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: The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes
    Moser, Florian N. ; Rijssel, Jacco van; Mwaiko, Salome ; Meier, Joana I. ; Ngatunga, Benjamin ; Seehausen, Ole - \ 2018
    University of Bern
    cichlid fish - adaptive radiation - incipient speciation - disruptive selection - niche expansion - fitness surfaces
    Adaptive radiation research typically relies on the study of evolution in retrospective, leaving the predictive value of the concept hard to evaluate. Several radiations, including the cichlid fish in the East African Great Lakes, have been studied extensively, yet no study has investigated the onset of the intraspecific processes of niche expansion and differentiation shortly after colonization of an adaptive zone by cichlids. Haplochromine cichlids of one of the two lineages that seeded the Lake Victoria radiation recently arrived in Lake Chala, a lake perfectly suited for within-lake cichlid speciation. Here we infer the colonization and demographic history, quantify phenotypic, ecological and genomic diversity and diversification, and investigate the selection regime to ask if the population shows signs of diversification resembling the onset of adaptive radiation. We find that since their arrival in the lake, haplochromines have colonized a wide range of depth habitats associated with ecological and morphological expansion and the beginning of phenotypic differentiation and potentially nascent speciation, consistent with the very early onset of an adaptive radiation process. Moreover, we demonstrate evidence of rugged phenotypic fitness surfaces, indicating that current ecological selection may contribute to the phenotypic diversification.
    Data from: Functional and evolutionary consequences of cranial fenestration in birds
    Gussekloo, S.W.S. ; Berthaume, Michael A. ; Pulaski, Daniel R. ; Westbroek, Irene ; Waarsing, Jan H. ; Heinen, R. ; Grosse, Ian R. ; Dumont, Elizabeth R. - \ 2017
    Wageningen University & Research
    avian evolution - cranial morphology - fenestration - finite element modelling - adaptive radiation
    Ostrich-like birds (Palaeognathae) show very little taxonomic diversity while their sister taxon (Neognathae) contains roughly 10000 species. The main anatomical differences between the two taxa are in the crania. Palaeognaths lack an element in the bill called the lateral bar that is present in both ancestral theropods and modern neognaths, have thin zones in the bones of the bill, and robust bony elements on the ventral surface of their crania. Here we use a combination of modelling and developmental experiments to investigate the processes that might have led to these differences. Engineering-based finite element analyses indicate that removing the lateral bars from a neognath increases mechanical stress in the upper bill and the ventral elements of the skull, regions that are either more robust or more flexible in palaeognaths. Surgically removing the lateral bar from neognath hatchlings led to similar changes. These results indicate that the lateral bar is load-bearing and suggest that this function was transferred to other bony elements when it was lost in palaeognaths. It is possible that the loss of the load-bearing lateral bar might have constrained diversification of skull morphology in palaeognaths and thus limited taxonomic diversity within the group.
    Birds in a bush : Toward an avian phylogenetic network
    Ottenburghs, Jente ; Hooft, Pim van; Wieren, Sipke E. van; Ydenberg, Ronald C. ; Prins, Herbert H.T. - \ 2016
    The Auk : a quarterly journal of ornithology 133 (2016)4. - ISSN 0004-8038 - p. 577 - 582.
    adaptive radiation - genomics - hybridization - phylogenetic networks - Phylogenetics

    Reconstructing the avian tree of life has become one of the major goals in ornithology. The use of genomic tools seemed a promising approach to reach this goal, but, instead, phylogenetic analyses of large numbers of genes uncovered high levels of incongruence between the resulting gene trees. This incongruence can be caused by several biological processes, such as recombination, hybridization, and rapid speciation (which can lead to incomplete lineage sorting). These processes directly or indirectly amount to deviations from tree-like patterns, thereby thwarting the use of phylogenetic trees. Phylogenetic networks provide an ideal tool to deal with these difficulties. We illustrate the usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches. With the increasing amount of genomic data in avian phylogenetic studies, capturing the evolutionary history of a set of taxa in a phylogenetic tree will become increasingly difficult. Moreover, given the widespread occurrence of hybridization and the numerous adaptive radiations in birds, phylogenetic networks provide a powerful tool to display and analyse the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

    Microbial Community Structure of Three Traditional Zambian Fermented Products: Mabisi, Chibwantu and Munkoyo
    Schoustra, S.E. ; Kasase, C. ; Toarta, C. ; Kassen, R. ; Poulain, A.J. - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    lactic-acid bacteria - adaptive radiation - ecology - foods - diversity - microorganisms - fermentations - systems - africa - safety
    Around the world, raw materials are converted into fermented food products through microbial and enzymatic activity. Products are typically produced using a process known as batch culture, where small volumes of an old culture are used to initiate a fresh culture. Repeated over many years, and provided samples are not shared among producers, batch culture techniques allow for the natural evolution of independent microbial ecosystems. While these products form an important part of the diets of many people because of their nutritional, organoleptic and food safety properties, for many traditional African fermented products the microbial communities responsible for fermentation are largely unknown. Here we describe the microbial composition of three traditional fermented non-alcoholic beverages that are widely consumed across Zambia: the milk based product Mabisi and the cereal based products Munkoyo and Chibwantu. Using culture and non-culture based techniques, we found that six to eight lactic acid bacteria predominate in all products. We then used this data to investigate in more detail the factors affecting community structure. We found that products made from similar raw materials do not harbor microbial communities that are more similar to each other than those made from different raw materials. We also found that samples from the same product taken at the same location were as different from each other in terms of microbial community structure and composition, as those from geographically very distant locations. These results suggest that microbial community structure in these products is neither a simple consequence of the raw materials used, nor the particular suite of microbes available in the environment but that anthropogenic variables (e. g., competition among sellers or organoleptic preferences by different tribes) are important in shaping the microbial community structures.
