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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    Fairly efficient, efficiently fair: Lessons from designing and testing payment schemes for ecosystem services in Asia
    Leimona, B. ; Noordwijk, M. van; Groot, J.C.J. ; Leemans, R. - \ 2015
    Ecosystem Services 12 (2015). - ISSN 2212-0416 - p. 16 - 28.
    pacific decadal oscillation - normalized burn ratio - western united-states - climate-change - interior alaska - north-america - landsat data - new-mexico - vegetation - area
    Paymentforecosystemservices(PES)iscommonlydefined asamarket-basedenvironmentalpolicy instrument toefficiently achieveecosystemservicesprovision.However,anincreasingbodyofliterature showsthatthisprescriptiveconceptualizationofPEScannotbeeasilygeneralizedandimplementedin practice, andthatthecommodification ofecosystemservices(ES)isproblematicandmayleadtounfair situations forrelevantPESactors.ThispapersynthesizescasestudiesinIndonesia,thePhilippinesand Nepal toprovideempiricalobservationsonemergingPESmechanismsinAsia.Lessonslearnedshow that fairnessandefficiency objectivesmustbeachievedsimultaneouslyindesigningandimplementing a sustainablePESscheme,especiallyindevelopingcountrycontexts.Neitherfairnessnorefficiency isa primary aimbutanintermediate ‘fairlyefficient andefficiently fair’ PES maybridgethegapbetweenPES theory andpracticetoincreasesustainableESprovisionandimprovelivelihoods.
    Estimating Asian terrestrial carbon fluxes from CONTRAIL aircraft and surface CO2 observations for the period 2006 to 2010
    Zhang, H.F. ; Chen, B.Z. ; Laan-Luijkx, I.T. van der; Machida, T. ; Matsueda, H. ; Sawa, Y. ; Peters, W. - \ 2014
    Atmospheric Chemistry and Physics 14 (2014)11. - ISSN 1680-7316 - p. 5807 - 5824.
    atmospheric co2 - interannual variability - parameterization sib2 - model formulation - transport models - dioxide exchange - north-america - south-asia - east-asia - china
    Current estimates of the terrestrial carbon fluxes in Asia show large uncertainties particularly in the boreal and mid-latitudes and in China. In this paper, we present an updated carbon flux estimate for Asia ("Asia" refers to lands as far west as the Urals and is divided into boreal Eurasia, temperate Eurasia and tropical Asia based on TransCom regions) by introducing aircraft CO2 measurements from the CONTRAIL (Comprehensive Observation Network for Trace gases by Airline) program into an inversion modeling system based on the CarbonTracker framework. We estimated the averaged annual total Asian terrestrial land CO2 sink was about -1.56 Pg C yr-1 over the period 2006–2010, which offsets about one-third of the fossil fuel emission from Asia (+4.15 Pg C yr-1). The uncertainty of the terrestrial uptake estimate was derived from a set of sensitivity tests and ranged from -1.07 to -1.80 Pg C yr-1, comparable to the formal Gaussian error of ±1.18 Pg C yr-1 (1-sigma). The largest sink was found in forests, predominantly in coniferous forests (-0.64 ± 0.70 Pg C yr-1) and mixed forests (-0.14 ± 0.27 Pg C yr-1); and the second and third large carbon sinks were found in grass/shrub lands and croplands, accounting for -0.44 ± 0.48 Pg C yr-1 and -0.20 ± 0.48 Pg C yr-1, respectively. The carbon fluxes per ecosystem type have large a priori Gaussian uncertainties, and the reduction of uncertainty based on assimilation of sparse observations over Asia is modest (8.7–25.5%) for most individual ecosystems. The ecosystem flux adjustments follow the detailed a priori spatial patterns by design, which further increases the reliance on the a priori biosphere exchange model. The peak-to-peak amplitude of inter-annual variability (IAV) was 0.57 Pg C yr-1 ranging from -1.71 Pg C yr-1 to -2.28 Pg C yr-1. The IAV analysis reveals that the Asian CO2 sink was sensitive to climate variations, with the lowest uptake in 2010 concurrent with a summer flood and autumn drought and the largest CO2 sink in 2009 owing to favorable temperature and plentiful precipitation conditions. We also found the inclusion of the CONTRAIL data in the inversion modeling system reduced the uncertainty by 11% over the whole Asian region, with a large reduction in the southeast of boreal Eurasia, southeast of temperate Eurasia and most tropical Asian areas.
