Chapter 10 Dates and Evolution

10.1 Dates / Times on Trees

If you look at your tree, you will notice the tips don’t “line up” on the right side. It’s as if not all species made it to the present day. This is only an appearance because branch lengths are in substitutions per site and not all species have the same substitution rate. We can adjust the branch lengths to match time using the rates. Usually we have calibration dates with complex probability distributions. In this case we are taking an extremely simple approach solely for the purpose of seeing a phylogeny where the branches appear to be time.

mrbayes_chronos <- chronos(mrbayes_phylo)

We can also generate the tree using a “strict clock model”.

### strict clock model:
clock_rate <- chronos.control(nb.rate.cat = 1)
mrbayes_chronos_clock <- chronos(mrbayes_phylo, model = "discrete", control = ctrl)

Now let’s plot all three trees together so you can compare the branch lengths.

par(mfrow = c(3,1))
plot(mrbayes_phylo, cex = 1)
plot(mrbayes_chronos, cex = 1)
plot(mrbayes_chronos_clock, cex = 1)