    Multivariate phenotypic divergence due to the fixation of beneficial mutations in experimentally evolved lineages of a filamentous fungus
    Schoustra, S.E. ; Punzalan, D. ; Dali, R. ; Rundle, H.D. ; Kassen, R. - \ 2012
    PLoS ONE 7 (2012)11. - ISSN 1932-6203
    variance-covariance matrices - genetic variance - aspergillus-nidulans - adaptive radiation - life-history - evolution - selection - fitness - adaptation - populations
    The potential for evolutionary change is limited by the availability of genetic variation. Mutations are the ultimate source of new alleles, yet there have been few experimental investigations of the role of novel mutations in multivariate phenotypic evolution. Here, we evaluated the degree of multivariate phenotypic divergence observed in a long-term evolution experiment whereby replicate lineages of the filamentous fungus Aspergillus nidulans were derived from a single genotype and allowed to fix novel (beneficial) mutations while maintained at two different population sizes. We asked three fundamental questions regarding phenotypic divergence following approximately 800 generations of adaptation: (1) whether divergence was limited by mutational supply, (2) whether divergence proceeded in relatively many (few) multivariate directions, and (3) to what degree phenotypic divergence scaled with changes in fitness (i.e. adaptation). We found no evidence that mutational supply limited phenotypic divergence. Divergence also occurred in all possible phenotypic directions, implying that pleiotropy was either weak or sufficiently variable among new mutations so as not to constrain the direction of multivariate evolution. The degree of total phenotypic divergence from the common ancestor was positively correlated with the extent of adaptation. These results are discussed in the context of the evolution of complex phenotypes through the input of adaptive mutations
    Evolution of blind beetles in isolated aquifers: a test of alternative modes of speciation
    Leys, R. ; Nes, E.H. van; Watts, C.H. ; Cooper, S.J.B. ; Humphreys, W.F. ; Hogendoorn, K. - \ 2012
    PLoS ONE 7 (2012)3. - ISSN 1932-6203 - 8 p.
    subterranean diving beetles - mitochondrial-dna phylogeography - size-structured populations - sympatric speciation - western-australia - adaptive radiation - ecological speciation - mathematical-models - oceanic island - yilgarn region
    Evidence is growing that not only allopatric but also sympatric speciation can be important in the evolution of species. Sympatric speciation has most convincingly been demonstrated in laboratory experiments with bacteria, but field-based evidence is limited to a few cases. The recently discovered plethora of subterranean diving beetle species in isolated aquifers in the arid interior of Australia offers a unique opportunity to evaluate alternative modes of speciation. This naturally replicated evolutionary experiment started 10-5 million years ago, when climate change forced the surface species to occupy geographically isolated subterranean aquifers. Using phylogenetic analysis, we determine the frequency of aquifers containing closely related sister species. By comparing observed frequencies with predictions from different statistical models, we show that it is very unlikely that the high number of sympatrically occurring sister species can be explained by a combination of allopatric evolution and repeated colonisations alone. Thus, diversification has occurred within the aquifers and likely involved sympatric, parapatric and/or microallopatric speciation
    Radiations and key innovations in an early branching angiosperm lineage (Annonaceae; Magnoliales)
    Erkens, R.H.J. ; Chatrou, L.W. ; Couvreur, T.L.P. - \ 2012
    Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 117 - 134.
