What units are mutation rates, root heights and population sizes expressed in?
If the sequence data are all from one time point, then the overall evolutionary rate must be specified with a strong prior. The units implied by the prior on the evolutionary rate will determine the units of the node heights in the tree (including the age of the most recent common ancestor) as well as the units of the demographic parameters such as the population size parameter and the growth rate. If the evolutionary rate is set to 1.0, then the node heights (and root height) will be in units of mutations per site (i.e. the units of branch lengths produced by common software packages such as MrBayes 3.0). Similarly the population size parameter will be an estimate of Ne*mu , (i.e., half of the standard population genetic parameter, theta=2*Ne*mu). However, if, for example, the evolutionary rate is expressed in mutations per site per year, then the branches in the tree will be in units of years. Furthermore the population size parameter of the demographic model will then be equal to Ne
