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: Snail shell colour evolution in urban heat islands detected via citizen science
    Kerstes, Niels A.G. ; Breeschoten, Thijmen ; Kalkman, Vincent J. ; Schilthuizen, Menno - \ 2019
    Dryad
    shell colour polymorphism - urban heat island - Cepaea nemoralis - citizen science - thermal adaptation - urban evolution
    The extreme environmental conditions that prevail in cities are known to cause selection pressures leading to adaptive changes in wild, city-dwelling, organisms (urban evolution). The urban heat island, elevated temperatures in the city centre due to a combination of generation, reflection, and trapping of heat, is one of the best recognised and most widespread urban environmental factors. Here, we use a citizen-science approach to study the effects of urban heat on genetically-determined shell colour in the land snail Cepaea nemoralis in the Netherlands. We use smartphone applications to obtain colour data on almost 8000 snails throughout the country. Our analysis shows that snails in urban centres are more likely to be yellow than pink, an effect predicted on the basis of thermal selection. Urban yellow snails are also more likely to carry dark bands at the underside of the shell; these bands might affect thermoregulation in yet underexplored ways
    Snail shell colour evolution in urban heat islands detected via citizen science
    Kerstes, Niels A.G. ; Breeschoten, Thijmen ; Kalkman, Vincent J. ; Schilthuizen, Menno - \ 2019
    Communications Biology 2 (2019). - ISSN 2399-3642

    The extreme environmental conditions that prevail in cities are known to cause selection pressures leading to adaptive changes in wild, city-dwelling, organisms (urban evolution). The urban heat island, elevated temperatures in the city centre due to a combination of generation, reflection, and trapping of heat, is one of the best recognised and most widespread urban environmental factors. Here, we use a citizen-science approach to study the effects of urban heat on genetically-determined shell colour in the land snail Cepaea nemoralis in the Netherlands. We use smartphone applications to obtain colour data on almost 8000 snails throughout the country. Our analysis shows that snails in urban centres are more likely to be yellow than pink, an effect predicted on the basis of thermal selection. Urban yellow snails are also more likely to carry dark bands at the underside of the shell; these bands might affect thermoregulation in yet underexplored ways.

    Dispatch from the field II: The mystery of the red and blue Opadometa male (Araneae, Tetragnathidae, Opadometa sarawakensis)
    Miller, Jeremy A. ; Freund, Christian ; Rambonnet, Liselotte ; Koets, Lianne ; Barth, Nadine ; Linden, Corné van der; Geml, József ; Schilthuizen, Menno ; Burger, Richard ; Goossens, Benoit - \ 2018
    Biodiversity Data Journal 6 (2018). - ISSN 1314-2828
    Borneo - Orb web - Sexual size dimorphism - Spider - Tropical field course

    Background Males of Opadometa are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex matching in this genus suggest finding a male in the web of a female, or better yet, mating pairs. New information A male Opadometa was observed hanging on a frame line of the web of a female Opadometa sarawakensis, a species for which the male was previously undescribed. This occurred during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description was completed as a course activity.

    Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, D. ; Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Gungor, Berivan ; Hartog, M.V. ; Hontelez, Jan ; Verver, J.W.G. ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
    Wageningen University & Research
    comparative genomics - copy number variation - evolution - nitrogen fixation - symbiosis - Parasponia andersonii - Parasponia rigada - Parasponia rugosa - Trema levigata - Trema orientalis - Trema tomentosa
    Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants
    Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, Defeng ; Purwana Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Güngör, Berivan ; Hartog, M.V. ; Hontelez, J. ; Verver, Jan ; Yang, Wei-Cai ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)20. - ISSN 0027-8424 - p. E4700 - E4709.
    Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
    Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia
    Velzen, R. van; Holmer, R. ; Bu, F. ; Rutten, L.J.J. ; Zeijl, A.L. van; Liu, W. ; Santuari, L. ; Cao, Q. ; Sharma, Trupti ; Shen, D. ; Purwana Roswanjaya, Yuda ; Wardhani, T. ; Seifi Kalhor, M. ; Jansen, Joelle ; Hoogen, D.J. van den; Gungor, Berivan ; Hartog, M.V. ; Hontelez, J. ; Verver, J.W.G. ; Yang, W.C. ; Schijlen, E.G.W.M. ; Repin, Rimi ; Schilthuizen, M. ; Schranz, M.E. ; Heidstra, R. ; Miyata, Kana ; Fedorova, E. ; Kohlen, W. ; Bisseling, A.H.J. ; Smit, S. ; Geurts, R. - \ 2017
    BioRxiv - 88 p.
    Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
    Dispatch from the field: Ecology of ground-webbuilding spiders with description of a new species (Araneae, Symphytognathidae)
    Miller, Jeremy A. ; Schilthuizen, Menno ; Burmester, Jennie Lilliendahl ; Graaf, Lot van der; Merckx, Vincent ; Jocqué, Merlijn ; Kessler, Paul Joseph Antonius ; Fayle, Tom Maurice ; Breeschoten, Thijmen ; Broeren, Regi ; Bouman, Roderick ; Chua, Wan Ji ; Feijen, Frida ; Fermont, Tanita ; Groen, Kevin ; Groen, Marvin ; Kil, Nicolaas Johannes Cornelis ; Laat, Henrica Allegonda de; Moerland, Michelangelo Sergio ; Moncoquet, Carole ; Panjang, Elisa ; Philip, Amelia Joyce ; Roca-Eriksen, Rebecca ; Rooduijn, Bastiaan ; Santen, Marit van; Swakman, Violet ; Evans, Meaghan N. ; Evans, Luke J. ; Love, Kieran ; Joscelyne, Sarah H. ; Tober, Anya Victoria ; Wilson, Hannah F. ; Ambu, Laurentius N. ; Goossens, Benoit - \ 2014
    Biodiversity Data Journal 2 (2014)1. - ISSN 1314-2828
    Borneo - Crassignatha - Disturbance - Inundation - Oil palm plantation - Riparian forest - Riverine forest - Tropical field course

