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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    Anthropogenic soils in central Amazonia: farmers’ practices, agrobiodiversity and land-use patterns
    Braga Junqueira, A. - \ 2015
    Wageningen University. Promotor(en): Paul Struik, co-promotor(en): Tjeerd-Jan Stomph; Conny Almekinders; C.R. Clement. - Wageningen : Wageningen University - ISBN 9789462574472 - 163
    antropogene horizonten - bodem - agro-ecologie - biodiversiteit - landgebruik - zwerflandbouw - intensivering - diversificatie - amazonia - anthropogenic horizons - soil - agroecology - biodiversity - land use - shifting cultivation - intensification - diversification - amazonia

    Keywords: Terra Preta; Amazonian Dark Earths; Shifting cultivation; Homegardens; Intensification; Diversification; Smallholder farming.

    André Braga Junqueira (2015). Anthropogenic soils in central Amazonia: farmers’ practices, agrobiodiversity and land-use patterns. PhD thesis, Wageningen University, The Netherlands, with summary in English, 163 pp.

    Rural Amazonia is increasingly experiencing environmental and socio-economic changes that directly affect smallholder farmers, with potential negative effects for environmental quality, agrobiodiversity and livelihoods. In this dynamic context, there is an urgent need to support pathways for smallholder agriculture that guarantee farmers’ economic and food security while maintaining and enhancing ecosystem functions. Amazonian Dark Earths (ADE, or Terra Preta) are anthropogenic soils created by pre-Columbian populations. Due to their high carbon content and enhanced fertility, ADE have been considered models for sustainable agriculture, based on the idea that transforming soils by mimicking some of the properties of ADE would benefit farmers, sequester carbon and reduce pressure on forests. Investigating the current use of ADE and surrounding soils by smallholder farmers allows us to evaluate the relevance of anthropogenic soils and of soil heterogeneity for smallholder farming in Amazonia, and to identify opportunities and constraints associated with the cultivation of fertile soils. The main objective of this thesis is to understand how ADE are understood and cultivated by smallholder farmers in Central Amazonia, and how these soils influence cultivation systems, agrobiodiversity and land-use patterns.

    Ethnographic data indicated that farmers’ understanding of ADE – and of soils in general – is based on their historical and shared knowledge about soil variation across the landscape, on physical attributes of the soil, and mainly on the recognition of different soil-vegetation interactions. A widespread perception about ADE is that these soils are suitable for the cultivation of ‘almost everything’ and always produce decent yields, but they require much more weeding during cultivation. Farmers’ decision-making in shifting cultivation is grounded in this differential understanding of soil-vegetation relationships, and weighed against the labor demands. Soil and vegetation inventories in swiddens used for shifting cultivation showed that the soil fertility gradient between surrounding soils and ADE was associated with more intensive cultivation (shorter fallow periods, shorter and more frequent cultivation cycles, higher labor requirements) and with changes in the crop assemblages, but with similar or larger numbers of species cultivated. In homegardens, vegetation structure and crop diversity were mainly influenced by natural variation in soil texture (homegardens on sandier soils being denser and more diverse), while the soil fertility gradient between ADE and adjacent soils influenced mainly the crop assemblages. At the farm level, the relationship between farmers’ use of ADE and the need to open areas for shifting cultivation was strongly dependent on the labor availability of the household. Instead of driving specific trends in land use, fertile soils are incorporated into local livelihoods as part of an extensive repertoire of resource management activities; most often, farmers with enough available labor manage multiple plots, combining more intensive cultivation on ADE with typical long-fallow shifting cultivation on poorer soils. Farmers’ access to increased soil fertility, therefore, does not necessarily lead to reduced pressure on forests.

