Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    (De)coding a technopolity: tethering the civic blockchain to political transformation
    Husain, Syed Omer - \ 2020
    Wageningen University. Promotor(en): H. Wiskerke, co-promotor(en): D. Roep; A. Franklin. - Wageningen : Wageningen University - ISBN 9789463953092 - 228

    This study rests at the intersection of technopolitics, translocal networks and political change. The overall aim of the thesis is to understand, and in turn, influence, the way technology interacts with political transformation. It responds to the fact that social science has thus far neglected to adequately account for and analyze how emerging technologies like blockchain and civic tech influence the way politics is practiced. The main research question guiding the study is how does the design, implementation and use of technopolitical innovations influence the practice of politics. The thesis foregrounds the idea that technopolitical experiments personify a ‘prefigurative politics by design’ i.e. they embody the politics and power structures they want to enable in society.

    Conducted as part of the EU-funded SUSPLACE project that explores the transformative capacity of sustainable place-shaping practices, the research was predominantly inspired by a hybrid digital ethnography methodology. The thesis confines its focus to three empirical clusters: technopolitical blockchain projects, government-led blockchain projects and place-based civic engagement technologies. The study delineates how differing politico-social imaginaries play a role in the design and implementation of technopolitical projects; addresses contemporary post-political phenomena such as the depoliticization of agency; and identifies the activation of a place-based geography of political action through digitally-mediated municipal networks. It articulates the language and frameworks necessary to analyze these present-day challenges, while simultaneously developing approaches that can be exported to different domains of political activism.

    Technology is not neutral; but neither are its designers and users. The thesis finds that it is through considerable, deliberate efforts, in conjunction with individual and collective choices, that technopolitical innovations can reframe our socio-economic and political realities. The study demonstrates the emphatic and urgent need for researchers, practitioners, politicians and citizens to collaboratively work on redrawing boundaries of access, empowering the citizenry, creating new forms of organization and re-politicizing the economy. It outlines a transdisciplinary research and practice agenda that aims at not only (de)coding the existing technopolitical innovations, but also (re)coding them to create a more equitable system of politics. The thesis concludes that since coding affordances and constraints in a technopolitical system is shown to regulate political agency and even influence the behavior of citizens, we must devise value-driven technology that incentivizes creating a more equitable political system. 

    The political imaginaries of blockchain projects: discerning the expressions of an emerging ecosystem
    Husain, Syed Omer ; Franklin, Alex ; Roep, Dirk - \ 2020
    Sustainability Science 15 (2020). - ISSN 1862-4065 - p. 379 - 394.
    Blockchain - Decentralization - Political imaginaries - Prefigurative politics - Technopolitics

    There is a wealth of information, hype around, and research into blockchain’s ‘disruptive’ and ‘transformative’ potential concerning every industry. However, there is an absence of scholarly attention given to identifying and analyzing the political premises and consequences of blockchain projects. Through digital ethnography and participatory action research, this article shows how blockchain experiments personify ‘prefigurative politics’ by design: they embody the politics and power structures which they want to enable in society. By showing how these prefigurative embodiments are informed and determined by the underlying political imaginaries, the article proposes a basic typology of blockchain projects. Furthermore, it outlines a frame to question, cluster, and analyze the expressions of political imaginaries intrinsic to the design and operationalization of blockchain projects on three analytic levels: users, intermediaries, and institutions.

    Prefigurative Post-Politics as Strategy: The Case of Government-Led Blockchain Projects
    Hussain, Syed Omer ; Roep, D. ; Franklin, Alex - \ 2020
    The Journal of The British Blockchain Association 3 (2020)1. - ISSN 2516-3949 - 11 p.
    Critically engaging with literature on post-politics, blockchain and algorithmic governance, and drawing also on knowledge gained from undertaking a three-year empirical study, the purpose of this article is to better understand the transformative capacity of government-led blockchain projects. Analysis of a diversity of empirical material, which was guided by a digital ethnography approach, is used to support the furthering of the existing debate on the nature of the post-political as a condition and/or strategy. Through these theoretical and empirical explorations, the article concludes that while the post-political represents a contingent political strategy by governmental actors, it could potentially impose an algorithmically enforced post-political ‘condition’ for the citizen. It is argued that the design, features and mechanisms of government-led projects are deliberately and strategically used to delimit a citizens’ political agency. In order to address this scenario, we argue that there is a need not only to analyse and contribute to the algorithmic design of blockchain projects (i.e. the affordances and constraints they set), but also to the metapolitical narrative underpinning them (i.e. the political imaginaries underlying the various government-led projects).
    Nitrogen and phosphorus constrain the CO2 fertilization of global plant biomass
    Terrer, César ; Jackson, Robert B. ; Prentice, I.C. ; Keenan, Trevor F. ; Kaiser, Christina ; Vicca, Sara ; Fisher, Joshua B. ; Reich, Peter B. ; Stocker, Benjamin D. ; Hungate, Bruce A. ; Peñuelas, Josep ; McCallum, Ian ; Soudzilovskaia, Nadejda A. ; Cernusak, Lucas A. ; Talhelm, Alan F. ; Sundert, Kevin Van; Piao, Shilong ; Newton, Paul C.D. ; Hovenden, Mark J. ; Blumenthal, Dana M. ; Liu, Yi Y. ; Müller, Christoph ; Winter, Klaus ; Field, Christopher B. ; Viechtbauer, Wolfgang ; Lissa, Caspar J. Van; Hoosbeek, Marcel R. ; Watanabe, Makoto ; Koike, Takayoshi ; Leshyk, Victor O. ; Polley, H.W. ; Franklin, Oskar - \ 2019
    Nature Climate Change 9 (2019). - ISSN 1758-678X - p. 684 - 689.

