[Taxacom] Clade age

Sergio Vargas sevragorgia at gmail.com
Thu Nov 10 15:37:06 CST 2011


thanks for the references, I wasn't aware of them.

sergio

On 11/10/11 10:32 PM, Michael Heads wrote:
> Hi Sergio,
> Yes, it's a serious problem. Trying to impose a poorly preserved, 
> fragmentary fossil on a beautifully resolved molecular phylogeny based 
> on millions of characters is like placing an angry bull in a china 
> shop. What a disaster. One tendency is to assume - 'it's a fossil, it 
> must be basal'. Smith et al. (2010, PNAS 107:5897) criticised ‘the 
> default practice of assigning fossils to the stem of the most 
> inclusive crown clade to which they probably belong, thereby possibly 
> biasing estimated ages (possibly throughout the tree) to be 
> younger’.Pennington et al. (2004 Phil. Trans. Roy. Soc. London//B 
> 359:1455) made the same point.
> 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
> *Sent:* Friday, 11 November 2011 8:32 AM
> *Subject:* [Taxacom] Clade age (was: Taxacom Digest)
>
> Hi,
>
> first, sorry for not changing the subject of my previous email.
>
> now, I would like to point out what to me is the biggest problem with 
> molecular dating. Interestingly it has nothing to do with the 
> algorithms or theory or modelling behind the dating analysis of with 
> whether you end up having minimal or maximal or hypothesized maximal 
> age, etc. Even more interestingly, and a bit surprising to me, was 
> that a complete systematics outsider pointed to the same problem after 
> a only seeing a figure showing the calibration points used for a 
> molecular dating analysis. Anyways, taking for example the fossil 
> polen of China and say that you can confidently assign it to Lamiaceae 
> but not to a specific genus of Lamiaceae (I don't how far can go 
> identifying polen anyways). Now, for a molecular dating analysis you 
> would assign use this fossil to constraint (calibrate) the age of 
> crown-group Lamiaceae but there is no reason or logical justification 
> to do this. Given that the polen could belong to any Lamiaceae you can 
> use it to constraint any node of the crown Lamiaceae, using the polen 
> to constraint the crown group artificially biases the origin of the 
> crown group to the age of the fossil but this is totally arbitrary, 
> because the polen could belong to any descendant of that 
> common-ancestor. You would need to evaluate the effect of uncertainty 
> in the calibration which will make the problem n-times as hard as it 
> already is. The main problem is that there is no reason to prefer 
> using the fossil to calibrate the age of crown-group Lamiaceae you 
> cannot argue that it is most parsimonious or that it is most likely, 
> so you need to evaluate all possible calibrations...
>
> sergio
>
> >In any case, if there is no pollen of Lamiaceae in the Cretaceous, 
> then we would have to go with the pollen in the Eocene of China (ca. 
> 44 million years ago), which would>indicate to me that Lamiaceae arose 
> far later than 85-89 million years, perhaps even after the 
> end-Cretaceous event (65 million years ago).  However, in that case,
> >any hypothetical age (by bracketing) is going to be less precise 
> given the longer ranges in time.  Anyway, I am mainly interested in 
> determining whether or not the>Conacian pollen belonged to Lamiaceae 
> or to some other family.  I clearly didn't anticipate getting dragged 
> into a debate involving Miocene fossils that are much more>recent.
>
>
>
> On 11/10/11 7:00 PM, taxacom-request at mailman.nhm.ku.edu 
> <mailto:taxacom-request at mailman.nhm.ku.edu> wrote:
> > P.S.  In any case, if there is no pollen of Lamiaceae in the
> > Cretaceous, then we would have to go with the pollen in the Eocene of
> > China (ca. 44 million years ago), which would indicate to me that
> > Lamiaceae arose far later than 85-89 million years, perhaps even after
> > the end-Cretaceous event (65 million years ago).  However, in that case,
> > any hypothetical age (by bracketing) is going to be less precise given
> > the longer ranges in time.  Anyway, I am mainly interested in
> > determining whether or not the Conacian pollen belonged to Lamiaceae or
> > to some other family.  I clearly didn't anticipate getting dragged into
> > a debate involving Miocene fossils that are much more recent.
>
> -- 
> 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
>
>
>
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-- 
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




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