    This thesis has shown that cultivation systems on ADE are associated with specific knowledge, practices and agrobiodiversity, providing increased opportunities for farmers to diversify their cultivation systems and grow a greater diversity of crops. Despite these advantages, ADE can also be associated with conventional intensification practices that can lead to environmental degradation and pose threats to local livelihoods. It cannot be assumed, therefore, that the use of more fertile soils will be associated with sustainable cultivation, neither that it will reduce pressure on forests. Initiatives aiming to promote sustainable pathways for agriculture in Amazonia should promote (and make use of) the heterogeneity of soils and of cultivation strategies, and should aim at increasing and not narrowing farmers’ opportunities for resource use and management.

    The butterfly plant arms-race escalated by gene and genome duplications
    Edger, P.P. ; Heidel-Fischer, H.M. ; Bekaert, K.M. ; Rota, J. ; Glockner, G. ; Platts, A.E. ; Heckel, D.G. ; Der, J.P. ; Wafula, E.K. ; Tang, M. ; Hofberger, J.A. ; Smithson, A. ; Hall, J.C. ; Blanchette, M. ; Bureau, T.E. ; Wright, S.I. ; dePamphilis, C.W. ; Schranz, M.E. ; Conant, G.C. ; Barker, M.S. ; Wahlberg, N. ; Vogel, H. ; Pires, J.C. ; Wheat, C.W. - \ 2015
    Proceedings of the National Academy of Sciences of the United States of America 112 (2015)27. - ISSN 0027-8424 - p. 8362 - 8366.
    evolutionaire genetica - co-evolutie - diversificatie - brassica - pieridae - papilionidae - glucosinolaten - fylogenie - evolutionary genetics - coevolution - diversification - brassica - pieridae - papilionidae - glucosinolates - phylogeny - diversity - defense - cytochrome-p450 - polymorphism - arabidopsis - metabolism - expression - speciation
    Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
    A complex interplay of tandem- and whole genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae
    Hofberger, J.A. ; Nsibo, D.L. ; Govers, F. ; Bouwmeester, K. ; Schranz, M.E. - \ 2015
    Genome Biology and Evolution 7 (2015)3. - ISSN 1759-6653 - p. 720 - 734.
    disease resistance genes - arabidopsis-thaliana - phylogenetic analysis - triggered immunity - provides insight - wide analysis - evolution - plants - diversification - expression
    The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding.
    A decade of uncertainty: Resolving the phyologenetic position of Diclinanona (Annonaceae), inlcuding taxonomic notes and a key to the species
    Erkens, R.H.J. ; Chatrou, L.W. ; Chaowasku, T. ; Westra, L.I.T. ; Maas, J.W. ; Maas, P.J.M. - \ 2014
    Taxon 63 (2014)6. - ISSN 0040-0262 - p. 1244 - 1252.
    palms sheds light - historical biogeography - global biogeography - evolution - diversification - speciation - genus - taxa - biodiversity - convergence
    The molecular phylogenetic placement of Diclinanona (Annonaceae) has been debated in the literature for a decade. On the basis of morphological studies the genus was thought to be related to genera now all placed in subfam. Annonoideae. This early hypothesis was supported by the first phylogenetic analyses of Annonaceae. However, more recently a placement in subfam. Malmeoideae was hypothesised based on an analysis of more plastid data, thus contradicting older but also new morphological findings and previous phylogenetic work. The current study uses newly sequenced plastid data for two species of Diclinanona to show that the earlier hypothesised placement was correct and discusses the (little) anatomical and morphological data on Diclinanona that is available in a phylogenetic framework. Furthermore, an online revision of the three species of Diclinanona is presented in order to update the taxonomic knowledge of this genus.
    Genetic divergence and evidence for sympatric host-races in the highly polyphagous brown tail moth, Euproctis chrysorrhoea (Lepidoptera: Erebidae)
    Marques, J.F. ; Wang, H.L. ; Svensson, G.P. ; Frago Clols, E. ; Anderbrant, O. - \ 2014
    Evolutionary Ecology 28 (2014)5. - ISSN 0269-7653 - p. 829 - 848.
