Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model

DOI10.1016/J.JTBI.2014.07.029MaRDI QIDQ739707zbMATH OpenOpenAlexWikidataFDO

Authors Elchanan Mossel, Mike Steel

Publication date 19 August 2016

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1404.2681

zbMATH Keywords

ancestral stateinformation lossMarkov processYule pure-birth tree

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 branching processes (60J85) Problems related to evolution (92D15)

Abstract: Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique -- majority rule -- estimates the root state by the most frequently occurring state at the leaves. Alternative methods -- such as maximum parsimony - explicitly take the tree structure into account. Since either method can outperform the other on particular trees, it is useful to consider the accuracy of the methods on trees generated under some evolutionary null model, such as a Yule pure-birth model. In this short note, we answer a recently posed question concerning the performance of majority rule on Yule trees under a symmetric 2-state Markovian substitution model of character state change. We show that majority rule is accurate precisely when the ratio of the birth (speciation) rate of the Yule process to the substitution rate exceeds the value $4$. By contrast, maximum parsimony has been shown to be accurate only when this ratio is at least 6. Our proof relies on a second moment calculation, coupling, and a novel application of a reflection principle.

Recommendations

• Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
• Sufficient condition for root reconstruction by parsimony on binary trees with general weights
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Cites work

• Broadcasting on trees and the Ising model.
• Choosing the best ancestral character state reconstruction method
• Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models
• Inferring ancestral sequences in taxon-rich phylogenies
• Information flow on trees
• Markov chains and mixing times. With a chapter on ``Coupling from the past by James G. Propp and David B. Wilson.

Cited in

(7)

• Sufficient condition for root reconstruction by parsimony on binary trees with general weights
• Ancestral state reconstruction with large numbers of sequences and edge-length estimation
• On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
• Phylogenetic confidence intervals for the optimal trait value
• A consistent estimator of the evolutionary rate
• Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree
• Topology and inference for Yule trees with multiple states

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