Who is Who in Phylogenetic Networks

Publications of Bengt Oxelman     Order by:   Type | Year

Associated keywords

duplication explicit-network from-multilabeled-tree from-trees phylogenetic-network phylogeny Program-PADRE reconstruction software

Article (Journal)

1 Martin Lott, Andreas Spillner, Katharina Huber, Anna Petri, Bengt Oxelman and Vincent Moulton. Inferring polyploid phylogenies from multiply-labeled gene trees. In BMCEB, Vol. 9:216, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://dx.doi.org/10.1186/1471-2148-9-216.         Toggle abstract "Background : Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. Results. We present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem. Conclusion. We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels. © 2009 Lott et al; licensee BioMed Central Ltd." 2 Katharina Huber, Bengt Oxelman, Martin Lott and Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):1784-1791, 2007. Keywords: duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784.         Toggle abstract "In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ ∼a043878/padre.html. © The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."