    Blood feeding on large grazers affects the transmission of Borrelia burgdorferi sensu lato by Ixodes ricinus
    Pacilly, F.C.A. ; Benning, M.E. ; Jacobs, F. ; Leidekker, J. ; Sprong, H. ; Wieren, S.E. van; Takken, W. - \ 2014
    Ticks and Tick-borne Diseases 5 (2014)6. - ISSN 1877-959X - p. 810 - 817.
    lyme borreliosis - tick infestation - north-america - endemic area - roe deer - netherlands - prevalence - density - disease - abundance
    The presence of Ixodes ricinus and their associated Borrelia infections on large grazers was investigated. Carcases of freshly shot red deer, mouflon and wild boar were examined for the presence of any stage of I. ricinus. Questing ticks were collected from locations where red deer and wild boar are known to occur. Presence of Borrelia burgdorferi s.l. DNA was examined in a fraction of the collected ticks. Larvae, nymphs and adult ticks were found on the three large grazers. Red deer had the highest tick burden, with many of the nymphs and adult females attached for engorgement. Most larvae had not attached. The mean number of ticks on the animals varied from 13 to 67. Ticks were highly aggregated amongst the animals: some animals had no ticks, while others had high numbers. Larvae and nymphs were mostly found on the ears, while adult ticks were attached to the axillae. The Borrelia infection rate of questing nymphs was 8.5%. Unengorged wandering nymphs on deer had a Borrelia infection rate of 12.5%, while only 0.9% of feeding nymphs carried a Borrelia infection. The infection rate of unengorged adult male ticks was 4.5%, and that of feeding female ticks was 0.7%. The data suggest that ticks feeding on red deer and wild boar lose their Borrelia infections. The implications of the results are discussed with respect to Borrelia epidemiology and maintenance of a Borrelia reservoir as well as the role of reproductive hosts for Ixodes ricinus.
    Anthropogenic emissions of NOx over China: Reconciling the difference of inverse modeling results using GOME-2 and OMI measurements
    Gu, D. ; Wang, Y. ; Smelzer, C. ; Boersma, K.F. - \ 2014
    Journal of Geophysical Research: Atmospheres 119 (2014)12. - ISSN 2169-897X - p. 7732 - 7740.
    ozone monitoring instrument - simulated tropospheric no2 - satellite-observations - convective-transport - seasonal-variations - north-america - lightning nox - past decade - east china - columns
    Inverse modeling using satellite observations of nitrogen dioxide (NO2) columns has been extensively used to estimate nitrogen oxides (NOx) emissions in China. Recently, the Global Ozone Monitoring Experiment-2 (GOME-2) and Ozone Monitoring Instrument (OMI) provide independent global NO2 column measurements on a nearly daily basis at around 9:30 and 13:30 local time across the equator, respectively. Anthropogenic NOx emission estimates by applying previously developed monthly inversion (MI) or daily inversion (DI) methods to these two sets of measurements show substantial differences. We improve the DI method by conducting model simulation, satellite retrieval, and inverse modeling sequentially on a daily basis. After each inversion, we update anthropogenic NOx emissions in the model simulation with the newly obtained a posteriori results. Consequently, the inversion-optimized emissions are used to compute the a priori NO2 profiles for satellite retrievals. As such, the a priori profiles used in satellite retrievals are now coupled to inverse modeling results. The improved procedure was applied to GOME-2 and OMI NO2 measurements in 2011. The new daily retrieval-inversion (DRI) method estimates an average NOx emission of 6.9 Tg N/yr over China, and the difference between using GOME-2 and OMI measurements is 0.4 Tg N/yr, which is significantly smaller than the difference of 1.3 Tg N/yr using the previous DI method. Using the more consistent DRI inversion results, we find that anthropogenic NOx emissions tend to be higher in winter and summer than spring (and possibly fall) and the weekday-to-weekend emission ratio tends to increase with NOx emission in China.