    Elevated CO2 (eCO2) experiments provide critical information to quantify the effects of rising CO2 on vegetation1–6. Many eCO2 experiments suggest that nutrient limitations modulate the local magnitude of the eCO2 effect on plant biomass1,3,5, but the global extent of these limitations has not been empirically quantified, complicating projections of the capacity of plants to take up CO2 7,8. Here, we present a data-driven global quantification of the eCO2 effect on biomass based on 138 eCO2 experiments. The strength of CO2 fertilization is primarily driven by nitrogen (N) in ~65% of global vegetation and by phosphorus (P) in ~25% of global vegetation, with N- or P-limitation modulated by mycorrhizal association. Our approach suggests that CO2 levels expected by 2100 can potentially enhance plant biomass by 12 ± 3% above current values, equivalent to 59 ± 13 PgC. The global-scale response to eCO2 we derive from experiments is similar to past changes in greenness9 and biomass10 with rising CO2, suggesting that CO2 will continue to stimulate plant biomass in the future despite the constraining effect of soil nutrients. Our research reconciles conflicting evidence on CO2 fertilization across scales and provides an empirical estimate of the biomass sensitivity to eCO2 that may help to constrain climate projections.

    Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation
    Almendros, Cristóbal ; Nobrega, Franklin L. ; McKenzie, Rebecca E. ; Brouns, Stan J.J. - \ 2019
    Nucleic acids research 47 (2019)10. - ISSN 0305-1048 - p. 5223 - 5230.

    Microbes have the unique ability to acquire immunological memories from mobile genetic invaders to protect themselves from predation. To confer CRISPR resistance, new spacers need to be compatible with a targeting requirement in the invader's DNA called the protospacer adjacent motif (PAM). Many CRISPR systems encode Cas4 proteins to ensure new spacers are integrated that meet this targeting prerequisite. Here we report that a gene fusion between cas4 and cas1 from the Geobacter sulfurreducens I-U CRISPR-Cas system is capable of introducing functional spacers carrying interference proficient TTN PAM sequences at much higher frequencies than unfused Cas4 adaptation modules. Mutations of Cas4-domain catalytic residues resulted in dramatically decreased naïve and primed spacer acquisition, and a loss of PAM selectivity showing that the Cas4 domain controls Cas1 activity. We propose the fusion gene evolved to drive the acquisition of only PAM-compatible spacers to optimize CRISPR interference.

