Efficient reconstruction of phylogenetic networks with constrained recombination

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Abstract
A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not treelike. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks. We consider the problem of determining whether the sequences can be derived on a phylogenetic network where the recombination cycles are node disjoint. In this paper, we call such a phylogenetic network a "galled-tree". By more deeply analysing the combinatorial constraints on cycle-disjoint phylogenetic networks, we obtain an efficient algorithm that is guaranteed to be both a necessary and sufficient test for the existence of a galled-tree for the data. If there is a galled-tree, the algorithm constructs one and obtains an implicit representation of all the galled trees for the data, and can create these in linear time for each one. We also note two additional results related to galled trees: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation is allowed per site; second, the site compatibility problem (which is NP-hard in general) can be solved in linear time for any set of sequences that can be derived on a galled tree. The combinatorial constraints we develop apply (for the most part) to node-disjoint cycles in any phylogenetic network (not just galled-trees), and can be used for example to prove that a given site cannot be on a node-disjoint cycle in any phylogenetic network. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in phylogenetic networks that go beyond galled-trees.