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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    Data from: Current climate, isolation and history drive global patterns of tree phylogenetic endemism
    Sandel, Brody ; Weigelt, Patrick ; Kreft, Holger ; Keppel, Gunnar ; Sande, Masha van der; Levin, Sam ; Smith, Stephen ; Craven, Dylan ; Knight, Tiffany M. - \ 2019
    trees - endemism - Biogeography - historical contingency - phylogenetic endemism - isolation - islands - current - species richness - climate stability
    Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions, and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants, and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g. mean annual temperature), geographical characteristics (e.g. isolation) and historical conditions (e.g. tree cover at the last glacial maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the last glacial maximum was a positive predictor of PE in the Paleotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographic, historical, and current factors. Some geographic variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographic drivers and regional climatic histories.
    Soil protists: A fertile frontier in soil biology research
    Geisen, Stefan ; Mitchell, Edward A.D. ; Adl, Sina ; Bonkowski, Michael ; Dunthorn, Micah ; Ekelund, Flemming ; Fernández, Leonardo D. ; Jousset, Alexandre ; Krashevska, Valentyna ; Singer, David ; Spiegel, Frederick W. ; Walochnik, Julia ; Lara, Enrique - \ 2018
    FEMS Microbiology Reviews 42 (2018)3. - ISSN 0168-6445 - p. 293 - 323.
    Biogeography - Functional diversity - Plant performance - Soil food web - Soil microbiome - Taxonomic diversity

    Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

    Classification of European and Mediterranean coastal dune vegetation
    Marcenò, Corrado ; Guarino, Riccardo ; Loidi, Javier ; Herrera, Mercedes ; Isermann, Maike ; Knollová, Ilona ; Tichý, Lubomír ; Tzonev, Rossen T. ; Acosta, Alicia Teresa Rosario ; Fitzpatrick, Úna ; Iakushenko, Dmytro ; Janssen, John A.M. ; Jiménez-Alfaro, Borja ; Kacki, Zygmunt ; Keizer-Sedláková, Iva ; Kolomiychuk, Vitaliy ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Chytrý, Milan - \ 2018
    Applied Vegetation Science 21 (2018)3. - ISSN 1402-2001 - p. 533 - 559.
    Ammophiletea - Biogeography - Expert system - Honckenyo-Elymetea - Koelerio-Corynephoretea canescentis - Phytosociology - Sand dune - Vegetation classification

    Aims: Although many phytosociological studies have provided detailed local and regional descriptions of coastal dune vegetation, a unified classification of this vegetation in Europe and the Mediterranean Basin has been missing. Our aim is to produce a formalized classification of this vegetation and to identify the main factors driving its plant species composition at a continental scale. Location: Atlantic and Baltic coasts of Europe, Mediterranean Basin and the Black Sea region. Methods: We compiled a database of 30,759 plots of coastal vegetation, which were resampled to reduce unbalanced sampling effort, obtaining a data set of 11,769 plots. We classified these plots with TWINSPAN, interpreted the resulting clusters and used them for developing formal definitions of phytosociological alliances of coastal dune vegetation, which were included in an expert system for automatic vegetation classification. We related the alliances to climatic factors and described their biogeographic features and their position in the coastal vegetation zonation. We examined and visualized the floristic relationships among these alliances by means of DCA ordination. Results: We defined 18 alliances of coastal dune vegetation, including the newly described Centaureo cuneifoliae-Verbascion pinnatifidi from the Aegean region. The main factors underlying the differentiation of these alliances were biogeographic and macroclimatic contrasts between the Atlantic-Baltic, Mediterranean and Black Sea regions, along with ecological differences between shifting and stable dunes. The main difference in species composition was between the Atlantic-Baltic and Mediterranean-Black Sea regions. Within the former region, the main difference was driven by the different ecological conditions between shifting and stable dunes, whereas within the latter, the main difference was biogeographic between the Mediterranean and the Black Sea. Conclusions: The first formal classification of the European coastal dune vegetation was established, accompanied by an expert system containing the formal definitions of alliances, which can be applied to new data sets. The new classification system critically revised the previous concepts and integrated them into a consistent framework, which reflects the main gradients in species composition driven by biogeographic influences, macroclimate and the position of the sites in the coast-inland zonation of the dune systems. A revision of the class concept used in EuroVegChecklist is also proposed.