    Crassignatha danaugirangensis sp. n. (Araneae: Symphytognathidae) was discovered during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description and accompanying ecological study were completed as course activities. To assess the ecology of this species, which belongs to the ground-webbuilding spider community, three habitat types were surveyed: riparian forest, recently inundated riverine forest, and oil palm plantation. Crassignatha danaugirangensis sp. n. is the most abundant ground-web-building spider species in riparian forest; it is rare or absent from the recently inundated forest and was not found in a nearby oil palm plantation. The availability of this taxonomic description may help facilitate the accumulation of data about this species and the role of inundated riverine forest in shaping invertebrate communities.

    The use of statistical tools in field testing of putative effects of genetically modified plants on nontarget organisms
    Semenov, A.V. ; Elsas, J.D. van; Glandorf, D.C.M. ; Schilthuizen, M. ; Boer, W.F. de - \ 2013
    Ecology and Evolution 3 (2013)8. - ISSN 2045-7758 - p. 2739 - 2750.
    herbicide-tolerant crops - farm-scale evaluations - gene flow - population-structure - habitat preference - land snail - dispersal - design - power - invertebrates
    To fulfill existing guidelines, applicants that aim to place their genetically modified (GM) insect-resistant crop plants on the market are required to provide data from field experiments that address the potential impacts of the GM plants on nontarget organisms (NTO's). Such data may be based on varied experimental designs. The recent EFSA guidance document for environmental risk assessment (2010) does not provide clear and structured suggestions that address the statistics of field trials on effects on NTO's. This review examines existing practices in GM plant field testing such as the way of randomization, replication, and pseudoreplication. Emphasis is placed on the importance of design features used for the field trials in which effects on NTO's are assessed. The importance of statistical power and the positive and negative aspects of various statistical models are discussed. Equivalence and difference testing are compared, and the importance of checking the distribution of experimental data is stressed to decide on the selection of the proper statistical model. While for continuous data (e.g., pH and temperature) classical statistical approaches - for example, analysis of variance (ANOVA) - are appropriate, for discontinuous data (counts) only generalized linear models (GLM) are shown to be efficient. There is no golden rule as to which statistical test is the most appropriate for any experimental situation. In particular, in experiments in which block designs are used and covariates play a role GLMs should be used. Generic advice is offered that will help in both the setting up of field testing and the interpretation and data analysis of the data obtained in this testing. The combination of decision trees and a checklist for field trials, which are provided, will help in the interpretation of the statistical analyses of field trials and to assess whether such analyses were correctly applied.
    Microgeographic evolution of snail shell shape and predator behavior
    Schilthuizen, M. ; Til, A. Van; Salverda, M. ; Liew, T.S. ; James, S. ; Elahan, B. Bin; Vermeulen, J.J. - \ 2006
    Evolution 60 (2006)9. - ISSN 0014-3820 - p. 1851 - 1858.
    land-snails - sexual selection - gene flow - speciation - dna - diversification - biodiversity - population - diversity - sequences
    AbstractGenetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.
    Phylogeography of the land snail Albinaria hippolyti (Pulmonata: Clausiliidae) from Crete, inferred from ITS-1 sequences
    Schilthuizen, M. ; Gutteling, E.W. ; Moorsel, C.H.M. van; Welter-Schultes, F.W. ; Haase, M. ; Gittenberger, E. - \ 2004
    Biological Journal of the Linnean Society 83 (2004)3. - ISSN 0024-4066 - p. 317 - 326.
    aegean islands - ribosomal dna - gastropoda - evolution - alignment