    plant-feeding insects - tree arbutus-unedo - evolutionary history - mitochondrial - populations - speciation - refugia - time - diversification - differentiation
    The brown tail moth (BTM) Euproctis chrysorrhoea (Linnaeus 1758) (Lepidoptera: Erebidae) is a forest and ornamental pest in Europe and the United States. Its extreme polyphagy, and documented phenological shift associated with host use suggest the presence of distinct host-races. To test this hypothesis, we sampled BTM infesting different host species in several locations along its distribution, and used DNA sequence data (a total of 1,672 bp from cytochrome c oxidase subunit I, elongation factor 1-alpha, and wingless) to produce haplotype networks and reconstruct the phylogenetic relationships between individuals. Population genetic diversity indices pointed out a higher genetic diversity in Europe, particularly in the samples from southern Spain and southern England. Lower F ST values were found between geographically closer populations when compared to more distant ones, but analyses of molecular variance and Mantel tests failed to reveal geographically associated genetic differentiation. However, haplotype networks and phylogenetic reconstructions revealed a previously unknown genetic differentiation within the BTM, with one lineage circumscribed to southern Europe. Although BTM haplotypes did not cluster according to their host plant, host-associated haplotypes were observed within certain geographic regions. Hence, our data support the existence of host-races of BTM within southern Spain and southern England, where populations from different hosts occur in sympatry.
    Annonaceae substitution rates - a codon model perspective
    Chatrou, L.W. ; Pirie, M.D. ; Velzen, R. van; Bakker, F.T. - \ 2014
    Revista Brasileira de Fruticultura 36 (2014)edição especial, e.. - ISSN 0100-2945 - p. 108 - 117.
    molecular evolution - flowering plants - phylogeny reconstruction - historical biogeography - nucleotide substitution - maximum-likelihood - genera - diversification - characters - patterns
    The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.
    Estimating farmers’ productive and marketing inefficiency: an application to vegetable producers in Benin
    Singbo, A.G. ; Oude Lansink, A.G.J.M. ; Emvalomatis, G. - \ 2014
    Journal of Productivity Analysis 42 (2014)2. - ISSN 0895-562X - p. 157 - 169.
    technical efficiency - distance functions - farming system - diversification - management - growth - impact
    This paper estimates the technical and marketing inefficiency of a sample of urban vegetable producers in Benin. Marketing inefficiency is defined as the failure of farmers to achieve better marketing output and is reflected in lower output price indices. The study proposes a Russell-type measure of inefficiency using a directional distance function that accounts simultaneously for the expansion of outputs and price indices and the contraction of variable inputs. A truncated bootstrap regression is used in the second stage to consistently analyze factors that underlie differences in inefficiency. The first-stage results suggest that vegetable producers are more inefficient with respect to marketing than production. The second-stage results indicate that technical inefficiency is affected by the production environment and private extension services. Marketing inefficiency is affected by the type of marketing arrangements.
    Farming with care: the evolution of care farming in the Netherlands
    Hassink, J. ; Hulsink, W. ; Grin, J. - \ 2014
    NJAS Wageningen Journal of Life Sciences 68 (2014). - ISSN 1573-5214 - p. 1 - 11.