    Net terrestrial CO2 exchange over China during 2001-2010 estimated with an ensemble data assimilation system for atmospheric CO 2
    Zhang, H.F. ; Chen, B.Z. ; Laan-Luijkx, I.T. van der; Peters, W. ; Chen, J. ; Xu, G. ; Yan, J.W. ; Zhou, X. ; Fukuyama, Y. ; Tans, P.P. - \ 2014
    Journal of Geophysical Research: Atmospheres 119 (2014)6. - ISSN 2169-897X - p. 3500 - 3515.
    carbon-dioxide exchange - flux inversion - north-america - ecosystems - sinks - transport - surface - temperature - forests - trends
    In this paper we present an estimate of net ecosystem CO2 exchange over China for the years 2001–2010 using the CarbonTracker Data Assimilation System for CO2 (CTDAS). Additional Chinese and Asian CO2 observations are used in CTDAS to improve our estimate. We found that the combined terrestrial ecosystems in China absorbed about -0.33 Pg C yr-1 during 2001–2010. The uncertainty on Chinese terrestrial carbon exchange estimates as derived from a set of sensitivity experiments suggests a range of -0.29 to -0.64 Pg C yr-1. This total Chinese terrestrial CO2 sink is attributed to the three major biomes (forests, croplands, and grass/shrublands) with estimated CO2 fluxes of -0.12 Pg C yr-1 (range from -0.09 to -0.19 Pg C yr-1), -0.12 Pg C yr-1 (range from -0.09 to -0.26 Pg C yr-1), and -0.09 Pg C yr-1 (range from -0.09 to -0.17 Pg C yr-1), respectively. The peak-to-peak amplitude of interannual variability of the Chinese terrestrial ecosystem carbon flux is 0.21 Pg C yr-1 (~64% of mean annual average), with the smallest CO2 sink (-0.19 Pg C yr-1) in 2003 and the largest CO2 sink (-0.40 Pg C yr-1) in 2007. We stress that our estimate of terrestrial ecosystem CO2 uptake based on inverse modeling strongly depends on a limited number of atmospheric CO2 observations used. More observations in China specifically and in Asia in general are needed to improve the accuracy of terrestrial carbon budgeting for this region
    Multilocus Sequence Typing for Characterization of Staphylococcus pseudintermedius
    Solyman, S.M. ; Black, C.C. ; Duim, B. ; Perreten, V. ; Duijkeren, E. van; Wagenaar, J.A. ; Eberlein, L.C. ; Sadeghi, L.N. ; Videla, R. ; Bemis, D.A. ; Kania, S.A. - \ 2013
    Journal of Clinical Microbiology 51 (2013)1. - ISSN 0095-1137 - p. 306 - 310.
    methicillin-resistant - antibiotic-resistance - north-america - dogs - intermedius - meca - clones - aureus - susceptibility - emergence
    Staphylococcus pseudintermedius is an opportunistic pathogen in dogs. Four housekeeping genes with allelic polymorphisms were identified and used to develop an expanded multilocus sequence typing (MLST) scheme. The new seven-locus technique shows S. pseudintermedius to have greater genetic diversity than previous methods and discriminates more isolates based upon host origin.
    Nested atmospheric inversion for the terrestrial carbon sources and sinks in China
    Jiang, F. ; Wang, H.W. ; Chen, J.M. ; Zhou, L.X. ; Ju, W.M. ; Peters, W. - \ 2013
    Biogeosciences 10 (2013)8. - ISSN 1726-4170 - p. 5311 - 5324.
    net primary production - interannual variability - dioxide exchange - flux inversion - north-america - co2 sources - transport - model - emissions - forests
    In this study, we establish a~nested atmospheric inversion system with a focus on China using the Bayes theory. The global surface is separated into 43 regions based on the 22 TransCom large regions, with 13 small regions in China. Monthly CO2 concentrations from 130 GlobalView sites and a Hong Kong site are used in this system. The core component of this system is atmospheric transport matrix, which is created using the TM5 model with a horizontal resolution of 3° × 2°. The net carbon fluxes over the 43 global land and ocean regions are inverted for the period from 2002 to 2009. The inverted global terrestrial carbon sinks mainly occur in Boreal Asia, South and Southeast Asia, eastern US and southern South America (SA). Most China areas appear to be carbon sinks, with strongest carbon sinks located in Northeast China. From 2002 to 2009, the global terrestrial carbon sink has an increasing trend, with the lowest carbon sink in 2002. The inter-annual variation (IAV) of the land sinks shows remarkable correlation with the El Niño Southern Oscillation (ENSO). However, no obvious trend is found for the terrestrial carbon sinks in China. The IAVs of carbon sinks in China show strong relationship with drought and temperature. The mean global and China terrestrial carbon sinks over the period 2002–2009 are -3.15 ± 1.48 and -0.21 ± 0.23 Pg C yr-1, respectively. The uncertainties in the posterior carbon flux of China are still very large, mostly due to the lack of CO2 measurement data in China.
    Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi
    Gomes, R.R. ; Glienke, C. ; Videira, S.I.R. ; Lombard, L. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 1 - 41.
    internal transcribed spacer - south-africa - species concepts - sp-nov - coelomycete phomopsis - foeniculum-vulgare - multigene analysis - north-america - ribosomal dna - twig dieback
    Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.
    Trend change detection in NDVI time series: Effects of inter-annual variability and methodology
    Forkel, M. ; Carvalhais, N. ; Verbesselt, J. ; Mahecha, M.D. ; Neigh, C. ; Reichstein, M. - \ 2013
    Remote Sensing 5 (2013)5. - ISSN 2072-4292 - p. 2113 - 2144.
    spectral vegetation indexes - satellite data - north-america - boreal forest - el-nino - alaska - modis - climate - disturbance - accuracy
    Changing trends in ecosystem productivity can be quantified using satellite observations of Normalized Difference Vegetation Index (NDVI). However, the estimation of trends from NDVI time series differs substantially depending on analyzed satellite datase
    Refugia: identifying and understanding safe havens for biodiversity under climate change
    Keppel, G. ; Niel, K.P. Van; Wardell-Johnson, G.W. ; Yates, C.J. ; Byrne, M. ; Mucina, L. ; Schut, A.G.T. ; Hopper, S.D. ; Franklin, S.E. - \ 2012
    Global Ecology and Biogeography 21 (2012)4. - ISSN 1466-822X - p. 393 - 404.
    postglacial dispersal limitation - species distribution models - glacial refugia - comparative phylogeography - north-america - vegetation distribution - pleistocene refugia - mediterranean basin - functional traits - genetic diversity
    Aim Identifying and protecting refugia is a priority for conservation under projected anthropogenic climate change, because of their demonstrated ability to facilitate the survival of biota under adverse conditions. Refugia are habitats that components of biodiversity retreat to, persist in and can potentially expand from under changing environmental conditions. However, the study and discussion of refugia has often been ad hoc and descriptive in nature. We therefore: (1) provide a habitat-based concept of refugia, and (2) evaluate methods for the identification of refugia. Location Global. Methods We present a simple conceptual framework for refugia and examine the factors that describe them. We then demonstrate how different disciplines are contributing to our understanding of refugia, and the tools that they provide for identifying and quantifying refugia. Results Current understanding of refugia is largely based on Quaternary phylogeographic studies on organisms in North America and Europe during significant temperature fluctuations. This has resulted in gaps in our understanding of refugia, particularly when attempting to apply current theory to forecast anthropogenic climate change. Refugia are environmental habitats with space and time dimensions that operate on evolutionary time-scales and have facilitated the survival of biota under changing environmental conditions for millennia. Therefore, they offer the best chances for survival under climate change for many taxa, making their identification important for conservation under anthropogenic climate change. Several methods from various disciplines provide viable options for achieving this goal. Main conclusions The framework developed for refugia allows the identification and description of refugia in any environment. Various methods provide important contributions but each is limited in scope; urging a more integrated approach to identify, define and conserve refugia. Such an approach will facilitate better understanding of refugia and their capacity to act as safe havens under projected anthropogenic climate change.
    Rapid identification of fusarium graminearum species complex using Rolling Circle Amplification (RCA)
    Davari, M. ; Diepeningen, A.D. van; Babai-Ahari, A. ; Arzanlou, M. ; Javad Najafzadeh, M. ; Lee, T.A.J. van der; Hoog, G.S. de - \ 2012
    Journal of Microbiological Methods 89 (2012)1. - ISSN 0167-7012 - p. 63 - 70.
