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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Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
A Study of Pig Chromosome X lncRNA Expression
Djebali, S. ; Palasca, O. ; Anthon, C. ; Derrien, T. ; Madsen, O. ; Thomas, M. ; Floden, E. ; Havgaard, J.H. ; Seemann, S.E. ; Gonzales, J.M. ; Junge, A. ; Pacholewska, A. ; Billis, K. ; Alkan, F. ; Eory, L. ; Amaral, A. ; Prieto Barja, P. ; Stadler, P.F. ; Notredame, C. ; Groenen, M. ; Harrow, J. ; Gorodkin, J. - \ 2017
What do we know about the ecological impacts of microplastic debris?
Rochman, Chelsea M. ; Browne, M.A. ; Underwood, A.J. ; Franeker, J.A. van; Thompson, R. ; Amaral-Zettler, Linda A. - \ 2016
Evaluating strategies for honey value chains in Brazil using a value chain structure-conduct-performance (SCP) framework
Santana de Figueiredo Junior, Hugo ; Meuwissen, Miranda P.M. ; Amaral Filho, Jair do; Oude Lansink, Alfons - \ 2016
International Food and Agribusiness Management Review 19 (2016)3. - ISSN 1096-7508 - p. 225 - 250.
Beekeeping - Economic development - Interventions - Supply chains

Development organizations have used value chain analysis in defining interventions for the honey business in major exporting countries like Brazil. Yet, the impact of interventions has been unclear. This paper aims at evaluating strategies of three honey value chain streams in Brazil, selected for a multiple case study between the years 2007-2011.Using the value chain Structure-Conduct-Performance (SCP) framework, likely successful strategies are identified by comparing stream performances. Next, the outcomes of this comparison are validated through questionnaires with experts. Understanding current stream strategies and local structural conditions, and fostering well-aligned strategies are found to be key for successful donor interventions.

Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: implications for dynamic global vegetation models
Johnson, Michelle O. ; Galbraith, David ; Gloor, Manuel ; Deurwaerder, Hannes De; Guimberteau, Matthieu ; Rammig, Anja ; Thonicke, Kirsten ; Verbeeck, Hans ; Randow, Celso Von; Monteagudo, Abel ; Phillips, Oliver L. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Lopez Gonzalez, Gabriela ; Fauset, Sophie ; Quesada, Carlos A. ; Christoffersen, Bradley ; Ciais, Philippe ; Sampaio, Gilvan ; Kruijt, Bart ; Meir, Patrick ; Moorcroft, Paul ; Zhang, Ke ; Alvarez-Davila, Esteban ; Alves De Oliveira, Atila ; Amaral, Ieda ; Andrade, Ana ; Aragao, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Aymard, Gerardo A. ; Baraloto, Christopher ; Barroso, Jocely ; Bonal, Damien ; Boot, Rene ; Camargo, Jose ; Chave, Jerome ; Cogollo, Alvaro ; Cornejo Valverde, Fernando ; Lola Da Costa, Antonio C. ; Fiore, Anthony Di; Ferreira, Leandro ; Higuchi, Niro ; Honorio, Euridice N. ; Killeen, Tim J. ; Laurance, Susan G. ; Laurance, William F. ; Licona, Juan ; Lovejoy, Thomas ; Malhi, Yadvinder ; Marimon, Bia ; Marimon, Ben Hur ; Matos, Darley C.L. ; Mendoza, Casimiro ; Neill, David A. ; Pardo, Guido ; Peña-Claros, Marielos ; Pitman, Nigel C.A. ; Poorter, Lourens ; Prieto, Adriana ; Ramirez-Angulo, Hirma ; Roopsind, Anand ; Rudas, Agustin ; Salomao, Rafael P. ; Silveira, Marcos ; Stropp, Juliana ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Toledo, Marisol ; Torres-Lezama, Armando ; Heijden, Geertje M.F. van der; Vasquez, Rodolfo ; Guimarães Vieira, Ima Cèlia ; Vilanova, Emilio ; Vos, Vincent A. ; Baker, Timothy R. - \ 2016
Global Change Biology 22 (2016)12. - ISSN 1354-1013 - p. 3996 - 4013.
