Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous

Sudhindra R. Gadagkar, Sudhir Kumar

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


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
Issue number11
StatePublished - Nov 2005


  • Heterotachy
  • Maximum likelihood
  • Maximum parsimony
  • Phylogenetic inference

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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