Maximum parsimony on subsets of taxa

DOI10.1016/J.JTBI.2009.06.010MaRDI QIDQ1625879zbMATH OpenOpenAlexWikidataFDO

Authors Mareike Fischer, Bhalchandra D. Thatte

Publication date 26 November 2018

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

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

zbMATH Keywords

ancestral state reconstructionmaximum parsimonytwo-state symmetric model

Mathematics Subject Classification ID

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

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.

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Cites work

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• Taxonomy with confidence

Cited in

(11)

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

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