Greedy selection of species for ancestral state reconstruction on phylogenies: Elimination is better than insertion

Guoliang Li, Jian Ma, Louxin Zhang

Research output: Contribution to journalArticle

Abstract

Accurate reconstruction of ancestral character states on a phylogeny is crucial in many genomics studies. We study how to select species to achieve the best reconstruction of ancestral character states on a phylogeny. We first show that the marginal maximum likelihood has the monotonicity property that more taxa give better reconstruction, but the Fitch method does not have it even on an ultrametric phylogeny. We further validate a greedy approach for species selection using simulation. The validation tests indicate that backward greedy selection outperforms forward greedy selection. In addition, by applying our selection strategy, we obtain a set of the ten most informative species for the reconstruction of the genomic sequence of the so-called boreoeutherian ancestor of placental mammals. This study has broad relevance in comparative genomics and paleogenomics since limited research resources do not allow researchers to sequence the large number of descendant species required to reconstruct an ancestral sequence.

Original languageEnglish (US)
Article numbere8985
JournalPloS one
Volume5
Issue number2
DOIs
StatePublished - Feb 4 2010

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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