Algorithmica

, Volume 54, Issue 1, pp 1–24 | Cite as

Why Neighbor-Joining Works

Article

Abstract

We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson’s optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson’s criterion is not satisfied. We also provide a proof for Atteson’s conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold for the quadratic time fast neighbor-joining algorithm, thus providing a theoretical basis for inferring very large phylogenies with neighbor-joining.

Keywords

Distance methods Edge radius Neighbor-joining Quartets 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Atteson, K.: The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251–278 (1999) MATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Bruno, W.J., Socci, N.D., Halpern, A.L.: Weighted neighbor-joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17(1), 189–197 (2000) Google Scholar
  3. 3.
    Bryant, D.: On the uniqueness of the selection criterion in neighbor-joining. J. Classif. 22(1), 3–15 (2005) MATHCrossRefGoogle Scholar
  4. 4.
    Dai, W., Xu, Y., Zhu, B.: On the edge l radius of Saitou and Nei’s method for phylogenetic reconstruction. Theor. Comput. Sci. 369(1–3), 448–455 (2006) MATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Desper, R., Gascuel, O.: The minimum evolution distance-based approach to phylogenetic inference. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford (2005) Google Scholar
  6. 6.
    Elias, I., Lagergren, J.: Fast neighbor joining. In: Proceedings of the International Colloquium on Automata, Languages and Programming (ICALP’05) (2005) Google Scholar
  7. 7.
    Erdös, P.L., Steel, M.A., Székely, L.A., Warnow, T.J.: A few logs suffice to build (almost) all trees, I. Random Struct. Algorithms 14(2), 153–184 (1999) MATHCrossRefGoogle Scholar
  8. 8.
    Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D., Kluge, A.G.: Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99–124 (1996) CrossRefGoogle Scholar
  9. 9.
    Felsenstein, J.: PHYLIP (phylogeny inference package) version 3.5c. Tech. report, Department of Genetics, University of Washington, Seattle (1993) Google Scholar
  10. 10.
    Gascuel, O.: A note on Sattath and Tversky’s, Saitou and Nei’s, and Studier and Keppler’s algorithms for inferring phylogenies from evolutionary distances. Mol. Biol. Evol. 11(6), 961–963 (1994) Google Scholar
  11. 11.
    Gascuel, O.: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14(7), 685–695 (1997) Google Scholar
  12. 12.
    Gascuel, O., Steel, M.: Neighbor-joining revealed. Mol. Biol. Evol. 23(11), 1997–2000 (2006) CrossRefGoogle Scholar
  13. 13.
    Hall, B.G.: Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol. Biol. Evol. 22(3), 792–802 (2005) CrossRefGoogle Scholar
  14. 14.
    Huelsenbeck, J., Hillis, D.: Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42(3), 247–264 (1993) Google Scholar
  15. 15.
    John, K.St., Warnow, T., Moret, B., Vawter, L.: Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor joining. J. Algorithms 48, 174–193 (2003) Google Scholar
  16. 16.
    Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459–468 (1994) Google Scholar
  17. 17.
    Kumar, S., Gadagker, S.R.: Efficiency of the neighbor-joining method in reconstructing evolutionary relationships in large phylogenies. J. Mol. Evol. 51, 544–553 (2000) Google Scholar
  18. 18.
    Levy, D., Yoshida, R., Pachter, L.: Beyond pairwise distances: neighbor joining with phylogenetic diversity estimates. Mol. Biol. Evol. 23, 491–498 (2006) CrossRefGoogle Scholar
  19. 19.
    Olsen, G.J., Matsuda, H., Hagstrom, R., Overbeek, R.: fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10, 41–48 (1994) Google Scholar
  20. 20.
    Ota, S., Li, W.H.: NJML: a hybrid algorithm for the neighbor-joining and maximum likelihood methods. Mol. Biol. Evol. 17(9), 1401–1409 (2000) Google Scholar
  21. 21.
    Pauplin, Y.: Direct calculation of tree length using a distance matrix. J. Mol. Evol. 51, 41–47 (2000) Google Scholar
  22. 22.
    Rambaut, A., Grassly, N.C.: Seq-Gen: an application for the Monte Carlo simulation of DNA sequences evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235–238 (1997) Google Scholar
  23. 23.
    Ranwez, V., Gascuel, O.: Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol. Biol. Evol. 19(11), 1952–1963 (2002) Google Scholar
  24. 24.
    Saitou, N., Nei, M.: The neighbor joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4), 406–425 (1987) Google Scholar
  25. 25.
    Sattath, S., Tversky, A.: Additive similarity trees. Psychometrika 42(6), 319–345 (1977) CrossRefGoogle Scholar
  26. 26.
    Semple, C., Steel, M.: Phylogenetics. Graduate Series in Mathematics and its Applications. Oxford University Press, Oxford (2003) MATHGoogle Scholar
  27. 27.
    Strimmer, K., von Haeseler, A.: Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964–969 (1996) Google Scholar
  28. 28.
    Studier, J.A., Keppler, K.J.: A note on the neighbor-joining method of Saitou and Nei. Mol. Biol. Evol. 5, 729–731 (1988) Google Scholar
  29. 29.
    Tamura, K., Nei, M., Kumar, S.: Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. 101, 11030–11035 (2004) CrossRefGoogle Scholar
  30. 30.
    Xu, Y., Dai, W., Zhu, B.: A lower bound on the edge l radius of Saitou and Nei’s method for phylogenetic reconstruction. Inf. Process. Lett. 94, 225–230 (2005) CrossRefMathSciNetGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceUC BerkeleyBerkeleyUSA

Personalised recommendations