Inferring the number of evolutionary events from DNA coding sequence differences

The estimation of the amount of evolutionary divergence that has taken place between two DNA coding sequences depends strongly on the degree of constraint on amino acid replacements. If amino acid replacements are relatively unconstrained, the individual nucleotide is the appropriate unit of analysi...

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Bibliographic Details
Published in:Molecular biology and evolution 1989, Vol.6 (1), p.15-32
Main Author: LEWONTIN, R. C
Format: Article
Language:English
Subjects:
Animals
Biological and medical sciences
Biological Evolution
Codon
DNA - genetics
Drosophila - genetics
Fundamental and applied biological sciences. Psychology
Genetics of eukaryotes. Biological and molecular evolution
Sequence Homology, Nucleic Acid
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Summary:The estimation of the amount of evolutionary divergence that has taken place between two DNA coding sequences depends strongly on the degree of constraint on amino acid replacements. If amino acid replacements are relatively unconstrained, the individual nucleotide is the appropriate unit of analysis and the method of Tajima and Nei can be used. If amino acid replacements are constrained, however, this method is shown to be inapplicable. For sequences with strong amino acid constraints, a method is outlined analogous to the Tajima and Nei method using codons as the unit of analysis. Only synonymous substitutions are used. Codon usage data can be employed to estimate the necessary parameters of the calculation, or a priori models of substitution may be employed. Sequences with significant but intermediate constraints on amino acid replacements are, in principle, unanalyzable.
ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/oxfordjournals.molbev.a040532