Showing papers by "Swedish University of Agricultural Sciences published in 2014"
American Museum of Natural History1, University of Tartu2, University of Colombo3, Royal Netherlands Academy of Arts and Sciences4, University of Florida5, University of Palermo6, Goethe University Frankfurt7, Hobart Corporation8, Nakhon Phanom University9, University of Bamenda10, University of Gothenburg11, Naturalis12, Swedish University of Agricultural Sciences13, Royal Botanic Gardens14, Universiti Malaysia Sabah15, United States Department of Agriculture16, Forest Research Institute Malaysia17, Humboldt State University18, Chinese Academy of Sciences19, Landcare Research20, University of Western Australia21, Estonian University of Life Sciences22, University of Southern Queensland23, Botanic Garden Meise24, Manchester Metropolitan University25, James Cook University26
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Abstract: Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
2,346 citations
Swedish University of Agricultural Sciences1, University of Veterinary Medicine Vienna2, KORA Organics3, University of Zagreb4, Spanish National Research Council5, The Nature Conservancy6, University of Porto7, University of Tirana8, University of Bern9, Czech University of Life Sciences Prague10, Indian Ministry of Environment and Forests11, Sapienza University of Rome12, Forest Research Institute13, Transilvania University of Brașov14, University of Ljubljana15, University of Sarajevo16, Friends of the Earth International17, Mendel University18, Environment Agency19, University of Göttingen20, University of Warsaw21, American Museum of Natural History22, Norwegian University of Life Sciences23, Hedmark University College24, Sofia University25
TL;DR: It is shown that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records, and coexistence alongside humans has become possible, argue the authors.
Abstract: The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success include protective legislation, supportive public opinion, and a variety of practices making coexistence between large carnivores and people possible. The European situation reveals that large carnivores and people can share the same landscape.
1,290 citations
Cornell University1, University of Missouri2, California State University, Fresno3, University of Leeds4, University of Massachusetts Amherst5, University of Melbourne6, North-West University7, University of Waikato8, Butler University9, Swedish University of Agricultural Sciences10, Helmholtz Centre for Environmental Research - UFZ11, Royal Institute of Technology12, Stellenbosch University13, Charles University in Prague14, Academy of Sciences of the Czech Republic15, University of Queensland16
TL;DR: It is found that the majority of urban bird and plant species are native in the world's cities, with the most common being Columba livia and Poa annua and few plants and birds are cosmopolitan.
Abstract: Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.
1,100 citations
Beijing Genomics Institute1, University of Copenhagen2, Royal Veterinary College3, Seoul National University4, University of Nebraska–Lincoln5, University of Porto6, University of South Carolina7, Montclair State University8, Uppsala University9, National University of Singapore10, University of California, Berkeley11, South China University of Technology12, Chinese Academy of Sciences13, Kunming Institute of Zoology14, Howard Hughes Medical Institute15, Aberystwyth University16, University of Kent17, University of California, Riverside18, Mississippi State University19, Austral University of Chile20, Swedish University of Agricultural Sciences21, China Agricultural University22, Cardiff University23, Copenhagen Zoo24, Louisiana State University25, Washington University in St. Louis26, Xi'an Jiaotong University27, University of California, Santa Cruz28, Nova Southeastern University Oceanographic Center29, Smithsonian Conservation Biology Institute30, National Museum of Natural History31, Natural History Museum32, University of California, San Francisco33, Harvard University34, University of Florida35, University of Edinburgh36, New Mexico State University37, Macau University of Science and Technology38, Curtin University39
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Abstract: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
872 citations
TL;DR: The current knowledge of mast cell secretory granules is discussed, which shows that mast cell granule proteases account for many of the protective and detrimental effects of mast cells in various inflammatory settings.
Abstract: Mast cells are important effector cells of the immune system and recent studies show that they have immunomodulatory roles in diverse processes in both health and disease. Mast cells are distinguished by their high content of electron-dense secretory granules, which are filled with large amounts of preformed and pre-activated immunomodulatory compounds. When appropriately activated, mast cells undergo degranulation, a process by which these preformed granule compounds are rapidly released into the surroundings. In many cases, the effects that mast cells have on an immune response are closely associated with the biological actions of the granule compounds that they release, as exemplified by the recent studies showing that mast cell granule proteases account for many of the protective and detrimental effects of mast cells in various inflammatory settings. In this Review, we discuss the current knowledge of mast cell secretory granules.
