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Re: How to Train Your New Papers

> Appendix 10 of my 2007 paper with Michel Laurin demonstrates this
> at excruciating length...

 I'm still waiting for somebody who has done and seen it all to
 publish a gold-standard review on what can go *wrong* with mol-phyl
 studies and how to avoid it.

I was talking about molecular dating, not molecular phylogenetics. Not the same thing; the methods are quite different. (Strictly speaking, it's not even the case that the latter is a prerequisite for the former; dating needs a tree, but the tree doesn't need to result from a phylogenetic analysis of the same data, or in fact any data. It's just more easily defensible when it does.)

 For birds, the name of the game these days seems to be multigene or
 even whole-mitogenomic studies. But given that gene trees do not
 equal species trees, this introduces an increasing probability of
 this particular error (which always leads to an overestimation of
 age). Essentially, without coalescent analysis, such studies are not
 very useful.

And coalescent analysis can't be used when tens of millions of years are involved, because there's no constant mutation rate across such timeframes.