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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    Welfare of Farmed Fish in Different Production Systems and Operations
    Vis, J.W. van de; Kolarevic, Jelena ; Stien, L.H. ; Kristiansen, T.S. ; Gerritzen, M.A. ; Braak, Karin van de; Abbink, W. ; Saether, B.S. ; Noble, C. - \ 2020
    In: The welfare of fish / Kristiansen, T.S., Fernö, A., Pavlidis, M.A., van de Vis, H., Cham : Springer (Animal Welfare ) - ISBN 9783030416744 - p. 323 - 361.
    When fish are reared for food production in aquaculture, they can be held in different types of rearing systems and subjected to various husbandry routines and operations. Each of these systems or operations can present different welfare risks to the fish, which in turn are dependent upon both the species and its life stage. In this chapter, we address and outline potential welfare hazards the fish may encounter in a wide range of existing and emerging rearing systems used for on-growing. These systems include: (1) pond-based aquaculture, (2) flow-through systems, (3) semi-closed containment systems, (4) RAS, (5) net cages and (6) farming offshore using sea cages in exposed conditions. We also outline potential welfare hazards for two key farming operations: transport and slaughter. We present the tools the farmer can use to assess fish welfare during on-growing and also outline relevant welfare actions that can be taken to militate against welfare hazards.
    De noodzaak van een nieuwe landbouwbenadering
    Zanten, H.H.E. van; Ittersum, M.K. van; Boer, I.J.M. de - \ 2020
    In: Beter weten over eten / van der Aalsvoort, J., Coebergh van den Braak, M., Domis-Hoos, M., Lever-de Vries, C., Nederlandse Vereniging voor het Onderwijs in de Natuurwetenschappen (NVON) (NVON-reeks 16) - ISBN 9789087970161 - p. 192 - 200.
    De gevolgen van het gevoerde landbouwbeleid; een circulair voedselsysteem; plantaardige biomassa, de basis van een circulair voedselsysteem; landbouwhuisdieren en hun rol in het circulaire voedselsysteem; hoe verder?
    Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes
    Möhlmann, Tim W.R. ; Vogels, Chantal B.F. ; Göertz, Giel P. ; Pijlman, Gorben P. ; Braak, Cajo J.F. ter; Beest, Dennis E. te; Hendriks, Marc ; Nijhuis, Els H. ; Warris, Sven ; Drolet, Barbara S. ; Overbeek, Leo van; Koenraadt, Constantianus J.M. - \ 2020
    Microbial Ecology 80 (2020)3. - ISSN 0095-3628 - p. 703 - 717.
    Arbovirus - Biting midge - Microbiome - Mosquito - Transmission

    Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.

    Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    Following publication of this Data Descriptor it was found that the affiliation of Oliver Purschke was stated incorrectly. The correct affiliations are stated below: Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden Biodiversity, Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden This has been corrected in both the HTML and PDF versions.

    Benthic invertebrate and microbial biodiversity in sub-tropical urban rivers: Correlations with environmental variables and emerging chemicals
    Peng, Feng Jiao ; Pan, Chang Gui ; Zhang, Nai Sheng ; Braak, Cajo J.F. ter; Salvito, Daniel ; Selck, Henriette ; Ying, Guang Guo ; Brink, Paul J. Van den - \ 2020
    Science of the Total Environment 709 (2020). - ISSN 0048-9697
    Benthic bacterial community - Benthic macroinvertebrates - Double constrained ordination - Traits - Urban rivers - WWTP effluents

    Urban rivers often function as sinks for various contaminants potentially placing the benthic communities at risk of exposure. We performed a comprehensive biological survey of the benthic macroinvertebrate and bacterial community compositions in six rivers from the suburb to the central urban area of Guangzhou city (South China), and evaluated their correlations with emerging organic contaminants, heavy metals and nutrients. Overall, the benthic macroinvertebrate community shifted from molluscs to oligochaete from the suburban to the central urban rivers that receive treated and untreated sewage. An exception was the site in the Sha River where chironomids were most abundant. The differences in macroinvertebrate community assemblages were significantly associated with chromium, total phosphorus, galaxolide, triclosan and sand content in the sediment. There was no significant difference in benthic macroinvertebrate composition between the dry and wet season. As assessed by double constrained ordination, sexual reproduction was the only trait of benthic macroinvertebrates that showed a significant correlation with pollution variables, as it was significantly positively correlated with chromium and total phosphorus. This suggests that r-strategist occurs in polluted sampling sites. The benthic bacterial community composition showed a significant difference between seasons and among the Liuxi River, Zhujiang River and central urban rivers. The differences in community composition of the benthic bacteria were significantly correlated with galaxolide, total phosphorus, lead and triclosan. These results suggest that input of treated and untreated sewage significantly altered the benthic macroinvertebrate and bacterial community compositions in urban rivers.

    Investigating microbial associations from sequencing survey data with co-correspondence analysis
    Alric, Benjamin ; Braak, Cajo J.F. ter; Desdevises, Yves ; Lebredonchel, Hugo ; Dray, Stéphane - \ 2020
    Molecular Ecology Resources 20 (2020)2. - ISSN 1755-098X - p. 468 - 480.
    co-correspondence analysis - co-occurrence network - Mamiellophyceae - microbial eukaryotes - next-generation sequencing - Prasinovirus

    Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.

    A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

    Compositional turnover and variation in Eemian pollen sequences in Europe
    Felde, Vivian A. ; Flantua, Suzette G.A. ; Jenks, Cathy R. ; Benito, Blas M. ; Beaulieu, Jacques Louis de; Kuneš, Petr ; Magri, Donatella ; Nalepka, Dorota ; Risebrobakken, Bjørg ; Braak, Cajo J.F. ter; Allen, Judy R.M. ; Granoszewski, Wojciech ; Helmens, Karin F. ; Huntley, Brian ; Kondratienė, Ona ; Kalniņa, Laimdota ; Kupryjanowicz, Mirosława ; Malkiewicz, Małgorzata ; Milner, Alice M. ; Nita, Małgorzata ; Noryśkiewicz, Bożena ; Pidek, Irena A. ; Reille, Maurice ; Salonen, Sakari ; Šeirienė, Vaida ; Winter, Hanna ; Tzedakis, Polychronis C. ; Birks, John B. - \ 2020
    Vegetation History and Archaeobotany 29 (2020)1. - ISSN 0939-6314 - p. 101 - 109.
    Detrended canonical correspondence analysis - Extrinsic and intrinsic processes - Inertia - Last interglacial dataset - Multivariate regression trees - Neutral processes - Principal curves

    The Eemian interglacial represents a natural experiment on how past vegetation with negligible human impact responded to amplified temperature changes compared to the Holocene. Here, we assemble 47 carefully selected Eemian pollen sequences from Europe to explore geographical patterns of (1) total compositional turnover and total variation for each sequence and (2) stratigraphical turnover between samples within each sequence using detrended canonical correspondence analysis, multivariate regression trees, and principal curves. Our synthesis shows that turnover and variation are highest in central Europe (47–55°N), low in southern Europe (south of 45°N), and lowest in the north (above 60°N). These results provide a basis for developing hypotheses about causes of vegetation change during the Eemian and their possible drivers.

    Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition
    Hartinger, Thomas ; Edwards, Joan E. ; Gómez Expósito, Ruth ; Smidt, Hauke ; Braak, Cajo J.F. ter; Gresner, Nina ; Südekum, Karl Heinz - \ 2019
    Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
    16S rRNA gene sequencing - anaerobic fungi - archaea - bacteria - lucerne silage - qPCR - rumen microbiota - Rusitec

    Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

    Biomarker Research in ADHD: The Impact of Nutrition (BRAIN) - Study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children
    Stobernack, Tim ; Vries, Stefan P.W. De; Rodrigues Pereira, Rob ; Pelsser, Lidy M. ; Braak, Cajo J.F. Ter; Aarts, Esther ; Baarlen, Peter Van; Kleerebezem, Michiel ; Frankena, Klaas ; Hontelez, Saartje - \ 2019
    BMJ Open 9 (2019)11. - ISSN 2044-6055
    ADHD - biomarker - brain activity - few-foods diet - fMRI - microbiota

