How do you calibrate the molecular clock?
How do you calibrate the molecular clock -- where you need a few known sequence divergence times -- when you only know a few speciation times?
Yesterday at a meeting (I'm not sure I can tell you which meeting; I'm not sure how open it is supposed to be :-/) we discussed the divergence time of human-orangutan and human-macaque. We need the sequence divergence time to calibrate a CoalHMM model for figuring out some speciation and population genetics parameters of ancestral species.
No definitive answer came up at the meeting, but there was a short discussion by email after the meeting. This paper was sent around, where the divergence times were estimated to 25MYA and 13MYA, respectively, although the last of those numbers is actually the calibration point used in the analysis, so it is an assumption more than an estimate.
The problem is, the 13MYA used for the calibration is based on fossil evidence, and as far as I can see, that would make it an estimate for the speciation time between human and orangutan. We need the sequence divergence time. Speciation time and divergence time can vary with millions of years (if the effective population size is large enough).
If 13MYA is the divergence time between human and orangutan, we get a speciation time that is unrealistically recent. If the divergence time is 18MYA instead, as we assumed in this paper, we would get a speciation time around 12MYA which would match the MBE paper.
But how do you figure out the divergence time needed to calibrate the clock? Is there any way to get it, rather than the speciation time, from fossil evidence?
For our purposes, I suppose we can just as well work with speciation times for our calibration, but not everyone is using CoalHMMs for their analysis, so how do you deal with this problem?