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  • 1.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Koch, Christin
    Edman, Mattias
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Testing the probability of finding major decomposing basidiomycetes in logs with T-RFLP - implications for field samplingManuscript (preprint) (Other academic)
    Abstract [en]

    In this article we examine the limitations and potential of T-RFLP for the accurate detection of fungal species in dead wood. We collected cross-sections of decayed logs to evaluate the number of fungal species domains that are likely to be hit when drilling a sawdust sample from a log. We used these estimates to simulate the number of species that would be found using a certain number of samples. We found that in 99% of the simulations, 4 or fewer species would be contained in a sample. Based on these results we tested the probability of detecting two species of wood-decaying basidiomycetes at three different DNA concentration ratios: 1:1, 1:5 and 1:20. An additional experiment was done with 3-5 species. It was possible to detect all species at ratios higher than 1:20 but lower than 1:5; in this range all peaks were easily detected. We were able to detect all species in the mixtures of 3-5 species, with extracts from both pure cultures and wood.

  • 2.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Olsson, Jörgen
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Strong clustering in a SNP study of Phlebiopsis gigantea in swedenManuscript (preprint) (Other academic)
    Abstract [en]

    The population structures of wood decaying basidomycetes depend on several factors; one is dispersal pattern of spores, another is age structure including lifespan and also environmental impacts like forest fires. Phlebiopsis gigantea has been shown to be in the group of basidomycetes that have a well developed tolerance to heat, is long-distance wind dispersed and whose fruit body show up early in succession on fallen logs. In a study of 132 individuals from 3 pairs of locations, 350 km apart, in middle to northern Sweden we used 26 SNP-markers in 6 loci to make a genetic clustering study using STRUCTURE (v. 2.3.4.). The hypothesis; first, clustering should follow the geographic sampling locations with more gene flow between geographically close locations, second; that genetic distance between different clusters should be low due to the long distance dispersal of spores, third; as markers are random we don’t expect to find a correlation between locations affected by forest fires and locations not affected by forest fires. In the study we found 5 clusters (Pr[K= 1]) with moderate to high Fst values (0,0697-03939). Clusters had a poor geographical correlation to sampled populations indicating a complicated population structure. Out of 132 individuals 119 had a private genotype showing a large genetic variation over the total area and a low level of clones in the field.         

  • 3.
    Novikova, P. Y.
    et al.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Hohmann, N.
    Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany .
    Nizhynska, V.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Tsuchimatsu, T.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Ali, J.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
    Muir, G.
    Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria .
    Guggisberg, A.
    Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland .
    Paape, T.
    Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland .
    Schmid, K.
    Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany .
    Fedorenko, O. M.
    Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Petrozavodsk, Russian Federation .
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Säll, T.
    Department of Biology, Lund University, Lund, Sweden .
    Schlötterer, C.
    Institut für Populationsgenetik, Vetmeduni, Vienna, Austria .
    Marhold, K.
    Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic .
    Widmer, A.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany .
    Sese, J.
    Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan .
    Shimizu, K. K.
    Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland .
    Weigel, D.
    Max Planck Institute for Developmental Biology, Tübingen, Germany .
    Krämer, U.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany .
    Koch, M. A.
    Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany .
    Nordborg, M.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria .
    Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism2016In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 9, p. 1077-1082Article in journal (Refereed)
    Abstract [en]

    The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection. © 2016 Nature America, Inc. All rights reserved.

  • 4.
    Westman, Anna-Karin
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Investigation of Progress in Peer Discussions Regarding Genetic ConceptsManuscript (preprint) (Other academic)
1 - 4 of 4
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