An algorithm for reconstructing level-2 phylogenetic networks from trinets

Leo van Iersel, Sjors Kole, Vincent Moulton, Leonie Nipius

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks is to develop algorithms for building such networks by amalgamating small networks into a single large network. The level of a phylogenetic network is a measure of its deviation from being a tree; the higher the level of network, the less treelike it becomes. Various algorithms have been developed for building level-1 networks from small networks. However, level-1 networks may not be able to capture the complexity of some data sets. In this paper, we present a polynomial-time algorithm for constructing a rooted binary level-2 phylogenetic network from a collection of 3-leaf networks or trinets. Moreover, we prove that the algorithm will correctly reconstruct such a network if it is given all of the trinets in the network as input. The algorithm runs in time $O(t\cdot n+n^4)$ with $t$ the number of input trinets and $n$ the number of leaves. We also show that there is a fundamental obstruction to constructing level-3 networks from trinets, and so new approaches will need to be developed for constructing level-3 and higher level-networks.

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