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Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods
The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to spec...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790797/ https://www.ncbi.nlm.nih.gov/pubmed/24124449 http://dx.doi.org/10.1371/journal.pone.0073667 |
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author | Nguyen, Thi-Hau Ranwez, Vincent Berry, Vincent Scornavacca, Celine |
author_facet | Nguyen, Thi-Hau Ranwez, Vincent Berry, Vincent Scornavacca, Celine |
author_sort | Nguyen, Thi-Hau |
collection | PubMed |
description | The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. |
format | Online Article Text |
id | pubmed-3790797 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37907972013-10-11 Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods Nguyen, Thi-Hau Ranwez, Vincent Berry, Vincent Scornavacca, Celine PLoS One Research Article The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree–gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. Public Library of Science 2013-10-04 /pmc/articles/PMC3790797/ /pubmed/24124449 http://dx.doi.org/10.1371/journal.pone.0073667 Text en © 2013 Nguyen et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Nguyen, Thi-Hau Ranwez, Vincent Berry, Vincent Scornavacca, Celine Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title | Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title_full | Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title_fullStr | Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title_full_unstemmed | Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title_short | Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods |
title_sort | support measures to estimate the reliability of evolutionary events predicted by reconciliation methods |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790797/ https://www.ncbi.nlm.nih.gov/pubmed/24124449 http://dx.doi.org/10.1371/journal.pone.0073667 |
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