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arXiv · 2607.11325

Proximity Measures for Classes of Phylogenetic Networks

Leo van Iersel·Mark Jones·Esther Julien·Yangjing Long·Yukihiro Murakami
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Abstract

Phylogenetic networks are used to represent the evolutionary history of species. Due to biological interpretations and computational advantages, researchers have focused on restricted classes of phylogenetic networks, such as tree-child, orchard, and tree-based. These classes capture different notions of tree-likeness: tree-child networks require every internal vertex to have a taxon reachable by a tree path, orchard networks are trees with horizontal arcs (for modelling histories rife with horizontal gene transfers), and tree-based networks are trees with additional (not-necessarily horizontal) arcs. A natural question to ask is ``how far is a given network from belonging to a particular class?'' This motivates the study of proximity measures, which measure the minimum number of graph modifications required to transform a network into one belonging to a particular class. In this paper, we consider three proximity measures based on leaf addition, valid arc deletion, and arc deletion. We study pairwise comparability of the proximity measures, prove complexity results, and derive extremal bounds for the classes of tree, tree-child, orchard, and tree-based networks.

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Leo van Iersel, Mark Jones, Esther Julien, Yangjing Long, Yukihiro Murakami. 2026-07-13. Proximity Measures for Classes of Phylogenetic Networks. https://arxiv.org/abs/2607.11325

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