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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Assessing effect of rainfall on rate of alien shrub expansion in a southern African savanna
Masocha, Mhosisi ; Dube, Timothy ; Skidmore, Andrew ; Holmgren Urba, Milena ; Prins, Herbert - \ 2017
African Journal of Range and Forage Science 34 (2017)1. - ISSN 1022-0119 - p. 39 - 44.
aerial photography - invasion - Kyle Game Reserve - Lantana camara - patch dynamics - rainfall variability

Understanding the environmental factors governing the spread of alien shrubs is crucial for conserving biodiversity. In the semi-arid savannas of Africa, alien shrub invasion often occurs simultaneously with native shrub encroachment but climate-dependent differences in encroachments of native and alien shrubs have never been properly quantified. A combination of historical aerial photographs and field measurements was used to compare the spread of the invasive shrub Lantana camara L. with that of native encroaching shrubs over a 31-year period in a protected semi-arid savanna in Zimbabwe, southern Africa. We tested whether the response of this invasive alien shrub to rainfall differs from that of native shrub encroachers. Both the invasive shrub L. camara and native encroaching shrubs spread significantly faster during high rainfall years than in dry years. However, the response of L. camara to annual rainfall was stronger than the response of native encroaching shrubs. During years of above-average rainfall, the mean annual rate of spread of L. camara was at least twice that of native shrub encroachers, whereas in other years natives spread at the same rate as the alien shrub. This is a novel finding suggesting that in water-limited savannas, pulses in rainfall may accelerate the spread of some invasive alien species.

Global Terrestrial Ecosystem Observations: Why, Where, What and How?
Jongman, R.H.G. ; Skidmore, A.K. ; Mücher, C.A. ; Bunce, R.G.H. ; Metzger, M. - \ 2017
In: The GEO-Handbook on Biodiversity Observation Networks / Walters, Michele, Scholes, Robert J., Cham, Switzerland : Springer - ISBN 9783319272863 - p. 19 - 38.
This chapter covers the questions of ecosystem definition and the organisation of a monitoring system. It treats where and how ecosystems should be measured and the integration between in situ and RS observations. Ecosystems are characterised by composition, function and structure. The ecosystem level is an essential link in biodiversity surveillance and monitoring between species and populations on the one hand and land use and landscapes on the other. Ecosystem monitoring requires a clear conceptual model that incorporates key factors influencing ecosystem dynamics to base the variables on that have to be monitored as well as data collection methods and statistics. Choices have to be made on the scale at which monitoring should be carried out and eco-regionalisation or ecological stratification are approaches for identification of the units to be sampled. This can be done on expert judgement but nowadays also on stratifications derived from multivariate statistical clustering. Data should also be included from individual research sites over the entire world and from organically grown networks covering many countries. An important added value in the available monitoring technologies is the integration of in situ and RS observations, as various RS technologies are coming into reach of ecosystem research. For global applications this development is essential. We can employ an array of instruments to monitor ecosystem characteristics, from fixed sensors and in situ measurements to drones, planes and satellite sensors. They allow to measure biogeochemical components that determine much of the chemistry of the environment and the geochemical regulation of ecosystems. Important global databases on sensor data are being developed and frequent high resolution RS scenes are becoming available. RS observations can complement field observations as they deliver a synoptic view and the opportunity to provide consistent information in time and space especially for widely distributed habitats. RS has a high potential for developing distribution maps, change detection and habitat quality and composition change at various scales. Hyperspectral sensors have greatly enhanced the possibilities of distinguishing related habitat types at very fine scales. The end-users can use such maps for estimating range and area of habitats, but they could also serve to define and update the sampling frame (the statistical ‘population’) of habitats for which field sample surveys are in place. Present technologies and data availability allow us to measure fragmentation through several metrics that can be calculated from RS data. In situ data have been collected in several countries over a longer term and these are fit for statistical analysis, producing statistics on species composition change, habitat richness and habitat structure. It is now possible to relate protocols for RS and in situ observations based on plant life forms, translate them and provide direct links between in situ and RS data.
