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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Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
Nature 571 (2019)7765. - ISSN 0028-0836

In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following, https://inventaire-forestier.ign.fr/spip.php?rubrique159, site accessed on 01 January 2015)’. All of these errors have been corrected online.

Recent Advances in Forest Observation with Visual Interpretation of Very High-Resolution Imagery
Schepaschenko, Dmitry ; See, Linda ; Lesiv, Myroslava ; Bastin, Jean-François ; Mollicone, Danilo ; Tsendbazar, Nandin-Erdene ; Bastin, Lucy ; McCallum, Ian ; Laso Bayas, Juan Carlos ; Baklanov, Artem ; Perger, Christoph ; Dürauer, Martina ; Fritz, Steffen - \ 2019
Surveys in Geophysics 40 (2019)4. - ISSN 0169-3298 - p. 839 - 862.
The land area covered by freely available very high-resolution (VHR) imagery has grown dramatically over recent years, which has considerable relevance for forest observation and monitoring. For example, it is possible to recognize and extract a number of features related to forest type, forest management, degradation and disturbance using VHR imagery. Moreover, time series of medium-to-high-resolution imagery such as MODIS, Landsat or Sentinel has allowed for monitoring of parameters related to forest cover change. Although automatic classification is used regularly to monitor forests using medium-resolution imagery, VHR imagery and changes in web-based technology have opened up new possibilities for the role of visual interpretation in forest observation. Visual interpretation of VHR is typically employed to provide training and/or validation data for other remote sensing-based techniques or to derive statistics directly on forest cover/forest cover change over large regions. Hence, this paper reviews the state of the art in tools designed for visual interpretation of VHR, including Geo-Wiki, LACO-Wiki and Collect Earth as well as issues related to interpretation of VHR imagery and approaches to quality assurance. We have also listed a number of success stories where visual interpretation plays a crucial role, including a global forest mask harmonized with FAO FRA country statistics; estimation of dryland forest area; quantification of deforestation; national reporting to the UNFCCC; and drivers of forest change.
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.

Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Changes throughout lactation in phenotypic and genetic correlations between methane emissions and milk fatty acid contents predicted from milk mid-infrared spectra
Vanrobays, M.L. ; Bastin, C. ; Vandenplas, J. ; Hammami, H. ; Soyeurt, H. ; Vanlierde, A. ; Dehareng, F. ; Froidmont, E. ; Gengler, N. - \ 2016
Journal of Dairy Science 99 (2016)9. - ISSN 0022-0302 - p. 7247 - 7260.
Dairy cattle - Fatty acid - Methane - Mid-infrared

The aim of this study was to estimate phenotypic and genetic correlations between methane production (MP) and milk fatty acid contents of first-parity Walloon Holstein cows throughout lactation. Calibration equations predicting daily MP (g/d) and milk fatty acid contents (g/100 dL of milk) were applied on milk mid-infrared spectra related to Walloon milk recording. A total of 241,236 predictions of MP and milk fatty acids were used. These data were collected between 5 and 305 DIM in 33,555 first-parity Holstein cows from 626 herds. Pedigree data included 109,975 animals. Bivariate (i.e., MP and a fatty acid trait) random regression test-day models were developed to estimate phenotypic and genetic parameters of MP and milk fatty acids. Individual short-chain fatty acids (SCFA) and groups of saturated fatty acids, SCFA, and medium-chain fatty acids showed positive phenotypic and genetic correlations with MP (from 0.10 to 0.16 and from 0.23 to 0.30 for phenotypic and genetic correlations, respectively), whereas individual long-chain fatty acids (LCFA), and groups of LCFA, monounsaturated fatty acids, and unsaturated fatty acids showed null to positive phenotypic and genetic correlations with MP (from -0.03 to 0.13 and from -0.02 to 0.32 for phenotypic and genetic correlations, respectively). However, these correlations changed throughout lactation. First, de novo individual and group fatty acids (i.e., C4:0, C6:0, C8:0, C10:0, C12:0, C14:0, SCFA group) showed low phenotypic or genetic correlations (or both) in early lactation and higher at the end of lactation. In contrast, phenotypic and genetic correlations between MP and C16:0, which could be de novo synthetized or derived from blood lipids, were more stable during lactation. This fatty acid is the most abundant fatty acid of the saturated fatty acid and medium-chain fatty acid groups of which correlations with MP showed the same pattern across lactation. Phenotypic and genetic correlations between MP and C17:0 and C18:0 were low in early lactation and increased afterward. Phenotypic and genetic correlations between MP and C18:1 . cis-9 originating from the blood lipids were negative in early lactation and increased afterward to become null from 18 wk until the end of lactation. Correlations between MP and groups of LCFA, monounsaturated fatty acids, and unsaturated fatty acids showed a similar or intermediate pattern across lactation compared with fatty acids that compose them. Finally, these results indicate that correlations between MP and milk fatty acids vary following lactation stage of the cow, a fact still often ignored when trying to predict MP from milk fatty acid profile.

