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)

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.

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

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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)

Cites Work

• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• A discrete Fourier analysis for evolutionary trees.
• A semialgebraic description of the general Markov model on phylogenetic trees
• Adventures in invariant theory
• Algebraic Statistics for Computational Biology
• An algebraic analysis of the two state Markov model on tripod trees
• Asynchronous Distance between Homologous DNA Sequences
• Fourier calculus on evolutionary trees
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
• Introduction to Lie algebras
• Invariants of phylogenies in a simple case with discrete states
• Invariants of some probability models used in phylogenetic inference
• Lie Markov models
• Lie Markov models with purine/pyrimidine symmetry
• Markov invariants and the isotropy subgroup of a quartet tree
• Markov invariants, plethysms, and phylogenetics
• On the ideals of equivariant tree models
• Phylogenetic ideals and varieties for the general Markov model
• Relevant phylogenetic invariants of evolutionary models
• Tensor rank, invariants, inequalities, and applications
• The Strand Symmetric Model
• The algebra of the general Markov model on phylogenetic trees and networks
• Toric Ideals of Phylogenetic Invariants

Cited In (9)

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

Uses Software

• Mathematica
• fastDNAml

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