Framing the concept of satellite remote sensing essential biodiversity variables: challenges and future directions
Pettorelli, Nathalie ; Wegmann, Martin ; Skidmore, Andrew ; Mücher, Sander ; Dawson, Terence P. ; Fernandez, Miguel ; Lucas, Richard ; Schaepman, Michael E. ; Wang, Tiejun ; O'Connor, Brian ; Jongman, Robert H.G. ; Kempeneers, Pieter ; Sonnenschein, Ruth ; Leidner, Allison K. ; Böhm, Monika ; He, Kate S. ; Nagendra, Harini ; Dubois, Grégoire ; Fatoyinbo, Temilola ; Hansen, Matthew C. ; Paganini, Marc ; Klerk, Helen M. De; Asner, Gregory P. ; Kerr, Jeremy T. ; Estes, Anna B. ; Schmeller, Dirk S. ; Heiden, Uta ; Rocchini, Duccio ; Pereira, Henrique M. ; Turak, Eren ; Fernandez, Nestor ; Lausch, Angela ; Cho, Moses A. ; Alcaraz-segura, Domingo ; Mcgeoch, Mélodie A. ; Turner, Woody ; Mueller, Andreas ; St-Louis, Véronique ; Penner, Johannes ; Vihervaara, Petteri ; Belward, Alan ; Reyers, Belinda ; Geller, Gary N. - \ 2016
Remote Sensing in Ecology and Conservation 2 (2016)3. - ISSN 2056-3485 - p. 122 - 131.
Although satellite-based variables have for long been expected to be key components to a unified and global biodiversity monitoring strategy, a definitive and agreed list of these variables still remains elusive. The growth of interest in biodiversity variables observable from space has been partly underpinned by the development of the essential biodiversity variable (EBV) framework by the Group on Earth Observations – Biodiversity Observation Network, which itself was guided by the process of identifying essential climate variables. This contribution aims to advance the development of a global biodiversity monitoring strategy by updating the previously published definition of EBV, providing a definition of satellite remote sensing (SRS) EBVs and introducing a set of principles that are believed to be necessary if ecologists and space agencies are to agree on a list of EBVs that can be routinely monitored from space. Progress toward the identification of SRS-EBVs will require a clear understanding of what makes a biodiversity variable essential, as well as agreement on who the users of the SRS-EBVs are. Technological and algorithmic developments are rapidly expanding the set of opportunities for SRS in monitoring biodiversity, and so the list of SRS-EBVs is likely to evolve over time. This means that a clear and common platform for data providers, ecologists, environmental managers, policy makers and remote sensing experts to interact and share ideas needs to be identified to support long-term coordinated actions.
Hyper-temporal SPOT-NDVI dataset parameterization captures species distributions
Girma, Atkilt ; Bie, C.A.J.M. de; Skidmore, Andrew K. ; Venus, Valentijn ; Bongers, Frans - \ 2016
International Journal of Geographical Information Science 30 (2016)1. - ISSN 1365-8816 - p. 89 - 107.
Boswellia papyrifera - HANTS - hyper-temporal - MAXENT - SPOT-NDVI

Hyper-temporal SPOT NDVI images contain useful information about the environment in which a species occurs, including information such as the beginning, end, peak, and curvature of photosynthetically active vegetation (PAV) greenness signatures. This raises the question: can parameterization of hyper-temporal SPOT NDVI images be useful to predict species distribution? A set of SPOT-NDVI images for the whole of Ethiopia covering nine years was classified using the unsupervised ISODATA clustering algorithm to group similar NDVI pixel values. The HANTS (Harmonic ANalysis of Time Series) algorithm, that fits series of smoothing cosine waves, was then applied to the time series for each of the NDVI classes to generate seven output Fourier components. These components, together with the topographic parameters slope and elevation, were used as predictors in a species distribution model using MAXENT. Presence-only data of one test species, Boswellia papyrifera, were modelled. This species is diminishing at an alarming rate and requires conservation. The performance of the model was evaluated by the area under curve (AUC) of the receiver-operating characteristics value. The output distribution map was tested for its agreement with the NDVI-clustering approach and conventional B. papyrifera distribution map using Kappa. The relative contributions of the first four predictors to the MAXENT in sequence were: 2nd harmonic phase, elevation, amplitude of the 1st harmonics, and amplitude of the 2nd harmonics. The average AUC test result for the 100 runs was 0.98 with a standard deviation of 0.002. The probability distribution map clearly shows high correlation with the B. papyrifera occurrence data. In addition, the distribution map was found to be in agreement with the NDVI-clustered and conventional map with improved details. Classifying hyper-temporal NDVI images and extracting their parameters through the use of the HANTS algorithm captures the PAV greenness behaviour (parameters) of the environment of the species studied. These parameters have proved successful in predicting the distribution of B. papyrifera.