Potential use of milk based biomarkers to assess and to select for heat tolerance in dairy cattle
Hammami, H. ; Vandenplas, J. ; Vanrobays, M.L. ; Bastin, C. ; Gengler, N. - \ 2015
In: Proceedings of the Second DairyCare Conference 2015. - Kopenhagen : DairyCare COST Action FA1308 - ISBN 9780993017612 - p. 61 - 61.
Heat stress (HS) has major impact on milk production, fertility, health, and welfare of dairy cows. Comfortable cows exhibiting minimal stress will consume, produce, and reproduce better. Therefore, controlling HS is important for animal welfare. Genetic selection has been proven as an effective tool to improve traits of interest and therefore potentially also heat tolerance, by inducing in a cost effective manner permanent and cumulative effects. Yet, direct measures of HS in routine remain complex and difficult. High!throughput analytic methods are increasingly available from milk recording schemes allowing routine quantification of several potential biomarkers in milk. Therefore, the main goals of this study were i) to estimate HS impacts on milk production, udder health, and milk fatty acids (FA) and ii) to assess the potential of milk FA as biomarkers of HS for dairy cattle. A total of 202,733 test!day records for milk, fat, and protein yields, fat and protein contents, somatic cell score, but also 7 groups of FA and 10 individual milk FA contents predicted by mid!infrared spectroscopy were collected from 34,468 Holstein cows in first lactation between 2007 and 2010 in 862 herds in the Walloon Region of Belgium. Test!day records were merged with a daily temperature humidity index (THI) measured at the nearest meteorological station to each herd. Reaction norm models without fixing priors for thresholds were used to estimate HS effects. Results show that when THI values increased, most milk and FA traits showed negative phenotypic and genetic trends. Moreover, genetic correlations between low and high THI values for these traits were relatively high (>0.80) indicating moderated influence of HS on genetic expression of traits. Conversely, somatic cell score, fat yield, unsaturated FA and specifically C18:1 cis!9 content in milk increased with THI. These traits showed lower genetic correlations (
Genetic correlations between methane production & milk fatty acid contents of Walloon Holstein cattle throughout the lactation
Vanrobays, M.L. ; Vandenplas, J. ; Bastin, C. ; Hammami, H. ; Soyeurt, H. ; Vanlierde, A. ; Dehareng, F. ; Froidmont, E. ; Gengler, N. - \ 2015
Seeing Central African forests through their largest trees
Bastin, J.F. ; Barbier, N. ; Réjou-Méchain, M. ; Fayolle, A. ; Gourlet-Fleury, S. ; Maniatis, D. ; Haulleville, T. De; Baya, F. ; Beeckman, H. ; Beina, D. ; Couteron, P. ; Chuyong, G. ; Dauby, G. ; Doucet, J.L. ; Droissart, V. ; Dufrêne, M. ; Ewango, C.E.N. ; Gillet, F. ; Gonmadje, C.H. ; Hart, T. ; Kavali, T. ; Kenfack, D. ; Libalah, M. ; Malhi, Y. ; Makana, J.R. ; Pélissier, R. ; Ploton, P. ; Serckx, S. ; Sonké, B. ; Stevart, T. ; Thomas, D.W. ; Cannière, C. De; Bogaert, J. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 8 p.
tropical forest - biomass - size - distributions - diversity - dynamics
Large tropical trees and a few dominant species were recently identified as the main structuring elements of tropical forests. However, such result did not translate yet into quantitative approaches which are essential to understand, predict and monitor forest functions and composition over large, often poorly accessible territories. Here we show that the above-ground biomass (AGB) of the whole forest can be predicted from a few large trees and that the relationship is proved strikingly stable in 175 1-ha plots investigated across 8 sites spanning Central Africa. We designed a generic model predicting AGB with an error of 14% when based on only 5% of the stems, which points to universality in forest structural properties. For the first time in Africa, we identified some dominant species that disproportionally contribute to forest AGB with 1.5% of recorded species accounting for over 50% of the stock of AGB. Consequently, focusing on large trees and dominant species provides precise information on the whole forest stand. This offers new perspectives for understanding the functioning of tropical forests and opens new doors for the development of innovative monitoring strategies.
