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Re: How to Train Your New Papers
> > We attached a prior probability to each
> fossil-based minimum age,
> Are there any maximum ages? (I don't have access to the
> paper here.) If not, it had to be _expected_ that many of
> the molecular dates would be too old. Minimum ages can only
> push molecular dates down (stratigraphically down), and when
> there's nothing to push them up, down is where they'll stay.
> 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
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. Also concatenation is
very shaky; it can save a lot of work, but before using it it must be checked
whether it *can* be used in this case (it's at least very risky to concatenate
indel-heavy sequences). Interesingly, the literature about things that can go
wrong with non-molecular cladistic analyses is quite extensive.
Another thing that is overdue is incorporation of geography into cladistic
analyses. Hard to quantify, and hasn't been much used for this reason. At first
I thought about quantifying it via polar coordinates, but that's not good.
Perhaps one could simply treat the general regions of an OTU's occurrence as
characters, and analyse it via a network of high/medium/low/"virtually
impossible" probability of dispersal to other regions (i.e. character
transition). E.g. something that is found in Jurassic Europe has a high
ppprobability of having relatives elsewhere in Europe, a medium probabilty of
relatives in Asia, a low probability for Africa, and a close relative
unexpectedly popping up in Australia would indicate either a significant ghost
record or that you should recheck your analysis.
Plate tectonics would need to be accounted for, but that can be done. The
interesting aspect is that it could be dealt with in a similar way as a
substitution model in mol-phyl
(http://en.wikipedia.org/wiki/Substitution_model), and would be open to ML
bootstrapping (regarding ML bootstrap vs MP PP, see also
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