In molecular evolution, I know that the instantaneous rate of the rate matrix is the limit of the rate as time approaches 0, but what I don't understand is how this rate is established or what I can do with this number.

For instance, if a discrete character is thought to have changed from 0 to 1 five times on a tree with a root age of 40 million years, is the proportion 5 / 40 million the same as the instantaneous rate of change? If not, how exactly are they different?

From a different perspective, let's assume an (absolute) instantaneous rate of 0.0001 and let's say I have a tree with a root age of 2 million years. Can I multiply 0.0001 by two million to get the expected number of transitions of that character across the tree?

  • $\begingroup$ related: bioinformatics.stackexchange.com/questions/13605/… $\endgroup$ Mar 15, 2021 at 19:28
  • $\begingroup$ @MaximilianPress I saw this post. Although both questions concern rate matrices, they are nevertheless quite distinct. $\endgroup$
    – Namenlos
    Mar 16, 2021 at 20:10
  • $\begingroup$ I agree; note that I didn't mark it as duplicate. However, they have a substantial overlap and it is worth annotating as such, for anyone coming across this question. $\endgroup$ Mar 16, 2021 at 20:14


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Browse other questions tagged or ask your own question.