2008/09/22 by Mareike Fischer, Fischer, Mareike, Bhalchandra D. Thatte +1
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Populations and Evolution (q-bio.PE) #Stochastic processes and statistical mechanics #Topological and Geometric Data Analysis
paper · pdf · doi:10.48550/arxiv.0809.3653
openalex publication_date 2008/09/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.