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.

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Statistical methods for QTL mapping and genomic prediction of multiple traits and environments: case studies in pepper
Alimi, Nurudeen Adeniyi - \ 2016
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Marco Bink. - Wageningen : Wageningen University - ISBN 9789462579361 - 153
capsicum - statistical analysis - statistics - genomics - quantitative trait loci - quantitative traits - quantitative methods - genetics - crop yield - statistische analyse - statistiek - genomica - loci voor kwantitatief kenmerk - kwantitatieve kenmerken - kwantitatieve methoden - genetica - gewasopbrengst

In this thesis we describe the results of a number of quantitative techniques that were used to understand the genetics of yield in pepper as an example of complex trait measured in a number of environments. Main objectives were; i) to propose a number of mixed models to detect QTLs for multiple traits and multiple environments, ii) to extend the multi-trait QTL models to a multi-trait genomic prediction model, iii) to study how well the complex trait yield can be indirectly predicted from its component traits, and iv) to understand the ‘causal’ relationships between the target trait yield and its component traits.

The thesis is part of an EU-FP7 project “Smart tools for Prediction and Improvements of Crop Yield” (SPICY- This project generated phenotypic data from four environments using 149 individuals from the sixth generation of recombinant inbred lines obtained from intraspecific cross between large – fruited inbred pepper cultivar ‘Yolo Wonder’ (YW) and the hot pepper cultivar ‘Criollo de Morelos 334’ (CM 334). A total of 16 physiological traits were evaluated across the four trials and various types of genetic parameters were estimated. In a first analysis, the traits were univariately analyzed using linear mixed model. Trait heritabilities were generally large (ranging between 0.43 – 0.96 with an average of 0.86) and mostly comparable across trials while many of the traits displayed heterosis and transgression. The same QTLs were detected across the four trials, though QTL magnitude differed for many of the traits. We also found that some QTLs affected more than one trait, suggesting QTL pleiotropy (a QTL region affecting more than one trait). We discussed our results in the light of previously reported QTLs for these and similar traits in pepper.

We addressed the presence of genotype-by-environment interaction (GEI) in yield and the other traits through a multi-environment (ME) mixed model methodology with terms for QTL-by-environment interaction (QEI). We opined that yield would benefit from joint analysis with other traits and so deployed two other mixed model based multi-response QTL approaches: a multi-trait approach (MT) and a multi-trait multi-environment approach (MTME). For yield as well as the other traits, MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. Many of the detected QTLs were pleiotropic and showed quantitative QEI. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.

The QTL methods considered thus far are not well suited for prediction purposes as only a limited set of QTL-related markers are used. Since the main interest of this research includes improvement of yield prediction, we explored both single-trait and multi-trait versions of genomic prediction (GP) models as alternatives to the QTL-based prediction (QP) models. This was termed direct prediction. The methods differed in their predictive accuracies with GP methods outperforming QP methods in both single and multi-traits situations. We borrowed ideas from crop growth model (CGM) to dissect complex trait yield into a number of its component traits. Here, we integrated QTL/genomic prediction and CGM approaches and showed that the target trait yield can be predicted via its component traits together with environmental covariables. This was termed indirect prediction. The CGM approach seemed to work well at first sight, but this is especially due to the fact that yield appeared to be strongly driven by just one of its components, the partitioning to fruit.

An alternative representation of the biological knowledge of a complex target trait such as yield is provided by network type models. We constructed both conditional and unconditional networks across the four environments to understand the ‘causal’ relationships between target trait yield and its component traits. The final networks for each environment from both conditional and unconditional methods were used in a structural equation model to assess the causal relationships. Conditioning QTL mapping on network structure improved detection of refined genetic architecture by distinguishing between QTL with direct and indirect effects, thereby removing non-significant effects found in the unconditional network and resolving QTL pleiotropy. Similar to the CGM topology, yield was established to be downstream to its component traits, indicating that yield can be studied and predicted from its component traits. Thus, the genetic improvements of yield would benefit from improvements on the component traits.

Finally, complex trait prediction can be enhanced by a full integration of the methods described in the different chapters. Recent research efforts have been channelled to incorporating both multivariate whole genome prediction models and crop growth models. Further research is required, but we hope that the present thesis presents useful steps towards better prediction models for complex traits exhibiting genotype by environment interaction.

