[Taxacom] Clade age (was: Taxacom Digest)

Michael Heads michael.heads at yahoo.com
Thu Nov 10 15:32:26 CST 2011


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.
LondonB 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 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
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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