Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees

Rates of molecular evolution vary substantially between lineages, and a
growing research effort is directed at uncovering the causes and
consequences of this variation. Comparing local-clocks (rates of molecular
evolution estimated from sets of branches of a phylogenetic tree) is a
common tool in this research effort. Here, I show that a commonly used
test (the Likelihood Ratio Test, LRT) will not be statistically valid for
comparing local-clocks in most cases. Instead, I propose the local-clock
permutation test (LCPT), a simple test which can be used to test the
significance of differences between local-clocks. The LCPT could also be
used to test for differences between any parameter that can be assigned to
individual branches on a phylogenetic tree. Using simulated data, I show
that the LCPT has good power to detect differences between local-clocks.