Environmental science : Agree on biodiversity metrics to track from space
Skidmore, A.K. ; Pettorelli, Nathalie ; Coops, N.C. ; Geller, G.N. ; Hansen, Matthew ; Lucas, Richard ; Mücher, Sander ; O'Connor, Brian ; Paganini, Marc ; Pereira, Henrique Miguel ; Schaepman, M.E. ; Turner, Woody ; Wang, Tiejun ; Wegmann, Martin - \ 2015
Nature 523 (2015)7561. - ISSN 0028-0836 - p. 403 - 405.
High Spectral Resolution Image Processing for Mapping, Quantifying and Detecting Biodiversity II
Skidmore, A.K. ; Mücher, C.A. ; Wegmann, M. ; Pettorelli, N. ; Wang, T. - \ 2015
Understanding Boswellia papyrifera tree secondary metabolites through bark spectral analysis
Girma, A. ; Skidmore, A.K. ; Bie, C.A.J.M. de; Bongers, F. - \ 2015
ISPRS Journal of Photogrammetry and Remote Sensing 105 (2015). - ISSN 0924-2716 - p. 30 - 37.
Decision makers are concerned whether to tap or rest Boswellia Papyrifera trees. Tapping for the production of frankincense is known to deplete carbon reserves from the tree leading to production of less viable seeds, tree carbon starvation and ultimately tree mortality. Decision makers use traditional experience without considering the amount of metabolites stored or depleted from the stem-bark of the tree. This research was designed to come up with a non-destructive B. papyrifera tree metabolite estimation technique relevant for management using spectroscopy. The concentration of biochemicals (metabolites) found in the tree bark was estimated through spectral analysis. Initially, a random sample of 33 trees was selected, the spectra of bark measured with an Analytical Spectral Device (ASD) spectrometer. Bark samples were air dried and ground. Then, 10 g of sample was soaked in Petroleum ether to extract crude metabolites. Further chemical analysis was conducted to quantify and isolate pure metabolite compounds such as incensole acetate and boswellic acid. The crude metabolites, which relate to frankincense produce, were compared to plant properties (such as diameter and crown area) and reflectance spectra of the bark. Moreover, the extract was compared to the ASD spectra using partial least square regression technique (PLSR) and continuum removed spectral analysis. The continuum removed spectral analysis were performed, on two wavelength regions (1275–1663 and 1836–2217) identified through PLSR, using absorption features such as band depth, area, position, asymmetry and the width to characterize and find relationship with the bark extracts. The results show that tree properties such as diameter at breast height (DBH) and the crown area of untapped and healthy trees were strongly correlated to the amount of stored crude metabolites. In addition, the PLSR technique applied to the first derivative transformation of the reflectance spectrum was found to estimate the concentration of the metabolites reliably at higher coefficient of determination. The most influential maximum slope positions of the spectrum obtained through PLSR analysis of the petroleum ether extract (crude metabolites) and the pure compounds (incensole acetate and boswellic acid) were found to coincide and concentrate in the region between 1383–1406 nm and 1861–1896 nm. However, analysis on these two individual specific region absorption features relationship with the bark extract, using the continuum removed approach, was not as robust as the PLSR analysis. This reveals that the ability to estimate metabolites in the stem-bark of B. papyrifera using spectral analysis opens a new approach on how to manage B. papyrifera tree. Development of such technique provides quick and reliable information for decision makers to decide on when to tap or for how long to rest the trees. However, to implement the technique, further research need to be conducted to determine how B. papyrifera tree metabolites vary due to tapping. In addition, research to determine the lowest metabolites quantity threshold, useful for management of the tree, needs to be conducted.
Eutrophication of mangroves linked to depletion of foliar and soil base cations
Fauzi, A. ; Skidmore, A.K. ; Heitkonig, I.M.A. ; Gils, H. van; Schlerf, M. - \ 2014
Environmental Monitoring and Assessment 186 (2014)12. - ISSN 0167-6369 - p. 8487 - 8498.
northeastern united-states - avicennia-marina - ammonium-sulfate - shrimp farms - pond culture - forest trees - red spruce - nitrogen - nutrient - phosphorus
There is growing concern that increasing eutrophication causes degradation of coastal ecosystems. Studies in terrestrial ecosystems have shown that increasing the concentration of nitrogen in soils contributes to the acidification process, which leads to leaching of base cations. To test the effects of eutrophication on the availability of base cations in mangroves, we compared paired leaf and soil nutrient levels sampled in Nypa fruticans and Rhizophora spp. on a severely disturbed, i.e. nutrient loaded, site (Mahakam delta) with samples from an undisturbed, near-pristine site (Berau delta) in East Kalimantan, Indonesia. The findings indicate that under pristine conditions, the availability of base cations in mangrove soils is determined largely by salinity. Anthropogenic disturbances on the Mahakam site have resulted in eutrophication, which is related to lower levels of foliar and soil base cations. Path analysis suggests that increasing soil nitrogen reduces soil pH, which in turn reduces the levels of foliar and soil base cations in mangroves.
