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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Plantaardige ketens in beeld
Bremmer, Johan ; Janssens, Bas ; Ruijs, Marc ; Benninga, Jan ; Stokkers, Robert ; Splinter, Gerben ; Smit, Pepijn ; Puister-Jansen, Linda ; Lakner, Dóra - \ 2019
Wageningen : Wageningen Economic Research (Wageningen Economic Research 2019-069) - 148
Data from: A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Sutherland, Chris ; Tenan, Simone - \ 2019
University of Florence
community structure - conservation - functional traits - mammals - trophic guild - tropical forest - camera traps
Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick A. ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Zvoleff, Alexander ; Sutherland, Chris ; Tenan, Simone - \ 2019
Ecography (2019). - ISSN 0906-7590
The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
Te veel natuur kan haast niet
Jansen, P.A. - \ 2019
Trouw (2019). - p. 11 - 11.
Comparing diel activity patterns of wildlife across latitudes and seasons: Time transformations using day length
Vazquez, Carmen ; Rowcliffe, Marcus ; Spoelstra, Kamiel ; Jansen, Patrick A. - \ 2019
Methods in Ecology and Evolution (2019). - ISSN 2041-210X
activity level - activity pattern - camera trapping - day length - diel activity - double anchoring - equinoctial anchoring - mouflon - red deer - seasonal variation

Camera trapping allows scientists to study activity patterns of animals under natural conditions. However, comparisons of activity patterns across seasons or latitudes can be biased, because activity is often attuned to sunrise and sunset, the timing of which varies with latitude and season. Existing transformation methods to solve this problem have limitations. Here, we explore whether and how activity patterns can be transformed more accurately using two alternative ‘double anchoring’ transformations – equinoctial and average anchoring – that anchor activity time to two chosen anchor points during the study period. Using simulated noisy datasets mimicking species with either crepuscular, diurnal or cathemeral activity patterns, we compared the ability of different transformation methods to extract the latent pattern and activity levels under different study conditions. We found that average anchoring best retrieved the original diel activity pattern and yielded accurate estimates of activity level. Two alternative transformation methods – single anchoring and equinoctial anchoring – performed less well. Bias in estimates from using untransformed clock times was most marked (up to 2.5-fold overestimation) for longer studies covering 4–5 months either side of an equinox at high latitude, and focusing on crepuscular species. We applied the average anchoring method to 9 months of data on Red deer Cervus elaphus, Wild boar Sus scrofa and Mouflon Ovis amon musimon activity as captured by camera traps in National Park Hoge Veluwe, the Netherlands. Average anchoring revealed more pronounced peaks of activity after sunset than was apparent from untransformed data in red deer and wild boar, but not for mouflon, a cathemeral species. Similarly, activity level was lower when calculated using average anchored time for red deer and wild boar, but no difference was observed for mouflon. We conclude that transformation of time might not be necessary at latitudes below 20°, or in studies with a duration of less than a month (below 40° latitude). For longer study periods and/or higher latitudes, average anchoring resolves the problem of variable day length. Code is provided. The transformation functions are incorporated in the r-package ‘activity’.

Chicken lines divergently selected on feather pecking differ in immune characteristics
Eijk, Jerine A.J. van der; Verwoolde, Michel B. ; Vries Reilingh, Ger de; Jansen, Christine A. ; Rodenburg, Bas ; Lammers, Aart - \ 2019
Physiology and Behavior 212 (2019). - ISSN 0031-9384
Feather pecking - Immune system - Natural (auto)antibodies - Nitric oxide production - Specific antibodies

It is crucial to identify whether relations between immune characteristics and damaging behaviors in production animals exist, as these behaviors reduce animal welfare and productivity. Feather pecking (FP) is a damaging behavior in chickens, which involves hens pecking and pulling at feathers of conspecifics. To further identify relationships between the immune system and FP we characterized high FP (HFP) and low FP (LFP) selection lines with regard to nitric oxide (NO) production by monocytes, specific antibody (SpAb) titers, natural (auto)antibody (N(A)Ab) titers and immune cell subsets. NO production by monocytes was measured as indicator for innate pro-inflammatory immune functioning, SpAb titers were measured as part of the adaptive immune system and N(A)Ab titers were measured as they play an essential role in both innate and adaptive immunity. Immune cell subsets were measured to identify whether differences in immune characteristics were reflected by differences in the relative abundance of immune cell subsets. Divergent selection on FP affected NO production by monocytes, SpAb and N(A)Ab titers, but did not affect immune cell subsets. The HFP line showed higher NO production by monocytes and higher IgG N(A)Ab titers compared to the LFP line. Furthermore the HFP line tended to have lower IgM NAAb titers, but higher IgM and IgG SpAb titers compared to the LFP line. Thus, divergent selection on FP affects the innate and adaptive immune system, where the HFP line seems to have a more responsive immune system compared to the LFP line. Although causation cannot be established in the present study, it is clear that relationships between the immune system and FP exist. Therefore, it is important to take these relationships into account when selecting on behavioral or immunological traits.