754 citations
Université du Québec à Montréal1, VU University Amsterdam2, Wageningen University and Research Centre3, Swiss Federal Institute of Aquatic Science and Technology4, University of Göttingen5, University of Toulouse6, Finnish Environment Institute7, Swedish University of Agricultural Sciences8, University of Zurich9, Centre national de la recherche scientifique10
TL;DR: Reducing the functional diversity of decomposer organisms and plant litter types slowed the cycling of litter carbon and nitrogen, and the emergence of this general mechanism and the coherence of patterns across contrasting terrestrial and aquatic ecosystems suggest that biodiversity loss has consistent consequences for litter decomposition and the Cycling of major elements on broad spatial scales.
Abstract: The decomposition of dead organic matter is a major determinant of carbon and nutrient cycling in ecosystems, and of carbon fluxes between the biosphere and the atmosphere. Decomposition is driven by a vast diversity of organisms that are structured in complex food webs. Identifying the mechanisms underlying the effects of biodiversity on decomposition is critical given the rapid loss of species worldwide and the effects of this loss on human well-being. Yet despite comprehensive syntheses of studies on how biodiversity affects litter decomposition, key questions remain, including when, where and how biodiversity has a role and whether general patterns and mechanisms occur across ecosystems and different functional types of organism. Here, in field experiments across five terrestrial and aquatic locations, ranging from the subarctic to the tropics, we show that reducing the functional diversity of decomposer organisms and plant litter types slowed the cycling of litter carbon and nitrogen. Moreover, we found evidence of nitrogen transfer from the litter of nitrogen-fixing plants to that of rapidly decomposing plants, but not between other plant functional types, highlighting that specific interactions in litter mixtures control carbon and nitrogen cycling during decomposition. The emergence of this general mechanism and the coherence of patterns across contrasting terrestrial and aquatic ecosystems suggest that biodiversity loss has consistent consequences for litter decomposition and the cycling of major elements on broad spatial scales.
573 citations
Durham University1, National Museum of Natural History2, University of Warwick3, New York University4, Uppsala University5, Swedish University of Agricultural Sciences6, University College London7, University of Pittsburgh8, Australian National University9, University of Aberdeen10, Oklahoma State University–Stillwater11, University of Copenhagen12, Ohio State University13, University of Guelph14, Washington University in St. Louis15, University of Missouri16, University of California, Davis17, University of Granada18
TL;DR: It is argued that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
Abstract: It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
555 citations
TL;DR: In this article, a systematic literature review was undertaken to analyse the linkages between different biodiversity attributes and 11 ecosystem services, and the majority of relationships between attributes and ecosystem services cited in the 530 studies were positive.
Abstract: A systematic literature review was undertaken to analyse the linkages between different biodiversity attributes and 11 ecosystem services. The majority of relationships between attributes and ecosystem services cited in the 530 studies were positive. For example, the services of water quality regulation, water flow regulation, mass flow regulation and landscape aesthetics were improved by increases in community and habitat area. Functional traits, such as richness and diversity, also displayed a predominantly positive relationship across the services, most commonly discussed for atmospheric regulation, pest regulation and pollination. A number of studies also discussed a positive correlation with stand age, particularly for atmospheric regulation. Species level traits were found to benefit a number of ecosystem services, with species abundance being particularly important for pest regulation, pollination and recreation, and species richness for timber production and freshwater fishing. Instances of biodiversity negatively affecting the examined ecosystem services were few in number for all ecosystem services, except freshwater provision. The review showed that ecosystem services are generated from numerous interactions occurring in complex systems. However, improving understanding of at least some of the key relationships between biodiversity and service provision will help guide effective management and protection strategies.
501 citations
University of Helsinki1, University of Aberdeen2, Rothamsted Research3, Royal Agricultural University4, University of Western Sydney5, University of Stirling6, Heriot-Watt University7, Swedish University of Agricultural Sciences8, University of Lleida9, Australian National University10, University of Edinburgh11, Pontifical Catholic University of Peru12, University of Exeter13
TL;DR: It is found that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.
Abstract: Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.
490 citations
TL;DR: Several genomic selection (GS) models are reviewed with respect to both the prediction accuracy and genetic gain from selection.
479 citations
TL;DR: Recent developments in climate change observations and projections, observed and projected impacts on European forests and the associated uncertainties are reviewed and synthesised with a view to understanding the implications for forest management.