Chemical variation in Jacobaea vulgaris is influenced by the interaction of season and vegetation successional stage
Almeida De Carvalho, S. ; Macel, M. ; Mulder, P.P.J. ; Skidmore, A. ; Putten, W.H. van der - \ 2014
Phytochemistry 99 (2014). - ISSN 0031-9422 - p. 86 - 94.
senecio-jacobaea - pyrrolizidine alkaloids - plant-communities - tyria-jacobaeae - cinnabar moth - life-history - dual role - soil - chronosequence - nitrogen
Knowledge on spatio-temporal dynamics of plant primary and secondary chemistry under natural conditions is important to assess how plant defence varies in real field conditions. Plant primary and secondary chemistry is known to vary with both season and vegetation successional stage, however, in few studies these two sources of variation have been examined in combination. Here we examine variations in primary and secondary chemistry of Jacobaea vulgaris (Asteraceae) throughout the growing season in early, mid, and late stages of secondary succession following land abandonment using a well-established chronosequence in The Netherlands.
Coupling socio-economic factors and eco-hydrological processes using a cascade-modeling approach
Odongo, V.O. ; Mulatu, D.W. ; Muthoni, F.K. ; Oel, P.R. van; Meins, F.M. ; Tol, C. van der; Skidmore, A.K. ; Groen, T.A. ; Becht, R. ; Onyando, J.O. ; Veen, A. van der - \ 2014
Journal of Hydrology 518 (2014)Part A. - ISSN 0022-1694 - p. 49 - 59.
land-use change - murray-darling basin - lake naivasha - population-dynamics - water availability - stream ecosystems - human impact - east-africa - kenya - rainfall
Most hydrological studies do not account for the socio-economic influences on eco-hydrological processes. However, socio-economic developments often change the water balance substantially and are highly relevant in understanding changes in hydrological responses. In this study a multi-disciplinary approach was used to study the cascading impacts of socio-economic drivers of land use and land cover (LULC) changes on the eco-hydrological regime of the Lake Naivasha Basin. The basin has recently experienced substantial LULC changes exacerbated by socio-economic drivers. The simplified cascade models provided insights for an improved understanding of the socio-ecohydrological system. Results show that the upstream population has transformed LULC such that runoff during the period 1986–2010 was 32% higher than during the period 1961–1985. Cut-flower export volumes and downstream population growth explain 71% of the water abstracted from Lake Naivasha. The influence of upstream population on LULC and upstream hydrological processes explained 59% and 30% of the variance in lake storage volumes and sediment yield respectively. The downstream LULC changes had significant impact on large wild herbivore mammal species on the fringe zone of the lake. This study shows that, in cases where observed socio-economic developments are substantial, the use of a cascade-modeling approach, that couple socio-economic factors to eco-hydrological processes, can greatly improve our understanding of the eco-hydrological processes of a catchment.
Ungulate herbivory overrides rainfall impacts on herbaceous regrouth and residual biomass in a key resource area
Muthoni, F.K. ; Groen, T.A. ; Skidmore, A.K. ; Oel, P.R. van - \ 2014
Journal of Arid Environments 100-101 (2014). - ISSN 0140-1963 - p. 9 - 17.
net primary productivity - papyrus cyperus-papyrus - lake naivasha - nonequilibrium concepts - semiarid savanna - kenya - vegetation - grassland - ecosystem - plants
Key grazing lands that provide dry season forage to both resident and migrating ungulates may experience heavy grazing impacts during the dry season, thereby jeopardizing future forage productivity. In this study a herbivore exclosure experiment was used to quantify the effects of grazing by large ungulates on herbaceous regrowth and residual aboveground biomass in a fragmented key resource area; the fringe zone around Lake Naivasha, Kenya. Top-down control mechanisms were prevalent in both the dry and wet seasons suggesting the existence of a high resident herbivore density. Intense grazing significantly reduced residual biomass that in turn reduced plant regrowth. An increased frequency of defoliation reduced regrowth during the dry season demonstrating the negative effect resulting from high herbivore densities during the dry season. This study indicates that grazing exerts a higher control on regrowth than rainfall as heavily grazed residual biomass did not recover during the following wet season.
