Rearrangement operations on unrooted phylogenetic networks
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection)...
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Georgia Southern University
2019-12-01
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Online Access: | https://digitalcommons.georgiasouthern.edu/tag/vol6/iss2/6/ |
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doaj-fd38f949e1e34355ba9a0301e863b4f92020-11-25T00:16:07ZengGeorgia Southern UniversityTheory and Applications of Graphs2470-98592019-12-016210.20429/tag.2019.060206Rearrangement operations on unrooted phylogenetic networksRemie JanssenJonathan KlawitterRearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks, which are generalisations of phylogenetic trees that can model reticulated evolutionary relationships. Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In particular, we prove connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-k networks. We also examine the behaviour of shortest TBR-sequence between two phylogenetic networks in a class, and whether the TBR-distance changes if intermediate networks from other classes are allowed: for example, the space of phylogenetic trees is an isometric subgraph of the space of phylogenetic networks under TBR. Lastly, we show that computing the TBR-distance and the PR-distance of two phylogenetic networks is NP-hard.https://digitalcommons.georgiasouthern.edu/tag/vol6/iss2/6/phylogenetic networkrearrangementlocal searchtbrsprnnidiameternp-hard |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Remie Janssen Jonathan Klawitter |
spellingShingle |
Remie Janssen Jonathan Klawitter Rearrangement operations on unrooted phylogenetic networks Theory and Applications of Graphs phylogenetic network rearrangement local search tbr spr nni diameter np-hard |
author_facet |
Remie Janssen Jonathan Klawitter |
author_sort |
Remie Janssen |
title |
Rearrangement operations on unrooted phylogenetic networks |
title_short |
Rearrangement operations on unrooted phylogenetic networks |
title_full |
Rearrangement operations on unrooted phylogenetic networks |
title_fullStr |
Rearrangement operations on unrooted phylogenetic networks |
title_full_unstemmed |
Rearrangement operations on unrooted phylogenetic networks |
title_sort |
rearrangement operations on unrooted phylogenetic networks |
publisher |
Georgia Southern University |
series |
Theory and Applications of Graphs |
issn |
2470-9859 |
publishDate |
2019-12-01 |
description |
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks, which are generalisations of phylogenetic trees that can model reticulated evolutionary relationships. Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In particular, we prove connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-k networks. We also examine the behaviour of shortest TBR-sequence between two phylogenetic networks in a class, and whether the TBR-distance changes if intermediate networks from other classes are allowed: for example, the space of phylogenetic trees is an isometric subgraph of the space of phylogenetic networks under TBR. Lastly, we show that computing the TBR-distance and the PR-distance of two phylogenetic networks is NP-hard. |
topic |
phylogenetic network rearrangement local search tbr spr nni diameter np-hard |
url |
https://digitalcommons.georgiasouthern.edu/tag/vol6/iss2/6/ |
work_keys_str_mv |
AT remiejanssen rearrangementoperationsonunrootedphylogeneticnetworks AT jonathanklawitter rearrangementoperationsonunrootedphylogeneticnetworks |
_version_ |
1725384437717270528 |