Draagkracht van de Oosterschelde en westelijke Waddenzee voor schelpdieren : evaluatie van veranderingen in de voedselcondities en schelpdierbestanden in relatie tot de mosselkweek in de periode 1990-2016
Jansen, Henrice ; Kamermans, Pauline ; Glorius, Sander ; Asch, Margriet van - \ 2019
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C096/19) - 46
Diergeneesmiddelen in het milieu - een synthese van de huidige kennis
Moermond, Caroline ; Lahr, Joost ; Montforts, Mark ; Derksen, Anja ; Bondt, Nico ; Puister-Jansen, Linda ; Koeijer, Tanja de; Hoeksma, Paul - \ 2019
Bilthoven : Rijksinstituut voor Volksgezondheid en Milieu (RIVM) - 15
Diergeneesmiddelen in het milieu : een synthese van de huidige kennis
Lahr, Joost ; Moermond, Caroline ; Montforts, Mark ; Derksen, Anja ; Bondt, Nico ; Puister-Jansen, Linda ; Koeijer, Tanja de; Hoeksma, Paul - \ 2019
Amersfoort : Stowa (Stowa rapport 2019-26) - ISBN 9789057738616 - 117
Import en export van het Nederlandse agrocomplex en de impact van kringlooplandbouw
Bergevoet, R. ; Jukema, G. ; Verhoog, D. ; Benninga, J. ; Horne, P. van; Hoste, R. ; Puister-Jansen, L. - \ 2019
Wageningen : Wageningen University & Research (Wageningen Economic Research 2019-059) - 35
Wild ungulates as forest engineers
Ramírez Chiriboga, Juan Ignacio - \ 2019
Wageningen University. Promotor(en): L. Poorter, co-promotor(en): J. den Ouden; P.A. Jansen. - Wageningen : Wageningen University - ISBN 9789463951074 - 159
A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. II. Tuber bulking and resource use efficiency
Khan, Muhammad Sohail ; Yin, Xinyou ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Struik, Paul C. - \ 2019
Field Crops Research 242 (2019). - ISSN 0378-4290
Genotype-by-environment interaction - Heritability - Maturity type - Path coefficient analysis - QTL mapping

Quantitative differences in tuber bulking of 100 genotypes in a segregating F1 population, their parents (SH, RH) and five contrasting cultivars of potato (Solanum tuberosum) grown in six environments were analysed using a piece-wise expolinear function. Tuber bulking was characterised by three parameters: cm, ED and wmax, where cm and ED were growth rate and effective duration, respectively, of the linear phase of tuber bulking, and wmax was the final tuber dry weight at the end of the linear phase (tE). We also analysed radiation (RUET) and nitrogen use efficiency (NUET), and their relationships with the model parameters. Values of cm and RUET were highest for early-maturing genotypes. Late-maturing genotypes had largest ED and NUET. As a result, wmax was higher in late genotypes than in early genotypes. Most traits exhibited high heritability and high genetic correlations with wmax. Path analysis showed that RUET, cm and a previously quantified parameter for total canopy cover Asum, had a major influence on wmax. Sixteen QTLs were detected for all traits explaining the phenotypic variance by up to 66%. One particular QTL on paternal linkage group V was detected for all traits with a major additive effect and maximum total phenotypic variance. Additional QTLs mostly associated with RH (cm, tE and ED) or both SH-RH linkage groups (NUET, wmax). Our study demonstrates that there are opportunities for improving tuber dry matter yield by selecting an optimal combination of important physiological traits.

Effecten van gebiedssluiting voor schelpdiervisserij op ontwikkeling meerjarige mosselbanken en bodemdiergemeenschap : Helpdeskvraag 1b in het kader van mosseltransitie (KD-2019-028)
Troost, Karin ; Bogaart, Lisanne van den; Jansen, Henrice - \ 2019
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C074/19) - 40
Climate change, reforestation/afforestation, and urbanization impacts on evapotranspiration and streamflow in Europe
Teuling, Adriaan J. ; Badts, Emile A.G. De; Jansen, Femke A. ; Fuchs, Richard ; Buitink, Joost ; Hoek Van Dijke, Anne J. ; Sterling, Shannon M. - \ 2019
Hydrology and Earth System Sciences 23 (2019)9. - ISSN 1027-5606 - p. 3631 - 3652.