    environmental cooperatives - agriculture - innovation - multifunctionality - diversification - organizations - transition - movements - networks - pathways
    The aim of this paper is to describe and understand the evolution of the care farming sector in one of its pioneering countries, the Netherlands. Care farms combine agricultural production with health and social services. Care farming is a phenomenon that faces specific challenges associated with connecting two different domains. Organizational ecology, social movement theory and the multi-level perspective are helpful concepts in interpreting and contextualizing the developments that have taken place. Organizational ecology explains how the number of care farms, and the legitimacy and diversity of the care farming sector, have increased rapidly over time. Strategic actions of dedicated boundary spanners have played an important role in the development of the sector. Social movement theory explains the impact of collaborative action in the pioneering and later stages. The multi-level perspective explains changes in the care regime, like the introduction of the personal budget of patients and the liberalization of the Dutch health care sector, helping to provide access of foundations of care farms to the collective health insurance for the costs of long-term care. Media exposure, contacts with ministries and politicians and the development of a quality system have contributed to the legitimacy of the sector. Changes in the care regime and collective action promoted a further expansion of the sector and provided direction to the ways the sector developed qualitatively, especially in terms of the emergence of structures aimed at facilitating existing and promoting new care farming practices. Our framework sheds light on changes in agriculture and transsectoral collaboration. Keywords care farming; social movement theory; organizational ecology; multi-level perspective; transition science; multi-functional agriculture
    Towards a new classification system for legumes: Progress report from the 6th International Legume Conference
    Pontes Coelho Borges, L.M. ; Bruneau, A. ; Cardoso, D. ; Crisp, M. ; Delgado-Salinas, A. ; Doyle, J.J. ; Egan, A. ; Herendeen, P.S. ; Hughes, C. ; Kenicer, G. ; Klitgaard, B. ; Koenen, E. ; Lavin, M. ; Lewis, G. ; Luckow, M. ; Mackinder, B. ; Malecot, V. ; Miller, J.T. ; Pennington, R.T. ; Queiroz, L.P. de; Schrire, B. ; Simon, M.F. ; Steele, K. ; Torke, B. ; Wieringa, J.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Estrella, M. de la; Mansano, V.D. ; Prado, D.E. ; Stirton, C. ; Wink, M. - \ 2013
    South African Journal of Botany 89 (2013). - ISSN 0254-6299 - p. 3 - 9.
    caesalpinioid legumes - phylogeny - leguminosae - evolution - diversification - dipsacales - sequences - lineages - gene - rbcl
    Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae, do not adequately represent relationships within the family. The occasion of the Sixth International Legume Conference in Johannesburg, South Africa in January 2013, with its theme "Towards a new classification system for legumes," provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guidelines, and draft classification were presented and debated at the conference. The objectives of the discussion were to develop consensus on the principles that should guide the development of the classification, to discuss the draft classification's strengths and weaknesses and make proposals for its revision, and identify and prioritize phylogenetic deficiencies that must be resolved before the classification could be published. This paper describes the collaborative process by a large group of legume systematists, publishing under the name Legume Phylogeny Working Group, to develop a new phylogenetic classification system for the Leguminosae. The goals of this paper are to inform the broader legume community, and others, of the need for a revised classification, and spell out clearly what the alternatives and challenges are for a new classification system for the family. (C) 2013 SAAB. Published by Elsevier B.V. All rights reserved.
    LysM effectors: secreted proteins supporting fungal life
    Kombrink, A. ; Thomma, B.P.H.J. - \ 2013
    PLoS Pathogens 9 (2013)12. - ISSN 1553-7366 - 4 p.
    chitin-triggered immunity - plant chitinases - virulence factor - pathogen - diversification - recognition - fragments - infection - receptor - binding
    Fishery livelihoods and (non)compliance with fishery regulations - A case study in Ca Mau Province, Mekong Delta, Vietnam
    Ha, T.T.P. ; Dijk, H. van - \ 2013
    Marine Policy 38 (2013). - ISSN 0308-597X - p. 417 - 427.
    climate-change - vulnerability - management - policy - diversification - risk
    Fishery in Ca Mau, Viet Nam’s most southern province in the Mekong Delta, plays locally an important role for human nutrition and has great potentials for export earnings. The overexploitation of inshore fishing resources is a major problem in Viet Nam’s coastal areas along the Mekong Delta. As a result, the Catch per Unit of Effort of small-scale fishing enterprises has decreased, undermining the sustainability of livelihoods of fishing families. The paper focuses on livelihoods’ strategies and diversification in the context of overexploitation and exhaustion of near-shore resources in relation to fishery policies. The results show that overexploitation is unavoidable in near-shore waters because of the lack of enforcement of fishery regulations for offshore vessels and the limitation of alternative sources of income and opportunities for livelihood diversification for small-scale fishers. The present policies to prevent overexploitation need to be reconciled with livelihood sustainability and fishery management, resource conservation and socio-economic goals
    Livelihood strategies in settlement projects in the Brazilian Amazon: Determining drivers and factors within the Agrarian Reform Program.
