Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous

Sudhindra R. Gadagkar, Sudhir Kumar

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in different species. In a recent study, the influence of heterotachy on the performance of different phylogenetic methods was examined using computer simulation for a four-species phylogeny. Maximum parsimony (MP) was reported to generally outperform maximum likelihood (ML). However, our comparisons of MP and ML methods using the methods and evaluation criteria employed in that study, but considering the possible range of proportions of sites involved in heterotachy, contradict their findings and indicate that, in fact, ML is significantly superior to MP even under heterotachy.

Original languageEnglish (US)
Pages (from-to)2139-2141
Number of pages3
JournalMolecular Biology and Evolution
Volume22
Issue number11
DOIs
StatePublished - Nov 2005

Fingerprint

Maximum likelihood
selection intensity
Sequence Alignment
DNA sequences
phylogeny
sequence alignment
Phylogeny
computer simulation
Computer Simulation
Amino Acid Sequence
amino acid sequences
amino acid
methodology
phylogenetics
nucleotide sequences
Amino Acids
DNA
Computer simulation
method
rate

Keywords

  • Heterotachy
  • Maximum likelihood
  • Maximum parsimony
  • Phylogenetic inference

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. / Gadagkar, Sudhindra R.; Kumar, Sudhir.

In: Molecular Biology and Evolution, Vol. 22, No. 11, 11.2005, p. 2139-2141.

Research output: Contribution to journalArticle

Gadagkar, Sudhindra R. ; Kumar, Sudhir. / Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. In: Molecular Biology and Evolution. 2005 ; Vol. 22, No. 11. pp. 2139-2141.
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