Work

Bridging Between Deviation Indices for Non-Tree-Based Phylogenetic Networks

Year: 2024

Type: article

Abstract: Phylogenetic networks are a useful model that can represent reticulate evolution and complex biological data. In recent years, mathematical and computational aspects of tree-based networks have been well studied. However, not all phylogenetic networks are tree-based, so it is meaningful to consider how close a given network is to being tree-based; Francis-Steel-Semple (2018) proposed several different indices to measure the degree of deviation of a phylogenetic network from being tree-based. One is the minimum number of leaves that need to be added to convert a given network to tree-based, and another is the number of vertices that are not included in the largest subtree covering its leaf-set. Both values are zero if and only if the network is tree-based. Both deviation indices can be computed efficiently, but the relationship between the above two is unknown, as each has been studied using different approaches. In this study, we derive a tight inequality for the values of the two measures and also give a characterisation of phylogenetic networks such that they coincide. This characterisation yields a new efficient algorithm for the Maximum Covering Subtree Problem based on the maximal zig-zag trail decomposition.

Source: IEEE Transactions on Computational Biology and Bioinformatics

DOI: 10.1109/tcbb.2024.3456575

Authors: Takatora Suzuki, Han Guo, Momoko Hayamizu

Institution: Waseda University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $2,495

Funder: Japan Science and Technology Agency