Genetic variance in micro-environmental sensitivity for milk and milk quality in Walloon Holstein cattle
Vandenplas, J. ; Bastin, C. ; Gengler, N. ; Mulder, H.A. - \ 2013
Journal of Dairy Science 96 (2013)9. - ISSN 0022-0302 - p. 5977 - 5990.
generalized linear-models - residual variance - breeding values - fatty-acids - production traits - bovine-milk - heterogeneity - variability - prediction - components
Animals that are robust to environmental changes are desirable in the current dairy industry. Genetic differences in micro-environmental sensitivity can be studied through heterogeneity of residual variance between animals. However, residual variance between animals is usually assumed to be homogeneous in traditional genetic evaluations. The aim of this study was to investigate genetic heterogeneity of residual variance by estimating variance components in residual variance for milk yield, somatic cell score, contents in milk (g/dL) of 2 groups of milk fatty acids (i.e., saturated and unsaturated fatty acids), and the content in milk of one individual fatty acid (i.e., oleic acid, C18:1 cis-9), for first-parity Holstein cows in the Walloon Region of Belgium. A total of 146,027 test-day records from 26,887 cows in 747 herds were available. All cows had at least 3 records and a known sire. These sires had at least 10 cows with records and each herd × test-day had at least 5 cows. The 5 traits were analyzed separately based on fixed lactation curve and random regression test-day models for the mean. Estimation of variance components was performed by running iteratively expectation maximization-REML algorithm by the implementation of double hierarchical generalized linear models. Based on fixed lactation curve test-day mean models, heritability for residual variances ranged between 1.01 × 10-3 and 4.17 × 10-3 for all traits. The genetic standard deviation in residual variance (i.e., approximately the genetic coefficient of variation of residual variance) ranged between 0.12 and 0.17. Therefore, some genetic variance in micro-environmental sensitivity existed in the Walloon Holstein dairy cattle for the 5 studied traits. The standard deviations due to herd × test-day and permanent environment in residual variance ranged between 0.36 and 0.45 for herd × test-day effect and between 0.55 and 0.97 for permanent environmental effect. Therefore, nongenetic effects also contributed substantially to micro-environmental sensitivity. Addition of random regressions to the mean model did not reduce heterogeneity in residual variance and that genetic heterogeneity of residual variance was not simply an effect of an incomplete mean model.
Implementation in breeding programmes
Coffey, M.P. ; McParland, S. ; Bastin, C. ; Wall, E. ; Berry, D.P. ; Veerkamp, R.F. - \ 2013
Advances in Animal Biosciences 4 (2013)3. - ISSN 2040-4700 - p. 626 - 630.
Genetic improvement is easy when selecting for one heritable and well-recorded trait at a time. Many industrialised national dairy herds have overall breeding indices that incorporate a range of traits balanced by their known or estimated economic value. Future breeding goals will contain more non-production traits and, in the context of this paper, traits associated with human health and cow robustness. The definition of Robustness and the traits used to predict it are currently fluid; however, the use of mid-infrared reflectance spectroscopic analysis of milk will help to create new phenotypes on a large scale that can be used to improve the human health characteristics of milk and the robustness of cows producing it. This paper describes the state-of-the-art in breeding strategies that include animal robustness (mainly energy status) and milk quality (as described by milk fatty acid profile), with particular emphasis on the research results generated by the FP7-funded RobustMilk project
Managing uncertainty in integrated environmental modelling: The UncertWeb framework.
Bastin, L. ; Cornford, D. ; Jones, R. ; Heuvelink, G.B.M. ; Pebesma, E. ; Stasch, C. ; Nativi, S. ; Mazzetti, P. - \ 2013
Environmental Modelling & Software 39 (2013). - ISSN 1364-8152 - p. 116 - 134.
sensitivity-analysis - parameter-estimation - bayesian-approach - watershed model - climate-change - error - calibration - systems - design - tools
Web-based distributed modelling architectures are gaining increasing recognition as potentially useful tools to build holistic environmental models, combining individual components in complex workflows. However, existing web-based modelling frameworks currently offer no support for managing uncertainty. On the other hand, the rich array of modelling frameworks and simulation tools which support uncertainty propagation in complex and chained models typically lack the benefits of web based solutions such as ready publication, discoverability and easy access. In this article we describe the developments within the UncertWeb project which are designed to provide uncertainty support in the context of the proposed ‘Model Web’. We give an overview of uncertainty in modelling, review uncertainty management in existing modelling frameworks and consider the semantic and interoperability issues raised by integrated modelling. We describe the scope and architecture required to support uncertainty management as developed in UncertWeb. This includes tools which support elicitation, aggregation/disaggregation, visualisation and uncertainty/sensitivity analysis. We conclude by highlighting areas that require further research and development in UncertWeb, such as model calibration and inference within complex environmental models.
