Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods

Abstract: Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems due to the number of taxa. We introduce the notion of an Efficient Quartet System (EQS) to represent a phylogenetic tree with a subset of the quartets displayed by the tree. We show mathematically that the set of quartets obtained from a tree via an EQS contains all of the combinatorial information of the tree itself. Using performance tests on simulated datasets, we also demonstrate that using an EQS to reduce the number of quartets in pipelines for summary methods of species tree inference and supertree inference results in only small reductions in accuracy.