    Introduction Attention deficit hyperactivity disorder (ADHD) is the most common childhood behavioural disorder, causing significant impediment to a child's development. It is a complex disorder with numerous contributing (epi)genetic and environmental factors. Currently, treatment consists of behavioural and pharmacological therapy. However, ADHD medication is associated with several side effects, and concerns about long-term effects and efficacy exist. Therefore, there is considerable interest in the development of alternative treatment options. Double-blind research investigating the effects of a few-foods diet (FFD) has demonstrated a significant decrease in ADHD symptoms following an FFD. However, an FFD requires a considerable effort of both child and parents, limiting its applicability as a general ADHD treatment. To make FFD intervention less challenging or potentially obsolete, we need to understand how, and in which children, an FFD affects ADHD behaviour and, consequently, the child's well-being. We hypothesise that an FFD affects brain function, and that the nutritional impact on ADHD is effectuated by a complex interplay between the microbiota, gut and brain, that is, the microbiota-gut-brain axis. Methods and analysis The Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) study is an open-label trial with researchers blinded to changes in ADHD symptoms during sample processing and initial data analyses. Ethics and dissemination The Medical Research and Ethics Committee of Wageningen University has approved this study (NL63851.081.17, application 17/24). Results will be disseminated through peer-reviewed journal publications, conference presentations, (social) media and the BRAIN study website. A summary of the findings will be provided to the participants. Trial registration number NCT03440346. Study dates Collection of primary outcome data started in March 2018 and will be ongoing until 100 children have participated in the study. Sample data analysis will start after all samples have been collected.

    New robust weighted averaging- and model-based methods for assessing trait–environment relationships
    Braak, Cajo J.F. ter - \ 2019
    Methods in Ecology and Evolution 10 (2019)11. - ISSN 2041-210X - p. 1962 - 1971.
    community assembly - community-weighted means - fourth-corner approach - generalized linear mixed models - species niche centroid - trait-based ecology - weighted averaging - Whittaker Siskiyou Mountains data

    Statistical analysis of trait–environment association is challenging owing to the lack of a common observation unit: Community-weighted mean regression (CWMr) uses site points, multilevel models focus on species points, and the fourth-corner correlation uses all species-site combinations. This situation invites the development of new methods capable of using all observation levels. To this end, new multilevel and weighted averaging-based regression methods are proposed. Compared to existing methods, the new multilevel method, called MLM3, has additional site-related random effects; they represent the unknowns in the environment that interact with the trait. The new weighted averaging method combines site-level CWMr with a species-level regression of Species Niche Centroids on to the trait. Because species can vary enormously in frequency and abundance giving diversity variation among sites, the regressions are weighted by Hill's effective number (N2) of occurrences of each species and the N2-diversity of a site, and are subsequently combined in a sequential test procedure known as the max test. Using the test statistics of these new methods, the permutation-based max test provides strong statistical evidence for trait–environment association in a plant community dataset, where existing methods show weak evidence. In simulations, the existing multilevel model showed bias and type I error inflation, whereas MLM3 did not. Out of the weighted averaging-based regression methods, the N2-weighted version best controlled the type I error rate. MLM3 was superior to the weighted averaging-based methods with up to 30% more power. Both methods can be extended (a) to account for phylogeny and spatial autocorrelation and (b) to select functional traits and environmental variables from a greater set of variables.

