Maximum parsimony on subsets of taxa

DOI10.1016/J.JTBI.2009.06.010zbMATH Open1402.92310arXiv0809.3653OpenAlexW2001892906WikidataQ51819255 ScholiaQ51819255MaRDI QIDQ1625879FDOQ1625879

Authors: Mareike Fischer, Bhalchandra D. Thatte 

Publication date: 26 November 2018

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

Abstract: In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.

Full work available at URL: https://arxiv.org/abs/0809.3653

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zbMATH Keywords

maximum parsimonyancestral state reconstructiontwo-state symmetric model

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10)

Cites Work

• Taxonomy with confidence
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
• Five surprising properties of parsimoniously colored trees

Cited In (11)

• On the number of binary characters needed to recover a phylogeny using maximum parsimony
• Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
• Pairwise sequence alignment at arbitrarily large evolutionary distance
• On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony
• Non-hereditary maximum parsimony trees
• Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model
• Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees
• Algebraic properties of the most parsimonious reconstructions of the hypothetical ancestors on a given tree
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
• Sufficient condition for root reconstruction by parsimony on binary trees with general weights
• Statistical inconsistency of maximum parsimony for \(k\)-tuple-site data

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