Smallholder Farms as Stepping Stone Corridors for Crop-Raiding Elephant in Northern Tanzania: Integration of Bayesian Expert System and Network Simulator
Pittiglio, C. ; Skidmore, A.K. ; Gils, H.A.M. van; McCall, M.K. ; Prins, H.H.T. - \ 2014
Ambio 43 (2014)2. - ISSN 0044-7447 - p. 149 - 161.
tarangire-manyara ecosystem - african elephants - land-use - national-park - conflict - conservation - patterns - wildlife - management - landscape
Crop-raiding elephants affect local livelihoods, undermining conservation efforts. Yet, crop-raiding patterns are poorly understood, making prediction and protection difficult. We hypothesized that raiding elephants use corridors between daytime refuges and farmland. Elephant counts, crop-raiding records, household surveys, Bayesian expert system, and least-cost path simulation were used to predict four alternative categories of daily corridors: (1) footpaths, (2) dry river beds, (3) stepping stones along scattered small farms, and (4) trajectories of shortest distance to refuges. The corridor alignments were compared in terms of their minimum cumulative resistance to elephant movement and related to crop-raiding zones quantified by a kernel density function. The "stepping stone" corridors predicted the crop-raiding patterns. Elephant presence was confirmed along these corridors, demonstrating that small farms located between refuges and contiguous farmland increase habitat connectivity for elephant. Our analysis successfully predicted elephant occurrence in farmland where daytime counts failed to detect nocturnal presence. These results have conservation management implications
Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling
Wielstra, B.M. ; Crnobrnja-Isailovic, J. ; Litvinchuk, S.N. ; Reijnen, B.T. ; Skidmore, A.K. ; Sotiropoulos, K. ; Toxopeus, A.G. ; Tzankov, N. ; Vukov, T. ; Arntzen, J.W. - \ 2013
Frontiers in Zoology 10 (2013)1. - ISSN 1742-9994 - 14 p.
crested newt - niche conservatism - climate-change - hybrid zone - gene flow - time - space - introgression - quaternary - evolution
Introduction The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial. Results We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps. Conclusions The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the ‘southern richness and northern purity’ paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an ‘extra-Mediterranean’ refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges
Hyperspectral reflectance of leaves and flowers of an outbreak species discriminates season and successional stage of vegetation
Almeida De Carvalho, S. ; Schlerf, M. ; Putten, W.H. van der; Skidmore, A. - \ 2013
International Journal of applied Earth Observation and Geoinformation 24 (2013). - ISSN 0303-2434 - p. 32 - 41.
absorption features - qinling mountains - leaf biochemistry - senecio-jacobaea - golden takin - plant - soil - chemistry - forest - chronosequence
Spectral reflectance can be used to assess large-scale performances of plants in the field based on plant nutrient balance as well as composition of defence compounds. However, plant chemical composition is known to vary with season – due to its phenology – and it may even depend on the succession stage of its habitat. Here we investigate (i) how spectral reflectance could be used to discriminate successional and phenological stages of Jacobaea vulgaris in both leaf and flower organs and (ii) if chemical content estimation by reflectance is flower or leaf dependent. We used J. vulgaris, which is a natural outbreak plant species on abandoned arable fields in north-western Europe and studied this species in a chronosequence representing successional development during time since abandonment. The chemical content and reflectance between 400 and 2500 nm wavelengths of flowers and leaves were measured throughout the season in fields of different successional ages. The data were analyzed with multivariate statistics for temporal discrimination and estimation of chemical contents in both leaf and flower organs. Two main effects were revealed by spectral reflectance measurements: (i) both flower and leaf spectra show successional and seasonal changes, but the pattern is complex and organ specific (ii) flower head pyrrolizidine alkaloids, which are involved in plant defence against herbivores, can be detected through hyperspectral reflectance.We conclude that spectral reflectance of both leaves and flowers can provide information on plant performance during season and successional stages. As a result, remote sensing studies of plant performance in complex field situations will benefit from considering hyperspectral reflectance of different plant organs. This approach may enable more detailed studies on the link between spectral information and plant defence dynamics both aboveground and belowground.
