Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes |
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Authors: | Nei M; Tajima F |
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Institution: | Center for Demographic and Population Genetics, University of Texas, Houston 77225. |
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Abstract: | A mathematical theory for the evolutionary change of restriction
endonuclease cleavage sites is developed, and the probabilities of various
types of restriction-site changes are evaluated. A computer simulation is
also conducted to study properties of the evolutionary change of
restriction sites. These studies indicate that parsimony methods of
constructing phylogenetic trees often make erroneous inferences about
evolutionary changes of restriction sites unless the number of nucleotide
substitutions per site is less than 0.01 for all branches of the tree. This
introduces a systematic error in estimating the number of mutational
changes for each branch and, consequently, in constructing phylogenetic
trees. Therefore, parsimony methods should be used only in cases where
nucleotide sequences are closely related. Reexamination of Ferris et al.'s
data on restriction-site differences of mitochondrial DNAs does not support
Templeton's conclusions regarding the phylogenetic tree for man and apes
and the molecular clock hypothesis. Templeton's claim that Nei and Li's
method of estimating the number of nucleotide substitutions per site is
seriously affected by parallel losses and loss-gains of restriction sites
is also unsupported.
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