Recovering normal networks from shortest inter-taxa distance information

Journal of Mathematical Biology
Magnus BordewichCharles Semple

Abstract

Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf vertex is the parent of a tree vertex or a leaf. Up to a certain equivalence, it has been recently shown that, under two different types of weightings, edge-weighted tree-child networks are determined by their collection of distances between each pair of taxa. However, the size of these collections can be exponential in the size of the taxa set. In this paper, we show that, if we have no "shortcuts", that is, the networks are normal, the same results are obtained with only a quadratic number of inter-taxa distances by using the shortest distance between each pair of taxa. The proofs are constructive and give cubic-time algorithms in the size of the taxa sets for building such weighted networks.

References

Nov 15, 2003·Molecular Phylogenetics and Evolution·C Donovan BaileyColin E Hughes
Mar 2, 2006·Systematic Biology·Mihaela BaroniMike Steel
Sep 29, 2006·Journal of Bioinformatics and Computational Biology·Ho-Leung ChanSiu-Ming Yiu
Feb 24, 2007·Bulletin of Mathematical Biology·Stephen J Willson
Jun 9, 2007·Bulletin of Mathematical Biology·Stephen J Willson
Oct 1, 2009·Bulletin of Mathematical Biology·Stephen J Willson
Oct 31, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gabriel CardonaGabriel Valiente
May 17, 2012·Algorithms for Molecular Biology : AMB·Stephen J Willson
Dec 17, 2015·Journal of Mathematical Biology·Magnus Bordewich, Charles Semple

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Citations

Jul 13, 2019·Bulletin of Mathematical Biology·Yukihiro MurakamiVincent Moulton
Sep 11, 2020·Journal of Mathematical Biology·Simone Linz, Charles Semple
Jan 17, 2021·Mathematical Biosciences·Allan BaiMike Steel
May 12, 2019·Mathematical Biosciences·Péter L ErdősMike Steel
Dec 14, 2021·Journal of Bioinformatics and Computational Biology·Remie Janssen, Pengyu Liu

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