Fortunately, intermediate models employing relaxed molecular clocks have been described.These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis.
These model the molecular rate among lineages as varying in an autocorrelated manner, with the rate in each branch being drawn (a priori) from a parametric distribution whose mean is a function of the rate on the parent branch.
For example, a lognormal distribution can be employed with the variance scaled relative to the length of the branch in units of time, implying that the evolutionary rate changes continuously along the branch.
Bayesian relaxed-clock methods, including those published by Thorne et al.
[ 15] and Aris-Brosou and Yang [ 17], present an enticing alternative to local clock models.
Alternatively, the use of an exponential distribution would imply that changes occurred at the nodes, with the size of the change being independent of the branch length.
Autocorrelation of rates from ancestral to descendant lineages will occur whenever the largest component of rate variation is due to inherited factors, whether these are life-history traits or biochemical mechanisms.We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme.With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.If this is a mistake, please don't panic - it's nothing personal.This practice has been regularly challenged by results from datasets showing considerable departures from clocklike evolution [ 3– 5], and rate variation among lineages can seriously mislead not only divergence date estimation [ 6] but also phylogenetic inference (e.g., [ 7, 8]).