And, like real gardening, you don’t so much come to *the* final result, but simply run out of time for the moment. (See Maddison’s Law of Phylogenetic Analysis: subulatepalpomere.com/category/phy...)
Posts about Phylogenetics written by David Maddison
This is a great blog post (I realize it isn't yours though). Divergence time inference is a dangerous thing and probably shouldn't be treated as "a" final analysis. This may be the way to go (unfortunately multiplies the number of analyses):
Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time-scaling phylogenetic tree...
One of my concerns, besides the delaying-a-paper-for-x-years is the carbon footprint that such "final" analyses require. HMC samplers hold a lot of promise for curtailing such woes, but (afaik, and I hope I am wrong) we are still years away from tools that scale.
