Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model

DOI10.1007/S00285-015-0951-7zbMATH Open1343.92352OpenAlexW1800712751WikidataQ40218751 ScholiaQ40218751MaRDI QIDQ304035FDOQ304035

Authors Peter D Jarvis, Jeremy G. Sumner

Publication date 23 August 2016

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

Full work available at URL https://arxiv.org/abs/1307.5574

zbMATH Keywords

phylogeneticsgroup theoryrepresentation theoryMarkov invariants

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Problems related to evolution (92D15) Symmetric functions and generalizations (05E05) Lie algebras of linear algebraic groups (17B45) Representation theory for linear algebraic groups (20G05)

Abstract: We consider the continuous-time presentation of the strand symmetric phylogenetic substitution model (in which rate parameters are unchanged under nucleotide permutations given by Watson-Crick base conjugation). Algebraic analysis of the model's underlying structure as a matrix group leads to a change of basis where the rate generator matrix is given by a two-part block decomposition. We apply representation theoretic techniques and, for any (fixed) number of phylogenetic taxa $L$ and polynomial degree $D$ of interest, provide the means to classify and enumerate the associated Markov invariants. In particular, in the quadratic and cubic cases we prove there are precisely 1/3$(3^L+(-1{)}^L)$ and $6^{L-1}$ linearly independent Markov invariants, respectively. Additionally, we give the explicit polynomial forms of the Markov invariants for (i) the quadratic case with any number of taxa $L$, and (ii) the cubic case in the special case of a three-taxa phylogenetic tree. We close by showing our results are of practical interest since the quadratic Markov invariants provide independent estimates of phylogenetic distances based on (i) substitution rates within Watson-Crick conjugate pairs, and (ii) substitution rates across conjugate base pairs.

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Cited in

(9)

• Dimensional reduction for the general Markov model on phylogenetic trees
• Tying up loose strands: defining equations of the strand symmetric model
• Markov invariants and the isotropy subgroup of a quartet tree
• Quantum channel simulation of phylogenetic branching models
• Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
• Phylosymmetric algebras: mathematical properties of a new tool in phylogenetics
• Markov invariants, plethysms, and phylogenetics
• Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies
• Lie-Markov models derived from finite semigroups

Describes a project that uses

Uses Software

• Mathematica
• fastDNAml

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