Shrimp pond effluent dominates foliar nitrogen in disturbed mangroves as mapped using hyperspectral imagery
Fauzi, A. ; Skidmore, A.K. ; Gils, H. ; Schlerf, M. ; Heitkonig, I.M.A. - \ 2013
Marine Pollution Bulletin 76 (2013)1-2. - ISSN 0025-326X - p. 42 - 51.
leaf-area index - species discrimination - absorption features - chlorophyll content - squares regression - vegetation indexes - avicennia-marina - canopy nitrogen - reflectance - forest
Conversion of mangroves to shrimp ponds creates fragmentation and eutrophication. Detection of the spatial variation of foliar nitrogen is essential for understanding the effect of eutrophication on mangroves. We aim (i) to estimate nitrogen variability across mangrove landscapes of the Mahakam delta using airborne hyperspectral remote sensing (HyMap) and (ii) to investigate links between the variation of foliar nitrogen mapped and local environmental variables. In this study, multivariate prediction models achieved a higher level of accuracy than narrow-band vegetation indices, making multivariate modeling the best choice for mapping. The variation of foliar nitrogen concentration in mangroves was significantly influenced by the local environment: (1) position of mangroves (seaward/landward), (2) distance to the shrimp ponds, and (3) predominant mangrove species. The findings suggest that anthropogenic disturbances, in this case shrimp ponds, influence nitrogen variation in mangroves. Mangroves closer to the shrimp ponds had higher foliar nitrogen concentrations.
Jacobaea through the eyes of spectroscopy : identifying plant interactions with the (a)biotic environment by chemical variation effects on spectral reflectance patterns
Almeida De Carvalho, S. - \ 2013
University. Promotor(en): Wim van der Putten; Andrew Skidmore, co-promotor(en): M. Macel; M. Schlerf. - S.l. : s.n. - ISBN 9789461737502 - 180
senecio jacobaea - senecio erucifolius - pyrrolizidinealkaloïden - voedingsstoffen - spectraalanalyse - spectroscopie - bodemmicrobiologie - metabolieten - chemische analyse - plantensuccessie - pyrrolizidine alkaloids - nutrients - spectral analysis - spectroscopy - soil microbiology - metabolites - chemical analysis - plant succession

Plants interact with a wide array of aboveground and belowground herbivores, pathogens, mutualists, and their natural enemies. These interactions are important drivers of spatio-temporal changes in vegetation, however, they may be difficult to be revealed without extensive sampling.In this thesis I investigated the potential of visible and near-infrared spectral measurements to detect plant chemical changes that may reflect interactions between plants and biotic or abiotic soil factors. First, I examined the relative contribution of pyrrolizidine alkaloids (PAs; these are defence compounds of Senecio-type plants against generalist herbivores) to the spectral reflectance features in the visible and short-wave infrared region. My hypothesis was that PAs can be predicted from specific spectral features of aboveground plant tissues. Since PA profiles and their relation to spectral features could be species specific I compared three different species, Jacobaea vulgaris, J. erucifolia and S. inaequidens subjected to nutrient and water treatments to stimulate plant chemical variation. Pyrrolizidine alkaloids were predicted best by spectral reflectance features in the case of Jacobaea vulgaris. I related the better results obtained with J. vulgaris to the existence of the correlation between PAs and nitrogen and the presence of the epoxide chemical structure in J. vulgaris.

I also examined if different soil microbial communities influenced plant shoot spectral reflectance. I grew the same three plant species as before in sterilized soil and living soil collected from fields with J. vulgaris. I expected that soil biota would change shoot defence content and hyperspectral reflectance in plant species-specific ways. Indeed, the exposure to different soils caused plant chemical profiles to change and both chemical and spectral patterns discriminated plants according to the soil biotic conditions.

I studied how primary and secondary plant metabolites varied during the growing season and vegetation successional stages. I used a well-studied chronosequence of abandoned arable fields and analysed the chemistry of both leaves and flowers of Jacobaea vulgaris throughout the seasons in fields of different successional status. My general hypothesis was that seasonal allocation of nutrients and defence metabolites to reproductive organs fitted the optimal defence theory, but that pattern was dependent on the successional stage of the vegetation. I found an interaction between season and succession stage, as plants from longer abandoned fields generally had flowers and leaves with higher N-oxides, especially in late Summer. Independent of the succession stage there was a seasonal allocation of nutrients and defence metabolites to flowers. Analyses of spectral reflectance of the field plants showed thatdefence compounds could be estimated more reliably in flowers, while in leaves primary compounds could be predicted best. Succession classes were successfully discriminated by the spectral patterns of flowers. Both chemical and spectral findings suggested that flowers are more sensitive to field ageing processes than leaves.


