Molecular Biology and Evolution, Vol 13, 437-444, Copyright © 1996 by Society for Molecular Biology and Evolution
M Wilkinson
Bootstrap analyses are usually summarized with majority-rule component
consensus trees. This consensus method is based on replicated components
and, like all component consensus methods, it is insensitive to other kinds
of agreement between trees. Recently developed reduced consensus methods
can be used to summarize much additional agreement on hypothesised
phylogenetic relationships among multiple trees. The new methods are
"strict" in the sense that they require agreement among all the trees being
compared for any relationships to be represented in a consensus tree.
Majority-rule reduced consensus methods are described and their use in
bootstrap analyses is illustrated with a hypothetical and a real example.
The new methods provide summaries of the bootstrap proportions of all
n-taxon statements/partitions and facilitate the identification of
hypotheses of relationships that are supported by high bootstrap
proportions, in spite of a lack of support for particular components or
clades. In practice majority-rule reduced consensus profiles may contain
many trees. The size of the profile can be reduced by constraints on
minimal bootstrap proportions and/or cardinality of the included trees.
Majority-rule reduced consensus trees can also be selected a posteriori
from the profile. Surrogates to the majority-rule reduced consensus methods
using partition tables or tree pruning options provided by widely used
phylogenetic inference software are also described. The methods are
designed to produce more informative summaries of bootstrap analyses and
thereby foster more informed assessment of the strengths and weaknesses of
complex phylogenetic hypotheses.
ORIGINAL ARTICLE
Majority-rule reduced consensus trees and their use in bootstrapping
School of Biological Sciences, University of Bristol, England. Mark.Wilkinson@bris.ac.uk
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