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  • 1.
    Huber, K T
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Watson, E E
    Institute of Biomolecular Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
    Hendy, M D
    Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
    An algorithm for constructing local regions in a phylogenetic network2001In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 19, no 1, p. 1-8Article, review/survey (Refereed)
    Abstract [en]

    The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a tree-building program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the tree-building program as “The Tree.” This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example.

  • 2.
    Huber, Katharina T
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Moulton, Vincent
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Lockhart, Peter
    Institute of Biomolecular Sciences, Massey University, PO Box 11-222, Palmerston North, New Zealand.
    Dress, A.
    FSPM-Strukturbildungsprozesse, University of Bielefeld, D-33501, Bielefeld, Germany.
    Pruned median networks: A technique for reducing the complexity of median networks2001In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 19, no 2, p. 302-310Article in journal (Refereed)
    Abstract [en]

    Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of-species diversification and/or processes of sequence evolution that are not tree-like. In these Cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.

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