[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ Skip to main content
Springer Nature Link
Log in

Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Summary

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
£29.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bajaj M, Blundell T (1984) Evolution and the tertiary structure of proteins. Ann Rev Biophys Bioeng 13:453–492

    Article  CAS  Google Scholar 

  • 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 82:149–152

    Article  PubMed  CAS  Google Scholar 

  • Cannon RE, White JA, Scandalios JG (1987) Cloning of cDNA for maize superoxide dismutase 2 (SOD2). Proc Natl Acad Sci USA 84:179–183

    Article  PubMed  CAS  Google Scholar 

  • Dayhoff MO, Eck RV (1968) Atlas of protein sequence and structure 1967–1968, National Biomedical Research Foundation, Silver Spring MD, p 19

    Google Scholar 

  • 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 7–16

    Google Scholar 

  • 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 345–358

    Google Scholar 

  • Doolittle RF (1981) Similar amino acid sequences: chance or common ancestry? Science 214:149–159

    Article  PubMed  CAS  Google Scholar 

  • Feng DF, Johnson MS, Doolittle RF (1985) Aligning amino acid sequences: comparison of commonly used methods. J Mol Evol 21:112–125

    Article  CAS  Google Scholar 

  • Fitch WM (1966) An improved method of testing for evolutionary homology. J Mol Biol 16:9–16

    Article  PubMed  CAS  Google Scholar 

  • Fitch WM (1970) Further improvements in the method of testing for evolutionary homology among proteins. J Mol Biol 49:1–14

    Article  PubMed  CAS  Google Scholar 

  • Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257

    Article  Google Scholar 

  • 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 18:60–67

    Article  PubMed  CAS  Google Scholar 

  • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 15:279–284

    Article  Google Scholar 

  • Fredman ML (1984) Computing evolutionary similarity measures with length independent gap penalties. Bull Math Biol 46:553–566

    Google Scholar 

  • Goodman M, Moore GW, Barnabas J, Matsuda G (1974) The phylogeny of human globin genes investigated by the maximum parsimony method. J Mol Evol 3:1–48

    Article  PubMed  CAS  Google Scholar 

  • Hogeweg P, Hesper B (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20:175–186

    Article  PubMed  CAS  Google Scholar 

  • Holmquist R (1979) The method of parsimony: an experimental test and theoretical analysis of the adequacy of molecular restoration studies. J Mol Biol 135:939–958

    Article  PubMed  CAS  Google Scholar 

  • Holmquist R, Jukes T (1981) The current status of REH theory. Reply to an essay by Fitch. J Mol Evol 18:47–59

    Article  PubMed  CAS  Google Scholar 

  • 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 229–249

    Google Scholar 

  • Jabusch JR, Farb DL, Kerschensteiner DA, Deutsch HF (1980) Some sulfhydryl properties and primary structure of human superoxide dismutase. Biochemistry 19:2310–2316

    Article  PubMed  CAS  Google Scholar 

  • 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 44:201–217

    Article  CAS  Google Scholar 

  • Johnson MS, Doolittle RF (1986) A method for the simultaneous alignment of three or more amino acid sequences. J Mol Evol 23:267–278

    Article  PubMed  CAS  Google Scholar 

  • Jue RA, Woodbury NW, Doolittle RF (1980) Sequence homologies amongE. coli ribosomal proteins: evidence for evolutionarily related groupings and internal duplications. J Mol Evol 15:129–148

    Article  PubMed  Google Scholar 

  • Kernighan BW, Ritchie DM (1978) The C programming language. Prentice-Hall, Englewood Cliffs NJ

    Google Scholar 

  • Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91:261–272

    Article  PubMed  CAS  Google Scholar 

  • Lee YM, Friedman DJ, Ayala FJ (1985) Superoxide dismutase: an evolutionary puzzle. Proc Natl Acad Sci USA 82:824–828

    Article  PubMed  CAS  Google Scholar 

  • Leunissen JAM, De Jong WW (1986) Copper/zinc superoxide dismutase: how likely is gene transfer from ponyfish toPhotobacterium leiognathi? J Mol Evol 23:250–258

    Article  CAS  Google Scholar 

  • Martin JP, Fridovich I (1981) Evidence for a natural gene transfer from the ponyfish to its bioluminescent bacterial symbiontPhotobacter leiognathi. J Biol Chem 256:6080–6089

    PubMed  CAS  Google Scholar 

  • 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 38:423–457

    Article  PubMed  CAS  Google Scholar 

  • Murata M, Richardson JS, Sussman JL (1985) Simultaneous comparison of three protein sequences. Proc Natl Acad Sci USA 82:3073–3077

    Article  PubMed  CAS  Google Scholar 

  • 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 48:443–453

    Article  PubMed  CAS  Google Scholar 

  • Penny D, Hendy M (1986) Estimating the reliability of evolutionary trees. Mol Biol Evol 3:403–417

    PubMed  CAS  Google Scholar 

  • Rocha HA, Bannister WH, Bannister JV (1984) The amino acid sequence of copper/zinc superoxide dismutase from swordfish liver. Eur J Biochem 145:477–484

    Article  PubMed  CAS  Google Scholar 

  • Sankoff D, Cedergren RJ, McKay WM (1982) A strategy for sequence phylogeny research. Nucleic Acids Res 10:421–431

    Article  PubMed  CAS  Google Scholar 

  • Sellers PH (1974) Evolutionary distances. SIAM J Appl Math 26:787–793

    Article  Google Scholar 

  • 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 364:675–690

    PubMed  CAS  Google Scholar 

  • Steinman HM, Naik VR, Abernathy JL, Hill RL (1974) Bovine erythrocyte superoxide dismutase J Biol Chem 249:7326–7338

    PubMed  CAS  Google Scholar 

  • Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J Mol Evol 18:387–404

    Article  PubMed  CAS  Google Scholar 

  • Wakabayashi S, Matsubara H, Webster DA (1986) Primary sequence of a dimeric bacterial hemoglobin fromVitreoscilla. Nature 322:481–483

    Article  PubMed  CAS  Google Scholar 

  • Zelenik M, Rudloff V, Braunitzer G (1979) Die Aminosaure-sequenz des monmeren Hamoglobins von Lampetra fluviatilis. Hoppe-Seyler's Z Physiol Chem 360:1879–1894

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, University of California-San Diego, 92093, La Jolla, California, USA

    Da-Fei Feng & Russell F. Doolittle

Authors
  1. Da-Fei Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Russell F. Doolittle
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Feng, DF., Doolittle, R.F. Progressive sequence alignment as a prerequisitetto correct phylogenetic trees. J Mol Evol 25, 351–360 (1987). https://doi.org/10.1007/BF02603120

Download citation

  • Received:

  • Revised:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02603120

Key words

Search

Navigation