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Open Access Open Badges Research article

Inferring polyploid phylogenies from multiply-labeled gene trees

Martin Lott1, Andreas Spillner1*, Katharina T Huber1, Anna Petri2, Bengt Oxelman2 and Vincent Moulton1

Author Affiliations

1 School of Computing Sciences, University of East Anglia, Norwich, UK

2 Department of Plant and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden

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BMC Evolutionary Biology 2009, 9:216  doi:10.1186/1471-2148-9-216

Published: 28 August 2009



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.


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.


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.