Journal of Molecular Evolution

, Volume 48, Issue 3, pp 264–273 | Cite as

A Novel Approach to Phylogeny Reconstruction from Protein Sequences

  • Nick V.  Grishin


The reliable reconstruction of tree topology from a set of homologous sequences is one of the main goals in the study of molecular evolution. If consistent estimators of distances from a multiple sequence alignment are known, the distance method is attractive because the tree reconstruction is consistent. To obtain a distance estimate d, the observed proportion of differences p (p-distance) is usually ``corrected'' for multiple and back substitutions by means of a functional relationship d=f(p). In this paper the conditions under which this correction of p-distances will not alter the selection of the tree topology are specified. When these conditions are not fulfilled the selection of the tree topology may depend on the correction function applied. A novel method which includes estimates of distances not only between sequence pairs, but between triplets, quadruplets, etc., is proposed to strengthen the proper selection of correction function and tree topology. A ``super'' tree that includes all tree topologies as special cases is introduced.

Key words: Substitution rates — Amniote phylogeny — Evolutionary distance — Phylogenetic tree 


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Copyright information

© Springer-Verlag New York Inc. 1999

Authors and Affiliations

  • Nick V.  Grishin
    • 1
  1. 1.Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75235-9041, USAUS

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