Genetic variance in environmental sensitivity for milk and milk quality in Walloon Holstein cattle
Vandenplas, J. ; Bastin, C. ; Mulder, H.A. ; Gengler, N. - \ 2012
In: Book of Abstracts of the 63rd Annual Meeting of the European Association for Animal Production, 27-31 August 2012, Bratislava, Slovakia, 27 - 31 August 2012. - Wageningen : Wageningen Academic Publishers - ISBN 9789086867615 - p. 15 - 15.
Animals that are robust to environmental changes are desirable in the current dairy industry. This difference in environmental sensitivity can be studied through the heterogeneity of residual variance while homogeneous residual variance between animals is usually assumed homogeneous in traditional genetic evaluations. The aim of this study was to study genetic heterogeneity of residual variance by the estimation of variance components in residual variance for 5 milk and milk quality traits. 146,027 test-day records from 26,887 Walloon Holstein first-parity cows in 747 herds were available. All cows had at least 3 records and had a known sire. These sires had at least 10 cows with records and each herd x test-day had at least 5 cows. Five traits, milk yield, somatic cell score, and content in milk (g/dL) of oleic acid (C18:1 cis-9), monounsaturated and unsaturated fatty acids, were analyzed separately. Estimation of variance components was performed by running iteratively Expectation Maximization-Restricted Maximum Likelihood algorithm by the implementation of double hierarchical generalized linear models. For all traits, the genetic standard deviation in residual variance (i.e. approximately the genetic coefficient of variation of residual variance) was low and ranged between 0.12 and 0.17. The standard deviations due to herd x test day and permanent environment in residual variance ranged between 0.35 and 0.44 for herd x test-day effect and between 0.55 and 0.96 for permanent environmental effect. This study shows the heterogeneity of residual variance and the existence of some genetic variance in environmental sensitivity for all studied traits in the Walloon Holstein dairy cattle.
Genetics and genomics of energy balance measured in milk using mid-infrared spectroscopy
McParland, S. ; Calus, M.P.L. ; Coffey, M.P. ; Wall, E. ; Soyeurt, H. ; Bastin, C. ; Veerkamp, R.F. ; Banos, G. ; Lewis, E. ; Bovenhuis, H. ; Berry, D.P. - \ 2012
In: Book of Abstracts of the 63rd Annual Meeting of the European Association for Animal Production. - Wageningen Academic Publishers - ISBN 9789086867615 - p. 92 - 92.
Genome-wide association study for milk fatty acid composition using cow versus bull data
Bastin, C. ; Gengler, N. ; Soyeurt, H. ; McParland, S. ; Wall, E. ; Calus, M.P.L. - \ 2012
In: Book of Abstracts of the 63rd Annual Meeting of the European Association for Animal Production. - Wageningen Academic Publishers - ISBN 9789086867615 - p. 93 - 93.
Cross-scale monitoring and assessment of land degradation and sustainable land management : a methodological framework for knowledge management
Reed, M.S. ; Buenemann, M. ; Atlhopheng, J. ; Akhtar-Schuster, M. ; Bachmann, F. ; Bastin, G. ; Bigas, H. ; Chanda, R. ; Dougill, A.J. ; Essahli, W. ; Evely, A.C. ; Fleskens, L. ; Geeson, N. ; Glass, J.H. ; Hessel, R. ; Holden, J. ; Ioris, A.A.R. ; Kruger, B. ; Liniger, H.P. ; Mphinyane, W. ; Nainggolan, D. ; Perkins, J. ; Raymond, C.M. ; Ritsema, C.J. ; Schwilch, G. ; Sebego, R. ; Seely, M. ; Stringer, L.C. ; Thomas, R. ; Twomlow, S. ; Verzandvoort, S. - \ 2011
Land Degradation and Development 22 (2011)2. - ISSN 1085-3278 - p. 261 - 271.
