The algebra of the general Markov model on phylogenetic trees and networks
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Publication:2429434
Directed graphs (digraphs), tournaments (05C20) Applications of graph theory (05C90) Applications of continuous-time Markov processes on discrete state spaces (60J28) Markov processes (60J99) Applications of statistics to biology and medical sciences; meta analysis (62P10) Systems biology, networks (92C42) Problems related to evolution (92D15)
Abstract: It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the K3ST model, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper we rectify this shortcoming by showing how to extend the general Markov model on trees to to include arbitrary splits; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity we proceed by discussing the two state case and note that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the previous approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give a tentative argument that our approach to extending to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for the possibility of convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.
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Cites work
- U(1) ×U(1) ×U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes
- Entanglement invariants and phylogenetic branching
- Hadamard phylogenetic methods and the \(n\)-taxon process
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
- Lie groups. An approach through invariants and representations
- Markov invariants, plethysms, and phylogenetics
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- Path integral formulation and Feynman rules for phylogenetic branching models
Cited in
(14)- A new family of Markov branching trees: the alpha-gamma model
- Lie Markov models
- Dimensional reduction for the general Markov model on phylogenetic trees
- The Aldous chain on cladograms in the diffusion limit
- Lie algebra solution of population models based on time-inhomogeneous Markov chains
- Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
- An algebraic analysis of the two state Markov model on tripod trees
- Quantum channel simulation of phylogenetic branching models
- Generalized Markov branching trees
- Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
- A distance-based model for convergent evolution
- Rank conditions on phylogenetic networks
- Convergence-divergence models: generalizations of phylogenetic trees modeling gene flow over time
- Markovian log-supermodularity, and its applications in phylogenetics
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