How much Biodiversity is in Natura 2000? : the “Umbrella Effect” of the European Natura 2000 protected area network : technical report
Sluis, T. van der; Foppen, R. ; Gillings, Simon ; Groen, T.A. ; Henkens, R.J.H.G. ; Hennekens, S.M. ; Huskens, K. ; Noble, David ; Ottburg, F.G.W.A. ; Santini, L. ; Sierdsema, H. ; Kleunen, A. van; Schaminee, J.H.J. ; Swaay, C. van; Toxopeus, Bert ; Wallis de Vries, M.F. ; Jones-Walters, L.M. - \ 2016
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2738) - 147 p.
biodiversity - habitats directive - birds directive - natura 2000 - statistical analysis - geographical information systems - biodiversiteit - habitatrichtlijn - vogelrichtlijn - statistische analyse - geografische informatiesystemen
In order to assess the significance of the presumed “umbrella effect” of Natura 2000 areas the European Commission initiated a study, in 2013, to address the following questions: 1) Which are, amongst the species regularly occurring within the European territory of the EU-28 Member States, those that significantly benefit from the site conservation under the EU Birds and Habitats Directive? 2) What is the percentage of all species occurring in the wild in the EU that benefit significantly from Natura 2000? 3) How significant is the contribution of Natura 2000 in relation to the objective of halting and reversing biodiversity loss? The approach used existing data, and covered the terrestrial mammals, birds, reptiles, amphibian, butterfly and plant species. The analysis is mostly based on statistical distribution models and GIS processing of species distribution data in relation to their presence within protected areas of the Natura 2000 network. The main findings for all species groups were: Animal species for which Natura 2000 areas were not specifically designated occur more frequently inside Natura 2000 than outside (in particular breeding birds and butterflies). These species do, therefore, gain benefit from the protected areas network. The species for which Natura 2000 areas were designated generally occur more frequently within the Natura 2000 site boundaries than the nonannex species; this is in particular the case for birds and butterflies, for amphibians and reptiles the difference is negligible. More specific conclusions and findings, as well as discussion of these results and implications for further studies are included in the report.
Indirect genetic effects for group-housed animals
Alemu, S.W. - \ 2015
University. Promotor(en): Johan van Arendonk, co-promotor(en): L.G. Janss; Piter Bijma; P. Berg. - Wageningen : Wageningen University - ISBN 9788793176713 - 228
nerts - pluimvee - groepshuisvesting - genetische effecten - sociaal gedrag - agressief gedrag - interacties - heritability - veredelingsprogramma's - statistische analyse - genetische parameters - selectief fokken - mink - poultry - group housing - genetic effects - social behaviour - aggressive behaviour - interactions - breeding programmes - statistical analysis - genetic parameters - selective breeding


Alemu, SW(2015) Indirect Genetic effects for Group-housed Animals. Joint PhD thesis between Aarhus University, Denmark and Wageningen University, the Netherlands.

Social interactions among individuals are common both in plants and animals. With social interactions, the trait value of an individual may be influenced by the genes of its interacting partners, a phenomenon known as indirect genetic effects (IGE). An IGE is heritable effect of an individual on trait values of another individual. A large body of literature has shown that social interactions can create addition heritable variation in both plants and animals, for both behavioural and production traits.

When IGE are estimated it is usually assumed that an individual interacts equally with all its group mates, irrespective of genetic relatedness. This assumption may not be true in mixed groups of kin and non-kin, where an individual may interact systematically different with kin and non-kin. Current IGE models ignore such systematically different interactions between kin and non-kin. Thus, the main aim of this thesis was to develop and apply statistical methods to estimate IGE when interactions differ between kin and non-kin.

Social interactions are important in mink that are kept in groups for the production of fur. Group housing of mink increases aggression behaviours, which is reflected by an increase in the number of bite marks on the pelts, and reduces the welfare of the animals. We estimated the genetic parameter for bite mark traits in group-housed mink, to investigate the prospects for genetic improvement of bite mark traits. We found that there are good prospects to produce mink that have a low level of biting. Finally, we further concluded that genetic parameter estimation for bite mark score should take into account systematic interactions due to sex or kin.