    Kosten van zwarte braak voor aaltjesbestrijding : Saldoverliezen en bewerkingskosten van zwarte braak bij sanering van Melodogyne soorten
    Smit, A.B. ; Jager, J.H. - \ 2019
    Wageningen : Wageningen Economic Research - 2 p.
    Relating ultrasonic vocalizations from a pair of rats to individual behavior : A composite link model approach
    Vendrig, Nadia J. ; Hemerik, Lia ; Pinter, Ilona J. ; Braak, Cajo J.F. ter - \ 2019
    Statistica Neerlandica 73 (2019)1. - ISSN 0039-0402 - p. 139 - 156.
    automated home cage - composite link model - model identification - social behavior - ultrasonic vocalization

    Ultrasonic vocalizations (USVs) are crucial in the social behavior of rats. We aim to relate USV rates of pairs of rats to individual activity in an automated home cage (PhenoTyper®) where USVs are recorded per pair and not per individual. We propose a composite link model approach to parametrize a mechanistic “sum-of-rates” model in which the pair's USV rate is the sum of the USV rates of individuals depending on their own behavior. In generalized linear models (GLMs), the individual's USV rates are multiplied. We verified through simulation that composite link model gave lower Poisson deviance than GLM. We analyzed the data from an experiment in which half of the cages did allow the pairs to interact (Pair Housing) and the other half did not (Individual Housing). The “sum-of-rates” model fits best for Individual Housing and GLM for Pair Housing. An additional simulation study strongly suggests that interaction between rats changes the underlying mechanism for vocalization behavior.

    Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait–environment relationships
    Braga, João ; Braak, Cajo J.F. ter; Thuiller, Wilfried ; Dray, Stéphane - \ 2018
    Ecology 99 (2018)12. - ISSN 0012-9658 - p. 2667 - 26764.
    community ecology - fourth-corner analysis - functional ecology - Moran's spectral randomization - null models - type I error

    The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental variables, mediated by site-specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are independent of each other. However, this fundamental hypothesis might be flawed because of phylogenetic relatedness between species and spatial autocorrelation in the environmental data. Here, using a simulation-based experiment, we demonstrate how the presence of spatial and phylogenetic autocorrelations can, in some circumstances, lead to inflated type I error rates, suggesting that significant associations can be misidentified. As an alternative, we propose a new randomization approach designed to avoid this issue, based on Moran's spectral randomization. In this approach, standard permutations are replaced by constrained randomizations so that the distribution of the statistic under the null hypothesis is built with additional constraints to preserve the phylogenetic and spatial structures of the observed data. The inclusion of this new randomization approach provides total control over type I error rates and should be used in real studies where spatial and phylogenetic autocorrelations often occur.

    Meer aardappels met minder water dankzij slimme irrigatie en andere rassen
    Blom-Zandstra, M. - \ 2018
    Simple parametric tests for trait–environment association
    Braak, Cajo J.F. ter; Peres-Neto, Pedro R. ; Dray, Stéphane - \ 2018
    Journal of Vegetation Science 29 (2018)5. - ISSN 1100-9233 - p. 801 - 811.
    community ecology - community-level test - CWM of traits - environmental gradients - fourth-corner - functional traits - modified test - species niche centroid - species-level test - statistical ecology - trait–environment relationship

    Question: The CWM approach is an easy way of analysing trait–environment association by regressing (or correlating) the mean trait per plot against an environmental variable and assessing the statistical significance of the slope or the associated correlation coefficient. However, the CWM approach does not yield valid tests, as random traits (or random indicator values) are far too often judged significantly related to the environmental variable, even when the trait and environmental variable are extrinsic to (not derived from) the community data. Existing solutions are the ZS-modified test (Zelený & Schaffers,) and the max (or sequential) test based on the fourth-corner correlation. Both tests are based on permutations which become cumbersome when many tests need to be carried out and many permutations are required, as in methods that correct for multiple testing. The main goal of this study was to compare these existing permutation-based solutions and to develop a quick and easy parametric test that can replace them. Methods: This study decomposes the fourth-corner correlation in two ways, which suggests a simple parametric approach consisting of assessing the significances of two linear regressions, one plot-level test as in the CWM approach and one species-level test, the reverse of the CWM approach, that regresses the environmental mean per species (i.e. the species niche centroid) on to the trait. The tests are combined by taking the maximum p-value. The type I error rates and power of this parametric max test are examined by simulation of one- and two-dimensional Gaussian models and log-linear models. Results: The ZS-modified test and the fourth-corner max test are conservative in different scenarios, the ZS-modified test being even more conservative than the fourth-corner. The new parametric max test is shown to control the type I error and has equal or even higher power than permutation tests based on the fourth-corner, the ZS-modified test and variants thereof. A weighted version of the new test showed inflated type I error. Conclusion: The combination of two simple regressions is a good alternative to the fourth-corner and the ZS-modified test. This combination is also applicable when multiple trait measurements are made per plot.