Understanding the processes that determine aboveground biomass (AGB) in Amazonian forests is important for predicting the sensitivity of these ecosystems to environmental change and for designing and evaluating dynamic global vegetation models (DGVMs). AGB is determined by inputs from woody productivity (woody NPP) and the rate at which carbon is lost through tree mortality. Here, we test whether two direct metrics of tree mortality (the absolute rate of woody biomass loss and the rate of stem mortality) and/or woody NPP, control variation in AGB among 167 plots in intact forest across Amazonia. We then compare these relationships and the observed variation in AGB and woody NPP with the predictions of four DGVMs. The observations show that stem mortality rates, rather than absolute rates of woody biomass loss, are the most important predictor of AGB, which is consistent with the importance of stand size-structure for determining spatial variation in AGB. The relationship between stem mortality rates and AGB varies among different regions of Amazonia, indicating that variation in wood density and height/diameter relationships also influence AGB. In contrast to previous findings, we find that woody NPP is not correlated with stem mortality rates, and is weakly positively correlated with AGB. Across the four models, basin-wide average AGB is similar to the mean of the observations. However, the models consistently overestimate woody NPP, and poorly represent the spatial patterns of both AGB and woody NPP estimated using plot data. In marked contrast to the observations, DGVMs typically show strong positive relationships between woody NPP and AGB. Resolving these differences will require incorporating forest size structure, mechanistic models of stem mortality and variation in functional composition in DGVMs
The ecological impacts of marine debris : Unraveling the demonstrated evidence from what is perceived
Rochman, Chelsea M. ; Browne, Mark Anthony ; Underwood, A.J. ; Franeker, Jan A. Van; Thompson, Richard C. ; Amaral-Zettler, Linda A. - \ 2016
Ecology 97 (2016)2. - ISSN 0012-9658 - p. 302 - 312.
Assemblage - Biological organization - Ecology - Plastic debris - Population - Systematic review

Anthropogenic debris contaminates marine habitats globally, leading to several perceived ecological impacts. Here, we critically and systematically review the literature regarding impacts of debris from several scientific fields to understand the weight of evidence regarding the ecological impacts of marine debris. We quantified perceived and demonstrated impacts across several levels of biological organization that make up the ecosystem and found 366 perceived threats of debris across all levels. Two hundred and ninety-six of these perceived threats were tested, 83% of which were demonstrated. The majority (82%) of demonstrated impacts were due to plastic, relative to other materials (e.g., metals, glass) and largely (89%) at suborganismal levels (e.g., molecular, cellular, tissue). The remaining impacts, demonstrated at higher levels of organization (i.e., death to individual organisms, changes in assemblages), were largely due to plastic marine debris (>1 mm; e.g., rope, straws, and fragments). Thus, we show evidence of ecological impacts from marine debris, but conclude that the quantity and quality of research requires improvement to allow the risk of ecological impacts of marine debris to be determined with precision. Still, our systematic review suggests that sufficient evidence exists for decision makers to begin to mitigate problematic plastic debris now, to avoid risk of irreversible harm.

Limited carbon and biodiversity co-benefits for tropical forest mammals and birds
Beaudrot, L. ; Kroetz, K. ; Alvarez-Loayza, P. ; Amaral, I. ; Breuer, T. ; Fletcher, C.D. ; Jansen, P.A. ; Kenfack, D. ; Andelman, S. - \ 2016
Ecological Applications 26 (2016)4. - ISSN 1051-0761 - p. 1098 - 1111.
The conservation of tropical forest carbon stocks offers the opportunity to curb climate change by reducing greenhouse gas emissions from deforestation and simultaneously conserve biodiversity. However, there has been considerable debate about the extent to which carbon storage will provide benefits to biodiversity in part because whether forests that contain high carbon density in their aboveground biomass also contain high animal diversity is unknown. Here, we empirically examined medium to large bodied ground-dwelling mammal and bird (hereafter "ground-dwelling endotherm") diversity and carbon stock levels within the tropics using camera trap and vegetation data from a pantropical network of sites. Specifically, we tested whether tropical forests that stored more carbon contained higher ground-dwelling endotherm species richness, taxonomic diversity and trait diversity. We found that carbon storage was not a significant predictor for any of these three measures of diversity, which suggests that benefits for ground-dwelling endotherm diversity will not be maximized unless endotherm diversity is explicitly taken into account; prioritizing carbon storage alone will not necessarily meet biodiversity conservation goals. We recommend conservation planning that considers both objectives because there is the potential for more terrestrial endotherm diversity and carbon storage to be achieved for the same total budget if both objectives are pursued in tandem rather than independently. Tropical forests with low elevation variability and low tree density supported significantly higher ground-dwelling endotherm diversity. These tropical forest characteristics may provide more affordable proxies of ground-dwelling endotherm diversity for future multi-objective conservation planning when fine scale data on wildlife are lacking.