    head blight pathogen - dna-sequence database - genealogical concordance - padlock probes - north-america - wheat - mycotoxins - cereals - barley - populations
    Rolling Circle Amplification (RCA) of DNA is a sensitive and cost effective method for the rapid identification of pathogenic fungi without the need for sequencing. Amplification products can be visualized on 1% agarose gel to verify the specificity of probe-template binding or directly by adding fluorescent dyes. Fusarium Head Blight (FHB) is currently the world's largest threat to the production of cereal crops with the production of a range of mycotoxins as an additional risk. We designed sets of RCA padlock probes based on polymorphisms in the elongation factor 1-a (EF-1a) gene to detect the dominant FHB species, comprising lineages of the Fusarium graminearum species complex (FGSC). The method also enabled the identification of species of the Fusarium oxysporum (FOSC), the Fusarium incarnatum-equiseti (FIESC), and the Fusarium tricinctum (FTSC) species complexes, and used strains from the CBS culture collection as reference. Subsequently probes were applied to characterize isolates from wheat and wild grasses, and inoculated wheat kernels. The RCA assays successfully amplified DNA of the target fungi, both in environmental samples and in the contaminated wheat samples, while no cross reactivity was observed with uncontaminated wheat or related Fusarium species. As RCA does not require expensive instrumentation, the technique has a good potential for local and point of care screening for toxigenic Fusarium species in cereals
    Clostridium difficile infections in the community: a zoonotic disease?
    Hensgens, M.P.M. ; Keessen, A.M. ; Squire, M.M. ; Riley, T.V. ; Koene, M.G.J. ; Boer, E. de; Lipman, L.J. ; Kuijper, E.J. - \ 2012
    Clinical Microbiology and Infection 18 (2012)7. - ISSN 1198-743X - p. 635 - 645.
    retail ground meat - general-practice - food animals - antimicrobial susceptibility - fatal enterocolitis - neonatal diarrhea - intestinal flora - north-america - pcr ribotypes - prevalence
    Clostridium difficile infections (CDIs) are traditionally seen in elderly and hospitalized patients who have used antibiotic therapy. In the community, CDIs requiring a visit to a general practitioner are increasingly occurring among young and relatively healthy individuals without known predisposing factors. C. difficile is also found as a commensal or pathogen in the intestinal tracts of most mammals, and various birds and reptiles. In the environment, including soil and water, C. difficile may be ubiquitous; however, this is based on limited evidence. Food products such as (processed) meat, fish and vegetables can also contain C. difficile, but studies conducted in Europe report lower prevalence rates than in North America. Absolute counts of toxigenic C. difficile in the environment and food are low, however the exact infectious dose is unknown. To date, direct transmission of C. difficile from animals, food or the environment to humans has not been proven, although similar PCR ribotypes are found. We therefore believe that the overall epidemiology of human CDI is not driven by amplification in animals or other sources. As no outbreaks of CDI have been reported among humans in the community, host factors that increase vulnerability to CDI might be of more importance than increased exposure to C. difficile. Conversely, emerging C. difficile ribotype 078 is found in high numbers in piglets, calves, and their immediate environment. Although there is no direct evidence proving transmission to humans, circumstantial evidence points towards a zoonotic potential of this type. In future emerging PCR ribotypes, zoonotic potential needs to be considered
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. - \ 2012
    Fungal Diversity 53 (2012)1. - ISSN 1560-2745 - p. 1 - 221.
    ribosomal dna-sequences - australian fresh-water - intertidal mangrove wood - sp-nov - north-america - marine fungi - molecular phylogeny - trematosphaeria-circinans - shiraia-bambusicola - multigene phylogeny
    One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.
    Can a 'state of the art' chemistry transport model really simulate Anazonian tropospheric chemistry
    Barkley, M. ; Palmer, P.I. ; Ganzeveld, L.N. - \ 2011
    Journal of Geophysical Research: Atmospheres 116 (2011). - ISSN 2169-897X - 28 p.