natural-resource management - local-communities - kalahari - desertification - rangeland - science - system - impact
For land degradation monitoring and assessment (M&A) to be accurate and for sustainable land management (SLM) to be effective, it is necessary to incorporate multiple knowledges using a variety of methods and scales, and this must include the (potentially conflicting) perspectives of those who use the land. This paper presents a hybrid methodological framework that builds on approaches developed by UN Food & Agriculture Organisation's land degradation Assessment in Drylands (LADA), the World Conservation Approaches and Technologies (WOCAT) programme and the Dryland Development Paradigm (DDP), and is being applied internationally through the EU-funded DESIRE project. The framework suggests that M&A should determine the progress of SLM towards meeting sustainability goals, with results continually and iteratively enhancing SLM decisions. The framework is divided into four generic themes: (i) establishing land degradation and SLM context and sustainability goals; (ii) identifying, evaluating and selecting SLM strategies; (iii) selecting land degradation and SLM indicators and (iv) applying SLM options and monitoring land degradation and progress towards sustainability goals. This approach incorporates multiple knowledge sources and types (including land manager perspectives) from local to national and international scales. In doing so, it aims to provide outputs for policy-makers and land managers that have the potential to enhance the sustainability of land management in drylands, from the field scale to the region, and to national and international levels. The paper draws on operational experience from across the DESIRE project to break the four themes into a series of methodological steps, and provides examples of the range of tools and methods that can be used to operationalise each of these steps.
Consequences of Selection for Milk Quality and Robustness Traits
Bastin, C. ; Berry, D.P. ; Strandberg, E. ; Urioste, J.I. ; Veerkamp, R.F. ; Gengler, N. - \ 2011
In: Proceedings of the 2011 Interbull meeting, 26-29 August 2011, Stavanger, Norway. - - p. 195 - 199.
Web Based Expert Elicitation of Uncertainties in Environmental Model Inputs
Bastin, L. ; Williams, M. ; Gosling, J.P. ; Truong, N.P. ; Cornford, D. ; Heuvelink, G.B.M. ; Achard, F. - \ 2011
Geophysical Research Abstracts 13 (2011). - ISSN 1029-7006 - p. 5384 - 5384.
Expert elicitation of input and model uncertainties
Heuvelink, G.B.M. ; Bastin, L. ; Cornford, D. ; Gossling, J.P. ; Truong, N.P. ; Williams, M. - \ 2011
The Uncertainty Enabled Model Web (Deliverable 3.1) - 61 p.
Monitoring Australian rangeland sites using landscape function indicators and ground- and remote-based techniques
Ludwig, J.A. ; Bastin, G.N. ; Eager, R.W. ; Karfs, R. ; Ketner, P. ; Pearce, G. - \ 2000
Environmental Monitoring and Assessment 64 (2000). - ISSN 0167-6369 - p. 167 - 178.
If the goal for managing rangelands is to achieve a balance between production and conservation, then monitoring is essential to detect change and apply corrective action. In some rangeland areas of northern Australia, monitoring has detected a tilt in the production-conservation balance towards excessive production. How big is this imbalance? Can it shift back? Robust monitoring is needed to answer these questions. The aim is to know what to monitor, and where. For example, to detect changes caused by livestock on rangeland forage production and soil erosion, indicators linking grazing disturbances to landscape function are needed, that is, indicators that signal how well landscapes are capturing, concentrating, and utilizing scarce water, nutrient, and organic resources. Studies in Australia and the USA document that simple vegetation and soil patch attributes can be measured as indicators of the ‘state of health’ of landscape function. For example, field and remote sensing-based grazing studies in Australia document that landscapes with a high cover of perennial plant patches function effectively to capture runoff water and nutrients in sediments, whereas landscapes with a low cover of these patches do not – they are dysfunctional – as indicated by large patches of bare soil. Aerial videography is proving to be a robust technique for measuring indicators of landscape function such as small patches of vegetation and the extent of bare soil. These indicators typically have a sigmoidal response to grazing impacts.We illustrate that if these indicators are measured on monitoring sites established near the sigmoidal ‘point of inflection’, then small changes in these indicators can be detected.
An application driven guide through infinite-dimensional systems theory.
Zwart, H.J. ; Bontsema, J. - \ 1997
In: Plenary lectures and mini-courses European Control Conference, G. Bastin and M. Gevers (Eds.), Brussel, Belgium - p. 289 - 328.
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