Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants

DOI10.1007/S00285-017-1129-2zbMATH Open1383.92056arXiv1608.04761OpenAlexW2963634228WikidataQ38824708 ScholiaQ38824708MaRDI QIDQ1679017FDOQ1679017

Authors: Jeremy G. Sumner, Amelia Taylor, Barbara R. Holland, Peter D Jarvis 

Publication date: 8 November 2017

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site patterns that, in expectation value, either vanish for particular evolutionary trees (in the case of phylogenetic invariants) or have well understood transformation properties (in the case of Markov invariants). While both approaches have been valued for their intrinsic mathematical interest, it is not clear how they relate to each other, and to what extent they can be used as practical tools for inference of phylogenetic trees. In this paper, by focusing on the special case of binary sequence data and quartets of taxa, we are able to view these two different polynomial-based approaches within a common framework. To motivate the discussion, we present three desirable statistical properties that we argue any phylogenetic method should satisfy: (1) sensible behaviour under reordering of input sequences; (2) stability as the taxa evolve independently according to a Markov process; and (3) ability to detect if the conditions of a continuous-time process are violated. Motivated by these statistical properties, we develop and explore several new phylogenetic inference methods. In particular, we develop a statistical bias-corrected version of the Markov invariants approach which satisfies all three properties. We also extend previous work by showing that the phylogenetic invariants can be implemented in such a way as to satisfy property (3). A simulation study shows that, in comparison to other methods, our new proposed approach based on bias-corrected Markov invariants is extremely powerful for phylogenetic inference.

Full work available at URL: https://arxiv.org/abs/1608.04761

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zbMATH Keywords

quartetsMarkov chainsrepresentation theoryphylogenetic invariants

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) Taxonomy, cladistics, statistics in mathematical biology (92B10)

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Cited In (7)

• Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
• Designing weights for quartet-based methods when data are heterogeneous across lineages
• Phylogenetic invariants for the general Markov model of sequence mutation
• Markov invariants and the isotropy subgroup of a quartet tree
• Title not available (Why is that?)
• QUARTET CONSISTENCY COUNT METHOD FOR RECONSTRUCTING PHYLOGENETIC TREES
• Evaluation of the relative performance of the subflattenings method for phylogenetic inference

Uses Software

• Mathematica
• fastDNAml

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