    tropical rain-forest - volatile organic-compounds - terrestrial isoprene emissions - master chemical mechanism - planetary boundary-layer - mcm v3 part - atmospheric chemistry - nonmethane hydrocarbons - united-states - north-america
    We present an evaluation of a nested high-resolution Goddard Earth Observing System (GEOS)-Chem chemistry transport model simulation of tropospheric chemistry over tropical South America. The model has been constrained with two isoprene emission inventories: (1) the canopy-scale Model of Emissions of Gases and Aerosols from Nature (MEGAN) and (2) a leaf-scale algorithm coupled to the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) dynamic vegetation model, and the model has been run using two different chemical mechanisms that contain alternative treatments of isoprene photo-oxidation. Large differences of up to 100 Tg C yr-1 exist between the isoprene emissions predicted by each inventory, with MEGAN emissions generally higher. Based on our simulations we estimate that tropical South America (30–85°W, 14°N–25°S) contributes about 15–35% of total global isoprene emissions. We have quantified the model sensitivity to changes in isoprene emissions, chemistry, boundary layer mixing, and soil NOx emissions using ground-based and airborne observations. We find GEOS-Chem has difficulty reproducing several observed chemical species; typically hydroxyl concentrations are underestimated, whilst mixing ratios of isoprene and its oxidation products are overestimated. The magnitude of model formaldehyde (HCHO) columns are most sensitive to the choice of chemical mechanism and isoprene emission inventory. We find GEOS-Chem exhibits a significant positive bias (10–100%) when compared with HCHO columns from the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI) for the study year 2006. Simulations that use the more detailed chemical mechanism and/or lowest isoprene emissions provide the best agreement to the satellite data, since they result in lower-HCHO columns
    Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA
    Kraus, R.H.S. ; Zeddeman, A. ; Hooft, W.F. van; Sartakov, D. ; Soloviev, S.A. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2011
    BMC Genetics 12 (2011). - ISSN 1471-2156
    duck anas-platyrhynchos - influenza-a viruses - avian influenza - bird migration - population-structure - north-america - black ducks - gene flow - hybridization - philopatry
    Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere.
    Dynamics and ecological consequences of avian influenza virus infection in greater white-fronted geese in their winter staging areas
    Kleijn, D. ; Munster, V.J. ; Ebbinge, B.S. ; Jonkers, D.A. ; Müskens, G.J.D.M. ; Randen, Y. van; Fouchier, R.A.M. - \ 2010
    Proceedings of the Royal Society. B: Biological Sciences 277 (2010)1690. - ISSN 0962-8452 - p. 2041 - 2048.
    wild mallard ducks - affect body condition - a virus - migratory waterfowl - branta-canadensis - north-america - vice-versa - birds - h5n1 - paramyxoviruses
    Recent outbreaks of highly pathogenic avian influenza (HPAI) in poultry have raised interest in the interplay between avian influenza (AI) viruses and their wild hosts. Studies linking virus ecology to host ecology are still scarce, particularly for non-duck species. Here, we link capture–resighting data of greater white-fronted geese Anser albifrons albifrons with the AI virus infection data collected during capture in The Netherlands in four consecutive winters. We ask what factors are related to AI virus prevalence and whether there are ecological consequences associated with AI virus infection in staging white-fronted geese. Mean seasonal (low pathogenic) AI virus prevalence ranged between 2.5 and 10.7 per cent, among the highest reported values for non-duck species, and occurred in distinct peaks with near-zero prevalence before and after. Throat samples had a 2.4 times higher detection frequency than cloacal samples. AI virus infection was significantly related to age and body mass in some but not other winters. AI virus infection was not related to resighting probability, nor to maximum distance travelled, which was at least 191 km during the short infectious lifespan of an AI virus. Our results suggest that transmission via the respiratory route could be an important transmission route of AI virus in this species. Near-zero prevalence upon arrival on their wintering grounds, in combination with the epidemic nature of AI virus infections in white-fronted geese, suggests that white-fronted geese are not likely to disperse Asian AI viruses from their Siberian breeding grounds to their European wintering areas.
    What explains the invading success of the aquatic mud snail Potamopyrgus antipodarum (Hydrobiidae, Mollusca)?
    Alonso, A. ; Castro-Diez, P. - \ 2008
    Hydrobiologia 614 (2008)1. - ISSN 0018-8158 - p. 107 - 116.
    fresh-water snail - new-zealand stream - life-history - predicting invasions - hypericum-perforatum - biological invaders - north-america - great-lakes - toxicity - jenkinsi
    The spread of non-native species is one of the most harmful and least reversible disturbances in ecosystems. Species have to overcome several filters to become a pest (transport, establishment, spread and impact). Few studies have checked the traits that confer ability to overcome these steps in the same species. The aim of the present study is to review the available information on the life-history and ecological traits of the mud snail, Potamopyrgus antipodarum Gray (Hydrobiidae, Mollusca), native from New Zealand, in order to explain its invasive success at different aquatic ecosystems around the world. A wide tolerance range to physico-chemical factors has been found to be a key trait for successful transport. A high competitive ability at early stages of succession can explains its establishment success in human-altered ecosystems. A high reproduction rate, high capacity for active and passive dispersal, and the escape from native predators and parasites explains its spread success. The high reproduction and the ability to monopolize invertebrate secondary production explain its high impact in the invaded ecosystems. However, further research is needed to understand how other factors, such as population density or the degree of human perturbation can modify the invasive success of this aquatic snail
    Modelling the effects of diving ducks on zebra mussels Dreissena polymorpha in lakes
    Nes, E.H. van; Noordhuis, R. ; Lammens, E.H.R.R. ; Portielje, R. ; Reeze, B. ; Peeters, E.T.H.M. - \ 2008
    Ecological Modelling 211 (2008)3-4. - ISSN 0304-3800 - p. 481 - 490.
