Towards systematic evaluation of crop model outputs for global land-use models

Land provides vital socioeconomic resources to the society, however at the cost of large environmental degradations. Global integrated models combining high resolution global gridded crop models (GGCMs) and global economic models (GEMs) are increasingly being used to inform sustainable solution for agricultural land-use. However, little effort has yet been done to evaluate and compare the accuracy of GGCM outputs. In addition, GGCM datasets require a large amount of parameters whose values and their variability across space are weakly constrained: increasing the accuracy of such dataset has a very high computing cost. Innovative evaluation methods are required both to ground credibility to the global integrated models, and to allow efficient parameter specification of GGCMs. We propose an evaluation strategy for GGCM datasets in the perspective of use in GEMs, illustrated with preliminary results from a novel dataset (the Hypercube) generated by the EPIC GGCM and used in the GLOBIOM land use GEM to inform on present-day crop yield, water and nutrient input needs for 16 crops x 15 management intensities, at a spatial resolution of 5 arc-minutes. We adopt the following principle: evaluation should provide a transparent diagnosis of model adequacy for its intended use. We briefly describe how the Hypercube data is generated and how it articulates with GLOBIOM in order to transparently identify the performances to be evaluated, as well as the main assumptions and data processing involved. Expected performances include adequately representing the sub-national heterogeneity in crop yield and input needs: i) in space, ii) across crop species, and iii) across management intensities. We will present and discuss measures of these expected performances and weight the relative contribution of crop model, input data and data processing steps in performances. We will also compare obtained yield gaps and main yield-limiting factors against the M3 dataset. Next steps include iterative improvement of parameter assumptions and evaluation of implications of GGCM performances for intended use in the IIASA EPIC-GLOBIOM model cluster. Our approach helps targeting future efforts at improving GGCM accuracy and would achieve highest efficiency if combined with traditional field-scale evaluation and sensitivity analysis

Towards Systematic Evaluation of Crop Model Outputs for Global Land-use Models

Land provides vital socioeconomic resources to the society; however, at the cost of large environmental degradation (Verburg et al., 2013). At the crossroads of these dimensions, agriculture becomes increasingly interconnected to various natural and human systems across various scales. In order to inform the design of policies to navigate land use towards a more sustainable operating space, comprehensive global assessment models are increasingly being used. They rely partly on the loose coupling of biophysical crop models to global economic models, via one-way exchange of output variables (Rosenzweig et al. 2013). Accuracy of variables exchanged strongly influences the outcomes assessed at various scales, and its improvement is likely to require iterative improvements. Yet there has been little effort to document, evaluate and compare these exchange variables across models (Mueller & Robertson et al. 2014). We here present a novel dataset (the Hypercube) generated by the Environmental Policy Integrated Model (EPIC) crop model and providing the Global Biosphere Management Model (GLOBIOM) with high-resolution information at global scale on the yield, water, and nutrient needs of 16 crops for 15 different combinations of management. We present the dataset and its links to the EPIC and GLOBIOM model, and the rationale for developing a systematic evaluation of the data, before illustrating them with preliminary results

Lipopeptide biodiversity in antifungal Bacillus strains isolated from Algeria

Several Bacillus strains have been well studied for their ability to control soil-borne plant diseases. This property is linked to the production of several families of lipopeptides. Depending of their structure, these compounds show antifungal and/or plant systemic resistance inducing activities. In this work, the biodiversity of lipopeptides produced by different antifungal Bacillus strains isolated from seeds, rhizospheric, and non-rhizospheric soils in Algeria was analyzed. Sixteen active strains were characterized by PCR for their content in genes involved in lipopeptide biosynthesis and by MALDI-ToF for their lipopeptide production, revealing a high biodiversity of products. The difficulty to detect kurstakin genes led us to design two new sets of specific primers. An interesting potential of antifungal activity and the synthesis of two forms of fengycins differing in the eighth amino acid (Gln/Glu) were found from the strain 8. Investigation of its genome led to the finding of an adenylation domain of the fengycin synthetase predicted to activate the glutamate residue instead of the glutamine one. According to the comparison of both the results of MALDI-ToF-MS and genome analysis, it was concluded that this adenylation domain could activate both residues at the same time. This study highlighted that the richness of the Algerian ecosystems in Bacillus strains is able to produce: surfactin, pumilacidin, lichenysin, kurstakin, and different types of fengycins. © 2018 Springer-Verlag GmbH Germany, part of Springer Natur

Hundreds of genetic barcodes of the species-rich hydroid superfamily Plumularioidea (Cnidaria, Medusozoa) provide a guide toward more reliable taxonomy

