Phylosymmetric algebras: mathematical properties of a new tool in phylogenetics

DOI10.1007/S11538-020-00832-WzbMATH Open1457.92127arXiv2009.11599OpenAlexW3107065762WikidataQ102320643 ScholiaQ102320643MaRDI QIDQ2227157FDOQ2227157

Authors: Michael Hendriksen, Julia A. Shore 

Publication date: 10 February 2021

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Abstract: In phylogenetics it is of interest for rate matrix sets to satisfy closure under matrix multiplication as this makes finding the set of corresponding transition matrices possible without having to compute matrix exponentials. It is also advantageous to have a small number of free parameters as this, in applications, will result in a reduction of computation time. We explore a method of building a rate matrix set from a rooted tree structure by assigning rates to internal tree nodes and states to the leaves, then defining the rate of change between two states as the rate assigned to the most recent common ancestor of those two states. We investigate the properties of these matrix sets from both a linear algebra and a graph theory perspective and show that any rate matrix set generated this way is closed under matrix multiplication. The consequences of setting two rates assigned to internal tree nodes to be equal are then considered. This methodology could be used to develop parameterised models of amino acid substitution which have a small number of parameters but convey biological meaning.

Full work available at URL: https://arxiv.org/abs/2009.11599

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zbMATH Keywords

graph theorymatrix modelsmatrix algebrasrooted treesphylogenetic methodsrate matrices

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15)

Cites Work

• Nineteen Dubious Ways to Compute the Exponential of a Matrix
• Phylogeny. Discrete and random processes in evolution
• Spectra of graphs
• Lie Markov models
• Lie Markov models with purine/pyrimidine symmetry
• Molecular evolution. A statistical approach
• Multiplicatively closed Markov models must form Lie algebras

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• Title not available (Why is that?)
• The impracticalities of multiplicatively-closed codon models: a retreat to linear alternatives

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