Journal of Molecular Evolution

, Volume 25, Issue 4, pp 351–360 | Cite as

Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

  • Da-Fei Feng
  • Russell F. Doolittle


A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: “once a gap, always a gap”. The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.

Key words

Multiple sequence alignments Evolutionary trees 


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  1. Bajaj M, Blundell T (1984) Evolution and the tertiary structure of proteins. Ann Rev Biophys Bioeng 13:453–492CrossRefGoogle Scholar
  2. Bannister JV, Parker MW (1985) The presence of a copper/ zinc superoxide dismutase in the bacteriumPhotobacterium leiognathi: a likely case of gene transfer from eukaryotes to prokaryotes. Proc Natl Acad Sci USA 82:149–152PubMedCrossRefGoogle Scholar
  3. Cannon RE, White JA, Scandalios JG (1987) Cloning of cDNA for maize superoxide dismutase 2 (SOD2). Proc Natl Acad Sci USA 84:179–183PubMedCrossRefGoogle Scholar
  4. Dayhoff MO, Eck RV (1968) Atlas of protein sequence and structure 1967–1968, National Biomedical Research Foundation, Silver Spring MD, p 19Google Scholar
  5. Dayhoff MO, Park CM, McLaughlin PJ (1972) Building a phylogenetic tree: cytochrome c. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5. National Biomedical Research Foundation, Washington DC, pp 7–16Google Scholar
  6. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model for evolutionary change. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington DC, pp 345–358Google Scholar
  7. Doolittle RF (1981) Similar amino acid sequences: chance or common ancestry? Science 214:149–159PubMedCrossRefGoogle Scholar
  8. Feng DF, Johnson MS, Doolittle RF (1985) Aligning amino acid sequences: comparison of commonly used methods. J Mol Evol 21:112–125CrossRefGoogle Scholar
  9. Fitch WM (1966) An improved method of testing for evolutionary homology. J Mol Biol 16:9–16PubMedCrossRefGoogle Scholar
  10. Fitch WM (1970) Further improvements in the method of testing for evolutionary homology among proteins. J Mol Biol 49:1–14PubMedCrossRefGoogle Scholar
  11. Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257CrossRefGoogle Scholar
  12. Fitch WM (1981) The old REH theory remains unsatisfactory and the new REH theory is problematical—a reply to Holmquist and Jukes. J Mol Evol 18:60–67PubMedCrossRefGoogle Scholar
  13. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 15:279–284CrossRefGoogle Scholar
  14. Fredman ML (1984) Computing evolutionary similarity measures with length independent gap penalties. Bull Math Biol 46:553–566Google Scholar
  15. Goodman M, Moore GW, Barnabas J, Matsuda G (1974) The phylogeny of human globin genes investigated by the maximum parsimony method. J Mol Evol 3:1–48PubMedCrossRefGoogle Scholar
  16. Hogeweg P, Hesper B (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20:175–186PubMedCrossRefGoogle Scholar
  17. Holmquist R (1979) The method of parsimony: an experimental test and theoretical analysis of the adequacy of molecular restoration studies. J Mol Biol 135:939–958PubMedCrossRefGoogle Scholar
  18. Holmquist R, Jukes T (1981) The current status of REH theory. Reply to an essay by Fitch. J Mol Evol 18:47–59PubMedCrossRefGoogle Scholar
  19. Hunt LT, Hurst-Calderone S, Dayhoff MO (1978) Globins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington DC, pp 229–249Google Scholar
  20. Jabusch JR, Farb DL, Kerschensteiner DA, Deutsch HF (1980) Some sulfhydryl properties and primary structure of human superoxide dismutase. Biochemistry 19:2310–2316PubMedCrossRefGoogle Scholar