    rain-forest trees - species-rich genus - adaptive radiation - diversification rates - rapid diversification - goniothalamus annonaceae - molecular phylogenetics - ecological opportunity - guatteria annonaceae - flowering plants
    Biologists are fascinated by species-rich groups and have attempted to discover the causes for their abundant diversification. Comprehension of the causes and mechanisms underpinning radiations and detection of their frequency will contribute greatly to the understanding of the evolutionary origin of biodiversity and its ecological structure. A dated and well-resolved phylogenetic tree of Annonaceae was used to study diversification patterns in the family in order to identify factors that drive speciation and the evolution of morphological (key) characters. It was found that, except for Goniothalamus, the largest genera in the family are not the result of radiations. Furthermore, the difference in species numbers between subfamilies Annonoideae (former long branch clade) and Malmeoideae (former short branch clade) cannot be attributed to significant differences in the diversification rate. Most of the speciation in Annonaceae is not distinguishable from a random branching process (i.e. chance), and no special explanations are therefore necessary for the distribution of species richness across the major part of the phylogenetic tree for Annonaceae. Only for a small number of clades can key innovations be invoked to explain the elevated rate of diversification
    Consistent phenological shifts in the making of biodiversity hotspots: the Cape flora.
    Warren, B. ; Bakker, F.T. ; Bellstedt, D.U. ; Bytebier, B. ; Claszen-Bockhoff, R. ; Dreyer, L.L. ; Edwards, A. ; Forest, F. ; Galley, C. ; Hardy, C.R. ; Linder, H.P. ; Muasya, A.M. ; Mummenhoff, K. ; Oberlander, K.C. ; Quint, M. ; Richardson, J.E. ; Savolainen, V. ; Schrire, B.D. ; Niet, T. van der; Verboom, G.A. ; Yesson, C. ; Hawkins, J.A. - \ 2011
    BMC Evolutionary Biology 11 (2011). - ISSN 1471-2148 - 11 p.
    climate-change - southern africa - ecological niches - flowering time - heterogeneous environments - evolutionary responses - adaptive radiation - rapid evolution - fossil record - sequence data
    Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.
    Death and cannibalism in a seasonal environment facilitate bacterial coexistence
    Rozen, D.E. ; Philippe, N. ; Visser, J.A.G.M. de; Lenski, R.E. ; Schneider, D. - \ 2009
    Ecology Letters 12 (2009)1. - ISSN 1461-023X - p. 34 - 44.
    term experimental evolution - escherichia-coli mutants - general stress-response - stationary-phase - adaptive radiation - balanced polymorphism - constant environment - microbial microcosms - prolonged starvation - niche construction
    Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct niches can subsequently coexist via frequency-dependent interactions. Here, we describe a novel form of niche construction that is based upon differential death and cannibalism, and which evolved during 20 000 generations of experimental evolution in Escherichia coli in a seasonal environment with alternating growth and starvation. In one of 12 populations, two monophyletic ecotypes, S and L, evolved that stably coexist with one another. When grown and then starved in monoculture, the death rate of S exceeds that of L, whereas the reverse is observed in mixed cultures. As shown by experiments and numerical simulations, the competitive advantage of S cells is increased by extending the period of starvation, and this advantage results from their cannibalization of the debris of lysed L cells, which allows the S cells to increase both their growth rate and total cell density. At the molecular level, the polymorphism is associated with divergence in the activity of the alternative sigma factor RpoS, with S cells displaying no detectable activity, while L cells show increased activity relative to the ancestral genotype. Our results extend the repertoire of known cross-feeding mechanisms in microbes to include cannibalism during starvation, and confirm the central roles for niche construction and seasonality in the maintenance of microbial polymorphisms
    Lacustrine spawning: is this a new reproductive strategy among 'large' African cyprinid fishes?
    Graaf, M. de; Nentwich, E.D. ; Osse, J.W.M. ; Sibbing, F.A. - \ 2005
    Journal of Fish Biology 66 (2005)5. - ISSN 0022-1112 - p. 1214 - 1236.
    barbus-intermedius complex - lake tana ethiopia - species flock - adaptive radiation - speciation - evolution - divergence - salmon - diversification - segregation
    Changes in the gonadosomatic index and abundance of the different Labeobarbus species in the mouths of four major afferent rivers of Lake Tana, Ethiopia, were monitored monthly during 1999 and 2000. Riverine spawning was characteristic for seven of Lake Tana's 15 contemporary Labeobarbus species. These seven did not show spatial segregation among afferent rivers but significant temporal segregation occurred in aggregating in the river mouths and migrating towards the upstream spawning areas during the breeding season (June¿October). Among the eight other species, peak gonad development occurred generally in the same period as in the riverine spawners. These species, however, did not aggregate in the river mouths during the breeding period and were absent from the upstream spawning areas. A derived, novel strategy, lacustrine spawning was hypothesized for these eight Labeobarbus species. This hypothesis was further supported by observations of running female fishes in the littoral zones distant from any of the afferent rivers. This derived strategy is only common among the littoraldwelling Labeobarbus species with restricted distribution patterns. At present it is thought that sequential waves of speciation and habitat divergence followed by trophic specialization, shaped the diversity of Lake Tana labeobarbs.
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