    The polytypic Cretan land snail Albinaria hippolyti has a range that is partly fragmented and partly subdivided by hybrid zones. For this reason, it has served as a model species for investigating speciation and radiation in Mediterranean Clausiliidae. The first internal transcribed spacer (ITS-1) of the nuclear ribosomal DNA was sequenced in 20 populations of A. hippolyti and phylogenetically analysed using maximum parsimony. We employed a novel method involving logarithmic weighting of gaps and topological constraints based on bootstrap values. The resulting phylogeography suggests that the species has undergone a recent cycle of range expansion and range reduction. Speciation cannot be linked to major geological vicariance events in the Miocene and Pliocene, as has been suggested previously. The subspecies A. h. arthuriana appears unrelated to other A. hippolyti subspecies, which supports recent suggestions, based on morphology, to regard it as a separate species. (C) 2004 The Linnean Society of London.
    Hybridization, rare alleles and adaptive radiation.
    Schilthuizen, M. ; Hoekstra, R.F. ; Gittenberger, E. - \ 2004
    Trends in Ecology and Evolution 19 (2004)8. - ISSN 0169-5347 - p. 404 - 405.
    hybrid zone
    The 'rare allele phenomenon' in a ribosomal spacer
    Schilthuizen, M. ; Hoekstra, R.F. ; Gittenberger, E. - \ 2001
    Molecular Ecology 10 (2001). - ISSN 0962-1083 - p. 1341 - 1345.
    We describe the increased frequency of a particular length variant of the internal transcribed spacer 1 (ITS-1) of the ribosomal DNA in a hybrid zone of the land snail Albinaria hippolyti. The phenomenon that normally rare alleles or other markers can increase in frequency in the centre of hybrid zones is not new. Under the term 'hybrizyme' or 'rare allele' phenomenon it has been recorded in many organisms and different genetic markers. However, this is the first time that it has been found in a multicopy locus. On the one hand, the pattern fits well with the view that purifying selection in hybrid populations works on many loci across the genome and should thus have its effect on many independent molecular markers. On the other hand, the results are puzzling, given that the multiple copies of rDNA are not expected to respond in unison. We suggest two possible explanations for these conflicting observations.
    Population structure in a snail species from isolated Malaysian limestone hills, inferred from ribosomal DNA sequences
    Schilthuizen, M. ; Vermeulen, J.J. ; Davison, G.W.H. ; Gittenberger, E. - \ 1999
    Malacologia 41 (1999). - ISSN 0076-2997 - p. 271 - 284.
    Cloning Odysseus and the seed of speciation
    Schilthuizen, M. - \ 1999
    Trends in Ecology and Evolution 14 (1999). - ISSN 0169-5347 - p. 90 - 91.
    Molecular characterization and phylogeny of the entomopathogenic fungus Aschersonia spp
    Obornik, M. ; Stouthamer, R. ; Meekes, E. ; Schilthuizen, M. - \ 1999
    Plant Protection Science 35 (1999). - ISSN 1212-2580 - p. 1 - 9.
    Selective maintenance of a rare haplotype in a land snail hybrid zone
    Schilthuizen, M. ; Hoekstra, R.F. ; Gittenberger, E. - \ 1999
    Proceedings of the Royal Society. B: Biological Sciences 266 (1999). - ISSN 0962-8452 - p. 2181 - 2185.
    Kevers op kadavers.
    Schilthuizen, M. ; Vallenduuk, H. - \ 1998
    Unknown Publisher (Wetenschappelijke Mededeling 222)
    Distribution of Wolbachia among the guild associated with the parthenogenetic gall wasp Diplolepis rosae.
    Schilthuizen, M. ; Stouthamer, R. - \ 1998
    Heredity 81 (1998). - ISSN 0018-067X - p. 270 - 274.
    Morphological and molecular phylogenetics in the genus Leptopilina (Hymenoptera: Cynipoidea: Eucoilidae).
    Schilthuizen, M. ; Nordlander, G. ; Stouthamer, R. ; Alphen, J.M. van - \ 1998
    Systematic Entomology 23 (1998). - ISSN 0307-6970 - p. 253 - 264.
    Parthenogenesis-Inducing Wolbachia in Trichogramma kaykai (Hymenoptera: Trichogrammatidae) originates from a single infection.
    Schilthuizen, M. ; Honda, J. ; Stouthamer, R. - \ 1998
    Annals of the Entomological Society Of America 91 (1998). - ISSN 0013-8746 - p. 410 - 414.
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