    Diniz, F.H. ; Hoogstra, M.A. ; Kok, K. ; Arts, B.J.M. - \ 2013
    Journal of Rural Studies 32 (2013). - ISSN 0743-0167 - p. 196 - 207.
    farm-level evidence - land-use patterns - climate-change - deforestation - cattle - diversification - colonists - dynamics - frontier - policies
    Over the last decades, hundreds of thousands of families have settled in the Brazilian Amazon within the framework of the Agrarian Reform Program (ARP). The rationale behind the program is to enable settlers to earn their living by small-scale farming and producing an agricultural surplus for the market. This paper aims to analyze the settlers' livelihood strategies under the framework of the ARP and its objectives. The paper considers more than just land use shares. Income composition, capital (human, physical, natural, social, and financial), mediating process, and context are also included, and these reveal three groups of livelihood strategies. Most of the settlers have achieved the ARP goals, mainly by deploying livestock strategies, particularly milk production
    Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in Madagascar
    Crottinia, A. ; Madsen, O. ; Poux, C. ; Straussa, A. ; Vieites, D.R. ; Vences, M. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)14. - ISSN 0027-8424 - p. 5358 - 5363.
    species richness - ocean currents - dispersal - diversification - divergence - hypothesis - vicariance - phylogeny - evolution - radiation
    The geographic and temporal origins of Madagascar's biota have long been in the center of debate. We reconstructed a time-tree including nearly all native nonflying and nonmarine vertebrate clades present on the island, from DNA sequences of two single-copy protein-coding nuclear genes (BDNF and RAG1) and a set of congruent time constraints. Reconstructions calculated with autocorrelated or independent substitution rates over clades agreed in placing the origins of the 31 included clades in Cretaceous to Cenozoic times. The two clades with sister groups in South America were the oldest, followed by those of a putative Asian ancestry that were significantly older than the prevalent clades of African ancestry. No colonizations from Asia occurred after the Eocene, suggesting that dispersal and vicariance of Asian/Indian groups were favored over a comparatively short period during, and shortly after, the separation of India and Madagascar. Species richness of clades correlates with their age but those clades that have a large proportion of species diversity in rainforests are significantly more species-rich. This finding suggests an underlying pattern of continuous speciation through time in Madagascar's vertebrates, with accelerated episodes of adaptive diversification in those clades that succeeded radiating into the rainforests.
    Care Farms in the Netherlands: An Underexplored Example of Multifunctional Agriculture—Toward an Empirically Grounded, Organization-Theory-Based Typology
    Hassink, J. ; Hulsink, W. ; Grin, J. - \ 2012
    Rural Sociology 77 (2012)4. - ISSN 0036-0112 - p. 569 - 600.
    rural-development - diversification - configurations - pluriactivity - strategy - arrangements - integration - management - resources - pathways
    For agricultural and rural development in Europe, multifunctionality is a leading concept that raises many questions. Care farming is a promising example of multifunctional agriculture that has so far received little attention. An issue that has not been examined thoroughly is the strategic mapping of different care farm organizations in this emerging field. The objective of this article is to develop a typology for care farms in the Netherlands and provide insight into the diversity of care farms. We have used different concepts from organization theory and information from regional organizations of care farmers to identify key dimensions and develop a typology of care farms. Key dimensions are the ratio between agriculture and care, the background of the initiators, and the degree of collaboration with formal care institutions. We found six main types of care farms with different identities, four of which were initiated by the farmers' families (mainly female partners). The other two types were started by new entrants in agriculture. On the basis of our findings, we confirmed, disputed, and supplemented insights to multifunctional farming literature. As a further contribution to that field, drawing from the organization theories underlying our typology, we have sought to understand how different types of care farms could emerge.
