Identifiability of phylogenetic networks and quintet concordance factors

Abstract

Several statistical methods of phylogenetic network inference and testing for non-tree-like relationships are based on assessing genomic data through quartet Concordance Factors, the frequencies of 4-taxon topological relationships on gene trees. While such an approach obviates making several undesirable modeling assumptions, it also results in non-identifiability issues for network roots and for small cycles. In this work, an algorithm and accompanying Macaulay2 implementation are provided for computing $n$-tet Concordance Factors on any phylogenetic network. We employ this algorithm on quintet Concordance Factors, summarizing 5-taxon gene trees, to explore identifiability of level-1 networks under the Network Multispecies Coalescent model. We show some additional network features become identifiable that are not through quartets. As identifiability is a necessary prerequisite to inference by any method, this lays a foundation for future inference work.