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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
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.