Phylogenetic diversity of Amazonian tree communities
Honorio Coronado, E.N. ; Dexter, K.G. ; Pennington, R.T. ; Chave, Jérôme ; Lewis, S.L. ; Alexiades, M.N. ; Alvarez, Esteban ; Alves de Oliveira, Atila ; Amaral, J.L. ; Araujo-Murakami, Alejandro ; Arets, E.J.M.M. - \ 2015
Diversity and Distributions 21 (2015)11. - ISSN 1366-9516 - p. 1295 - 1307.
Amazon basin - Eudicots - Magnoliids - Monocots - Phylogenetic diversity - Species richness

Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.

Expression studies in the embryo and in the micropylar endosperm of germinating coffee (Coffea arabica cv. Rubi) seeds
Farias, E.T. de; Amaral da Silva, E.A. ; Toorop, P.E. ; Bewley, J.D. ; Hilhorst, H.W.M. - \ 2015
Plant Growth Regulation 75 (2015)2. - ISSN 0167-6903 - p. 575 - 581.
beta-mannanase - growth - purification - cloning
Germination of coffee (Coffea arabica L.) seed is slow and uneven. Its germination is the net result of events that occur simultaneously in the embryo and endosperm and which are controlled by abscisic acid (ABA). The aim of the study was to monitor the expression of genes related to the cell cycle and to cell wall modifications, including an actin (ACT), a cyclin-dependent kinase (CDK2a) and a-expansin (a-EXP) in the embryo, and a-galactosidase (a-GAL), ß-mannosidase (LeMSIDE2), endo-ß-mannanase (MANA) in the micropylar endosperm. The first seed germinated after 5 days of imbibition and 50 % germination was reached after 10 days. The embryo grew inside the seed prior to radicle protrusion and ABA inhibited both embryo growth and radicle protrusion. The expression of the genes associated with the embryo growth increased during germination and ABA partially inhibited expression. The expression of ß-mannosidase and endo-ß-mannanase increased during imbibition and ABA completely inhibited expression of these genes. However, a-galactosidase displayed a more constitutive expression and was less affected by ABA. ABA plays a dual role in the regulation of coffee seed germination; it concomitantly controls both endosperm weakening and embryo growth.
Transmission of Xanthomonas campestris pv. campestris in seed production crops of cauliflower
Kastelein, P. ; Krijger, M.C. ; Zouwen, P.S. van der; Steen, J.J.M. van der; Stevens, L.H. ; Wolf, J.M. van der; Fernandes Vieira, J. ; Amaral Villela, F. - \ 2014
In: Proceedings of the IInd International Symposium on Organic Greenhouse Horticulture. - Leuven, Belgium : ISHS - ISBN 9789462610309 - p. 197 - 2014.
n 2011, two polytunnel greenhouse experiments were conducted on seed production farms, one under conventional conditions in the South-West (Rilland) and the other under organic conditions in the East (Voorst) of the Netherlands, to study transmission routes of Xanthomonas campestris pv. campestris (Xcc), that can result in seed infections of cauliflower plants (Brassica oleracea var. botrytis). Each experiment consisted of three plots. Before head formation, plants in the two outside plots were spray-inoculated with either Xcc strain IPO 3076 or IPO 3078, and plants in the central plot were sprayed with water. A colony of honeybees (Apis mellifera) was placed in each tunnel to provide pollination. At Rilland, incidences of black rot were low, and seed infections were not detected in a plating assay, although peduncles were infected in a high percentage of the plants. At Voorst, black rot symptoms developed in almost all Xcc-inoculated plants, resulting in plant losses. The incidence of plants with infected seeds in the plot inoculated with Xcc IPO 3076 was higher than in the two other plots. Identification of Xcc isolates by BOX-PCR revealed that Xcc IPO 3076 was transmitted to the other plots of the experiment. Xcc IPO 3078, however, was only recovered from plants inoculated with this strain. The routes of seed infection for Xcc and then transmission of the pathogen are discussed
Phylogenetics, ancestral state reconstruction, and a new infrafamilial classification of the pantropical Ochnaceae (Medusagynaceae, Ochnaceae s.str., Quiinaceae) based on five DNA regions
Schneider, J.V. ; Bissiengou, P. ; Amaral, M.D. ; Tahir, A. ; Fay, M.F. ; Thines, M. ; Sosef, M.S.M. ; Zizka, G. ; Chatrou, L.W. - \ 2014
Molecular Phylogenetics and Evolution 78 (2014)20. - ISSN 1055-7903 - p. 199 - 214.
chain monte-carlo - angiosperm phylogeny - venezuelan guayana - matk sequences - malpighiales - evolution - morphology - inference - systematics - taxa
Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.
