[Taxacom] Taxacom Digest, Vol 68, Issue 8

Sergio Vargas sevragorgia at gmail.com
Wed Nov 9 16:49:14 CST 2011


Yes, I agree, but that's how you end up obtaining maximum ages from 
minimum ages. That's the price you pay. The problem in most cases is not 
been able to clearly state that your conclusions are valid only GIVEN 
all the modelling you place in between the minimum age and the estimated 
region were the maximum age could be. That means of course that the next 
time a new (older) fossil is found your ages will change and so on until 
no older fossil is found which doesn't mean you found the older. So in 
any case you will need to resort to some kind of modelling if you really 
want to date a node using molecular clock like analysis. You can use 
uniform priors on your nodes. Most biologists feel better using flat 
priors because most of us recognized that there is no good way to choose 
a prior for the age of a node but then you tend to get wide error bars. 
In my experience, biologists and palaeontologists working to molecular 
dating get very nervous when they see huge error bars after the 
analysis. The uncertainty is so high that you cannot really say 
anything. The usual answer is to play around with the priors and the 
root age until they feel comfortable with the results, i.e. the error 
bars are not too large. Also at some point the user becomes very 
pragmatic and recognizes that the priors are so because... well 
because... and since no one knows which one to pick is justifiable to 
pick just one that "works good". My problem is what "good" generally 
means in this context: I like what I see because it is what I though. So 
I am not testing anything, I am biasing the analysis using my favorite 
priors and I am finding that what I thought (my priors) were very good! 
This might be self-fulfilling for some, but reviewers should filter such 
inconsistencies very quickly, ask for more robust analyses: 
cross-validation, effect of different priors and root ages, and prevent 
that authors sale their date as The Dates. This is simply reminding 
authors that the dates are only approximations given the model.

cheers

sergio

On 11/9/11 10:58 PM, Michael Heads wrote:
> Hi Sergio,
> You wrote: 'Most authors agree that fossils provide only minimal ages, 
> I don't think they ignore this but they base their conclusions on the 
> credible region obtained from the analysis, and treat this credible 
> region as an approximation to the maximal age of the clade'.
>    In other words, they transform a minimal age into a maximum age 
> (the maximum age of the 95% credibility interval). But how can you 
> actually do this? They do it simply by decree: they stipulate an 
> exponential or log normal prior for the clade age, with rapidly 
> decreasing probabilities for clade ages older than the oldest 
> fossil. An exponential prior even attributes the most likely clade age 
> to the age of the oldest fossil! It's all smoke and mirrors.
> Michael
> Wellington, New Zealand.
>
> My papers on biogeography are at: http://tiny.cc/RiUE0
> Information on my new book, 'Molecular panbiogeography of the 
> tropics', is at: http://www.ucpress.edu/book.php?isbn=9780520271968
>
> *From:* Sergio Vargas <sevragorgia at gmail.com>
> *To:* taxacom at mailman.nhm.ku.edu; jgrehan at sciencebuff.org
> *Sent:* Thursday, 10 November 2011 10:08 AM
> *Subject:* Re: [Taxacom] Taxacom Digest, Vol 68, Issue 8
>
> Hi,
>
> I have a couple of questions:
>
> >Don't just take the word of 'experts' (experts in what anyway). You 
> should be able to determine for yourself what the empirical reality is 
> and what is theoretically>claimed.
>
> by theoretically claimed you mean hypothesized?
>
> >With molecular clocks you will often see the dates represented as 
> actual or maximal, but the empirical proof of that is lacking (that 
> you can read for yourself, no need to>take anyone's word for it either 
> way). You will also see so-called mathematical modeling or statistic 
> estimations claiming some sort of average and probability spread>which 
> is ok as it stands as a theoretical claim that may or may not have an 
> empirical foundation. You will also see authors contradict themselves 
> within a paper, saying on>the one hand that the dates are minimal and 
> then later ignoring that understanding. Anyway, glad you are aware of 
> the pitfalls.
>
> well... if you had empirical evidence for the maximal/actual age of a 
> clade you would not need molecular dating. I would like to know what 
> the empirical evidence for the maximal age of a clade could be? There 
> is no way to demonstrate that a fossil is of maximal age, you can only 
> approximate the maximal age of a clade hypothesizing that there is no 
> fossil of taxon A that is older that the oldest known fossil of taxon 
> A, or using molecular dating to provide a credible interval for the 
> maximal age of the clade given the calibrations (minimal ages) and 
> prior distributions for the node ages (to model the maximal age). Most 
> authors agree that fossils provide only minimal ages, I don't think 
> they ignore this but they base their conclusions on the credible 
> region obtained from the analysis, and treat this credible region as 
> an approximation to the maximal age of the clade. Of course some 
> authors really want to have The Date of cladogenesis, but with 
> bayesian methods this is getting less common.
>
> cheers
>
> sergio
>
> -- 
> Sergio Vargas R., M.Sc.
> Dept. of Earth&  Environmental Sciences
> Palaeontology&  Geobiology
> Ludwig-Maximilians-Universität München
> Richard-Wagner-Str. 10
> 80333 München
> Germany
> tel. +49 89 2180 17929
> s.vargas at lrz.uni-muenchen.de <mailto:s.vargas at lrz.uni-muenchen.de>
> sevra at marinemolecularevolution.org 
> <mailto:sevra at marinemolecularevolution.org>
>
> check my webpage:
> http://www.marinemolecularevolution.org
>
> check my research ID:
> http://www.researcherid.com/rid/A-5678-2011
>
>
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu <mailto:Taxacom at mailman.nhm.ku.edu>
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of 
> these methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
>

-- 
Sergio Vargas R., M.Sc.
Dept. of Earth&  Environmental Sciences
Palaeontology&  Geobiology
Ludwig-Maximilians-Universität München
Richard-Wagner-Str. 10
80333 München
Germany
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sevra at marinemolecularevolution.org

check my webpage:
http://www.marinemolecularevolution.org

check my research ID:
http://www.researcherid.com/rid/A-5678-2011




More information about the Taxacom mailing list