The estimation of pyrrolizidine alkaloids by spectral reflectance features was better in Jacobaea vulgaris than in Senecio inaequidens or Jacobaea erucifolia (chapter 2). Differences in soil communities affect plant leaves’ chemistry and spectral reflectance patterns (chapter 3). Jacobaea vulgarisplants from recent and longer-abandoned fields showed the largest differences in chemical concentration, composition of defence compounds, and spectral reflectance patterns. Flowers were more discriminatory than leaves (chapters 4 and 5). There is a potential to detect plant-biotic interactions by analyzing spectral reflectance patterns (this thesis).
Non-linear partial least square regression increases the estimation accuracy of grass nitrogen and phosphorus using in situ hyperspectral and environmental data
Ramoelo, A. ; Skidmore, A.K. ; Cho, M.A. ; Mathieu, R. ; Heitkonig, I.M.A. ; Dudeni-Tlhone, N. ; Schlerf, M. ; Prins, H.H.T. - \ 2013
ISPRS Journal of Photogrammetry and Remote Sensing 82 (2013). - ISSN 0924-2716 - p. 27 - 40.
kruger-national-park - multiple linear-regression - band-depth analysis - vegetation indexes - south-africa - chlorophyll estimation - imaging spectroscopy - absorption features - biochemical content - mineral-nutrition
Grass nitrogen (N) and phosphorus (P) concentrations are direct indicators of rangeland quality and provide imperative information for sound management of wildlife and livestock. It is challenging to estimate grass N and P concentrations using remote sensing in the savanna ecosystems. These areas are diverse and heterogeneous in soil and plant moisture, soil nutrients, grazing pressures, and human activities. The objective of the study is to test the performance of non-linear partial least squares regression (PLSR) for predicting grass N and P concentrations through integrating in situ hyperspectral remote sensing and environmental variables (climatic, edaphic and topographic). Data were collected along a land use gradient in the greater Kruger National Park region. The data consisted of: (i) in situ-measured hyperspectral spectra, (ii) environmental variables and measured grass N and P concentrations. The hyperspectral variables included published starch, N and protein spectral absorption features, red edge position, narrow-band indices such as simple ratio (SR) and normalized difference vegetation index (NDVI). The results of the non-linear PLSR were compared to those of conventional linear PLSR. Using non-linear PLSR, integrating in situ hyperspectral and environmental variables yielded the highest grass N and P estimation accuracy (R2 = 0.81, root mean square error (RMSE) = 0.08, and R2 = 0.80, RMSE = 0.03, respectively) as compared to using remote sensing variables only, and conventional PLSR. The study demonstrates the importance of an integrated modeling approach for estimating grass quality which is a crucial effort towards effective management and planning of protected and communal savanna ecosystems.
Elephant response to spatial heterogeneity in a savanna landscape of northern Tanzania
Pittiglio, C. ; Skidmore, A.K. ; Gils, H.A.M.J. van; Prins, H.H.T. - \ 2013
Ecography 36 (2013)7. - ISSN 0906-7590 - p. 819 - 831.
habitat heterogeneity - wavelet analysis - time-series - vegetation - ecology - scale - conservation - stability - patterns - models
Landscape heterogeneity, namely the variation of a landscape property across space and time, can influence the distribution of a species and its abundance. Quantifying landscape heterogeneity is important for the management of semi-natural areas through predicting species response to landscape changes, such as habitat fragmentation. In this paper, we tested whether the change in spatial heterogeneity of the vegetation cover due to farming expansion affected the distribution of the African elephant in the Tarangire-Manyara ecosystem, northern Tanzania. Spatial heterogeneity (based on the normalized difference vegetation index) was characterized at multiple spatial scales using the wavelet transform and the intensity-dominant scale method. Elephant distribution was estimated from time-series aerial surveys using a kernel density function. The intensity, which relates to the contrast in vegetation cover, quantified the maximum variation in NDVI across multiple spatial scales, whereas the dominant scale, which represents the scale at which this maximum variation occurs, identified the dominant inter-patches distance, i.e. the size of dominant landscape features. We related the dominant scale of spatial heterogeneity to the probability of elephant occurrence in order to identify: 1) the scale that maximizes elephant occurrence, and 2) its change between 1988 and 2001. Neither the dominant scale and intensity of spatial heterogeneity, nor the probability of the elephant occurrence changed significantly between 1988 and 2001. The spatial scale maximizing elephant occurrence remained constant at 7000 to 8000 m during each wet season. Compared to the findings of a recent, similar study in Zimbabwe, our results suggest that the change in the dominant scale was relatively small in Tarangire-Manyara ecosystem and well within the critical threshold for elephant persistence. The method is a useful tool for monitoring ecosystems and their properties.