Gomphrena claussenii, the first South-American metallophyte species with indicator-like Zn and Cd accumulation and extreme metal tolerance
Tomaz Villafort Carvalho, M. ; Amaral, D.C. ; Guilherme, L.R. ; Aarts, M.G.M. - \ 2013
Frontiers in Plant Science 4 (2013). - ISSN 1664-462X - 10 p.
sedum-alfredii hance - hyperaccumulator thlaspi-caerulescens - arabidopsis-thaliana - molecular-mechanisms - copper tolerance - zinc tolerance - plants - cadmium - soils - phytoremediation
Plant species with the capacity to tolerate heavy metals are potentially useful for phytoremediation since they have adapted to survive and reproduce under toxic conditions and to accumulate high metal concentrations. Gomphrena claussenii Moq., a South-American species belonging to the Amaranthaceae, is found at a zinc (Zn) mining area in the state of Minas Gerais, Brazil. Through soil and hydroponic experiments, the metal tolerance and accumulation capacities of G. claussenii were assessed and the effects on physiological characteristics were compared with a closely related non-tolerant species, G. elegans Mart. G. claussenii plants grown in soil sampled at the Zn smelting area accumulated up to 5318µgg-1 of Zn and 287 µg g-1 of cadmium (Cd) in shoot dry biomass after 30 days of exposure. Plants were grown in hydroponics containing up to 3000 µM of Zn and 100 µM of Cd for G. claussenii and 100 µM of Zn and 5 µM of Cd for G. elegans. G. claussenii proved to be an extremely tolerant species to both Zn and Cd, showing only slight metal toxicity symptoms at the highest treatment levels, without significant decrease in biomass and no effects on root growth, whereas the non-tolerant species G. elegans showed significant toxicity effects at the highest exposure levels. Both species accumulated more Zn and Cd in roots than in shoots. In G. elegans, over 90% of the Cd remained in the roots, but G. claussenii showed a root:shoot concentration ratio of around 2, with shoots reaching 0.93% Zn and 0.13% Cd on dry matter base. In G. claussenii shoots, the concentrations of other minerals, such as iron (Fe) and manganese (Mn), were only affected by the highest Zn treatment while in G. elegans the Fe and Mn concentrations in shoots decreased drastically at both Zn and Cd treatments. Taking together, these results indicate that G. claussenii is a novel metallophyte, extremely tolerant of high Zn and Cd exposure and an interesting species for further phytoremediation studies Keywords: phytoremediation, Zn/Cd hypertolerance, hyperaccumulation, metal contamination, Gomphrena claussenii, Gomphrena elegans
Large trees drive forest aboveground biomass variation in moist lowland forests across the tropics
Slik, J.W.F. ; Paoli, G. ; McGuire, K. ; Amaral, I. ; Barroso, J. ; Bongers, F. ; Poorter, L. - \ 2013
Global Ecology and Biogeography 22 (2013)12. - ISSN 1466-822X - p. 1261 - 1271.