    Keeping crispr in check: diverse mechanisms of phage-encoded anti-crisprs
    Trasanidou, Despoina ; Gerós, Ana Sousa ; Mohanraju, Prarthana ; Nieuwenweg, Anna Cornelia ; Nobrega, Franklin L. ; Staals, Raymond H.J. - \ 2019
    FEMS Microbiology Letters 366 (2019)9. - ISSN 0378-1097
    crispr-cas - anti-crispr - genome editing - phage
    CRISPR-Cas represents the only adaptive immune system of prokaryotes known to date. These immune systems are widespread among bacteria and archaea, and provide protection against invasion of mobile genetic elements, such as bacteriophages and plasmids. As a result of the arms-race between phages and their prokaryotic hosts, phages have evolved inhibitors known as anti-CRISPR (Acr) proteins to evade CRISPR immunity. In the recent years, several Acr proteins have been described in both temperate and virulent phages targeting diverse CRISPR-Cas systems. Here, we describe the strategies of Acr discovery and the multiple molecular mechanisms by which these proteins operate to inhibit CRISPR immunity. We discuss the biological relevance of Acr proteins and speculate on the implications of their activity for the development of improved CRISPR-based research and biotechnological tools.
    Decentralising geographies of political action: civic tech and placebased municipalism
    Husain, S.O. ; Franklin, Alex ; Roep, D. - \ 2019
    The Journal of Peer Production 2019 (2019)13. - ISSN 2213-5316 - 22 p.
    This article introduces the concept of ‘place-based civic tech’ — citizen engagement technology codesigned by local government, civil society and global volunteers. It investigates to what extent creating such a digital space for autonomous self-organization allows for the emergence of a parallel, self-determining and more place-based geography of politics and political action. It finds that combining online tools with offline collaborative practices presents a unique opportunity for decentralization of power and decision-making in a manner which both politically motivates civil society and begins to update the infrastructure of democracy. The discussion is supported by a combination of primary and secondary data, with research methods including ethnographic and participatory observation techniques. Research data is drawn from a range of empirical sources, including an in-depth case study of the radical municipalist movement in Spain. The article concludes that there is a clear and compelling narrative of cities taking power back, in the form of a plural and globally networked movement. As such, this study contributes to both the theory and practice of civic tech, collective impact, municipalism and place-based urban politics while emphasizing the need for further research on experiments and movements currently existing below the academic radar.
    Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds
    Nunes-Nesi, Adriano ; Alseekh, Saleh ; Oliveira Silva, Franklin Magnum de; Omranian, Nooshin ; Lichtenstein, Gabriel ; Mirnezhad, Mohammad ; González, Roman R.R. ; y Garcia, Julia Sabio ; Conte, Mariana ; Leiss, Kirsten A. ; Klinkhamer, Peter G.L. ; Nikoloski, Zoran ; Carrari, Fernando ; Fernie, Alisdair R. - \ 2019
    Metabolomics 15 (2019)4. - ISSN 1573-3882
    Leaf metabolism - Metabolite network - Metabolite QTL - Tomato

    Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

    Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing
    Koopal, Balwina ; Kruis, Aleksander J. ; Claassens, Nico J. ; Nobrega, Franklin L. ; Oost, John Van Der - \ 2019
    ACS synthetic biology 8 (2019)2. - ISSN 2161-5063 - p. 216 - 222.
    Cas9 - CRISPR-Cas - CRISPRi - gene silencing - synthetic amino acid

    The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoters that regulate the expression of the dcas9 gene. However, as dCas9-mediated gene silencing is very efficient, even slightly leaky dcas9 expression leads to significant background levels of repression of the target gene. In this study, we report on the development of optimized control of dCas9-mediated silencing through additional regulation at the translation level. We have introduced the TAG stop codon in the dcas9 gene in order to insert a synthetic amino acid, l-biphenylalanine (BipA), at a permissive site in the dCas9 protein. In the absence of BipA, a nonfunctional, truncated dCas9 is produced, but when BipA is present, the TAG codon is translated resulting in a functional, full-length dCas9 protein. This synthetic, BipA-containing dCas9 variant (dCas9-BipA) could still fully repress gene transcription. Comparison of silencing mediated by dCas9 to dCas9-BipA revealed a 14-fold reduction in background repression by the latter system. The here developed proof-of-principle system thus reduces unwanted background levels of gene silencing, allowing for tight and timed control of target gene expression.

    Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?
    Tytgat, Hanne L.P. ; Nobrega, Franklin L. ; Oost, John van der; Vos, Willem M. de - \ 2019
    Trends in Microbiology 27 (2019)1. - ISSN 0966-842X - p. 17 - 25.
    biofilm - colorectal cancer - microbiota - tipping points

    Bacterial communities are known to impact human health and disease. Mixed species biofilms, mostly pathogenic in nature, have been observed in dental and gastric infections as well as in intestinal diseases, chronic gut wounds and colon cancer. Apart from the appendix, the presence of thick polymicrobial biofilms in the healthy gut mucosa is still debated. Polymicrobial biofilms containing potential pathogens appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut mucosa. Key biofilm-forming pathogens and associated molecules hold promise as biomarkers. Criteria to distinguish microcolonies from biofilms are crucial to provide clarity when reporting biofilm-related phenomena in health and disease in the gut.

    Molecular and Evolutionary Determinants of Bacteriophage Host Range
    Jonge, Patrick A. de; Nobrega, Franklin L. ; Brouns, Stan J.J. ; Dutilh, Bas E. - \ 2019
    Trends in Microbiology 27 (2019)1. - ISSN 0966-842X - p. 51 - 63.
    bacteriophage - broad-host-range phages - phage therapy - specificity - virus–host interaction

    The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.