In this thesis we also investigated genomic selection for socially affected traits, considering survival time in two lines of brown egg layers showing cannibalistic behaviour. Despite the limited reference population of ~234 progeny tested sires, the accuracy of estimated breeding values (EBV) was ~35% higher for genomic selection compared with the parent average-EBV. We found that the response to genomic selection per year for line B1 was substantially higher than for the traditional breeding scheme, whereas for line BD response was slightly higher than for the traditional breeding scheme. In conclusion, genetic selection with IGE combined with marker information can substantially reduce detrimental social behaviours such as cannibalism in layers and biting in group-housed mink.

Neerschalen van ruimtelijke informatie : Perceelsinformatie uit kaarten voor postcodegebieden
Brus, D.J. ; Orton, T.G. ; Walvoort, D.J.J. ; Reijneveld, J.A. ; Oenema, O. ; Knotters, M. - \ 2014
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 31 (2014)3. - ISSN 0169-6300 - p. 165 - 168.
bodemkwaliteit - organische stof - velden - landbouwgronden - kaarten - bepaling - kriging - statistische analyse - innovaties - soil quality - organic matter - fields - agricultural soils - maps - determination - statistical analysis - innovations
Kaarten kunnen informatie geven over grotere eenheden, bijvoorbeeld postcodegebieden, of nog kleinere, zoals percelen. Met een variant op een interpolatietechniek is het mogelijk informatie te verkrijgen over een kleiner gebied. We illustreren dit aan de hand van organische stofgehalten in de bodem. De methodiek is breed toepasbaar op allerlei vormen van ruimtelijke informatie en maakt een betere benutting van data mogelijk.
Trendanalyse van contaminanten in diervoeders : mogelijkheden en problemen bij het gebruik van historische monitoringsgegens
Adamse, P. ; Boer, W.J. de; Nijs, W.C.M. de - \ 2014
Wageningen : RIKILT Wageningen UR (RIKILT report 2014.007) - 53
besmetters - diervoeding - historische verslagen - tendensen - statistische analyse - gevalsanalyse - voedselveiligheid - voedingsnormen - gegevensverwerking - analytische methoden - contaminants - animal nutrition - historical records - trends - statistical analysis - case studies - food safety - feeding standards - data processing - analytical methods
Voor het verkrijgen van inzicht in het basisniveau van een contaminant in een diervoeder kan gebruik worden gemaakt van monitoringsgegevens. Zowel de gegevens als de te gebruiken technieken moeten wel aan bepaalde voorwaarden voldoen. In een vorig rapport (Adamse, 2014) staat beschreven hoe met redelijk eenvoudige statistische basistools analyses kunnen worden uitgevoerd. In het huidige rapport staan meer complexe statistische analyses beschreven met daarbij de mogelijkheden en potentiele problemen.
Trendanalyse van historische gegevens : handleiding voor het gebruik van monitoringsgegevens
Adamse, P. - \ 2014
Wageningen : RIKILT Wageningen UR (RIKILT report 2014.001) - 22
tendensen - historische verslagen - monitoring - analytische methoden - statistische analyse - diervoeding - besmetters - voedselveiligheid - voedingsnormen - gegevensverwerking - voederveiligheid - trends - historical records - analytical methods - statistical analysis - animal nutrition - contaminants - food safety - feeding standards - data processing - feed safety
Het doel van dit rapport is om aan te geven welke technieken gebruikt kunnen worden om inzicht te krijgen in het achtergrondniveau van contaminanten in diervoeders en diervoederproducten. Beschreven is tevens met welke factoren rekening gehouden moet worden bij het gebruik van historische monitoringsgegevens. Deze gegevens zijn verzameld in het kader van monitoringsprogramma’s.
Spatial precipitation patterns and trends in The Netherlands during 1951–2009
Daniels, E.E. ; Lenderink, G. ; Hutjes, R.W.A. ; Holtslag, A.A.M. - \ 2014
International Journal of Climatology 34 (2014)6. - ISSN 0899-8418 - p. 1773 - 1784.
neerslag - klimaatverandering - statistische analyse - regionale verkenningen - seizoenen - nederland - precipitation - climatic change - statistical analysis - regional surveys - seasons - netherlands - coastal precipitation - urban land - europe - rainfall - temperatures - extremes - feedback - impacts - indexes - soils
