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The rigid hybrid number for two phylogenetic trees
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number. Such networks are useful for representing the evolution of sp...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7997861/ https://www.ncbi.nlm.nih.gov/pubmed/33770290 http://dx.doi.org/10.1007/s00285-021-01594-2 |
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author | Huber, Katharina T. Linz, Simone Moulton, Vincent |
author_facet | Huber, Katharina T. Linz, Simone Moulton, Vincent |
author_sort | Huber, Katharina T. |
collection | PubMed |
description | Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number. Such networks are useful for representing the evolution of species whose genomes have undergone processes such as lateral gene transfer and recombination that cannot be represented appropriately by a phylogenetic tree. Even so, as was recently pointed out in the literature, insisting that a network displays the set of trees can be an overly restrictive assumption when modeling certain evolutionary phenomena such as incomplete lineage sorting. In this paper, we thus consider the less restrictive notion of rigidly displaying which we introduce and study here. More specifically, we characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences. These are sequences of special subconfigurations of the two trees related to the well-studied cherry-picking sequences. We also show that, in case it exists, the rigid hybrid number for two phylogenetic trees is given by a minimum weight fork-picking sequence for the trees. Finally, we consider the relationship between the rigid hybrid number and three closely related numbers; the weak, beaded, and temporal hybrid numbers. In particular, we show that these numbers can all be different even for a fixed pair of trees, and also present an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of n leaves can grow at least linearly with n. |
format | Online Article Text |
id | pubmed-7997861 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-79978612021-04-27 The rigid hybrid number for two phylogenetic trees Huber, Katharina T. Linz, Simone Moulton, Vincent J Math Biol Article Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number. Such networks are useful for representing the evolution of species whose genomes have undergone processes such as lateral gene transfer and recombination that cannot be represented appropriately by a phylogenetic tree. Even so, as was recently pointed out in the literature, insisting that a network displays the set of trees can be an overly restrictive assumption when modeling certain evolutionary phenomena such as incomplete lineage sorting. In this paper, we thus consider the less restrictive notion of rigidly displaying which we introduce and study here. More specifically, we characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences. These are sequences of special subconfigurations of the two trees related to the well-studied cherry-picking sequences. We also show that, in case it exists, the rigid hybrid number for two phylogenetic trees is given by a minimum weight fork-picking sequence for the trees. Finally, we consider the relationship between the rigid hybrid number and three closely related numbers; the weak, beaded, and temporal hybrid numbers. In particular, we show that these numbers can all be different even for a fixed pair of trees, and also present an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of n leaves can grow at least linearly with n. Springer Berlin Heidelberg 2021-03-26 2021 /pmc/articles/PMC7997861/ /pubmed/33770290 http://dx.doi.org/10.1007/s00285-021-01594-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Huber, Katharina T. Linz, Simone Moulton, Vincent The rigid hybrid number for two phylogenetic trees |
title | The rigid hybrid number for two phylogenetic trees |
title_full | The rigid hybrid number for two phylogenetic trees |
title_fullStr | The rigid hybrid number for two phylogenetic trees |
title_full_unstemmed | The rigid hybrid number for two phylogenetic trees |
title_short | The rigid hybrid number for two phylogenetic trees |
title_sort | rigid hybrid number for two phylogenetic trees |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7997861/ https://www.ncbi.nlm.nih.gov/pubmed/33770290 http://dx.doi.org/10.1007/s00285-021-01594-2 |
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