    Transportation where people leave: An introduction
    Franklin, Rachel S. ; Leeuwen, Eveline S. van; Paez, Antonio - \ 2018
    In: Advances in Transport Policy and Planning / Franklin, Rachel S., Van Leeuwen, Eveline S., Paez, Antonio, Elsevier B.V. (Advances in Transport Policy and Planning ) - ISBN 9780128154540 - p. 1 - 14.
    Cities - Demographic aging - Exurbia - Population loss - Rural - Suburbia - Transportation

    Transportation means access: to jobs, information, communities, and services. When depopulation occurs a number of questions arise around the central query: what was and will be the role of transportation? This volume engages with several aspects of the depopulation-transportation topic and at multiple geographic scales—from the national and regional to the city- and neighborhood-level. In this chapter, we provide an overview of the challenges associated with population loss and how various aspects of transportation research intersect with these issues. We then summarize the chapters included in this volume, showing how they connect to larger emerging research themes, as well as to each other.

    Carbon storage potential in degraded forests of Kalimantan, Indonesia
    Ferraz, António ; Saatchi, Sassan ; Xu, Liang ; Hagen, Stephen ; Chave, Jerome ; Yu, Yifan ; Meyer, Victoria ; Garcia, Mariano ; Silva, Carlos ; Roswintiart, Orbita ; Samboko, Ari ; Sist, Plinio ; Walker, Sarah ; Pearson, Timothy R.H. ; Wijaya, Arief ; Sullivan, Franklin B. ; Rutishauser, Ervan ; Hoekman, Dirk ; Ganguly, Sangram - \ 2018
    Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
    aboveground biomass mapping - airborne lidar - carbon - forest degradation - Indonesia - Kalimantan - peat swamp forests

    The forests of Kalimantan are under severe pressure from extensive land use activities dominated by logging, palm oil plantations, and peatland fires. To implement the forest moratorium for mitigating greenhouse gas emissions, Indonesia's government requires information on the carbon stored in forests, including intact, degraded, secondary, and peat swamp forests. We developed a hybrid approach of producing a wall-to-wall map of the aboveground biomass (AGB) of intact and degraded forests of Kalimantan at 1 ha grid cells by combining field inventory plots, airborne lidar samples, and satellite radar and optical imagery. More than 110 000 ha of lidar data were acquired to systematically capture variations of forest structure and more than 104 field plots to develop lidar-biomass models. The lidar measurements were converted into biomass using models developed for 66 439 ha of drylands and 44 250 ha of wetland forests. By combining the AGB map with the national land cover map, we found that 22.3 Mha (106 ha) of forest remain on drylands ranging in biomass from 357.2 ±12.3 Mgha-1 in relatively intact forests to 134.2 ±6.1 Mgha-1 in severely degraded forests. The remaining peat swamp forests are heterogeneous in coverage and degradation level, extending over 3.62 Mha and having an average AGB of 211.8 ±12.7 Mgha-1. Emission factors calculated from aboveground biomass only suggest that the carbon storage potential of more than 15 Mha of degraded and secondary dryland forests will be about 1.1 PgC.

    Targeting mechanisms of tailed bacteriophages
    Nobrega, Franklin L. ; Vlot, Marnix ; Jonge, Patrick A. de; Dreesens, Lisa L. ; Beaumont, Hubertus J.E. ; Lavigne, Rob ; Dutilh, Bas E. ; Brouns, Stan J.J. - \ 2018
    Nature Reviews Microbiology 16 (2018). - ISSN 1740-1526 - p. 760 - 773.

    Phages differ substantially in the bacterial hosts that they infect. Their host range is determined by the specific structures that they use to target bacterial cells. Tailed phages use a broad range of receptor-binding proteins, such as tail fibres, tail spikes and the central tail spike, to target their cognate bacterial cell surface receptors. Recent technical advances and new structure–function insights have begun to unravel the molecular mechanisms and temporal dynamics that govern these interactions. Here, we review the current understanding of the targeting machinery and mechanisms of tailed phages. These new insights and approaches pave the way for the application of phages in medicine and biotechnology and enable deeper understanding of their ecology and evolution.

    Complete genome sequences of two T4-like Escherichia coli bacteriophages
    Costa, Ana R. ; Brouns, Stan J.J. ; Nobrega, Franklin L. - \ 2018
    Genome Announcements 6 (2018)26. - ISSN 2169-8287

    Bacteriophages and their proteins have potential applications in biotechnology for the detection and control of bacterial diseases. Here, we describe the sequencing and genome annotations of two strictly virulent Escherichia coli bacteriophages that may be explored for biocontrol strategies and to expand the understanding of phage-host interactions.