rain-forest - wood density - species composition - spatial-patterns - landscape-scale - carbon stocks - amazon - diversity - climate - monodominance
Aim - Large trees (d.b.h.¿=¿70¿cm) store large amounts of biomass. Several studies suggest that large trees may be vulnerable to changing climate, potentially leading to declining forest biomass storage. Here we determine the importance of large trees for tropical forest biomass storage and explore which intrinsic (species trait) and extrinsic (environment) variables are associated with the density of large trees and forest biomass at continental and pan-tropical scales. Location - Pan-tropical. Methods - Aboveground biomass (AGB) was calculated for 120 intact lowland moist forest locations. Linear regression was used to calculate variation in AGB explained by the density of large trees. Akaike information criterion weights (AICc-wi) were used to calculate averaged correlation coefficients for all possible multiple regression models between AGB/density of large trees and environmental and species trait variables correcting for spatial autocorrelation. Results - Density of large trees explained c. 70% of the variation in pan-tropical AGB and was also responsible for significantly lower AGB in Neotropical [287.8 (mean)¿±¿105.0 (SD) Mg ha-1] versus Palaeotropical forests (Africa 418.3¿±¿91.8 Mg ha-1; Asia 393.3¿±¿109.3 Mg ha-1). Pan-tropical variation in density of large trees and AGB was associated with soil coarseness (negative), soil fertility (positive), community wood density (positive) and dominance of wind dispersed species (positive), temperature in the coldest month (negative), temperature in the warmest month (negative) and rainfall in the wettest month (positive), but results were not always consistent among continents. Main conclusions - Density of large trees and AGB were significantly associated with climatic variables, indicating that climate change will affect tropical forest biomass storage. Species trait composition will interact with these future biomass changes as they are also affected by a warmer climate. Given the importance of large trees for variation in AGB across the tropics, and their sensitivity to climate change, we emphasize the need for in-depth analyses of the community dynamics of large trees
Global Optimization Simplex Bisection Revisited Based on Considerations by Reiner Horst
Hendrix, E.M.T. ; Casado, L.G. ; Amaral, P. - \ 2012
In: Proceedings of the 12th International Conference, 18-21 June 2012, Salvador de Bahia, Brazil, Proceedings Part III / Murgante, B., Osvaldo, G., Misra, S., Heidelberg : Springer (Lecture Notes in Computer Science ) - ISBN 9783642311376 - p. 159 - 173.
In this paper, the use of non-optimality spheres in a simplicial branch and bound (B&B) algorithm is investigated. In this context, some considerations regarding the use of bisection on the longest edge in relation with ideas of Reiner Horst are reminded. Three arguments highlight the merits of bisection of simplicial subsets in B&B schemes.
Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Amaral, A.J. ; Ferretti, L. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Nie, H. ; Ramos-Onsins, S.E. ; Perez-Enciso, M. ; Schook, L.B. ; Groenen, M.A.M. - \ 2011
PLoS One 6 (2011)4. - ISSN 1932-6203 - 12 p.
major histocompatibility complex - recent positive selection - class-i region - linkage disequilibrium - genetic diversity - breeds - generation - signatures - chimpanzee - mutation
Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.
The Porcine HapMap Project: Genome-Wide Assessment Of Nucleotide Diversity, Haplotype Diversity And Footprints Of Selection In The Pig
Groenen, M.A.M. ; Amaral, A.J. ; Megens, H.J.W.C. ; Larson, B.A. ; Archibald, A.L. ; Muir, W.M. ; Malhi, Y. ; Crooijmans, R.P.M.A. ; Ferretti, L. ; Perez-Encizo, M. ; Schook, L.B. - \ 2010
In: Book of Abstracts of the Plant and Animal Genome XVIII Conference, San Diego, California, USA, 9-13 Januari 2010. - - p. w609 - w609.
The Porcine HapMap Consortium The pig has a complex and long history of domestication and breed formation and has been domesticated independently multiple times and has likely experienced introgression of local Wild boar after the spread of agriculture. Using the Illumina GA sequencing platform thousand s of SNPs were identified in the porcine genome and used these to develop the Illumin porcine 60K iSelect Beadchip. This chip has enabled whole-genome characterization of linkage disequilibrium and haplotype structure in commercial and local breeds and comparison with the Wild boar. The chip has also allowed an investigation into whole-genome patterns of variation, including signatures of selection associated with domestication and breed formation as well as elucidating demographic events such as population bottlenecks, and providing insights into the complex origin of domesticated populations by examining patterns of haplotype sharing. Signatures of selection were also identified using Illumina short read sequences generated from pooled reduced representation libraries of different breeds and covering approximately 2% of the genome. Signals of positive selection were identified and a GO term/KEGG pathway enrichment analysis provided evidence for specific gene families under selection in domesticated pigs and Wild boar. Currently approximately 2,000 pigs were been genotyped with the porcine 60K beadchip, including approximatley 50 pig breeds, and about 20 different Wild boar populations distributed throughout Eurasia. In addition, museum and archeological samples were included to provide a wider insight into domestication and geographic history. Inclusion of a range of other Suidae as outgroup species, supported an estimation of ancestral alleles and the origin and relative age of the porcine SNPs.