Significant increases in precipitation have been observed in The Netherlands over the last century. At the same time persistent spatial variations are apparent. The objective of this study is to analyse and explain these spatial patterns, focussing on changes in means and extremes for the period 1951–2009. To investigate different possibilities for the causes of spatial variations, a distinction was made between six regions based on mean precipitation, soil type and elevation, and four zones at different distances to the coast. Spatial maxima in mean precipitation inland and over elevated areas are mainly formed in winter and spring, while maxima along the coast are generated in autumn. Daily precipitation maxima are found in the central West coast and over elevated areas. Upward trends in daily precipitation are highest from February to April and lowest from July to September. The strongest and most significant increases are found along the coast. For several seasonal and climatological periods diverging behaviour between coastal and inland zones is observed. We find that distance to the coast gives a more consistent picture for the seasonal precipitation changes than a classification based on surface characteristics. Therefore, from the investigated surface factors, we consider sea surface temperature to have the largest influence on precipitation in The Netherlands.
SST and circulation trend biases cause an underestimation of European precipitation trends
Haren, R. van; Oldenborgh, G.J. van; Lenderink, G. ; Collins, M. ; Hazeleger, W. - \ 2013
Climate Dynamics 40 (2013)1-2. - ISSN 0930-7575 - p. 1 - 20.
neerslag - klimaatverandering - statistische analyse - temperatuur - mariene gebieden - europa - atlantische oceaan - precipitation - climatic change - statistical analysis - temperature - marine areas - europe - atlantic ocean - air-flow influences - climate-change - model projections - united-kingdom - local climate - 20th-century - simulations - extremes
Clear precipitation trends have been observed in Europe over the past century. In winter, precipitation has increased in north-western Europe. In summer, there has been an increase along many coasts in the same area. Over the second half of the past century precipitation also decreased in southern Europe in winter. An investigation of precipitation trends in two multi-model ensembles including both global and regional climate models shows that these models fail to reproduce the observed trends. In many regions the model spread does not cover the trend in the observations. In contrast, regional climate model (RCM) experiments with observed boundary conditions reproduce the observed precipitation trends much better. The observed trends are largely compatible with the range of uncertainties spanned by the ensemble, indicating that the boundary conditions of RCMs are responsible for large parts of the trend biases. We find that the main factor in setting the trend in winter is atmospheric circulation, for summer sea surface temperature (SST) is important in setting precipitation trends along the North Sea and Atlantic coasts. The causes of the large trends in atmospheric circulation and summer SST are not known. For SST there may be a connection with the well-known ocean circulation biases in low-resolution ocean models. A quantitative understanding of the causes of these trends is needed so that climate model based projections of future climate can be corrected for these precipitation trend biases.
Canoco reference manual and user's guide: software for ordination, version 5.0
Braak, C.J.F. ter; Smilauer, P. - \ 2012
Ithaca USA : Microcomputer Power - 496
computer software - gegevensanalyse - statistische analyse - multivariate analyse - ecologie - biologie - handleidingen - data analysis - statistical analysis - multivariate analysis - ecology - biology - guide books
Canoco is a software package for multivariate data analysis, with an emphasis on dimesional reduction (ordination), regression analysis, and the combination of the two, constrained ordination. Canoco makes effective and powerful ordination methods easilyt accessible for scientists wanting to infer and visualize pattern and structure in complex multivariate data, e.g. biologists researching the relations between plant and animal communities and their environment. Canoco contains linear and unimodal ordination methods, with the possibility to account for background variation specified by covariates. In combination with extensive facilities for permutation tests, these methods have proven to be remarkably effective in solving applied research problems.
Nutritional Systems Biology of Fat : integration and modeling of transcriptomics datasets related to lipid homeostasis
Ohid Ullah, M. - \ 2012
University. Promotor(en): Michael Muller, co-promotor(en): Guido Hooiveld. - S.l. : s.n. - ISBN 9789461733818 - 158
vetzuren - genexpressie - lipidenmetabolisme - obesitas - transcriptomica - statistische analyse - wiskundige modellen - fatty acids - gene expression - lipid metabolism - obesity - transcriptomics - statistical analysis - mathematical models