    Thirteen decades of antimicrobial copper compounds applied in agriculture. A review
    Lamichhane, Jay Ram ; Osdaghi, Ebrahim ; Behlau, Franklin ; Köhl, Jürgen ; Jones, Jeffrey B. ; Aubertot, Jean Noël - \ 2018
    Agronomy for Sustainable Development 38 (2018)3. - ISSN 1774-0746
    Chemical control - Copper compounds - Crop protection - Organic farming - Pathogen resistance development - Phytotoxicity - Soil accumulation - Sustainable agriculture

    Since the initial use of Bordeaux mixture in 1885 for plant disease control, a large number of copper-based antimicrobial compounds (CBACs) have been developed and applied for crop protection. While these compounds have revolutionized crop protection in the twentieth century, their continuous and frequent use has also raised concerns about the long-term sustainability of copper (Cu)-based crop protection system. Here, we review CBACs used in crop protection and highlight their benefits and risks, and potential for their improvement and opportunities for further research to develop alternatives to CBACs. The major findings are (i) the relatively high toxicity to plant pathogens, low cost, low mammalian toxicity of the fixed Cu compounds, and their chemical stability and prolonged residual effects are major benefits of these compounds; (ii) phytotoxicity, development of copper-resistant strains, soil accumulation, and negative effects on soil biota as well as on food quality parameters are key disadvantages of CBACs; (iii) regulatory pressure in agriculture worldwide to limit the use of CBACs has led to several restrictions, including that imposed by the regulation 473/2002 in the European Union; and (iv) mitigation strategies to limit the negative effects of CBACs include their optimized use, soil remediation, and development and application of alternatives to CBACs for a sustainable crop protection. We conclude that recent research and policy efforts have led to the development of a number of alternatives to CBACs, which should be further intensified to ensure that growers have sufficient tools for the implementation of sustainable crop protection strategies.

    Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation
    Kieper, Sebastian N. ; Almendros, Cristóbal ; Behler, Juliane ; McKenzie, Rebecca E. ; Nobrega, Franklin L. ; Haagsma, Anna C. ; Vink, Jochem N.A. ; Hess, Wolfgang R. ; Brouns, Stan J.J. - \ 2018
    Cell Reports 22 (2018)13. - ISSN 2211-1247 - p. 3377 - 3384.
    Cas4 - CRISPR adaptation - spacer acquisition - type I-D CRISPR-Cas system
    CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Kieper et al. demonstrate that the ubiquitous protein Cas4 assists Cas1 and Cas2 in the selection of new CRISPR spacers with a PAM licensing efficient CRISPR interference.
    Phylogenetic classification of the world's tropical forests
    Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
    Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

    Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

    Introduction to the Alonso’s Five Bells : Insights for Spatial Inequality and Population Decline Special Issue
    Leeuwen, Eveline S. van; Franklin, Rachel S. - \ 2018
    International Regional Science Review 41 (2018)2. - ISSN 0160-0176 - p. 131 - 133.
    For Whom the Bells Toll : Alonso and a Regional Science of Decline
    Franklin, Rachel S. ; Leeuwen, Eveline S. van - \ 2018
    International Regional Science Review 41 (2018)2. - ISSN 0160-0176 - p. 134 - 151.
    population decline - regional science - spatial inequality
    In his presidential address to the Regional Science Association over thirty years ago, William Alonso presented the case for “Five Bell Shapes in Development” and argued that “the developed countries will enter fully in to the realm of the right-hand tail of these curves” (p. 16) and that this transition might result in several surprises. He proposed, therefore, that we should study the right tail of these “curves” as well as interactions among them. Much of what Alonso suggested has come to pass, although his prognostications were not always exact. And although he touched on several issues of relevance to regional scientists, the discipline has been slow to move away from a growth-centered paradigm. The strength of regional science—the capacity to consider economic, demographic, and geographical aspects of an issue simultaneously—has yet to be focused on some of the “right-hand” challenges that have arisen, population loss, for example. In this article, we provide a review of regional science research within the context of Alonso’s five bells and hypothesize how Alonso’s propositions might differ in today’s world. We then focus more specifically on one particular area: population loss. Using these examples allows us to highlight how regional science might contribute to the conceptualization of “right-hand tail” development challenges, especially where theory, issues of spatial scale, and interregional dependencies are concerned.
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