    Priorities for research in soil ecology
    Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
    Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
    Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
    The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
    Globally intertwined evolutionary history of giant barrel sponges
    Swierts, Thomas ; Peijnenburg, Katja T.C.A. ; Leeuw, Christiaan A. de; Breeuwer, Johannes A.J. ; Cleary, Daniel F.R. ; Voogd, Nicole J. de - \ 2017
    Coral Reefs 36 (2017)3. - ISSN 0722-4028 - p. 933 - 945.
    Biogeography - Mitochondrial DNA - Nuclear DNA - Porifera - Species complex - Xestospongia
    Three species of giant barrel sponge are currently recognized in two distinct geographic regions, the tropical Atlantic and the Indo-Pacific. In this study, we used molecular techniques to study populations of giant barrel sponges across the globe and assessed whether the genetic structure of these populations agreed with current taxonomic consensus or, in contrast, whether there was evidence of cryptic species. Using molecular data, we assessed whether giant barrel sponges in each oceanic realm represented separate monophyletic lineages. Giant barrel sponges from 17 coral reef systems across the globe were sequenced for mitochondrial (partial CO1 and ATP6 genes) and nuclear (ATPsβ intron) DNA markers. In total, we obtained 395 combined sequences of the mitochondrial CO1 and ATP6 markers, which resulted in 17 different haplotypes. We compared a phylogenetic tree constructed from 285 alleles of the nuclear intron ATPsβ to the 17 mitochondrial haplotypes. Congruent patterns between mitochondrial and nuclear gene trees of giant barrel sponges provided evidence for the existence of multiple reproductively isolated species, particularly where they occurred in sympatry. The species complexes in the tropical Atlantic and the Indo-Pacific, however, do not form separate monophyletic lineages. This rules out the scenario that one species of giant barrel sponge developed into separate species complexes following geographic separation and instead suggests that multiple species of giant barrel sponges already existed prior to the physical separation of the Indo-Pacific and tropical Atlantic.
    Big data integration : Pan-European fungal species observations' assembly for addressing contemporary questions in ecology and global change biology
    Andrew, Carrie ; Heegaard, Einar ; Kirk, Paul M. ; Bässler, Claus ; Heilmann-Clausen, Jacob ; Krisai-Greilhuber, Irmgard ; Kuijper, Thomas ; Senn-Irlet, Beatrice ; Büntgen, Ulf ; Kauserud, Håvard - \ 2017
    Fungal Biology Reviews 31 (2017)2. - ISSN 1749-4613 - p. 88 - 98.
    Biogeography - Citizen science - Fungi - Global change - Meta-database - Open-source

    Species occurrence observations are increasingly available for scientific analyses through citizen science projects and digitization of museum records, representing a largely untapped ecological resource. When combined with open-source data, there is unparalleled potential for understanding many aspects of the ecology and biogeography of organisms. Here we describe the process of assembling a pan-European mycological meta-database (ClimFun) and integrating it with open-source data to advance the fields of macroecology and biogeography against a backdrop of global change. Initially 7.3 million unique fungal species fruit body records, spanning nine countries, were processed and assembled into 6 million records of more than 10,000 species. This is an extraordinary amount of fungal data to address macro-ecological questions. We provide two examples of fungal species with different life histories, one ectomycorrhizal and one wood decaying, to demonstrate how such continental-scale meta-databases can offer unique insights into climate change effects on fungal phenology and fruiting patterns in recent decades.

