A Semialgebraic Description of the General Markov Model on Phylogenetic Trees

DOI10.1137/120901568zbMATH Open1300.60085arXiv1212.1200OpenAlexW2962993072MaRDI QIDQ3192161FDOQ3192161

John A. Rhodes, Amelia Taylor, Elizabeth S. Allman

Publication date: 26 September 2014

Published in: SIAM Journal on Discrete Mathematics (Search for Journal in Brave)

Abstract: Many of the stochastic models used in inference of phylogenetic trees from biological sequence data have polynomial parameterization maps. The image of such a map --- the collection of joint distributions for a model --- forms the model space. Since the parameterization is polynomial, the Zariski closure of the model space is an algebraic variety which is typically much larger than the model space, but has been usefully studied with algebraic methods. Of ultimate interest, however, is not the full variety, but only the model space. Here we develop complete semialgebraic descriptions of the model space arising from the k-state general Markov model on a tree, with slightly restricted parameters. Our approach depends upon both recently-formulated analogs of Cayley's hyperdeterminant, and the construction of certain quadratic forms from the joint distribution whose positive (semi-)definiteness encodes information about parameter values. We additionally investigate the use of Sturm sequences for obtaining similar results.

Full work available at URL: https://arxiv.org/abs/1212.1200

zbMATH Keywords

phylogenetic treesemialgebraic setphylogenetic varietygeneral Markov model

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) Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20) Semialgebraic sets and related spaces (14P10)

Cited In (16)

• Markovian log-supermodularity, and its applications in phylogenetics
• Designing weights for quartet-based methods when data are heterogeneous across lineages
• Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
• Gaussian tree constraints applied to acoustic linguistic functional data
• An algebraic analysis of the two state Markov model on tripod trees
• The inertia of the symmetric approximation for low-rank matrices
• Bounded-rank tensors are defined in bounded degree
• Phylogenetic reconstruction based on algebra
• Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants
• Evolutionary trees can be learned in polynomial time in the two-state general Markov model
• Parsimony and the rank of a flattening matrix
• Fixed points of the EM algorithm and nonnegative rank boundaries
• Tensors of nonnegative rank two
• The algebra of the general Markov model on phylogenetic trees and networks
• Conditional independence ideals with hidden variables
• A new family of Markov branching trees: the alpha-gamma model

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