Fatty acids, in the form of triglycerides, are the main constituent of the class of dietary lipids. They not only serve as a source of energy but can also act as potent regulators of gene transcription. It is well accepted that an energy rich diet characterized by high intakes of dietary fat is linked to the dramatic increase in the prevalence of obesity in both developed and developing countries in the last several decades. Obese individuals are at increased risk of developing the metabolic syndrome, a cluster of metabolic abnormalities that ultimately increase the risk of developing vascular diseases and type 2 diabetes. Many studies have been performed to uncover the role of fatty acids on gene expression in different organs, but integrative studies in different organs over time driven by high throughput data are lacking. Therefore, we first aimed to develop integrative approaches on the level of individual genes but also pathways using genome-wide transcriptomics datasets of mouse liver and small intestine that are related to fatty acid sensing transcription factor peroxisome proliferator activated receptor alpha (PPARα). We also aimed to uncover the behavior of PPARαtarget genes and their corresponding biological functions in a short time series experiment, and integrated and modeled the influence of different levels of dietary fat and the time dependency on transcriptomics datasets obtained from several organs by developing system level approaches.

We developed an integrative statistical approach that properly adjusted for multiple testing while integrating data from two experiments, and was driven by biological inference. By quantifying pathway activities in different mouse tissues over time and subsequent integration by partial least squares path model, we found that the induced pathways at early time points are the main drivers for the induced pathways at late time points. In addition, using a time course microarray study of rat hepatocytes, we found that most of the PPARα target genes at early stage are involved in lipid metabolism-related processes and their expression level could be modeled using a quadratic regression function. In this study, we also found that the transcription factorsNR2F, CREB, EREF and RXR might work together with PPARα in the regulation of genes involved in lipid metabolism. By integrating time and dose dependent gene expression data of mouse liver and white adipose tissue (WAT), we found a set of time-dose dependent genes in liver and WAT including potential signaling proteinssecreted from WAT that may induce metabolic changes in liver, thereby contributing to the pathogenesis of obesity.

Taken together, in this thesis integrative statistical approaches are presented that were applied to a variety of datasets related to metabolism of fatty acids. Results that were obtained provide a better understanding of the function of the fatty acid-sensor PPARa, and identified a set of secreted proteins that may be important for organ cross talk during the development of diet induced obesity.

