appropriate model of cultivation, and highlight the consequences of these agricultural practices for our understanding of Neolithic societies in central Europe.
eBook
Ethnobotany in the New Europe
The study of European wild food plants and herbal medicines is an old discipline that has been invigorated by a new generation of researchers pursuing ethnobotanical studies in fresh contexts. Modern botanical and medical science itself was built on studies of Medieval Europeans' use of food plants and medicinal herbs. In spite of monumental changes introduced in the Age of Discovery and Mercantile Capitalism, some communities, often of immigrants in foreign lands, continue to hold on to old recipes and traditions, while others have adopted and enculturated exotic plants and remedies into their diets and pharmacopoeia in new and creative ways. Now in the 21st century, in the age of the European Union and Globalization, European folk botany is once again dynamically responding to changing cultural, economic, and political contexts. The authors and studies presented in this book reflect work being conducted across Europe's many regions. They tell the story of the on-going evolution of human-plant relations in one of the most bioculturally dynamic places on the planet, and explore new approaches that link the re-evaluation of plant-based cultural heritage with the conservation and use of biocultural diversity.
eBook
Neonicotinoid Insecticides and Their Impacts on Bees: A Systematic Review of Research Approaches and Identification of Knowledge Gaps
It has been suggested that the widespread use of neonicotinoid insecticides threatens bees, but research on this topic has been surrounded by controversy. In order to synthesize which research approaches have been used to examine the effect of neonicotinoids on bees and to identify knowledge gaps, we systematically reviewed research on this subject that was available on the Web of Science and PubMed in June 2015. Most of the 216 primary research studies were conducted in Europe or North America (82%), involved the neonicotinoid imidacloprid (78%), and concerned the western honey bee Apis mellifera (75%). Thus, little seems to be known about neonicotinoids and bees in areas outside Europe and North America. Furthermore, because there is considerable variation in ecological traits among bee taxa, studies on honey bees are not likely to fully predict impacts of neonicotinoids on other species. Studies on crops were dominated by seed-treated maize, oilseed rape (canola) and sunflower, whereas less is known about potential side effects on bees from the use of other application methods on insect pollinated fruit and vegetable crops, or on lawns and ornamental plants. Laboratory approaches were most common, and we suggest that their capability to infer real-world consequences are improved when combined with information from field studies about realistic exposures to neonicotinoids. Studies using field approaches often examined only bee exposure to neonicotinoids and more field studies are needed that measure impacts of exposure. Most studies measured effects on individual bees. We suggest that effects on the individual bee should be linked to both mechanisms at the sub-individual level and also to the consequences for the colony and wider bee populations. As bees are increasingly facing multiple interacting pressures future research needs to clarify the role of neonicotinoids in relative to other drivers of bee declines.
Journal Article
Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)
Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.
Journal Article
Revisiting territories of relegation
In the postindustrial city, relegation takes the form of real or imaginary consignment to distinctive sociospatial formations variously and vaguely referred to as 'inner cities,' 'ghettos,' 'enclaves,' 'nogo areas,' 'problem districts' or simply 'rough neighborhoods'. How are we to characterise and differentiate these spaces; what determines their trajectory (birth, growth, decay and death); whence comes the intense stigma attached to them; and what constellations of class, ethnicity and state do they both materialise and signify? These are the questions I pursued in my book Urban Outcasts (Wacquant, 2008a) through a methodical comparison of the trajectories of the black American ghetto and the European working-class peripheries in the era of neoliberal ascendancy. In this article, I revisit this cross-continental sociology of 'advanced marginality' to tease out its broader lessons for our understanding of the tangled nexus of symbolic, social and physical space in the polarising metropolis at century's threshold in particular, and for bringing the core principles of Bourdieu's sociology to bear on comparative urban studies in general.
Journal Article
Climatic Niche Shifts Are Rare Among Terrestrial Plant Invaders
The assumption that climatic niche requirements of invasive species are conserved between their native and invaded ranges is key to predicting the risk of invasion. However, this assumption has been challenged recently by evidence of niche shifts in some species. Here, we report the first large-scale test of niche conservatism for 50 terrestrial plant invaders between Eurasia, North America, and Australia. We show that when analog climates are compared between regions, fewer than 15% of species have more than 10% of their invaded distribution outside their native climatic niche. These findings reveal that substantial niche shifts are rare in terrestrial plant invaders, providing support for an appropriate use of ecological niche models for the prediction of both biological invasions and responses to climate change.
Journal Article