A stepwise algorithm for finding minimum evolution trees

Sudhir Kumar

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m - 1)1/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.

Original languageEnglish (US)
Pages (from-to)584-593
Number of pages10
JournalMolecular Biology and Evolution
Volume13
Issue number4
StatePublished - Apr 1996
Externally publishedYes

Fingerprint

Trees (mathematics)
Topology
Statistical tests
Joining
topology
Sampling
Computer simulation
Selection Bias
Least-Squares Analysis
methodology
computer simulation
Computer Simulation
least squares
statistical analysis

Keywords

  • distance method
  • minimum evolution trees
  • neighbor-joining
  • phylogeny

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

A stepwise algorithm for finding minimum evolution trees. / Kumar, Sudhir.

In: Molecular Biology and Evolution, Vol. 13, No. 4, 04.1996, p. 584-593.

Research output: Contribution to journalArticle

Kumar, Sudhir. / A stepwise algorithm for finding minimum evolution trees. In: Molecular Biology and Evolution. 1996 ; Vol. 13, No. 4. pp. 584-593.
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