Estimate of veterinary antibiotic usage in the Netherlands in 2011
Bondt, N. ; Puister-Jansen, L.F. ; Veen, H.B. van der; Bergevoet, R.H.M. ; Douma, B.E. ; Vliet, A.L.J. van; Wehling, K.W. - \ 2011
Den Haag : LEI, onderdeel van Wageningen UR - 4
dierhouderij - antibiotica - veterinaire producten - verkoopbaar volume - toepassing - statistische analyse - animal husbandry - antibiotics - veterinary products - merchantable volume - application - statistical analysis
The information presented on the MARAN website is based on a collation of data from ongoing surveillance systems on the sales and use of antimicrobial agents in animal husbandry in the Netherlands.
Quantification of dynamics of soil-borne pathogens and their consequences for yield in crop rotations
Berg, W. van den - \ 2011
University. Promotor(en): Johan Grasman, co-promotor(en): Walter Rossing. - [S.l.] : S.n. - ISBN 9789461730497 - 127
gewassen - rotaties - bodempathogenen - plantenparasitaire nematoden - populatiedynamica - oogstvoorspelling - proefopzet - modellen - dynamische modellen - statistische analyse - crops - rotations - soilborne pathogens - plant parasitic nematodes - population dynamics - yield forecasting - experimental design - models - dynamic models - statistical analysis
Sturen op verantwoord antibioticagebruik
Kuipers, A. ; Wemmenhove, H. ; Bakker, J. ; Kuipers, F. - \ 2010
Veeteelt (2010). - ISSN 0168-7565 - p. 3 - 4.
melkveehouderij - melkkoeien - mastitis - antibiotica - dosering - uiers - indexen - statistische analyse - antibioticaresistentie - dairy farming - dairy cows - antibiotics - dosage - udders - indexes - statistical analysis - antibiotic resistance
Resistentieontwikkeling verscherpt de aandacht voor het antibioticumgebruik in de veehouderij. Het project ‘Transparant en efficiënt medicijngebruik’ brengt antibioticumgebruik in kaart via aantal dagdoseringen. Dat getal varieert van bedrijf tot bedrijf.
Naar objectieve schatting van aantallen Muskusratten in Nederland
Belle, J. van; Wieren, S.E. van; Ydenberg, R.C. ; Goedhart, P. - \ 2010
De Levende Natuur 111 (2010)2. - ISSN 0024-1520 - p. 94 - 99.
ondatra zibethicus - plagenbestrijding - geboorteregeling - statistische analyse - dierecologie - waterbeheer - pest control - population control - statistical analysis - animal ecology - water management
Discussies over Muskusratten en muskusrattenbestrijding worden gehinderd door een gebrek aan inzicht in de feiten, en een gebrekkig begrip ten aanzien van de populatiedynamiek van deze dieren in Nederland. Welk effect heeft bestrijding in haar huidige vorm op aanwezige aantallen? Wat zijn die aantallen ongeveer en hoe beïnvloeden de Muskusratten bij deze dichtheden de omgeving? In dit artikel laten de auteurs een methode zien om meer grip te krijgen op deze vragen.
Statistiek voor onderzoekers, met voorbeelden uit de landbouw- en milieuwetenschappen
Burgers, S.L.G.E. ; Oude Voshaar, J.H. - \ 2010
Wageningen : Wageningen Academic Publishers - ISBN 9789086861385 - 352
statistische analyse - landbouw - proefopzet - milieuwetenschappen - regressieanalyse - landbouwwetenschappen - statistical analysis - agriculture - experimental design - environmental sciences - regression analysis - agricultural sciences
Dit boek helpt onderzoekers statistiek toe te passen in hun onderzoek. Theoretisch (wiskundige) details zijn hierbij zoveel mogelijk achterwege gebleven. De in dit boek besproken methoden sluiten aan bij het onderzoek van Wageningen UR. De methoden worden toegelicht aan de hand van voorbeelden.
On some surprising statistical properties of a DNA fingerprinting technique called AFLP
Gort, G. - \ 2010
University. Promotor(en): A. Stein; Fred van Eeuwijk. - [S.l. : S.n. - ISBN 9789085855378 - 154
planten - statistische analyse - dna-fingerprinting - genomen - biometrie - moleculaire genetica - dna - aflp - biostatistiek - toegepaste statistiek - plants - statistical analysis - dna fingerprinting - genomes - biometry - molecular genetics - amplified fragment length polymorphism - biostatistics - applied statistics
AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary system, and are separated by length, with shorter fragments traveling further. Multiple individuals are simultaneously fingerprinted on a gel. One of the applications of AFLP is the estimation of genetic similarity between individuals, e.g. in diversity and phylogenetic studies. In that case, profiles of two individuals are compared, and the fraction of shared (comigrating) bands is calculated, e.g. using the Dice similarity coefficient. Two comigrating bands may share the same fragment, but band sharing could also be due to chance, if two equally sized, but different fragments are amplified. This is called homoplasy. Homoplasy biases similarity coefficients. Homoplasy could also occur within a lane, if two different fragments of equal length are amplified, resulting in a single band. We call this collision. The main objective of this thesis is the study of collision and homoplasy in AFLP. The length distribution of AFLP fragments plays an important role. This distribution is highly skewed with more abundant short fragments. By simulation the expected similarity for unrelated genotypes is calculated. As much as 40% of the bands may be shared by chance in case of profiles with 120 bands. The collision problem is analogous to the birthday problem, which has a surprising solution. The collision problem is even more extreme, making it even more surprising. Profiles with only 19 bands contain collision(s) with probability 1/2. These findings have consequences for practice. In some cases it is better to prevent the occurrence of collisions by decreasing the number of bands, in other cases a correction for homoplasy and collision is preferred. Modified similarity coefficients are proposed, that estimate the fraction of homologous fragments, correcting for homoplasy and collision. Partially related to homoplasy and collision, we study the codominant scoring of AFLP in association panels. Examples of AFLP in lettuce and tomato serve as illustrations.
