On encodings of phylogenetic networks of bounded level
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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? For the large class of level-1 (phylogenetic) networks we characterize those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. In addition, we show that three known distance measures for comparing phylogenetic networks are in fact metrics on the resulting subclass and give the diameter for two of them. Finally, we investigate the related concept of indistinguishability and also show that many properties enjoyed by level-1 networks are not satisfied by networks of higher level.
KeywordsPhylogenetic networks Triplets Clusters Supernetwork Level-1 network Level-k network Weak hierarchy Consistency Metric Indistinguishable
Mathematics Subject Classification (2000)92B10
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- Bandelt HJ, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human population using median networks. Genetics 141: 743–753Google Scholar
- Choy C, Jansson J, Sadakane K, Sung WK (2004) Computing the maximum agreement of phylogenetic networks. In: Proceedings of computing: the tenth Australasian theory symposium (CATS’04). Electronic notes in theoretical computer science, vol 91, pp 134–147Google Scholar
- Gambette P, Berry V, Paul C (2009) The structure of level-k phylogenetic networks. In: Proceedings of the 20th annual symposium on combinatorial pattern matching (CPM’09)Google Scholar
- Grünewald S, Huber KT (2007) Identifying and defining trees. In: Gascuel O, Steel M (eds) Reconstructing evolution, new mathematical and computational advances. Oxford University Press, Oxford, pp 217–246Google Scholar
- Gusfield D, Eddhu S, Langley C (2003) Efficient reconstruction of phylogenetic networks with constrained recombination. In: Proceedings of the 2003 IEEE computational systems bioinformatics conference (CSB2003), pp 363–374Google Scholar
- Huson DH, Rupp R (2008) Summarizing multiple gene trees using cluster networks. In: Proceedings of the eighth workshop on algorithms in bioinformatics (WABI’08). Lecture notes in computer science, vol 5251. Springer, New York, pp 296–305Google Scholar
- Huson DH, Rupp R, Scornavacca C (2011) Phylogenetic networks. Cambridge University Press, CambridgeGoogle Scholar
- Semple C (2007) Hybridization networks. In: Gascuel O, Steel M (eds) Reconstructing evolution new mathematical and computational advances. Oxford University Press, Oxford, pp 277–314Google Scholar
- To TH, Habib M (2009) Level-k phylogenetic network can be constructed from a dense triplet set in polynomial time. In: Proceedings of the 20th annual symposium on combinatorial pattern matching (CPM’09)Google Scholar
- Wang L, Zhang K, Zhang L (2001) Perfect phylogenetic networks with recombination. In: Proceedings of the 16th ACM symposium on applied computing (SAC’01), pp 46–50Google Scholar