On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters

Philippe Gambette, K. T. Huber, S. Kelk

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Abstract

Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet systems and cluster systems, the motivation being that any network $N$ induces a triplet system $\mathcal R(N)$ and a softwired cluster system $\mathcal S(N)$. Since in real-world studies it cannot be guaranteed that all triplets/softwired clusters induced by a network are available, it is of particular interest to understand whether subsets of $\mathcal R(N)$ or $\mathcal S(N)$ allow one to uniquely reconstruct the underlying network $N$. Here we show that even within the highly restricted yet biologically interesting space of level-1 phylogenetic networks it is not always possible to uniquely reconstruct a level-1 network $N$\kelk{,} even when all triplets in $\mathcal R(N)$ or all clusters in $\mathcal S(N)$ are available. On the positive side, we introduce a reasonably large subclass of level-1 networks the members of which are uniquely determined by their induced triplet/softwired cluster systems. Along the way, we also establish various enumerative results, both positive and negative, including results which show that certain special subclasses of level-1 networks $N$ can be uniquely reconstructed from proper subsets of $\mathcal R(N)$ and $\mathcal S(N)$. We anticipate these results to be of use in the design of algorithms for phylogenetic network inference.
Original languageEnglish
Pages (from-to)1729–1751
JournalJournal of Mathematical Biology
Volume74
Issue number7
Early online date31 Oct 2016
DOIs
Publication statusPublished - Jun 2017

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