On encodings of phylogenetic networks of bounded level
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Publication:455730
DOI10.1007/S00285-011-0456-YzbMATH Open1303.92080arXiv0906.4324OpenAlexW3102216859WikidataQ51548537 ScholiaQ51548537MaRDI QIDQ455730FDOQ455730
Authors: Philippe Gambette, Katharina T. Huber 
Publication date: 22 October 2012
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Abstract: Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case.
Full work available at URL: https://arxiv.org/abs/0906.4324
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consistencyclustersmetricphylogenetic networksindistinguishablelevel-\(k\) networklevel-1 networksupernetworktripletsweak hierarchy
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Cited In (24)
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
- Trinets encode orchard phylogenetic networks
- Trinets encode tree-child and level-2 phylogenetic networks
- Beyond representing orthology relations by trees
- Encodings of cladograms and labeled trees
- Level-\(2\) networks from shortest and longest distances
- Encoding and constructing 1-nested phylogenetic networks with trinets
- Computing the rooted triplet distance between galled trees by counting triangles
- On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters
- Classes of explicit phylogenetic networks and their biological and mathematical significance
- Display sets of normal and tree-child networks
- An efficient algorithm for the rooted triplet distance between galled trees
- Computing the rooted triplet distance between phylogenetic networks
- Computing consensus networks for collections of 1-nested phylogenetic networks
- The weighted total cophenetic index: a novel balance index for phylogenetic networks
- A class of phylogenetic networks reconstructable from ancestral profiles
- An algorithm for reconstructing level-2 phylogenetic networks from trinets
- Uprooted phylogenetic networks
- Reconstruction of LGT networks from tri-LGT-nets
- Caterpillars on three and four leaves are sufficient to binary normal networks
- Comparing and simplifying distinct-cluster phylogenetic networks
- Encoding and ordering \(X\)-cactuses
- Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
- Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations
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