Reducing distortion in phylogenetic networks

Daniel H. Huson, Mike A. Steel, James Bryan Whitfield

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

When multiple genes axe used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
PublisherSpringer-Verlag
Pages150-161
Number of pages12
ISBN (Print)3540395830, 9783540395836
StatePublished - Jan 1 2006
Event6th International Workshop on Algorithms in Bioinformatics, WABI 2006 - Zurich, Switzerland
Duration: Sep 11 2006Sep 13 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4175 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other6th International Workshop on Algorithms in Bioinformatics, WABI 2006
CountrySwitzerland
CityZurich
Period9/11/069/13/06

Fingerprint

Phylogenetic Network
Genes
Gene
Combinatorial Analysis
Scenarios
Plug-in
Phylogenetics
False Positive
Filter
Computing

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Huson, D. H., Steel, M. A., & Whitfield, J. B. (2006). Reducing distortion in phylogenetic networks. In Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings (pp. 150-161). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4175 LNBI). Springer-Verlag.

Reducing distortion in phylogenetic networks. / Huson, Daniel H.; Steel, Mike A.; Whitfield, James Bryan.

Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer-Verlag, 2006. p. 150-161 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4175 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Huson, DH, Steel, MA & Whitfield, JB 2006, Reducing distortion in phylogenetic networks. in Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4175 LNBI, Springer-Verlag, pp. 150-161, 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, Zurich, Switzerland, 9/11/06.
Huson DH, Steel MA, Whitfield JB. Reducing distortion in phylogenetic networks. In Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer-Verlag. 2006. p. 150-161. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Huson, Daniel H. ; Steel, Mike A. ; Whitfield, James Bryan. / Reducing distortion in phylogenetic networks. Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer-Verlag, 2006. pp. 150-161 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
@inproceedings{8cdba6e6beb04ce79f5e8a271feeec11,
title = "Reducing distortion in phylogenetic networks",
abstract = "When multiple genes axe used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.",
author = "Huson, {Daniel H.} and Steel, {Mike A.} and Whitfield, {James Bryan}",
year = "2006",
month = "1",
day = "1",
language = "English (US)",
isbn = "3540395830",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer-Verlag",
pages = "150--161",
booktitle = "Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings",

}

TY - GEN

T1 - Reducing distortion in phylogenetic networks

AU - Huson, Daniel H.

AU - Steel, Mike A.

AU - Whitfield, James Bryan

PY - 2006/1/1

Y1 - 2006/1/1

N2 - When multiple genes axe used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.

AB - When multiple genes axe used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.

UR - http://www.scopus.com/inward/record.url?scp=33750265162&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33750265162&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:33750265162

SN - 3540395830

SN - 9783540395836

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 150

EP - 161

BT - Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings

PB - Springer-Verlag

ER -