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Inferring polyploid phylogenies from multiply-labeled gene trees

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 o...

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Autores principales: Lott, Martin, Spillner, Andreas, Huber, Katharina T, Petri, Anna, Oxelman, Bengt, Moulton, Vincent
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748082/
https://www.ncbi.nlm.nih.gov/pubmed/19715596
http://dx.doi.org/10.1186/1471-2148-9-216
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author Lott, Martin
Spillner, Andreas
Huber, Katharina T
Petri, Anna
Oxelman, Bengt
Moulton, Vincent
author_facet Lott, Martin
Spillner, Andreas
Huber, Katharina T
Petri, Anna
Oxelman, Bengt
Moulton, Vincent
author_sort Lott, Martin
collection PubMed
description 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.
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spelling pubmed-27480822009-09-22 Inferring polyploid phylogenies from multiply-labeled gene trees Lott, Martin Spillner, Andreas Huber, Katharina T Petri, Anna Oxelman, Bengt Moulton, Vincent BMC Evol Biol Research Article 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. BioMed Central 2009-08-28 /pmc/articles/PMC2748082/ /pubmed/19715596 http://dx.doi.org/10.1186/1471-2148-9-216 Text en Copyright © 2009 Lott et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Lott, Martin
Spillner, Andreas
Huber, Katharina T
Petri, Anna
Oxelman, Bengt
Moulton, Vincent
Inferring polyploid phylogenies from multiply-labeled gene trees
title Inferring polyploid phylogenies from multiply-labeled gene trees
title_full Inferring polyploid phylogenies from multiply-labeled gene trees
title_fullStr Inferring polyploid phylogenies from multiply-labeled gene trees
title_full_unstemmed Inferring polyploid phylogenies from multiply-labeled gene trees
title_short Inferring polyploid phylogenies from multiply-labeled gene trees
title_sort inferring polyploid phylogenies from multiply-labeled gene trees
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748082/
https://www.ncbi.nlm.nih.gov/pubmed/19715596
http://dx.doi.org/10.1186/1471-2148-9-216
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