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

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 ℛ(N) and a softwired cluster system 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 ℛ(N) or 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 , even when all triplets in ℛ(N) or all clusters in 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 ℛ(N) and 𝒮(N) . We anticipate these results to be of use in the design of algorithms for phylogenetic network inference.