    aythya-fuligula - north-america - water-quality - great-lakes - populations - dynamics - impact - river - individuals - unionidae
    An individual-based model describing the growth of zebra mussels (Dreissena polymorpha) is presented. The model is spatially explicit and predicts length¿frequency distributions of zebra mussels. The parameters and model inputs with the strongest effect on the model outcomes were identified using a Monte Carlo sensitivity analysis. Using a cluster analysis we could subsequently identify five clusters of parameters with similar multivariate effect on the model outcomes. We applied the model to two shallow lakes in the Netherlands (Lake Veluwemeer and Lake Gooimeer) that differed strongly in densities of diving ducks in winter. The parameters describing predation by diving ducks were estimated from literature based on a detailed study on the diets of the dominant species (tufted duck Aythya fuligula, pochard Aythya ferina and coot Fulica atra). Growth parameters of zebra mussels were also obtained from literature. The only parameters that were calibrated were those describing the densities and timing of larval settlement. The measured length¿frequency distributions of larger mussels (>8 mm) did not differ significantly from the modelled distributions in Lake Veluwemeer (Kolmogorov¿Smirnov test p > 0.05, N = 1056) and was satisfactory in Lake Gooimeer. However, the smaller size classes (8 mm by 90% whereas in Lake Gooimeer this reduction was only about 10%.
    AFLP Markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae)
    Koopman, W.J.M. ; Wissemann, V. ; Cock, K. de; Huylenbroeck, J. van; Riek, J. de; Sabatino, G.J.H. ; Visser, D.L. ; Vosman, B. ; Ritz, K. ; Maes, B. ; Werlemark, G. ; Nybom, H. ; Debener, T. ; Linde, M. ; Smulders, M.J.M. - \ 2008
    American Journal of Botany 95 (2008)3. - ISSN 0002-9122 - p. 353 - 366.
    bayesian phylogenetic inference - internal transcribed spacers - genus rosa - genetic-relationships - dna-sequences - chloroplast dna - reticulate evolution - molecular evidence - north-america - sect. caninae
    The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.
    Scale-dependent homogenization: changes in breeding bird diversity in the Netherlands over a 25-year period
    Turnhout, C.A.M. van; Foppen, R.P.B. ; Leuven, R.S.E.W. ; Siepel, H. ; Esselink, H. - \ 2007
    Biological Conservation 134 (2007)4. - ISSN 0006-3207 - p. 505 - 516.
    biotic homogenization - atmospheric deposition - north-america - urbanization - population - biodiversity - abundance - declines - britain - trends
    Changes in breeding bird diversity in the Netherlands between 1973-1977 and 1998-2000 were evaluated by testing three hypotheses related to the loss of biodiversity: (1) species diversity is declining, (2) biotic homogenization is increasing and (3) rare species are declining more severely than abundant species. Using data collected for two successive national breeding bird atlases, changes in diversity were assessed at different spatial scales (local, regional and national) and among species characteristic for different landscapes (farmland, woodland, heathland, wetland, coastal habitats and urban habitats). National species richness, diversity and equitability had increased between the two atlas periods, with more species increasing than decreasing in range and abundance. Most species in the large groups of woodland and wetland birds showed positive trends, whereas most in the smaller groups of heathland, reed-breeding and meadow birds showed negative trends. However, findings varied between regions and localities. Increases in species richness occurred mainly in regions in the low-lying, western part of the country which were previously relatively poor in species. By contrast, species richness decreased in some previously species-rich regions in the eastern part of the country. This has resulted in a homogenization of breeding bird communities between regions. We advocate the conservation and restoration of regional identity as a priority for landscape planning in the Netherlands. We did not find a clear relation between species abundance and trends, although both rare and very abundant species tended to decrease on average.
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