Marine hydroids are important benthic components of shallow and deep waters worldwide, but their taxonomy is controversial because diagnostic morphological characters to categorize taxa are limited. Their genetic relationships are also little investigated. We tested taxonomic hypotheses within the highly speciose superfamily Plumularioidea by integrating a classical morphological approach with DNA barcoding of the 16S and COI mitochondrial markers for 659 and 196 specimens of Plumularioidea, respectively. Adding Genbank sequences, we inferred systematic relationships among 1,114 plumularioids, corresponding to 123 nominal species and 17 novel morphospecies in five families of Plumularioidea. We found considerable inconsistencies in the systematics of nominal families, genera and species. The families Kirchenpaueriidae and Plumulariidae were polyphyletic and the Halopterididae paraphyletic. Most genera of Plumularioidea are not monophyletic. Species diversity is considerably underestimated. Within our study, at least 10% of the morphologically-distinctive morphospecies are undescribed, and about 40% of the overall species richness is represented by cryptic species. Convergent evolution and morphological plasticity therefore blur systematic relationships. Additionally, cryptic taxa occur frequently in sympatry or parapatry, complicating correspondence with type material of described species. Sometimes conspecificity of different morphotypes was found. The taxonomy of hydroids requires continued comprehensive revision.This work relied on several hydrozoan samples collected from various sites, with the aid of many people. Supplementary Table S1 refers many of the people involved in the collection and/or preservation of the samples. C.J.M. acknowledges his great buddy-divers Jaime N.-Ruiz (CIMAR, Univ. Costa Rica), Axel Calderon, Nathaniel Chu, Eleni Petrou (STRI, Smiths. Inst.), Hanae Spathias, Karen Koltes (at the Belize station, Smith. Inst.), Freya Sommer (Hopkins Marine Station), Remilson Ferreira ('Costa Norte', Sao Tome), Frederico Cardigos (DOP, Univ. Azores) and others that assisted the dives. C.J.M. also acknowledges Rita Castillo (CIMAR, Univ. Costa Rica), Plinio Gondola, Ligia Calderon, Laura Geyer, Maria Castillo (STRI, Smiths. Inst.), Gregory Ruiz (SERC, Smiths. Inst.), Paul Greenhall, William Keel (MSC, Smith. Inst.), Manuel Enes, Valentina Matos (IMAR/DOP, Univ. Azores), Filipe Porteiro, Joao Goncalves (OKEANOS/IMAR, Univ. Azores), Marina Cunha, Ascensao Ravara (CESAM, Univ. Aveiro), Shirley Pomponi (Harbor Branch, Florida Atlantic Univ.), Estrela Matilde (Fundacao Principe Trust), Monica Albuquerque, Ines Tojeira (EMEPC), Diana Carvalho (Nat. Mus. Nat. Hist., Lisbon) and many others colleagues that facilitated the morphologic classifications and deposition of the samples. Peter Schuchert (Mus. d'Hist. Nat. Geneve) kindly provided some DNA extractes. Todd Kincaid and his team of GUE divers (Project Baseline - Azores) collected valuable samples from unusual depths. Joana Boavida (CIIMAR, Univ. Algarve) facilitated some samples of the 'DeepReefs' project. Jim Drewery (Marine Scotland Science Inst.) also provided few samples. Dale Calder (Royal Ontario Museum) provided some bibliography to C.J.M. and discussed/resolved some dubios taxonomic classifications. Colleagues at the L.A.B. (NMNH, Smith. Inst.) were very supportive. The APC fees for open access publication were supported by a program of the Regional Government of the Azores ("Apoio ao funcionamento e gestao dos centros de I&D regionais: 2018 - DRCT-medida 1

Global priority areas for ecosystem restoration

Extensive ecosystem restoration is increasingly seen as being central to conserving biodiversity1 and stabilizing the climate of the Earth2. Although ambitious national and global targets have been set, global priority areas that account for spatial variation in benefits and costs have yet to be identified. Here we develop and apply a multicriteria optimization approach that identifies priority areas for restoration across all terrestrial biomes, and estimates their benefits and costs. We find that restoring 15% of converted lands in priority areas could avoid 60% of expected extinctions while sequestering 299 gigatonnes of CO2—30% of the total CO2 increase in the atmosphere since the Industrial Revolution. The inclusion of several biomes is key to achieving multiple benefits. Cost effectiveness can increase up to 13-fold when spatial allocation is optimized using our multicriteria approach, which highlights the importance of spatial planning. Our results confirm the vast potential contributions of restoration to addressing global challenges, while underscoring the necessity of pursuing these goals synergistically.Fil: Strassburg, Bernardo B. N.. Pontifícia Universidade Católica do Rio de Janeiro; Brasil. Universidade Federal do Rio de Janeiro; BrasilFil: Iribarrem, Alvaro. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Beyer, Hawthorne L.. The University of Queensland; Australia. University of Queensland; AustraliaFil: Cordeiro, Carlos Leandro. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Crouzeilles, Renato. Universidade Federal do Rio de Janeiro; Brasil. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Jakovac, Catarina C.. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Braga Junqueira, André. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Lacerda, Eduardo. Pontifícia Universidade Católica do Rio de Janeiro; Brasil. Universidade Federal Fluminense; BrasilFil: Latawiec, Agnieszka E.. University of East Anglia; Reino Unido. Pontifícia Universidade Católica do Rio de Janeiro; BrasilFil: Balmford, Andrew. University of Cambridge; Estados UnidosFil: Brooks, Thomas M.. University Of The Philippines Los Banos; Filipinas. Institute For Marine And Antarctic Studies; Australia. International Union For Conservation Of Nature And Natural Resources; SuizaFil: Butchart, Stuart H. M.. University of Cambridge; Estados UnidosFil: Chazdon, Robin L.. University Of The Sunshine Coast; Australia. University of Connecticut; Estados UnidosFil: Erb, Karl-Heinz. Universitat Fur Bodenkultur Wien; AustriaFil: Brancalion, Pedro. Universidade de Sao Paulo; BrasilFil: Buchanan, Graeme. Royal Society For The Protection Of Birds; Reino UnidoFil: Cooper, David. Secretariat Of The Convention On Biological Diversity; CanadáFil: Díaz, Sandra Myrna. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Donald, Paul F.. University of Cambridge; Estados UnidosFil: Kapos, Valerie. United Nations Environment Programme World Conservation Monitoring Centre; Reino UnidoFil: Leclère, David. International Institute For Applied Systems Analysis, Laxenburg; AustriaFil: Miles, Lera. United Nations Environment Programme World Conservation Monitoring Centre; Reino UnidoFil: Obersteiner, Michael. Oxford Social Sciences Division; Reino Unido. International Institute For Applied Systems Analysis, Laxenburg; AustriaFil: Plutzar, Christoph. Universitat Fur Bodenkultur Wien; Austria. Universidad de Viena; AustriaFil: de M. Scaramuzza, Carlos Alberto. International Institute For Sustainability; BrasilFil: Scarano, Fabio R.. Universidade Federal do Rio de Janeiro; BrasilFil: Visconti, Piero. International Institute For Applied Systems Analysis, Laxenburg; Austri

