Sanderson & Donoghue 1996

I like the fact that the authors provide a summary of the methods used for reconstructing diversification rates in Table 1. I understand that the sample size for a phylogeny with known branch times is the number of terminal taxa. For a phylogeny lacking time estimates the sample size is “now of the order of 2-10, the maximum number of clades that can be considered given available methods and computational constraints” (pg 19). What computational constraints limit the estimation of sample size in tree-based methods without time?

The concluding discussion of molecular clocks offers three options for non-clock-like behavior of which the second appears the most promising to me. With the current models of molecular evolution, and all of the sequence data available, why is it not possible to develop rate models for different genes? When a molecular clock is rejected, is there a way of measuring to what degree the data deviate from clock-like behavior? What is known about the causes of rate heterogeneity across sites and across time? Is it possible to break the tree down into rate partitions that are clock-like?