2024/08/28 by Johanna Heiss, Heiss, Johanna, Daniel H. Huson +3
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #05C05 92D15 05C20 #Biomedical Text Mining and Ontologies #Evolution and Paleontology Studies #FOS: Biological sciences #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.2408.16156
openalex publication_date 2024/08/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.