Hello
I have an alignment of roughly 1 million bp ddRAD data and I'm planning to run a BSP analysis on three closely related species to detect past changes in effective population sizes for each of them separately. Since I don't have any reasonable node age priors for nodes within all three species I was planning on fixing the clock rate for the strict molecular clock with values obtained from literature (e.g. 1.4E-9 subst/site/year from McGowen et al 2012, Proc Biol Sci).
One thing I'm struggling with is understanding what dimension the x axis of the resulting skyline plot will be in. If I set the clock rate at 0.0014, which would be subst/site/million years, will the x-axis in the resulting skyline plot be in millions of years as well (obviously I would have to make sure all other priors I may have make sense together with this fixed substitution rate)?
Thanks in advance!
