On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony

DOI10.1007/S11538-018-0407-5zbMATH Open1390.92093arXiv1706.06085OpenAlexW2719896867WikidataQ87866725 ScholiaQ87866725MaRDI QIDQ1636052FDOQ1636052

Authors: Lina Herbst, Mareike Fischer 

Publication date: 4 June 2018

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

Abstract: We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric 4-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

Full work available at URL: https://arxiv.org/abs/1706.06085

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zbMATH Keywords

maximum parsimonyreconstruction accuracyancestral sequence reconstructionsymmetric four-state model

Mathematics Subject Classification ID

Problems related to evolution (92D15) Trees (05C05)

Cites Work

• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
• Maximum parsimony on subsets of taxa
• Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees

Cited In (8)

• Generating most parsimonious reconstructions on a tree: A generalization of the Farris-Swofford-Maddison method
• Ancestral state reconstruction with large numbers of sequences and edge-length estimation
• Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
• Pairwise sequence alignment at arbitrarily large evolutionary distance
• Title not available (Why is that?)
• Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees
• Maximum parsimony on subsets of taxa
• Sufficient condition for root reconstruction by parsimony on binary trees with general weights

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