greedy selection of species for ancestral state reconstruction on phylogenies elimination is better than insertion贪婪选择物种的祖先的国家重建的发展史消除比插入.pdfVIP
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greedy selection of species for ancestral state reconstruction on phylogenies elimination is better than insertion贪婪选择物种的祖先的国家重建的发展史消除比插入
Greedy Selection of Species for Ancestral State
Reconstruction on Phylogenies: Elimination Is Better
than Insertion
1 2 3
Guoliang Li , Jian Ma , Louxin Zhang *
1 Computational Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore, 2 Department of Bioengineering, University of Illinois at Urbana-
Champaign, Urbana, Illinois, United States of America, 3 Department of Mathematics, National University of Singapore, Singapore, Singapore
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.
Citation: Li G, Ma J, Zhang L (2010) Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies: Elimination Is Better than Insertion. PLoS
ONE 5(2): e8985. doi:10.1371/journal.pone.0008985
Editor: I. King Jordan, Georgia Institute of Technology, United States of America
Recei
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