TL;DR: Because of the continuous emission of PFASs, further information about their ecotoxicological potential among multiple generations, species interactions, and mixture toxicity seems fundamental to reliably assess the risks forPFASs to affect ecosystem structure and function in the aquatic environment.
Abstract: Polyfluoroalkyl and perfluoroalkyl substances (PFASs) are distributed ubiquitously in the aquatic environment, which raises concern for the flora and fauna in hydrosystems. The present critical review focuses on the fate and adverse effects of PFASs in the aquatic environment. The PFASs are continuously emitted into the environment from point and nonpoint sources such as sewage treatment plants and atmospheric deposition, respectively. Although concentrations of single substances may be too low to cause adverse effects, their mixtures can be of significant environmental concern. The production of C8 -based PFASs (i.e., perfluorooctane sulfonate [PFOS] and perfluorooctanoate [PFOA]) is largely phased out; however, the emissions of other PFASs, in particular short-chain PFASs and PFAS precursors, are increasing. The PFAS precursors can finally degrade to persistent degradation products, which are, in particular, perfluoroalkane sulfonates (PFSAs) and perfluoroalkyl carboxylates (PFCAs). In the environment, PFSAs and PFCAs are subject to partitioning processes, whereby short-chain PFSAs and PFCAs are mainly distributed in the water phase, whereas long-chain PFSAs and PFCAs tend to bind to particles and have a substantial bioaccumulation potential. However, there are fundamental knowledge gaps about the interactive toxicity of PFAS precursors and their persistent degradation products but also interactions with other natural and anthropogenic stressors. Moreover, because of the continuous emission of PFASs, further information about their ecotoxicological potential among multiple generations, species interactions, and mixture toxicity seems fundamental to reliably assess the risks for PFASs to affect ecosystem structure and function in the aquatic environment.
TL;DR: It is shown that the evolution of preference for human odour in domestic mosquitoes is tightly linked to increases in the expression and ligand-sensitivity of the odorant receptor AaegOr4, which recognizes a compound present at high levels in human Odour.
Abstract: Female mosquitoes are major vectors of human disease and the most dangerous are those that preferentially bite humans. A 'domestic' form of the mosquito Aedes aegypti has evolved to specialize in biting humans and is the main worldwide vector of dengue, yellow fever, and chikungunya viruses. The domestic form coexists with an ancestral, 'forest' form that prefers to bite non-human animals and is found along the coast of Kenya. We collected the two forms, established laboratory colonies, and document striking divergence in preference for human versus non-human animal odour. We further show that the evolution of preference for human odour in domestic mosquitoes is tightly linked to increases in the expression and ligand-sensitivity of the odorant receptor AaegOr4, which we found recognizes a compound present at high levels in human odour. Our results provide a rare example of a gene contributing to behavioural evolution and provide insight into how disease-vectoring mosquitoes came to specialize on humans.
TL;DR: It is observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups, thus underpinning the importance of community structure for N2O emissions.
Abstract: Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N2O emissions.
TL;DR: In this article, the capacity of soils to take up Nitrous Oxide (N2O) is mostly explained by the abundance and diversity of a newly described N2O-reducing microbial group.
Abstract: Nitrous oxide (N2O) is a greenhouse gas and an important ozone-depleting substance. Microbial nitrogen cycling in agricultural soils is a major source of atmospheric N2O. Now, research shows that the capacity of soils to take up N2O is mostly explained by the abundance and diversity of a newly described N2O-reducing microbial group.
TL;DR: In this article, a conceptual model based on a framework of consumers' quality perception process is presented and applied, and seven main categories of credence characteristics can be identified in the literature: (a) health; (b) organic food; (c) origin; (d) brand; (e) production methods; (f) ethics; (g) descriptive food names and ingredients).
TL;DR: A web-survey is used to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
Abstract: To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
TL;DR: In this paper, the authors reviewed empirical findings on the species richness in urban parks across all species groups that have been studied and discussed the overall species richness of urban parks, its community attributes and drivers.
Abstract: There is growing recognition of urban areas as hosts for innovative ways to conserve and promote biodiversity. Parks, as one specific type of urban green space, constitute particularly important biodiversity hotspots in the cityscape. We reviewed empirical findings on the species richness in urban parks across all species groups that have been studied. The aim was to assess and discuss the overall species richness of urban parks, its community attributes and drivers. Search and subsequent selection process resulted in 62 papers from 25 different countries. For all examined species groups, the findings consistently show that parks are among the most species rich types of urban green spaces, but also that exotics constitute large shares, especially of plant species. Key ecological theories like the gradient approach and the island habitat ecological theory, and fundamental ecological relationships such as the species-area relationship are valid despite the manipulated ‘nature’ of parks and the surrounding urban matrix. Most studies surveyed large number of parks and applied ‘multi-scale’ approaches in tests of confounding variables, providing methodological strength. While matrix effects are consistently found to affect species richness negatively, the diversity of habitats and microhabitat heterogeneity contained in urban parks appears as the most decisive factor for the overall species richness. However, a constraint of research to date is the limitation of individual studies to one or a few species groups, rarely bridging between flora and fauna. Adopting ‘multi-species group’ approaches in future research is needed to further advance the understanding of the overall biodiversity of urban parks, and its drivers.
Max Planck Society1, Macquarie University2, Oak Ridge National Laboratory3, Boston University4, Goethe University Frankfurt5, University of Oklahoma6, CSIRO Marine and Atmospheric Research7, University of Illinois at Urbana–Champaign8, Natural Resources Canada9, Lund University10, Princeton University11, Colorado State University12, University of Bordeaux13, Institut national de la recherche agronomique14, Imperial College London15, Swedish University of Agricultural Sciences16, Duke University17
TL;DR: The results suggest that improved representation of above-ground–below-ground interactions and better constraints on plant stoichiometry are important for a predictive understanding of eCO2 effects and improved accuracy of soil organic matter inventories is pivotal to reduce uncertainty in the observed C–N budgets.
Abstract: We analysed the responses of 11 ecosystem models to elevated atmospheric [CO2] (eCO(2)) at two temperate forest ecosystems (Duke and Oak Ridge National Laboratory (ORNL) Free-Air CO2 Enrichment (FACE) experiments) to test alternative representations of carbon (C)-nitrogen (N) cycle processes. We decomposed the model responses into component processes affecting the response to eCO(2) and confronted these with observations from the FACE experiments. Most of the models reproduced the observed initial enhancement of net primary production (NPP) at both sites, but none was able to simulate both the sustained 10-yr enhancement at Duke and the declining response at ORNL: models generally showed signs of progressive N limitation as a result of lower than observed plant N uptake. Nonetheless, many models showed qualitative agreement with observed component processes. The results suggest that improved representation of above-ground-below-ground interactions and better constraints on plant stoichiometry are important for a predictive understanding of eCO(2) effects. Improved accuracy of soil organic matter inventories is pivotal to reduce uncertainty in the observed C-N budgets. The two FACE experiments are insufficient to fully constrain terrestrial responses to eCO(2), given the complexity of factors leading to the observed diverging trends, and the consequential inability of the models to explain these trends. Nevertheless, the ecosystem models were able to capture important features of the experiments, lending some support to their projections. (Less)
Swedish University of Agricultural Sciences1, Royal Holloway, University of London2, University of Tasmania3, Australian National University4, United States Forest Service5, Estonian University of Life Sciences6, Vancouver Island University7, University of Washington8, University of Eastern Finland9, University of Alberta10, Université du Québec en Outaouais11, Norwegian University of Life Sciences12
TL;DR: A meta-analysis of 78 studies using a systematic review protocol provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity, a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention.
Abstract: Summary 1. Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests. 2. Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna. 3. Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts. 4. Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts. 5. Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively. 6. Synthesis and applications. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising
University of Porto1, Science for Life Laboratory2, Norwich University3, Massachusetts Institute of Technology4, Max Planck Society5, Swedish University of Agricultural Sciences6, Ain Shams University7, European Bioinformatics Institute8, Wellcome Trust Sanger Institute9, University of Cambridge10, Institut national de la recherche agronomique11, University of Bologna12, National Institutes of Health13, United States Department of Energy14, Spanish National Research Council15, University of Montana16, Texas A&M University17
TL;DR: It is proposed that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
Abstract: The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
TL;DR: It is shown that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later, which implies that speciation rate is ultimately set by niche filling, rather than by the rate of acquisition of reproductive isolation.
