Dimensional reduction for the general Markov model on phylogenetic trees

DOI10.1007/S11538-017-0249-6MaRDI QIDQ2012319zbMATH OpenOpenAlexWikidataFDO

Authors Jeremy G. Sumner

Publication date 28 July 2017

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

Full work available at URL https://arxiv.org/abs/1602.07780

zbMATH Keywords

Markov chainsrepresentation theoryaffine group

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)

Abstract: We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.

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Cited in

(5)

• Markovian log-supermodularity, and its applications in phylogenetics
• Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
• Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants
• The algebra of the general Markov model on phylogenetic trees and networks
• Evaluation of the relative performance of the subflattenings method for phylogenetic inference

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Uses Software

• fastDNAml

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