Relaxed molecular clock dating

Instead, those clades/lineages are allowed to evolve according different evolutionary rates while rate constancy is assumed across the remainder of the tree (see e.g. In BEAST, the ‘Fixed local clock’ option assumes that the user has created one or more taxon sets. BEAST then uses all of the taxon sets defined and assumes a change of evolutionary rate at their (time to) most recent common ancestor (MRCA). The relaxed clock implementation in BEAST works by assigning each branch one rate from a fixed number of discrete rates. Basically, the underlying distribution is discretized into a number of categories equal to the number of branches and each branch receives a unique evolutionary rate from that discretization. When a stretch of DNA does indeed behave like a molecular clock, it becomes a powerful tool for estimating the dates of lineage-splitting events.

Each branch in a phylogeny (subtending a clade) is a possible location for a change of rate from one local clock to a new one. For example,the gene that codes for the protein alpha-globin (a component of hemoglobin) experiences base changes at a rate of .56 changes per base pair per billion years*.If this rate is reliable, the gene could be used as a molecular clock.BEAST estimates that the former has a high evolutionary rate and the latter has a low evolutionary rate, with those rates being constant within each clade.

The shift in evolutionary rate occurs at the (T)MRCA of those defined clades, and hence no shifts are allowed to occur at random times on a branch.

That means that the two DNA versions differ by 100 million years of evolution and that their common ancestor lived 50 million years ago.