Journal of Molecular Evolution

, Volume 57, Supplement 1, pp S233–S240

Estimating Changes in Mutational Mechanisms of Evolution


DOI: 10.1007/s00239-003-0032-1

Cite this article as:
Ota, R. & Penny, D. J Mol Evol (2003) 57: S233. doi:10.1007/s00239-003-0032-1


By considering three DNA sequences simultaneously there is sufficient information to recover a full Markov model with three transition matrices from the root to each of the sequences. It is necessary to have relatively long sequences because, for nucleotides, the full model requires 39 parameters that are estimated from 63 observable values. This triplet Markov method is evaluated for the protein coding genes of mammalian vertebrate mitochondrial genomes, and, in addition, version for two-statecharacters (such as R/Y coding) is implemented. A key finding is that some changes in mutational mechanism differentially affect the mutation rate between pairs of nucleotides; there does not appear to be a universal change in “rate” of evolution. It remains to be explored whether detecting changes in certain nucleotide interchanges can be localized to a particular part of the DNA replication/repair system. In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change.


Differences in DNA repairMolecular clockMutation rateTensor

Copyright information

© Springer-Verlag New York LLC 2003

Authors and Affiliations

  1. 1.Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciencesMassey University, Palmerston NorthNew Zealand