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Orchard Networks are Trees with Additional Horizontal Arcs

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional ho...

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Autores principales: van Iersel, Leo, Janssen, Remie, Jones, Mark, Murakami, Yukihiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9213324/
https://www.ncbi.nlm.nih.gov/pubmed/35727410
http://dx.doi.org/10.1007/s11538-022-01037-z
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author van Iersel, Leo
Janssen, Remie
Jones, Mark
Murakami, Yukihiro
author_facet van Iersel, Leo
Janssen, Remie
Jones, Mark
Murakami, Yukihiro
author_sort van Iersel, Leo
collection PubMed
description Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely related to tree-based networks, where the difference is that in tree-based networks the additional arcs do not need to be horizontal. Then, we use this new characterization to show that the space of orchard networks on n leaves with k reticulations is connected under the rNNI rearrangement move with diameter [Formula: see text] .
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spelling pubmed-92133242022-06-23 Orchard Networks are Trees with Additional Horizontal Arcs van Iersel, Leo Janssen, Remie Jones, Mark Murakami, Yukihiro Bull Math Biol Original Article Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely related to tree-based networks, where the difference is that in tree-based networks the additional arcs do not need to be horizontal. Then, we use this new characterization to show that the space of orchard networks on n leaves with k reticulations is connected under the rNNI rearrangement move with diameter [Formula: see text] . Springer US 2022-06-21 2022 /pmc/articles/PMC9213324/ /pubmed/35727410 http://dx.doi.org/10.1007/s11538-022-01037-z Text en © The Author(s) 2022 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 Original Article
van Iersel, Leo
Janssen, Remie
Jones, Mark
Murakami, Yukihiro
Orchard Networks are Trees with Additional Horizontal Arcs
title Orchard Networks are Trees with Additional Horizontal Arcs
title_full Orchard Networks are Trees with Additional Horizontal Arcs
title_fullStr Orchard Networks are Trees with Additional Horizontal Arcs
title_full_unstemmed Orchard Networks are Trees with Additional Horizontal Arcs
title_short Orchard Networks are Trees with Additional Horizontal Arcs
title_sort orchard networks are trees with additional horizontal arcs
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9213324/
https://www.ncbi.nlm.nih.gov/pubmed/35727410
http://dx.doi.org/10.1007/s11538-022-01037-z
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