Since the 1950s, Europe has undergone large shifts in climate and land cover. Previous assessments of past and future changes in evapotranspiration or streamflow have either focussed on land use/cover or climate contributions or on individual catchments under specific climate conditions, but not on all aspects at larger scales. Here, we aim to understand how decadal changes in climate (e.g. precipitation, temperature) and land use (e.g. deforestation/afforestation, urbanization) have impacted the amount and distribution of water resource availability (both evapotranspiration and streamflow) across Europe since the 1950s. To this end, we simulate the distribution of average evapotranspiration and streamflow at high resolution (1 km2) by combining (a) a steady-state Budyko model for water balance partitioning constrained by long-term (lysimeter) observations across different land use types, (b) a novel decadal high-resolution historical land use reconstruction, and (c) gridded observations of key meteorological variables. The continental-scale patterns in the simulations agree well with coarser-scale observation-based estimates of evapotranspiration and also with observed changes in streamflow from small basins across Europe. We find that strong shifts in the continental-scale patterns of evapotranspiration and streamflow have occurred between the period around 1960 and 2010. In much of central-western Europe, our results show an increase in evapotranspiration of the order of 5 %-15 % between 1955-1965 and 2005-2015, whereas much of the Scandinavian peninsula shows increases exceeding 15 %. The Iberian Peninsula and other parts of the Mediterranean show a decrease of the order of 5 %-15 %. A similar north-south gradient was found for changes in streamflow, although changes in central-western Europe were generally small. Strong decreases and increases exceeding 45 % were found in parts of the Iberian and Scandinavian peninsulas, respectively. In Sweden, for example, increased precipitation is a larger driver than large-scale reforestation and afforestation, leading to increases in both streamflow and evapotranspiration. In most of the Mediterranean, decreased precipitation combines with increased forest cover and potential evapotranspiration to reduce streamflow. In spite of considerable local- and regional-scale complexity, the response of net actual evapotranspiration to changes in land use, precipitation, and potential evaporation is remarkably uniform across Europe, increasing by ĝ1/4 35-60 km3 yr-1, equivalent to the discharge of a large river. For streamflow, effects of changes in precipitation (ĝ1/4 95 km3 yr-1) dominate land use and potential evapotranspiration contributions (ĝ1/4 45-60 km3 yr-1). Locally, increased forest cover, forest stand age, and urbanization have led to significant decreases and increases in available streamflow, even in catchments that are considered to be near-natural.

Biodiversity monitoring in seaweed farms by DNA metabarcoding using settlement plates and water samples
Bernard, M.S. ; Tonk, L. ; Groot, G.A. de; Glorius, S. ; Jansen, Henrice - \ 2019
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C070/19) - 35
Robustness of trait connections across environmental gradients and growth forms
Flores-Moreno, Habacuc ; Fazayeli, Farideh ; Banerjee, Arindam ; Datta, Abhirup ; Kattge, Jens ; Butler, Ethan E. ; Atkin, Owen K. ; Wythers, Kirk ; Chen, Ming ; Anand, Madhur ; Bahn, Michael ; Byun, Chaeho ; Cornelissen, Hans C. ; Craine, Joseph ; Gonzalez-Melo, Andres ; Hattingh, Wesley N. ; Jansen, Steven ; Kraft, Nathan J.B. ; Kramer, Koen ; Laughlin, Daniel C. ; Minden, Vanessa ; Niinemets, Ülo ; Onipchenko, Vladimir ; Peñuelas, Josep ; Soudzilovskaia, Nadejda A. ; Dalrymple, Rhiannon L. ; Reich, Peter B. - \ 2019
Global Ecology and Biogeography 28 (2019)12. - ISSN 1466-822X - p. 1806 - 1826.
leaf traits - plant functional traits - plant strategy integration - seed traits - stem traits - trait interdependence - trait networks

Aim: Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We identified the direct and indirect connections across plant traits relevant to competition, resource acquisition and reproductive strategies using a global database and explored whether connections within and between traits from different tissue types vary across climates and growth forms. Location: Global. Major taxa studied: Plants. Time period: Present. Methods: We used probabilistic graphical models and a database of 10 plant traits (leaf area, specific leaf area, mass- and area-based leaf nitrogen and phosphorous content, leaf life span, plant height, stem specific density and seed mass) with 16,281 records to describe direct and indirect connections across woody and non-woody plants across tropical, temperate, arid, cold and polar regions. Results: Trait networks based on direct connections are sparser than those based on correlations. Land plants had high connectivity across traits within and between tissue types; leaf life span and stem specific density shared direct connections with all other traits. For both growth forms, two groups of traits form modules of more highly connected traits; one related to resource acquisition, the other to plant architecture and reproduction. Woody species had higher trait network modularity in polar compared to temperate and tropical climates, while non-woody species did not show significant differences in modularity across climate regions. Main conclusions: Plant traits are highly connected both within and across tissue types, yet traits segregate into persistent modules of traits. Variation in the modularity of trait networks suggests that trait connectivity is shaped by prevailing environmental conditions and demonstrates that plants of different growth forms use alternative strategies to cope with local conditions.

