AAM writes:
I tried myself the simple quantification based on Krings, 1999 (substitution rate - 0.94x10-7 per site per year per lineage) paper but I got quite strange results that do not correlate to the paper, so I presume that I did not understand methodology:
Krings et al 1999 (in PNAS Vol. 96, Issue 10, pp 5581-5585, May 11, 1999) cite the following paper for their mathematical methods:
The paper is on-line at
Professor Nei's own pages. He has a heap of publications in this area, and many are available there. Unfortunately there are some bad links. I’ve given a link to the paper in question that seems to work. You may need to replace "Nei" with "Nei/Lab" in some URLs.
The maths in this paper is very detailed; I won't try to summarize here.
Abtract:
Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition / transversion ratio for the entire control region was ~15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.
Hope this helps.
Cheers -- Sylas
Added in edit: link and cite for Krings et al 1999
This message has been edited by Sylas, 12-19-2004 10:06 PM
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