Nucleotide variation and footprints of selection in the porcine and chicken genomes
Amaral, A.J. - \ 2010
University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Henri Heuven. - [S.l. : S.n. - ISBN 9789085856559 - 160 p.
varkens - kippen - genomen - nucleotiden - genetische diversiteit - kunstmatige selectie - selectief fokken - rassen (dieren) - genetica - pigs - fowls - genomes - nucleotides - genetic diversity - artificial selection - selective breeding - breeds - genetics
Finding selection footprints in the swine genome using massive parallel sequencing.
Amaral, A.J. ; Feretti, L. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Nie, H. ; Groenen, M.A.M. - \ 2009
We investigated whether selection footprints can be identified from GA (Genome analyzer) sequences generated from pooled Reduced Representation Libraries and covering approximately 2% of the genome of Large White, Landrace, Pietrain, Duroc and Wild Boar. Methods were developed to estimate Nucleotide Diversity (ND) considering that, GA sequences were obtained from pooled DNA, singletons were removed and the sequencing error rate. The average ND ranged from 0.0008 to 0.002 depending on chromosome and breed. Genomic locations that have been, putatively, under selection were identified. We found signals of positive selection on SSC8 in the region containing the KIT gene, for white breeds but not for Duroc and Wild Boar. Signals of balancing selection were found for regions on SSC7 containing genes from the MHC complex and from the olfactory receptors complex. Enrichment analysis of KEGG-pathways showed that for regions under positive selection, swine breeds showed higher enrichment of pathways related to growth whereas Wild Boar showed higher enrichment of pathways related to immunity and robustness. Balancing selection resulted in the significant enrichment of pathways related to the olfactory receptors activities in all swine breeds and Wild Boar. Our results raise the possibility of using GA sequencing of pools for identification of selection footprints and present the first global map of regions under selection in the swine genome
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology
Ramos, A. ; Crooijmans, R.P.M.A. ; Affara, N.A. ; Amaral, A.J. ; Kerstens, H.H.D. ; Megens, H.J.W.C. ; Groenen, M.A.M. - \ 2009
PLoS One 4 (2009)8. - ISSN 1932-6203 - 13 p.
Background: The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings: A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
Amaral, A.J. ; Kerstens, H.H.D. ; Megens, H.J.W.C. ; Heuven, H.C.M. ; Dibbits, B.W. ; Dungen, J. den; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164 - p. 374 - 374.
single-nucleotide polymorphisms - reduced representation - linkage disequilibrium - pig genome - technologies - populations - diversity - selection - sites - swine
Background - Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the International Porcine SNP Chip Consortium, this pilot study aimed to evaluate the impact of the quality level of the sequenced bases on mapping quality and identification of true SNPs on a large scale. Results - DNA pooled from five animals from a commercial boar line was digested with DraI; 150–250-bp fragments were isolated and end-sequenced using the Illumina 1 G Genome Analyzer, yielding 70,348,064 sequences 36-bp long. Rules were developed to select sequences, which were then aligned to unique positions in a reference genome. Sequences were selected based on quality, and three thresholds of sequence quality (SQ) were compared. The highest threshold of SQ allowed identification of a larger number of SNPs (17,489), distributed widely across the pig genome. In total, 3,142 SNPs were validated with a success rate of 96%. The correlation between estimated minor allele frequency (MAF) and genotyped MAF was moderate, and SNPs were highly polymorphic in other pig breeds. Lowering the SQ threshold and maintaining the same criteria for SNP identification resulted in the discovery of fewer SNPs (16,768), of which 259 were not identified using higher SQ levels. Validation of SNPs found exclusively in the lower SQ threshold had a success rate of 94% and a low correlation between estimated MAF and genotyped MAF. Base change analysis suggested that the rate of transitions in the pig genome is likely to be similar to that observed in humans. Chromosome X showed reduced nucleotide diversity relative to autosomes, as observed for other species. Conclusion - Large numbers of SNPs can be identified reliably by creating strict rules for sequence selection, which simultaneously decreases sequence ambiguity. Selection of sequences using a higher SQ threshold leads to more reliable identification of SNPs. Lower SQ thresholds can be used to guarantee sufficient sequence coverage, resulting in high success rate but less reliable MAF estimation. Nucleotide diversity varies between porcine chromosomes, with the X chromosome showing less variation as observed in other species
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