Abstract: In Himalayan songbirds, the speciation rate is ultimately set by ecological competition, rather than by the rate of acquisition of reproductive isolation. The beginnings of adaptive radiation and speciation have been widely studied — in Darwin's finches, sticklebacks and cichlid fish, for example — but relatively little is known about what happens next. Specifically, what is the rate-limiting step for the establishment of new species? This seven-year study of the 358 songbird species found on the Himalayan slopes suggests that it is the rates at which new niches are created and occupied that limits diversification, not the rate at which new species form through reproductive isolation. Speciation generally involves a three-step process—range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations1,2. Speciation relies on cycling through these three steps and each may limit the rate at which new species form1,3. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions4, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation5. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed2,3,6; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.
TL;DR: A new antibody is described that prevents thrombosis and facilitates blood flow in a specific heart-lung machine without causing bleeding in large animal models and shows an anticoagulation therapy without bleeding risk based on a plasma protease factor XII function-neutralizing antibody.
Abstract: Currently used anticoagulants prevent thrombosis but increase bleeding. We show an anticoagulation therapy without bleeding risk based on a plasma protease factor XII function-neutralizing antibody. We screened for antibodies against activated factor XII (FXIIa) using phage display and demonstrated that recombinant fully human antibody 3F7 binds into the FXIIa enzymatic pocket. 3F7 interfered with FXIIa-mediated coagulation, abolished thrombus formation under flow, and blocked experimental thrombosis in mice and rabbits. We adapted an extracorporeal membrane oxygenation (ECMO) cardiopulmonary bypass system used for infant therapy to analyze clinical applicability of 3F7 in rabbits. 3F7 provided thromboprotection as efficiently as heparin, and both drugs prevented fibrin deposition and thrombosis within the extracorporeal circuit. Unlike heparin, 3F7 treatment did not impair the hemostatic capacity and did not increase bleeding from wounds. These data establish that targeting of FXIIa is a safe mode of thromboprotection in bypass systems, and provide a clinically relevant anticoagulation strategy that is not complicated by excess bleeding.
TL;DR: It is observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives, and DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study.
Abstract: Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
Natural Environment Research Council1, University of Malaya2, Monash University3, Swedish University of Agricultural Sciences4, National Institute of Water and Atmospheric Research5, Lamont–Doherty Earth Observatory6, University of Siena7, University of Waikato8, Antarctica New Zealand9, University of Bristol10, Ohio State University11, University of Tasmania12, Autonomous University of Madrid13, University of Wollongong14, University of Genoa15, Colorado State University16
TL;DR: In this paper, the authors synthesized current knowledge on environmental variability across terrestrial, freshwater, and marine Antarctic biomes and related this to the observed biotic patterns, showing that the most important physical driver of Antarctic terrestrial communities is the availability of liquid water, itself driven by solar irradiance intensity.
Abstract: Patterns of environmental spatial structure lie at the heart of the most fundamental and familiar patterns of diversity on Earth. Antarctica contains some of the strongest environmental gradients on the planet and therefore provides an ideal study ground to test hypotheses on the relevance of environmental variability for biodiversity. To answer the pivotal question, “How does spatial variation in physical and biological environmental properties across the Antarctic drive biodiversity?” we have synthesized current knowledge on environmental variability across terrestrial, freshwater, and marine Antarctic biomes and related this to the observed biotic patterns. The most important physical driver of Antarctic terrestrial communities is the availability of liquid water, itself driven by solar irradiance intensity. Patterns of biota distribution are further strongly influenced by the historical development of any given location or region, and by geographical barriers. In freshwater ecosystems, free water is also crucial, with further important influences from salinity, nutrient availability, oxygenation, and characteristics of ice cover and extent. In the marine biome there does not appear to be one major driving force, with the exception of the oceanographic boundary of the Polar Front. At smaller spatial scales, ice cover, ice scour, and salinity gradients are clearly important determinants of diversity at habitat and community level. Stochastic and extreme events remain an important driving force in all environments, particularly in the context of local extinction and colonization or recolonization, as well as that of temporal environmental variability. Our synthesis demonstrates that the Antarctic continent and surrounding oceans provide an ideal study ground to develop new biogeographical models, including life history and physiological traits, and to address questions regarding biological responses to environmental variability and change.
TL;DR: Fluorescence spectroscopy was used to explore DOM quality from 560 lakes distributed across Sweden and encompassed a wide climatic gradient typical of the boreal ecozone, suggesting that DOM reactivity depends more heavily on the duration of time taken to pass through the landscape, rather than temperature.
