Abstract:
: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-state-characters (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.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Ota R,Penny Ddoi
10.1007/s00239-003-0032-1keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
S233-40eissn
0022-2844issn
1432-1432journal_volume
57 Suppl 1pub_type
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