  21. Johansen JT, Overballe-Petersen C, Martin B, Hasemann B, Svendsen I (1979) The complete amino acid sequence of copper-zinc superoxide dismutase fromSaccharomyces cerevisiae. Carlsberg Res Commun 44:201–217CrossRefGoogle Scholar
  22. Johnson MS, Doolittle RF (1986) A method for the simultaneous alignment of three or more amino acid sequences. J Mol Evol 23:267–278PubMedCrossRefGoogle Scholar
  23. Jue RA, Woodbury NW, Doolittle RF (1980) Sequence homologies amongE. coli ribosomal proteins: evidence for evolutionarily related groupings and internal duplications. J Mol Evol 15:129–148PubMedCrossRefGoogle Scholar
  24. Kernighan BW, Ritchie DM (1978) The C programming language. Prentice-Hall, Englewood Cliffs NJGoogle Scholar
  25. Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91:261–272PubMedCrossRefGoogle Scholar
  26. Lee YM, Friedman DJ, Ayala FJ (1985) Superoxide dismutase: an evolutionary puzzle. Proc Natl Acad Sci USA 82:824–828PubMedCrossRefGoogle Scholar
  27. Leunissen JAM, De Jong WW (1986) Copper/zinc superoxide dismutase: how likely is gene transfer from ponyfish toPhotobacterium leiognathi? J Mol Evol 23:250–258CrossRefGoogle Scholar
  28. Martin JP, Fridovich I (1981) Evidence for a natural gene transfer from the ponyfish to its bioluminescent bacterial symbiontPhotobacter leiognathi. J Biol Chem 256:6080–6089PubMedGoogle Scholar
  29. Moore GM, Goodman M, Barnabas J (1973) An iterative approach from the standpoint of the additive hypothesis to the dendrogram problem posed by molecular data sets. J Theor Biol 38:423–457PubMedCrossRefGoogle Scholar
  30. Murata M, Richardson JS, Sussman JL (1985) Simultaneous comparison of three protein sequences. Proc Natl Acad Sci USA 82:3073–3077PubMedCrossRefGoogle Scholar
  31. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453PubMedCrossRefGoogle Scholar
  32. Penny D, Hendy M (1986) Estimating the reliability of evolutionary trees. Mol Biol Evol 3:403–417PubMedGoogle Scholar
  33. Rocha HA, Bannister WH, Bannister JV (1984) The amino acid sequence of copper/zinc superoxide dismutase from swordfish liver. Eur J Biochem 145:477–484PubMedCrossRefGoogle Scholar
  34. Sankoff D, Cedergren RJ, McKay WM (1982) A strategy for sequence phylogeny research. Nucleic Acids Res 10:421–431PubMedCrossRefGoogle Scholar
  35. Sellers PH (1974) Evolutionary distances. SIAM J Appl Math 26:787–793CrossRefGoogle Scholar
  36. Steffens GJ, Bannister JV, Bannister WH, Flohe L, Gunzler WA, Kim S-MA, Otting F (1983) The primary structure of Cu-Zn superoxide dismutase fromPhotobacterium leiognathi: evidence for a separate evolution of Cu-Zn superoxide dismutase in bacteria. Hoppe-Seyler's Z Physiol Chem 364:675–690PubMedGoogle Scholar
  37. Steinman HM, Naik VR, Abernathy JL, Hill RL (1974) Bovine erythrocyte superoxide dismutase J Biol Chem 249:7326–7338PubMedGoogle Scholar
  38. Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J Mol Evol 18:387–404PubMedCrossRefGoogle Scholar
  39. Wakabayashi S, Matsubara H, Webster DA (1986) Primary sequence of a dimeric bacterial hemoglobin fromVitreoscilla. Nature 322:481–483PubMedCrossRefGoogle Scholar
  40. Zelenik M, Rudloff V, Braunitzer G (1979) Die Aminosaure-sequenz des monmeren Hamoglobins von Lampetra fluviatilis. Hoppe-Seyler's Z Physiol Chem 360:1879–1894PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc. 1987

Authors and Affiliations

  • Da-Fei Feng
    • 1
  • Russell F. Doolittle
    • 1
  1. 1.Department of ChemistryUniversity of California-San DiegoLa JollaUSA

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