Ongemerkt en ongewild doen we allemaal mee aan de vernietiging van de natuur
Jansen, P.A. - \ 2019
Trouw (2019).
A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. I. Canopy cover dynamics
Khan, Muhammad Sohail ; Struik, Paul C. ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Yin, Xinyou - \ 2019
Field Crops Research 242 (2019). - ISSN 0378-4290
Genotype-by-environment interaction - Haulm growth - Heritability - Maturity type - QTL mapping

We designed a model to quantify the canopy cover dynamics in potato (Solanum tuberosum L.). It describes the dynamics during the build-up phase, maximum cover phase, and decline phase of canopy development through five parameters defining timing of three phases and maximum canopy cover (vmax). These five parameters were estimated for 100 individuals of an F1 population, their parents, and five standard cultivars, using data from six field experiments, and used to estimate secondary traits, related to duration and area under the canopy cover curve for the three phases. The duration of the canopy build-up phase (DP1) was rather conserved, but the duration of maximum canopy cover (DP2) and the decline phase (DP3) varied greatly, with late maturing genotypes having longer DP2 and DP3 and thus a higher area under the canopy cover curve (Asum). High genetic variability coupled with high heritability was recorded for end of canopy senescence (te), DP2 and Asum. Strong positive phenotypic and genetic correlations were observed between DP2 and te, vmax or Asum indicating that genotypes with longer DP2 could be indirectly obtained by selecting for these traits. Several quantitative trait loci (QTLs) were detected for model traits explaining the variance by up to 74%. Clustering of many QTLs were found on position 18.2 cM on paternal linkage group V with major additive effects. Many additional QTLs with minor effects were mostly associated with maternal linkage groups. Our model approach could be used to exploit available genetic variability in canopy cover dynamics of potato.

Effectiveness of Panama as an intercontinental land bridge for large mammals
Meyer, Ninon F.V. ; Moreno, Ricardo ; Sutherland, Christopher ; Torre, J.A. de la; Esser, Helen J. ; Jordan, Christopher A. ; Olmos, Melva ; Ortega, Josué ; Reyna-Hurtado, Rafael ; Valdes, Samuel ; Jansen, Patrick A. - \ 2019
Conservation Biology (2019). - ISSN 0888-8892
Bayesian statistics - community-level distribution - hierarchical occupancy modeling - landscape connectivity - Mesoamerican Biological Corridor - Neotropical forest

Habitat fragmentation is a primary driver of wildlife loss, and establishment of biological corridors is a common strategy to mitigate this problem. A flagship example is the Mesoamerican Biological Corridor (MBC), which aims to connect protected forest areas between Mexico and Panama to allow dispersal and gene flow of forest organisms. Because forests across Central America have continued to degrade, the functioning of the MBC has been questioned, but reliable estimates of species occurrence were unavailable. Large mammals are suitable indicators of forest functioning, so we assessed their conservation status across the Isthmus of Panama, the narrowest section of the MBC. We used large-scale camera-trap surveys and hierarchical multispecies occupancy models in a Bayesian framework to estimate the occupancy of 9 medium to large mammals and developed an occupancy-weighted connectivity metric to evaluate species-specific functional connectivity. White-lipped peccary (Tayassu pecari), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), white-tailed deer (Odocoileus virginianus), and tapir (Tapirus bairdii) had low expected occupancy along the MBC in Panama. Puma (Puma concolor), red brocket deer (Mazama temama), ocelot (Leopardus pardalis), and collared peccary (Pecari tajacu), which are more adaptable, had higher occupancy, even in areas with low forest cover near infrastructure. However, the majority of species were subject to ≥1 gap that was larger than their known dispersal distances, suggesting poor connectivity along the MBC in Panama. Based on our results, forests in Darien, Donoso–Santa Fe, and La Amistad International Park are critical for survival of large terrestrial mammals in Panama and 2 areas need restoration.

Neem tekens aan de wand serieus
Jansen, Patrick - \ 2019
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