A 4D view on the evolution of metamorphic dehydration reactions

Metamorphic reactions influence the evolution of the Earth's crust in a range of tectonic settings. For example hydrous mineral dehydration in a subducting slab can produce fluid overpressures which may trigger seismicity. During reaction the mechanisms of chemical transport, including water expulsion, will dictate the rate of transformation and hence the evolution of physical properties such as fluid pressure. Despite the importance of such processes, direct observation of mineral changes due to chemical transport during metamorphism has been previously impossible both in nature and in experiment. Using time-resolved (4D) synchrotron X-ray microtomography we have imaged a complete metamorphic reaction and show how chemical transport evolves during reaction. We analyse the dehydration of gypsum to form bassanite and H2O which, like most dehydration reactions, produces a solid volume reduction leading to the formation of pore space. This porosity surrounds new bassanite grains producing fluid-filled moats, across which transport of dissolved ions to the growing grains occurs via diffusion. As moats grow in width, diffusion and hence reaction rate slow down. Our results demonstrate how, with new insights into the chemical transport mechanisms, we can move towards a more fundamental understanding of the hydraulic and chemical evolution of natural dehydrating systems

A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios

To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land-use and climate change on biodiversity and ecosystem services (i.e., nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs)-SSP1xRCP2.6, SSP3xRCP6.0, SSP5xRCP8.6-to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenario selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem services models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modeling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modeling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios

Trends in incidence, mortality and survival in women with breast cancer from 1985 to 2012 in Granada, Spain: a population-based study

The incidence of breast cancer has increased since the 1970s. Despite favorable trends in prognosis, the role of changes in clinical practice and the introduction of screening remain controversial. We examined breast cancer trends to shed light on their determinants Overall, age-adjusted (European Standard Population) incidence rates increased from 48.0 cases × 100,000 women in 1985–1989 to 83.4 in 2008–2012, with an annual percentage change (APC) of 2.5% (95%CI, 2.1–2.9) for 1985–2012. The greatest increase was in women younger than 40 years (APC 3.5, 95%CI, 2.4–4.8). For 2000–2012 the incidence trend increased only for stage I tumors (APC 3.8, 95%CI, 1.9–5.8). Overall age-adjusted breast cancer mortality decreased (APC − 1, 95%CI, − 1.4 – − 0.5), as did mortality in the 50–69 year age group (APC − 1.3, 95%CI, − 2.2 – − 0.4). Age-standardized net survival increased from 67.5% at 5 years in 1985–1989 to 83.7% in 2010–2012. All age groups younger than 70 years showed a similar evolution. Five-year net survival rates were 96.6% for patients with tumors diagnosed in stage I, 88.2% for stage II, 62.5% for stage III and 23.3% for stage IV. Breast cancer incidence is increasing – a reflection of the evolution of risk factors and increasing diagnostic pressure. After screening was introduced, the incidence of stage I tumors increased, with no decrease in the incidence of more advanced stages. Reductions were seen for overall mortality and mortality in the 50–69 year age group, but no changes were found after screening implementation. Survival trends have evolved favorably except for the 70–84 year age group and for metastatic tumors.This study was supported by a grant from the Acción Estratégica en Salud plan for the High Resolution Project on Prognosis and Care of Cancer Patients (No. AC14/00036) awarded by the Spanish Ministry of Economy and Competitiveness and co-funded by the European Regional Development Fund (ERDF)

Evolution of protein domain architectures

This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution