Molecular Biology and Evolution, Vol 3, 403-417, Copyright © 1986 by Society for Molecular Biology and Evolution
D Penny and M Hendy
Six protein sequences from the same 11 mammalian taxa were used to estimate
the accuracy and reliability of phylogenetic trees using real, rather than
simulated, data. A tree comparison metric was used to measure the increase
in similarity of minimal trees as larger, randomly selected subsets of
nucleotide positions were taken. The ratio of the observed to the expected
number of incompatibilities for each nucleotide position (character) is a
good predictor of the number of changes required at that position on the
minimal (most-parsimonious) tree. This allows a higher weighting of
nucleotide positions that have changed more slowly and should result in the
minimal length tree converging to the correct tree as more sequences are
obtained. An estimate was made of the smallest subset of trees that need to
be considered to include the actual historical tree for a given set of
data. It was concluded that it is possible to give a reasonable estimate of
the reliability of the final tree, at least when several sequences are
combined. With the present data, resolving the rodent- primate-lagomorph
(rabbit) trichotomy is the least certain aspect of the final tree, followed
then by establishing the position of dog. In our opinion, it is
unreasonable to publish an evolutionary tree derived from sequence data
without giving an idea of the reliability of the tree.
ORIGINAL ARTICLE
Estimating the reliability of evolutionary trees
Department of Botany and Zoology, Massey University, Palmerston North, New Zealand.
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