Recognizing Level-k-Based Phylogenetic Networks is NP-Complete

Abstract

Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are from being tree-based, Suzuki and Hayamizu (2025) formulated the problem of finding the support network with minimum level of a given rooted almost-binary phylogenetic network. They conjectured that this problem is NP-hard and provided exponential-time algorithms. In this paper, we prove this conjecture by showing that, for every fixed integer $k \geq 1$, it is NP-complete to decide whether the minimum level is at most $k$.