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Molecular Clock Calibration

mwooten at ducvax.auburn.edu mwooten at ducvax.auburn.edu
Mon Feb 15 09:56:59 EST 1993

In article <9302121613.ad24816 at Note2.nsf.gov>, rhoneycu at NSF.GOV writes:
Since someone asked in a later post,    _________^^^^^^   the response
I am addressing here was from Rodney Honeycutt, Systematic Biology Program
at the NSF.   

Now, let me see if I can explain myself. 

>           mwooten at ducvax.auburn.edu had several questions concerning
>           using fossils to calibrate the molecular clock.  This is a
>           response to those questions and comments.
>                I am not for sure what Mike Wooten is arguing.  The
>           divergence time estimate for Mus and Rattus is based on the
>           fossil record, and the age of fossils has nothing to do with
>           the phenotype and the environment.  In fact, I don't even
>           know what this has to do with calibration of the molecular
>           clock.  <discussion following deleted>
What I was arguing (trying to be polite) was that due to the fact that 
the fossil record is by its very nature, quite incomplete, I see very
little evidence that phylogenetic topologies generated from these data
are stable.  From my limited experience with the subject, I would argue
that this statement is true for rodents.  Now, first let me admit that
I have very little data on which to base this statement because to my
knowledge, very few studies that statistically examine stablility in
fossil based topologies have been published.  But from just random
review of the literature, I see many different phylogenetic hypotheses
presented for many mammal taxa, including rodents.  I point is that
with out some evidence that the topologies are accurate (stable?) how
can they be used to calibrate anything?  
  To further my point, take the human phylogenetic tree.  From what I
have read, the evidence is ambiguous relative to the evolutionary history
of our species.  This is true for even relatively 'recent' events (i.e.
the heated discussion of the relationship between H. erectus and H. sapiens).
In the recent literature, the age of H. sapiens has been reported as being
as old as 500,000 ya or as young as 50,000 ya.  This does not even include
the problems that arise when the entire primate lineage is examined.  Now,
let's think about this.  Consider the amount of intellectual effort put
into this one issue ( producing a stable phylogenetic topology for humans).
This effort has surely dwarfed all research involving rodent phylogenetics.
Again, no data for this statement but Honeycutt can address this if it is
far off base as his division has funded much of this work.  To the point:
Can we really rely on existing fossil-based human phylogenies for 
calibrating molecular clocks?  All that the data tells us with any certainty
is that species X was present during X time period.  Without an understanding
of how X actually relates to Y, I fail to see how calibration works.  My
opinion is that the matter is even less resolved for rodents.     
Why did I mention environment?  Basically my point was this, morphological
differences among populations -- species, etc. --- are often related to
environmental differences.  This is a commonly documented issue (Ecogeographic
Rules etc).  The spatial variation often observed in morphological features
has clearly impacted systematics studies (i.e. look at the large effort put
into discussion relative to sub-species <--> species classifications of many
mammal taxa).  I think that this same issue must be considered when fossils
are used as the data source.  This appears to be well understood by 
researchers building fossil-based topologies.  The point was that if
environment induces instability in topologies, then fossil-based topologies
suffer from the same problem as do topologies generated from living species.
We know much less about ancient environments than recent conditions so
therefore we understand less about how this issue effects our evolutionary
hypotheses for fossil species.  Again, with increasing uncertainty in the
relationships among the taxa of interest, the greater the potential increase
in uncertainty relative to calibration ability.  Look at the discussions
relative to dispersal vs. in situ speciation in humans.  Here is a good
example of how potential environmental differences can impact an evolutionary
hypothesis and thus the usefullness of these data for calibration.  
>                I disagree with Wooten's statement that morphology and
>           fossils have nothing to offer.  To the contrary, without
>           this information it would be difficult to examine processes
>           of molecular evolution, at least so far as rates are
>           concerned.  Also, Wooten might also remember that
>           convergence cannot be ruled out at the molecular level.
>           There is beginning to more and more evidence of convergence
>           and even positive selection, at least in some cases.
Please re-read my original post.  I did not say (nor did I mean to imply)
that "fossils have nothing to offer".  My comment was that I did not see
that fossil-based hypotheses were any less circular than molecular ones (
which is what the original poster had implied).  I, in fact, went on to make
the point that, since none of the data were perfect, all of what
we had *should* be considered!  I would not argue that the results from
relative rate tests etc. are any more *or* less useful than fossil dates.
Both types of data lack precision but they are currently what we have to work
with.  Thus, I did not agree with the original poster that fossil data was
the only important data for calibration work.
Wooten understands very well that convergence cannot be ruled out at the 
molecular level (I was co-PI on a proposal to examine this very issue 
which NSF rejected <--*sorry* flame on for a second there).  Well but again
maybe that proves that I do not understand the issue at all....  

| Michael C. Wooten                
| Dept. of Zoology                
| Auburn University              
| Auburn, AL  36849-5414        
| mwooten at auducvax.bitnet     
| mwooten at ducvax.auburn.edu  
| Disclaimer: All statements made are my opinions only and do not     |
|             reflect, in any form, the views of my employer.         |

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