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

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

SUBMITTER: Li G 

PROVIDER: S-EPMC2816206 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature