Generating Markov evolutionary matrices for a given branch length

DOI10.1016/J.LAA.2012.11.009MaRDI QIDQ1938705zbMATH OpenOpenAlexWikidataFDO

Authors Anna M. Kedzierska, Marta Casanellas

Publication date 22 February 2013

Published in Linear Algebra and its Applications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1112.3529

zbMATH Keywords

algorithmbranch lengthdeterminantdiscrete-time modelevolutionary modelMarkov matrixnonhomogeneous evolutionary processesstochastic matrices

Mathematics Subject Classification ID

Determinants, permanents, traces, other special matrix functions (15A15) Stochastic matrices (15B51) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10)

Abstract: Under a markovian evolutionary process, the expected number of substitutions per site (also called branch length) that have occurred when a sequence has evolved from another according to a transition matrix $P$ can be approximated by $-1/4logdetP.$ When the Markov process is assumed to be continuous in time, i.e. $P=expQt$ it is easy to simulate this evolutionary process for a given branch length (this amounts to requiring $Q$ of a certain trace). For the more general case (what we call discrete-time models), it is not trivial to generate a substitution matrix $P$ of given determinant (i.e. corresponding to a process of given branch length). In this paper we solve this problem for the most well-known discrete-time models JC*, K80*, K81*, SSM and GMM. These models lie in the class of nonhomogeneous evolutionary models. For any of these models we provide concise algorithms to generate matrices $P$ of given determinant. Moreover, in the first four models, our results prove that any of these matrices can be generated in this way. Our techniques are mainly based on algebraic tools.

Review text

Under a Markovian evolutionary process, the expected number of substitutions per site (branch length) that occur when a sequence evolves from another via a transition matrix \(P\) can be approximated by \(-\frac 14 \log(\det P)\). In continuous-time models, it is easy to simulate the process for any given branch length. For discrete-time models, it is not so trivial. In this article, the authors solve this problem for the most well-known discrete-time models JC69*, K80*, K81*, SSM, and GMM. They also provide concise algorithms to generate stochastic matrices of given determinant. These models have the advantage to be nonhomogeneous evolutionary processes.

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Cites work

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(7)

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• Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA
• An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
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• Generating embeddable matrices whose principal logarithm is not a Markov generator
• Closed form modeling of evolutionary rates by exponential Brownian functionals
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