    Een eureka-moment dat nog een beetje natrilt : over zwaartekrachtgolven en Bayesiaans rekenen
    Braak, C.J.F. ter - \ 2018
    Stator, periodiek van VVS 19 (2018)2. - ISSN 1567-3383 - p. 14 - 17.
    Out of the box : Statistical methods for the analysis of automated home cage experiments
    Vendrig, Nadia J. - \ 2018
    Wageningen University. Promotor(en): C.J.F. ter Braak, co-promotor(en): L. Hemerik. - Wageningen : Wageningen University - ISBN 9789463432627 - 181

    Automated home cage experiments have been proposed as an alternative to the classical tests used for behavioural phenotyping. As the name implies, automated home cage experiments are conducted in home cage environments and the behaviour is recorded automatically. The experiments can thus be conducted without human interference and can last for several days.

    All data incorporated in this thesis is collected using a PhenoTyper® system (Noldus Information Technology, Wageningen, The Netherlands). The Pheno- Typer is a home cage environment with an integrated top-view camera. The ex- act location of the rat or mouse is determined for every frame in the video. Be- havioural response variables such as Distance Moved or Duration Progressing are extracted from the location.

    Data from automated home cage experiments typically consists of multiple re- sponse variables that can be highly correlated. In addition to the location-based activity response variables, automated home cage environments have the poten- tial to incorporate data from other sources such as biometric parameters.

    The aim of this thesis is to expand the methodology available to analyse these data.

    In Chapter 2, the use of multivariate statistics for data from automated home cage experiments is demonstrated in two case studies. Data from automated home cage experiments is pre-dominantly analysed using univariate statistics in which the significance and magnitude of the effect of a treatment on a single response variable is tested. By analysing single response variables the benefit that au- tomated home cage experiments allow for the collection of numerous response variables simultaneously is not fully utilized. The use of multivariate statistics allows for simultaneous analysis of multiple response variables. The multivari- ate methods described in Chapter 2 are Redundancy Analysis (RDA) and Principal Response Curves (PRC). Both of these methods are frequently used in (aquatic) ecology, toxicology, and microbiology. RDA is a constrained form of Principal Components Analysis (PCA). RDA describes the underlying structure of a data set in terms of the explanatory variables (such as experimental treatment). It quan- tifies the proportion of variance in the data set that can be described using these explanatory variables. PRC is a special case of RDA used to describe experimen- tal multivariate longitudinal data. It estimates differences among treatments on a collection of response variables over time and the extent to which the response of those individual response variables resembles the overall response. In both case studies, the multivariate analyses were able to draw the same main conclusions as the contrasting univariate analyses. The advantages of using a multivariate analysis rather than a univariate analysis on a single response variable is that the multivariate methods provide a graphical representation of the data set, are easy to interpret, and allow for estimation of the relation between response variables.

    In Chapter 3, a novel extension to PRC is presented that allows for response variable selection using permutation testing. Often, not all of the response vari- ables included in PRC are affected by the treatment which can make response vari- able selection desirable. One approach is to use a straightforward cut-off value for coefficient size. Because coefficient size of response variables are affected by more factors than effect-size alone, results of this approach can be variable between data sets. A backward selection approach was expected to give a more robust result. Four backward selection approaches based on permutation testing were presented. The approaches differ in whether coefficient size is used or not in ranking the response variables to test. The performance of these approaches was demonstrated in a simulation study using a well known data set in the field of aquatic ecology. The permutation testing approach that uses information on coefficient size of RVs sped up the algorithm without affecting its performance. This most successful permutation testing approach removed roughly 95% of the response variables that are unaffected by the treatment irrespective of the char- acteristics of the data set (which is a desirable property of a statistical test) and, in the simulations, correctly identified up to 97% of response variables affected by the treatment.

