%0 Journal Article
%T Inferring polyploid phylogenies from multiply-labeled gene trees
%A Martin Lott
%A Andreas Spillner
%A Katharina T Huber
%A Anna Petri
%A Bengt Oxelman
%A Vincent Moulton
%J BMC Evolutionary Biology
%D 2009
%I BioMed Central
%R 10.1186/1471-2148-9-216
%X 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.Polyploidy is an important evolutionary process in plants, as well as in some animal groups (e.g. [1,2]), accounting for a significant proportion of speciation events [2]. Most eukaryotes have a life cycle which includes a haploid (one set of chromosomes) and a diploid (two sets of chromosomes) part. A polyploid can arise from a sterile hybrid which has resulted from the fusion of two incompatible haploid gametes. If, for example due to meiotic errors, the hybrid doubles its chromosomes, it can develop into a new, fertile lineage that is instantaneously reproductively isolated from its parents (but see e.g. [3]), so called allopolyploidy. Genome doubling within a lineage is called autopolyploidy.Despite the importance of polyploidy, molecular phylogenetic studies of plants, even at shallow levels where reticulate patterns due to allopolyploidy are to be expected, have been dominated by the use of sequence regions that are unable to trace biparentally inherited evolutionary history. For example, sequences from the cytoplasmatic genomes are usually maternally inherited only, and for nuclear ribosomal DNA it is thought that concerted evolution can eradicate evidence for hybridization (e.g. [4]). Moreover, most phylogenetic studies aiming at tracing polyploid histori
%U http://www.biomedcentral.com/1471-2148/9/216