[Taxacom] minimal estimates

[John Grehan]

This is a good illustration of the perils of mistaking a technological
advance for a conceptual advance.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Sergio Vargas
Sent: Wednesday, May 18, 2011 2:36 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] minimal estimates

  Hi all,

I just want to point that most molecular clock estimates rely on a 
maximum age for the root. Without this strong assumption (i.e. a maximum

age for the root cannot be justified in most cases, I would say in all 
cases) the method just doesn't work.

Is also important the way in which you model the rates. I've seen nodes 
showing outliers going back 2000 million years back in time. Most of the

time you don't detect this outliers because they are not included in the

95% CI of the mean root age reported by the program. Anyways, the 
analysis is generally hard from the beginning (establishing the fossil 
calibration) to the end (interpreting the dates), and most researchers 
don't like to acknowledge that the dates are conditional on the root age

used.

sergio


> John Grehan and co-thinkers point to a very important limitation of
molecular dating exercises - that the first appearance of a clade in the
fossil record provides only a minimal age for that clade.
>
> However, it does not follow from this that molecular clock dates for
clades calibrated on the basis of such fossils are necessarily minimum
estimates.
>
> Why? Because there are many potential sources of error to be
considered. Some of these, such as misspecified substitution models,
ancestral sequence polymorphism, incorrectly estimated phylogenies,
hemiplasy, and among lineage rate variation can all result in
over-estimates of clade ages. If errors leading to age-estimate
exaggeration are greater than any fossil record related error causing
age underestimation, then the age-estimate be to old.
>
> It is not helpful to seize on one source of error alone, we need to
consider all the potential sources of error, and preferably quantify
them.
>
> Not all of these estimates are of equal reliability, and in general I
do agree with John that they need to be treated with scepticism.
However, to label them minimum estimates is incorrect, even if it does
tend to favour panbiogeographer's eccentric ideas about the age of taxa.
>
> Cheers
> Rob


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