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Deciding the existence of a cherry-picking sequence is hard on two trees

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Abstract

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which proved hardness for eight or more trees. Via a known equivalence between cherry-picking sequences and temporal phylogenetic networks, our result proves that it is NP-complete to determine the existence of a temporal phylogenetic network that contains topological embeddings of both trees. The hardness result also greatly strengthens previous inapproximability results for the minimum temporal-hybridization number problem. This is the optimization version of the problem where we wish to construct a temporal phylogenetic network that topologically embeds two given rooted binary phylogenetic trees and that has a minimum number of indegree-2 nodes, which represent events such as hybridization and horizontal gene transfer. We end on a positive note, pointing out that fixed parameter tractability results in this area are likely to ensure the continued relevance of the temporal phylogenetic network model.

    Research areas

  • COMPLEXITY, Elimination orders, NP-hardness, PHYLOGENETIC NETWORKS, Phylogenetic networks, Phylogenetics, Satisfiability, TEMPORAL HYBRIDIZATION NUMBER, Temporal networks
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Details

Original languageEnglish
Pages (from-to)131-143
Number of pages13
JournalDiscrete Applied Mathematics
Volume260
Early online date2019
DOIs
Publication statusPublished - 15 May 2019