Changes in plant defense chemistry (pyrrolizidine alkaloids) revealed through high-resolution spectroscopy
Almeida De Carvalho, S. ; Macel, M. ; Schlerf, M. ; Moghaddam, F.E. ; Mulder, P.P.J. ; Skidmore, A.K. ; Putten, W.H. van der - \ 2013
ISPRS Journal of Photogrammetry and Remote Sensing 80 (2013). - ISSN 0924-2716 - p. 51 - 60.
near-infrared spectroscopy - senecio-jacobaea - red edge - nitrogen - leaf - reflectance - forest - regression - vegetation - prediction
Plant toxic biochemicals play an important role in defense against natural enemies and often are toxic to humans and livestock. Hyperspectral reflectance is an established method for primary chemical detection and could be further used to determine plant toxicity in the field. In order to make a first step for pyrrolizidine alkaloids detection (toxic defense compound against mammals and many insects) we studied how such spectral data can estimate plant defense chemistry under controlled conditions. In a greenhouse, we grew three related plant species that defend against generalist herbivores through pyrrolizidine alkaloids: Jacobaea vulgaris, Jacobaea erucifolia and Senecio inaequidens, and analyzed the relation between spectral measurements and chemical concentrations using multivariate statistics. Nutrient addition enhanced tertiary-amine pyrrolizidine alkaloids contents of J. vulgaris and J. erucifolia and decreased N-oxide contents in S. inaequidens and J. vulgaris. Pyrrolizidine alkaloids could be predicted with a moderate accuracy. Pyrrolizidine alkaloid forms tertiary-amines and epoxides were predicted with 63% and 56% of the variation explained, respectively. The most relevant spectral regions selected for prediction were associated with electron transitions and CH, OH, and NH bonds in the 1530 and 2100 nm regions. Given the relatively low concentration in pyrrolizidine alkaloids concentration (in the order of mg g-1) and resultant predictions, it is promising that pyrrolizidine alkaloids interact with incident light. Further studies should be considered to determine if such a non-destructive method may predict changes in PA concentration in relation to plant natural enemies. Spectroscopy may be used to study plant defenses in intact plant tissues, and may provide managers of toxic plants, food industry and multitrophic-interaction researchers with faster and larger monitoring possibilities
Estimating tropical forest biomass more accurately by integrating ALOS PALSAR and Landsat-7 ETM+ data
Basuki, T.M. ; Skidmore, A.K. ; Hussin, Y.A. ; Duren, I.C. van - \ 2013
International Journal of Remote Sensing 34 (2013)13. - ISSN 0143-1161 - p. 4871 - 4888.
multisensor image fusion - aboveground biomass - wavelet transform - jers-1 sar - satellite estimation - band sar - decomposition - multiresolution - lidar - queensland
Integration of multisensor data provides the opportunity to explore benefits emanating from different data sources. A fusion between fraction images derived from spectral mixture analysis of Landsat-7 ETM+ and phased array L-band synthetic aperture radar (PALSAR) is introduced. The aim of this fusion is to improve the estimation accuracy of above-ground biomass (AGB) in lowland mixed dipterocarp forest. Spectral mixture analysis was applied to decompose a mixture of spectral components of Landsat-7 ETM+ into vegetation, soil, and shade fractions. These fraction images were integrated with PALSAR data using the discrete wavelet transform (DWT) and Brovey transform. As a comparison, spectral reflectance of Landsat-7 ETM+ was fused directly with PALSAR data. Backscatter of horizontal-horizontal and horizontal-vertical polarizations was also used to estimate AGB. Forest inventory was carried out in 77 randomly distributed plots, the data being used for either model development or validation. A local allometric equation was applied to calculate AGB per plot. Regression models were developed by integrating field measurements of 50 sample plots with remotely sensed data, e.g. fraction images, reflectance of Landsat-7 ETM+, and PALSAR data. The models developed were validated using 27 independent sample plots. The results showed that not all fused images significantly improved the accuracy of AGB estimation. The model based on Brovey transform using the reflectance of Landsat-7ETM+ and PALSAR produced an R 2 of only 0.03-0.10. By contrast, fusion between PALSAR data and fraction images using Brovey transform improved the accuracy of R 2 to 0.33-0.46. Further improvement in the accuracy of estimating AGB was observed when DWT was applied to integrate PALSAR with the reflectance of Landsat-7ETM+ (R 2 = 0.69-0.72) and PALSAR with fraction images (R 2 = 0.70-0.75).
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