    In Chapter 4, a case study is used to illustrate the power of combining mecha- nistic and statistical modelling, and the benefits of simulation studies. In this case study, an integrated analysis of two streams of information: activity response variables per rat and Ultrasonic Vocalisations (USVs) per cage (containing a pair of rats). USVs are crucial in the social behaviour of rats. The aim of the first part of the chapter was to develop methodology to predict the USV-rate of the pair of rats as a function of the activity of the individuals. A mechanistic model is that the USV-rate of the pair of rats is the sum of the USV-rates of the two individuals depending on their own behaviour (“sum-of-rates” model). It turns out that this “sum-of-rates” model can be fitted to data using a Composite Link Model (CLM) approach. In generalized linear models (GLM) the individual’s USV-rates are mul- tiplied rather than summed. A simulation study verified that CLM gave a better fit (lower Poisson Deviance) than GLM. In the second part of the chapter, data from an experiment in which half of the cages did allow the rats of the pair to interact (Pair Housing) and the other half did not (Individual Housing). A num- ber of models was fitted to investigate whether there is evidence that interaction between rats affects their behaviour. The “sum-of-rates” model fit best for In- dividual Housing and GLM for Pair Housing. This difference in fit supports the hypothesis that interaction between rats affects their behaviour. An additional simulation study strongly suggested that this difference was not due to chance and that the underlying mechanism that links activity and USVs structurally dif- fered between Pair Housing and Individual Housing.

    In Chapter 5, a simulation study is described that evaluates the performance of a new and promising statistical learning method under circumstances relevant for automated home cage experiments. Targeted Maximum Likelihood Estima- tion (TMLE) is a new and promising statistical method for causal effect estima- tion, even in observational studies, that can use machine learning methods to increase performance. The intended role of TMLE in the analysis of home cage ex- periments was to account for inter-individual variation in behaviour when test- ing specific treatment effects. TMLE is a doubly robust method, which means that it is robust to misspecification of either the treatment outcome model or the treatment assignment model. A treatment outcome model predicts the effect of a treatment on the response variable given the covariates. A treatment assignment model predicts the probability that an individual is in a treatment group given the covariates. In theory, when all assumptions are correct, TMLE should thus pro- vide unbiased causal effect estimators even when either the treatment outcome or treatment assignment model is misspecified. When TMLE is applied in prac- tice however, it is possible that these required theoretical assumptions such as the positivity assumption and no unobserved confounders are violated. The sim- ulation study in Chapter 5 illustrates the effects of unobserved (non-)confounding covariates and noise covariates on bias, mean square error, and coverage of TMLE on near-balanced data sets (with low risk of positivity violations) and unbalanced data sets (with higher risks of positivity violations). The conclusion was that TMLE is able to estimate average causal effects with low bias and mean square error, compared to the golden standard linear regression, given that the sample size is large, the data set is near-balanced, and the assignment model is specified cor- rectly. In unbalanced data sets TMLE did not live up to expectations, also in data sets in which the positivity assumption was not violated. The conclusion from the simulation study is that TMLE is as yet not suited for the intended use in home cage experiments.

    In Chapter 6, the General Discussion, the main findings of the thesis are sum- marised and discussed in relation to the aim of the thesis. In addition, several hot topics in biostatistics for automated home cage experiments are discussed.

    Achteruitgang insectenpopulaties in Nederland: trends, oorzaken en kennislacunes
    Kleijn, David ; Bink, Ruud J. ; Braak, Cajo J.F. ter; Grunsven, Roy van; Ozinga, Wim A. ; Roessink, Ivo ; Scheper, Jeroen A. ; Schmidt, Anne M. ; Wallis de Vries, Michiel F. ; Wegman, Ruut ; Zee, Friso F. van der; Zeegers, Th. - \ 2018
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2871) - 85
    Canoco reference manual and user's guide : software for ordination (version 5.10)
    Braak, Cajo J.F. ter; Šmilauer, Petr - \ 2018
    Wageningen : Biometris, Wageningen University & Research - 536
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