    Exploring opportunities for diversification of specialized tobacco farms in the Northwest of Argentina
    Chavez Clemente, M.D. - \ 2012
    Wageningen University. Promotor(en): Alfons Oude Lansink, co-promotor(en): Paul Berentsen. - S.l. : s.n. - ISBN 9789461734204 - 161
    tabak - gespecialiseerde landbouw - gewasproductie - landbouwbedrijven - diversificatie - specialisatie - inkomen - risico - bodemdegradatie - argentinië - tobacco - specialized farming - crop production - farms - diversification - specialization - income - risk - soil degradation - argentina
    In the Northwest of Argentina tobacco (Nicotiana tabacum L.) is economically and socially important. Tobacco mono-cropping, excessive tillage and inadequate irrigation management cause soil degradation. This and also tobacco production dependence on government subsidies and concern about health damage from tobacco consumption calls for research on diversification. The aim of this thesis was to explore opportunities for diversification of specialized tobacco farms in the Northwest of Argentina.
    Institutions in the Mexican coffee sector : changes and responses
    Rodriguez Padron, B. - \ 2012
    Wageningen University. Promotor(en): Erwin Bulte; Ruerd Ruben, co-promotor(en): Kees Burger. - [S.l.] : s.n. - ISBN 9789461734181 - 201
    instellingen - institutionele economie - mexico - koffie - landbouwsector - verandering - samenwerking - contracten - diversificatie - onzekerheid - markten - markthandelaars - institutions - institutional economics - mexico - coffee - agricultural sector - change - cooperation - contracts - diversification - uncertainty - markets - market traders

    Keywords: Cooperation, contract arrangements, traders´ performance, market uncertainty, diversification, coffee, Mexico.

    The main aim of this thesis is to investigate the institutional environment prevailing in the Mexican coffee sector and its effect on the producers, traders and households. Specific topics we examine are the contract arrangements and trade performance, the factors influencing the growers´ willingness to join a cooperative, the effects of cooperation on price variability, the influence of cooperation on the growers’ welfare, and coffee producers’ response to the falling coffee price through their engagement in diversification activities. To accomplish the main objectives we have used primary and secondary data. We applied ordinarily least squares, logistic, probit and multivariate probit regressions in the analysis. The main findings indicate that farmers were better off under the quota system than they are under the free market. Results also indicate that being a roaster and selling cherry coffee negatively affects traders’ use of contracts, whereas being vertically integrated has a positive effect on contracting. On the other hand, selling cherry coffee, participating in a competitive environment and having contracts positively influence intermediaries’ performance. Other results show that some individual, family and farm factors, as well as variability of the coffee price at the municipal level favour cooperative affiliation; whereas housing conditions, the proportion of farmers in the municipality and the level of producers selling to intermediaries at the municipal level negatively affect prospects for cooperative membership. We discovered overall positive effects of cooperative participation on household welfare through an increase in the price and total coffee income; results also indicate that households responded to the low coffee price periods with an increase in diversification.

    The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
    Hont, A. D'; Denoeud, F. ; Aury, J.M. ; Kema, G.H.J. ; Dita Rodriguez, M.A. ; Waalwijk, C. - \ 2012
    Nature 488 (2012). - ISSN 0028-0836 - p. 213 - 217.
    in-situ hybridization - sequence count data - dna-sequences - differential expression - maximum-likelihood - gene - rice - diversification - identification - resource
    Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3, 4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence
    The tomato genome sequence provides insights into fleshy fruit evolution
    Sato, S. ; Tabata, S. ; Hirakawa, H. ; Klein Lankhorst, R.M. ; Jong, H. de; Ham, R.C.H.J. van; Datema, E. ; Smit, S. ; Schijlen, E.G.W.M. ; Haarst, J.C. van; Peters, S.A. ; Henkens, M.H.C. ; Staveren, M.J. van; Mooijman, P.J.W. ; Hesselink, T. ; Belt, J. van de; Szinay, D. ; Bai, Y. ; Visser, R.G.F. - \ 2012
    Nature 485 (2012). - ISSN 0028-0836 - p. 635 - 641.
