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Path integral formulation and Feynman rules for phylogenetic branching models

Citation

Jarvis, PD and Bashford, JD and Sumner, JG, Path integral formulation and Feynman rules for phylogenetic branching models, Journal of Physics A: Mathematical and General, 38, (44) pp. 9621-9647. ISSN 0305-4470 (2005) [Refereed Article]

DOI: doi:10.1088/0305-4470/38/44/002

Abstract

A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the number of taxa under consideration, and hence the rank of the underlying joint probability state tensor. We point out the combinatorial necessity for a second-quantized, or Fock space setting, incorporating discrete counting labels for taxa and character types, to allow for a description in the number basis. Rate operators describing both time evolution without branching, and also phylogenetic branching events, are identified. A detailed development of these ideas is given, using standard transcriptions from the microscopic formulation of non-equilibrium reaction-diffusion or birth-death processes. These give the relations between stochastic rate matrices, the matrix elements of the corresponding evolution operators representing them, and the integral kernels needed to implement these as path integrals. The 'free' theory (without branching) is solved, and the correct trilinear 'interaction' terms (representing branching events) are presented. The full model is developed in perturbation theory via the derivation of explicit Feynman rules which establish that the probabilities (pattern frequencies of leaf colourations) arising as matrix elements of the time evolution operator are identical with those computed via the standard analysis. Simple examples (phylogenetic trees with two or three leaves), are discussed in detail. Further implications for the work are briefly considered including the role of time reparametrization covariance. © 2005 IOP Publishing Ltd.

Item Details

Item Type:Refereed Article
Research Division:Physical Sciences
Research Group:Other Physical Sciences
Research Field:Physical Sciences not elsewhere classified
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Physical Sciences
Author:Jarvis, PD (Dr Peter Jarvis)
Author:Bashford, JD (Dr James Bashford)
Author:Sumner, JG (Dr Jeremy Sumner)
ID Code:36499
Year Published:2005
Funding Support:Australian Research Council (DP0344996)
Web of Science® Times Cited:7
Deposited By:Physics
Deposited On:2005-08-01
Last Modified:2006-03-29
Downloads:0

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