In the light of deep coalescence: revisiting trees within networks
| dc.citation.journalTitle | BMC Bioinformatics | |
| dc.contributor.author | Zhu, Jiafan | |
| dc.contributor.author | Yu, Yun | |
| dc.contributor.author | Nakhleh, Luay K. | |
| dc.date.accessioned | 2016-11-11T17:03:12Z | |
| dc.date.available | 2016-11-11T17:03:12Z | |
| dc.date.issued | 2016 | |
| dc.date.updated | 2016-11-11T17:03:11Z | |
| dc.description.abstract | Abstract Background Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network. Results In this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network. We formally define the set of parental trees of a network and make three contributions based on this definition. First, we extend the notion of anomaly zone to phylogenetic networks and report on anomaly results for different networks. Second, we demonstrate how coalescence events could negatively affect the ability to infer a species tree that could be augmented into the correct network. Third, we demonstrate how a phylogenetic network can be viewed as a mixture model that lends itself to a novel inference approach via gene tree clustering. Conclusions Our results demonstrate the limitations of focusing on the set of trees displayed by a network when analyzing and inferring the network. Our findings can form the basis for achieving higher accuracy when inferring phylogenetic networks and open up new venues for research in this area, including new problem formulations based on the notion of a network’s parental trees. | |
| dc.identifier.citation | Zhu, Jiafan, Yu, Yun and Nakhleh, Luay K.. "In the light of deep coalescence: revisiting trees within networks." <i>BMC Bioinformatics,</i> (2016) BioMed Central: http://dx.doi.org/10.1186/s12859-016-1269-1. | |
| dc.identifier.doi | http://dx.doi.org/10.1186/s12859-016-1269-1 | |
| dc.identifier.uri | https://hdl.handle.net/1911/92706 | |
| dc.language.iso | eng | |
| dc.publisher | BioMed Central | |
| dc.rights | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | |
| dc.rights.holder | The Author(s) | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| dc.title | In the light of deep coalescence: revisiting trees within networks | |
| dc.type | Journal article | |
| dc.type.dcmi | Text | |
| dc.type.publication | publisher version | |
| local.sword.agent | BioMed Central |