    Formalized classification of European fen vegetation at the alliance level
    Peterka, Tomáš ; Hájek, Michal ; Jiroušek, Martin ; Jiménez-Alfaro, Borja ; Aunina, Liene ; Bergamini, Ariel ; Dítě, Daniel ; Felbaba-Klushyna, Ljuba ; Graf, Ulrich ; Hájková, Petra ; Hettenbergerová, Eva ; Ivchenko, Tatiana G. ; Jansen, Florian ; Koroleva, Natalia E. ; Lapshina, Elena D. ; Lazarević, Predrag M. ; Moen, Asbjørn ; Napreenko, Maxim G. ; Pawlikowski, Paweł ; Plesková, Zuzana ; Sekulová, Lucia ; Smagin, Viktor A. ; Tahvanainen, Teemu ; Thiele, Annett ; Biţǎ-Nicolae, Claudia ; Biurrun, Idoia ; Brisse, Henry ; Ćušterevska, Renata ; Bie, Els De; Ewald, Jörg ; FitzPatrick, Úna ; Font, Xavier ; Jandt, Ute ; Kącki, Zygmunt ; Kuzemko, Anna ; Landucci, Flavia ; Moeslund, Jesper E. ; Pérez-Haase, Aaron ; Rašomavičius, Valerijus ; Rodwell, John S. ; Schaminée, Joop H.J. ; Šilc, Urban ; Stančić, Zvjezdana ; Chytrý, Milan ; Schwabe-Kratochwil, Angelika - \ 2017
    Applied Vegetation Science 20 (2017)1. - ISSN 1402-2001 - p. 124 - 142.
    Biogeography - Ecological gradients - Endangered habitats - Mires - Relevés - Supervised vegetation classification - Unsupervised vegetation classification - Vegetation plots - Wetlands
    Aims: Phytosociological classification of fen vegetation (Scheuchzerio palustris-Caricetea fuscae class) differs among European countries. Here we propose a unified vegetation classification of European fens at the alliance level, provide unequivocal assignment rules for individual vegetation plots, identify diagnostic species of fen alliances, and map their distribution. Location: Europe, western Siberia and SE Greenland. Methods: 29 049 vegetation-plot records of fens were selected from databases using a list of specialist fen species. Formal definitions of alliances were created using the presence, absence and abundance of Cocktail-based species groups and indicator species. DCA visualized the similarities among the alliances in an ordination space. The ISOPAM classification algorithm was applied to regional subsets with homogeneous plot size to check whether the classification based on formal definitions matches the results of unsupervised classifications. Results: The following alliances were defined: Caricion viridulo-trinervis (sub-halophytic Atlantic dune-slack fens), Caricion davallianae (temperate calcareous fens), Caricion atrofusco-saxatilis (arcto-alpine calcareous fens), Stygio-Caricion limosae (boreal topogenic brown-moss fens), Sphagno warnstorfii-Tomentypnion nitentis (Sphagnum-brown-moss rich fens), Saxifrago-Tomentypnion (continental to boreo-continental nitrogen-limited brown-moss rich fens), Narthecion scardici (alpine fens with Balkan endemics), Caricion stantis (arctic brown-moss rich fens), Anagallido tenellae-Juncion bulbosi (Ibero-Atlantic moderately rich fens), Drepanocladion exannulati (arcto-boreal-alpine non-calcareous fens), Caricion fuscae (temperate moderately rich fens), Sphagno-Caricion canescentis (poor fens) and Scheuchzerion palustris (dystrophic hollows). The main variation in the species composition of European fens reflected site chemistry (pH, mineral richness) and sorted the plots from calcareous and extremely rich fens, through rich and moderately rich fens, to poor fens and dystrophic hollows. ISOPAM classified regional subsets according to this gradient, supporting the ecological meaningfulness of this classification concept on both the regional and continental scale. Geographic/macroclimatic variation was reflected in the second most important gradient. Conclusions: The pan-European classification of fen vegetation was proposed and supported by the data for the first time. Formal definitions developed here allow consistent and unequivocal assignment of individual vegetation plots to fen alliances at the continental scale.
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