I saw this sentence "4DTv is the transversion rate at fourfold synonymous codon positions, and ranged from zero (for recently duplicated paralogs) to ~0.5 (for paralogs derived from an ancient evolutionary past)." at this paper and another paper.

I have searched 4DTv or four-fold synonymous on google, but I did not find the answers showed at the following lines.

And my questions:

(1) Does the value of 4DTv range from 0 to 0.5?

(2) Why 4DTv closed to 0.5 indicate that an ancient evolutionary was happended?

  • I was about to ask the same question: did you answer yourself? Can you post your answer in that case? – Macspider Nov 13 at 10:14

After one month of research, I have some insights about it.

First of all, more than "fourfold-synonymous", the correct research is fourfold degeneracy. The genetic code is degenerate, in the sense that there is usually more than 1 codon encoding a certain amino-acid. The degeneracy usually takes place in the third position of the codon, that can be 2-, 3- or 4-fold degenerate. A 4-fold degenerate site would be the third position of a codon, where regardless of which nucleotide you have, the outcome doesn't change. Example: GGT, GGC, GGA, GGG all code for Glycine. As there are four variants at the third site of the codon, the third site is said to be fourfold-degenerate (4D). As the encoded amino-acid does not change, there is virtually no selective pressure on these variants, therefore they can be used as a "clock" to estimate times, given that you know the mutation rates per position.

Now for your other questions: Yes, the value ranges from 0 to ~0.5, and this can be explained in a simple way. Transversions (Tv) are considered to be more rare than transitions (Ti). Therefore, if you calculate the ratio of Tv among all the variants, you expect this value to be < 0.5 (i.e. to have less Tv than Ti, otherwise it would be >= 0.5). Now, in order to accumulate Tv at 4D sites you need time to pass, so the more of them you have, the more time has passed, and that's why 4DTv ratios define time.

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