    lycopersicon-esculentum - gene - diversification - arabidopsis - patterns - ortholog - history - sorghum - potato
    Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
    Scenarios of long-term farm structural change for application in climate change impact assessment
    Mandryk, M. ; Reidsma, P. ; Ittersum, M.K. van - \ 2012
    Landscape Ecology 27 (2012)4. - ISSN 0921-2973 - p. 509 - 527.
    klimaatadaptatie - klimaatverandering - landbouw - structurele verandering - agrarische bedrijfsvoering - bedrijfsstructuur in de landbouw - scenario-analyse - flevoland - nederland - climate adaptation - climatic change - agriculture - structural change - farm management - farm structure - scenario analysis - flevoland - netherlands - agricultural land-use - future - policy - adaptation - diversification - vulnerability - productivity - consequences - variability - performance
    Towards 2050, climate change is one of the possible drivers that will change the farming landscape, but market, policy and technological development may be at least equally important. In the last decade, many studies assessed impacts of climate change and specific adaptation strategies. However, adaptation to climate change must be considered in the context of other driving forces that will cause farms of the future to look differently from today’s farms. In this paper we use a historical analysis of the influence of different drivers on farm structure, complemented with literature and stakeholder consultations, to assess future structural change of farms in a region under different plausible futures. As climate change is one of the drivers considered, this study thus puts climate change impact and adaptation into the context of other drivers. The province of Flevoland in the north of The Netherlands was used as case study, with arable farming as the main activity. To account for the heterogeneity of farms and to indicate possible directions of farm structural change, a farm typology was developed. Trends in past developments in farm types were analyzed with data from the Dutch agricultural census. The historical analysis allowed to detect the relative importance of driving forces that contributed to farm structural changes. Simultaneously, scenario assumptions about changes in these driving forces elaborated at global and European levels, were downscaled for Flevoland, to regional and farm type level in order to project impacts of drivers on farm structural change towards 2050. Input from stakeholders was also used to detail the downscaled scenarios and to derive historical and future relationships between drivers and farm structural change. These downscaled scenarios and future driver-farm structural change relationships were used to derive quantitative estimations of farm structural change at regional and farm type level in Flevoland. In addition, stakeholder input was used to also derive images of future farms in Flevoland. The estimated farm structural changes differed substantially between the two scenarios. Our estimations of farm structural change provide a proper context for assessing impacts of and adaptation to climate change in 2050 at crop and farm level
    Multifunctionele landbouw in Nederland : meer dan boeren alleen
    Kierkels, T. ; Ypma, T. ; Kars, J. ; Veen, E.J. ; Vijn, M.P. ; Elings, M. ; Oostindië, H.A. ; Methorst, R.G. ; Winter, M.A. de; Engelsma, K.A. ; Kempenaar, J. ; Visser, A.J. ; Alebeek, F.A.N. van - \ 2012
    Zutphen : Roodbont - ISBN 9789087401184 - 140
    multifunctionele landbouw - inkomsten van buiten het landbouwbedrijf - ondernemerschap - diversificatie - boerderijwinkels - zorgboerderijen - boerderijeducatie - dagopvang - agrarisch natuurbeheer - boerderijtoerisme - multifunctional agriculture - non-farm income - entrepreneurship - diversification - on-farm sales - social care farms - farm education - day care - agri-environment schemes - farm tourism
    Multifunctionele landbouw combineert verschillende functies op het boerenbedrijf: een agrarische tak met bijvoorbeeld huisverkoop of zorglandbouw. Inmiddels vormt de sector met bijna een half miljard euro omzet, die vergelijkbaar is met de bollensector, een sterke economische drager van het platteland. In het boek komen thema’s aan bod als economie, ondernemerschap, verbinding, vers voedsel en beleving. Verder worden de belangrijkste deelsectoren belicht: kinderopvang, boerderijverkoop, zorglandbouw, agrarisch natuurbeheer, recreatie/toerisme en boerderij-educatie. In tien ‘dubbelportretten’ komen mensen aan het woord die via de multifunctionele landbouw met elkaar in verbinding staan, zoals gastvrouw en gast, leverancier en verwerker, educatieboerin en docent.
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