Ontwikkeling en toepassing van een poweranalyse voor de vogelmonitoringgegevens in het kader van de nieuwe gaswinning
Wiersma, P. ; Roodbergen, M. ; Goedhart, P.W. ; Ens, B.J. - \ 2009
Beek-Ubbergen : SOVON Vogelonderzoek Nederland (SOVON-onderzoeksrapport 2009/11)
vogels - aardgas - extractie - bodemdaling - bevolkingsafname - statistische analyse - watervogels - broedplaatsen - waddenzee - lauwersmeergebied - birds - natural gas - extraction - subsidence - population decrease - statistical analysis - waterfowl - breeding places - wadden sea
De NAM is in 2007 gestart met nieuwe aardgaswinning in het Waddenzeegebied en de Lauwersmeer. Hierbij wordt het principe van ‘hand aan de kraan’ gehanteerd: de gaswinning moet worden gestaakt wanneer blijkt dat er schadelijke effecten zijn op abiotische, dan wel biotische parameters. Daarom heeft de NAM aan SOVON Vogelonderzoek Nederland de opdracht gegeven vogelsoorten in het Waddengebied en de Lauwersmeer te monitoren en een plan op te stellen om deze gegevens te analyseren. Het gaat om gegevens van watervogels en broedvogels in de Lauwersmeer (en eventuele referentiegebieden) en het Waddengebied, waarbij onderscheid wordt gemaakt in gebieden met en zonder verwachte bodemdaling. Bij een poweranalyse wordt onderzocht welk effect, in dit geval een afname in aantallen vogels, statistisch nog aantoonbaar is. Er wordt in beginsel geen uitspraak gedaan over de oorzaak van het effect.
Populatiedynamica van muskusratten. Huidige en alternatieve strategieën van bestrijding in Nederland
Bos, D. ; Belle, J. van; Goedhart, P.W. ; Wieren, S.E. van; Ydenberg, R.C. - \ 2009
Feanwâlden : Altenburg & Wymenga (A&W-rapport 1250) - 79
ondatra zibethicus - populatiedynamica - plagenbestrijding - geboorteregeling - statistische analyse - dierecologie - nederland - waterbeheer - population dynamics - pest control - population control - statistical analysis - animal ecology - netherlands - water management
Er is behoefte aan een modelmatige benadering van de muskusrattenproblematiek, uitgevoerd in samenhang met de eventueel uit te voeren veldproeven. Met als doel: beter onderbouwd bestrijden, effectiever in termen van tijd en geld en met zo mogelijk vermindering van dierenleed. Dit rapport (geschreven in het engels, maar ruimschoots voorzien van nederlandstalige inleiding en samenvatting en bijlagen) presenteert de resultaten van een statistische analyse van vangsten in de afgelopen twintig jaar in Nederland. Daarbij is de Groep Biometrie van Wageningen UR betrokken geweest, uitgevoerd door Altenburg & Wymenga
Proficiency test for antibiotics in beef
Berendsen, B.J.A. ; Stolker, A.A.M. - \ 2009
Wageningen : RIKILT (Report / RIKILT 2009.015) - 43
rundvlees - antibiotica - testen - screenen - statistische analyse - kwantitatieve analyse - eigenschappen - toegepaste wiskunde - toegepaste statistiek - beef - antibiotics - testing - screening - statistical analysis - quantitative analysis - properties - applied mathematics - applied statistics
The aim of this proficiency study was to give laboratories the possibility to evaluate or demonstrate their competence for the analysis of antibiotics in bovine tissues, including the screening analysis. This study also provided an evaluation of the methods applied for screening and quantitative and confirmatory analysis of antibiotics in beef.
The CMGS statistical tool for yield forecasting
Hoek, S.B. ; Goedhart, P.W. ; Akkermans, L.M.W. - \ 2009
Agro Informatica 22 (2009)2. - ISSN 0925-4455 - p. 19 - 20.
gewasopbrengst - oogstvoorspelling - remote sensing - modellen - statistische analyse - gewasmonitoring - biostatistiek - crop yield - yield forecasting - models - statistical analysis - crop monitoring - biostatistics
Official EU forecasts for crop yields are calculated several times per year by crop analysts of the Joint Research Centre (JRC). In general the forecasts for a certain region are based on statistical models which describe historical yields in terms of a time trend combined with a relationship with CGMS indicator data. Since 1994 the so-called CGMS statistical module has been in use at JRC - to facilitate crop yield forecasting at national and sub-national level. Now, an improved version has been developed, for use by the crop analysts of JRC. The tool was developed by two subdivisions of the Wageningen UR: Alterra-CGI and Biometris. Aim was to enable the analysts to construct more elaborate models (regression and scenario models) than they could construct with the previous module and to make it easier to include more indicators, i.e. weather indicator and remote sensing data.
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