Abstract
The use of pairwise comparisons of correctly aligned DNA and protein sequences for the measurement of time in historical biology remains a contentious matter. However, the limited success of some molecular evolutionary clocks provides a stimulus to attempt to improve their resolution by the judicious selection of sequences for ease of alignment, commonality of function, taxonomic breadth and appropriate rates of evolution. Existing algorithms for correcting observed distances for superimposed nucleotide substitutions or amino acid replacements appear adequate for the task, given the noise that results from the inherent variability of the process. Some possible approaches are illustrated through the use of gene and protein sequences of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase: an enzyme that is demonstrably homologous from purple bacteria to flowering plants.
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