Novel Triple-Based Problems for the Construction of Phylogenetic Networks via Least Common Ancestors

Abstract

Evolutionary histories are often represented by rooted phylogenetic networks, whose leaves correspond to extant taxa and whose internal vertices represent ancestral lineages. Since such histories must usually be inferred from incomplete data, in particular from genomic sequences of present-day taxa, one often obtains only local information about relative evolutionary proximity. For instance, sequence data may suggest that two taxa $x$ and $y$ are more closely related to each other than either is to a third taxon $z$. This information is classically encoded by a rooted triple $xy|z$. In this paper, we study rooted triples in phylogenetic networks under an ancestor-based interpretation: $xy|z$ is displayed if the unique least common ancestor (LCA) of $x$ and $y$ lies strictly below the unique LCA of $x$ and $z$, respectively of $y$ and $z$, and the latter two LCAs coincide. We also introduce anchored triples $\underline{x}y|z$, which retain only the asymmetric comparison that the LCA of $x$ and $y$ lies below the LCA of $x$ and $z$. This relaxation is natural in networks, where different pairwise ancestral relationships need not behave as they do in trees. We consider several variants of consistency problems for ordinary and anchored triples, both with and without forbidden triples. Somewhat surprisingly, these ancestor-based consistency questions for triples in phylogenetic networks do not appear to have been addressed before despite their direct biological interpretation and the fact that such constraints can be inferred naturally from genomic sequence data. By translating these questions into realization problems for required and forbidden LCA-constraints, we show that all resulting problems can be solved in polynomial time. Moreover, whenever a solution exists, a suitable realizing DAG and phylogenetic network can be constructed within the same time bound.