Abstract: Inland waters transport large amounts of dissolved organic matter (DOM) from terrestrial environments to the oceans, but DOM also reacts en route, with substantial water column losses by mineralization and sedimentation. For DOM transformations along the aquatic continuum, lakes play an important role as they retain waters in the landscape allowing for more time to alter DOM. We know DOM losses are significant at the global scale, yet little is known about how the reactivity of DOM varies across landscapes and climates. DOM reactivity is inherently linked to its chemical composition. We used fluorescence spectroscopy to explore DOM quality from 560 lakes distributed across Sweden and encompassed a wide climatic gradient typical of the boreal ecozone. Six fluorescence components were identified using parallel factor analysis (PARAFAC). The intensity and relative abundance of these components were analyzed in relation to lake chemistry, catchment, and climate characteristics. Land cover, particularly the percentage of water in the catchment, was a primary factor explaining variability in PARAFAC components. Likewise, lake water retention time influenced DOM quality. These results suggest that processes occurring in upstream water bodies, in addition to the lake itself, have a dominant influence on DOM quality. PARAFAC components with longer emission wavelengths, or red-shifted components, were most reactive. In contrast, protein-like components were most persistent within lakes. Generalized characteristics of PARAFAC components based on emission wavelength could ease future interpretation of fluorescence spectra. An important secondary influence on DOM quality was mean annual temperature, which ranged between � 6.2 and +7.5 °C. These results suggest that DOM reactivity depends more heavily on the duration of time taken to pass through the landscape, rather than temperature. Projected increases in runoff in the boreal region may force lake DOM toward a higher overall amount and proportion of humic-like substances.
TL;DR: The concept of panarchy provides a framework that characterizes complex systems of people and nature as dynamically organized and structured within and across scales of space and time and a set of testable hypotheses to evaluate key propositions that follow from panarchy theory are forward.
Abstract: The concept of panarchy provides a framework that characterizes complex systems of people and nature as dynamically organized and structured within and across scales of space and time. It has been more than a decade since the introduction of panarchy. Over this period, its invocation in peer-reviewed literature has been steadily increasing, but its use remains primarily descriptive and abstract. Here, we discuss the use of the concept in the literature to date, highlight where the concept may be useful, and discuss limitations to the broader applicability of panarchy theory for research in the ecological and social sciences. Finally, we forward a set of testable hypotheses to evaluate key propositions that follow from panarchy theory.
Swiss Federal Institute for Forest, Snow and Landscape Research1, University of Copenhagen2, University of Freiburg3, University of Ljubljana4, Swedish University of Agricultural Sciences5, University of Natural Resources and Life Sciences, Vienna6, Wageningen University and Research Centre7, Bern University of Applied Sciences8, University of Florence9, Czech University of Life Sciences Prague10
TL;DR: This review identifies and evaluates six principles for enhancing the adaptive capacity of European temperate forests in a changing climate and uses these principles to examine how three CNS systems (single-tree selection, group selection and shelterwood) serve adaptation strategies.
Abstract: In many parts of Europe, close-to-nature silviculture (CNS) has been widely advocated as being the best approach for managing forests to cope with future climate change. In this review, we identify and evaluate six principles for enhancing the adaptive capacity of European temperate forests in a changing climate: (1) increase tree species richness, (2) increase structural diversity, (3) maintain and increase genetic variation within tree species, (4) increase resistance of individual trees to biotic and abiotic stress, (5) replace high-risk stands and (6) keep average growing stocks low. We use these principles to examine how three CNS systems (single-tree selection, group selection and shelterwood) serve adaptation strategies. Many attributes of CNS can increase the adaptive capacity of European temperate forests to a changing climate. CNS promotes structural diversity and tree resistance to stressors, and growing stocks can be kept at low levels. However, some deficiencies exist in relation to the adaptation principles of increasing tree species richness, maintaining and increasing genetic variation, and replacing high-risk stands. To address these shortcomings, CNS should make increased use of a range of regeneration methods, in order to promote light-demanding tree species, non-native species and non-local provenances.
TL;DR: In this article, the authors present a review of the attributes that evoke fear of crime in urban green spaces and highlight their complex interaction by adopting a social-ecological framework, which can help guide future research.
TL;DR: It is shown that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species and it is found that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype.
Abstract: Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.