In article <01IFDFBOSJF600UCVY at RL0002.RULIMBURG.NL>, F.Schaap at FYS.UNIMAAS.NL writes:
>I am (still) searching a a reliable method for calculating divergence time
>between members of a multigene family, with the members having different
>evolutionary rates? Between orthologous sequences synonymous substitution
>rates are fairly constant (3*10-9 per site per year), while nonsynonymous
>substitution rates range from 0.021-0.76*10-9. Between paralogous sequences
>the number of synonymous substitutions per site can not be accurately
The number of substitutions, synonymous or non synonymous, can be
estimated in exactly the same way for orthologous and paralogous
genes, as far as I can judge. If you want to infer divergence times
from this, you need an estimate of substitution rate, which is
variable both for synonymous and non synonymous substitutions,
between genes and between lineages.
You may be able to calibrate the rate of genes by comparing
orthologous copies, if you know divergence dates of species, then
use this calibration in comparing paralogous copies.
Is this what you are looking for ?
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