A Fixed-Parameter Tractable Algorithm for Finding Agreement Cherry-Reduced Subnetworks in Level-1 Orchard Networks

Phylogenetic networks are increasingly being considered better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that have received a lot of attention recently is the class of orchard networks, which is composed of networks that...

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Vydáno v:Journal of computational biology Ročník 31; číslo 4; s. 360
Hlavní autoři: Landry, Kaari, Tremblay-Savard, Olivier, Lafond, Manuel
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 01.04.2024
Témata:
Algorithms
Biological Evolution
Models, Genetic
Phylogeny
orchard networks
network distance
MACRS
cherry picking
cherry operations
phylogenetic networks
ISSN:1557-8666, 1557-8666
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Shrnutí:Phylogenetic networks are increasingly being considered better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that have received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry reductions. Cherry reductions, also called cherry-picking operations, remove either a leaf of a simple cherry (sibling leaves sharing a parent) or a reticulate edge of a reticulate cherry (two leaves whose parents are connected by a reticulate edge). In this article, we present a fixed-parameter tractable algorithm to solve the problem of finding a maximum agreement cherry-reduced subnetwork (MACRS) between two rooted binary level-1 networks. This is the first exact algorithm proposed to solve the MACRS problem. As proven in an earlier work, there is a direct relationship between finding an MACRS and calculating a distance based on cherry operations. As a result, the proposed algorithm also provides a distance that can be used for the comparison of level-1 networks.Phylogenetic networks are increasingly being considered better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that have received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry reductions. Cherry reductions, also called cherry-picking operations, remove either a leaf of a simple cherry (sibling leaves sharing a parent) or a reticulate edge of a reticulate cherry (two leaves whose parents are connected by a reticulate edge). In this article, we present a fixed-parameter tractable algorithm to solve the problem of finding a maximum agreement cherry-reduced subnetwork (MACRS) between two rooted binary level-1 networks. This is the first exact algorithm proposed to solve the MACRS problem. As proven in an earlier work, there is a direct relationship between finding an MACRS and calculating a distance based on cherry operations. As a result, the proposed algorithm also provides a distance that can be used for the comparison of level-1 networks.
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2023.0317