[Taxacom] Morphology vs Molecular

[Michael Heads]

Hi Richard,
 
You wrote: 'I tend to subscribe to the common understanding that there is one species history, and that during speciation or at least isolation of two lineages from one, a process goes on that eliminates all but one of the ancestral polymorphisms in each of the new lineages...'.
 
In fact retention of ancestral polymorphism is very common (there are more than 12 000 hits for 'incomplete lineage sorting' on Google) and 'It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference' (Maddison & Knowles, 2006. Syst Bol. 55, 21-30). 
 
Michael Heads


Wellington, New Zealand.

My papers on biogeography are at: http://tiny.cc/RiUE0

--- On Wed, 8/19/09, Richard Zander <Richard.Zander at mobot.org> wrote:


From: Richard Zander <Richard.Zander at mobot.org>
Subject: Re: [Taxacom] Morphology vs Molecular
To: Taxacom at mailman.nhm.ku.edu
Date: Wednesday, August 19, 2009, 11:09 AM


A loose end:

Hope no one thought I agreed that differential lineage sorting meant that ancestors were so undifferentiated molecularly that molecular analysis was impossible if there was any evidence of different gene histories. No, no. I tend to subscribe to the common understanding that there is one species history, and that during speciation or at least isolation of two lineages from one, a process goes on that eliminates all but one of the ancestral polymorphisms in each of the new lineages, a process called reciprocal monophyly. New sets of polymorphisms are created, but these can be distinguished as derivative. 

Evidence that polymorphisms are rather random is that when three taxa (e.g. man, gorilla, chimp) are analyzed with multiple genes and differential sorting is discovered, one generally gets one rather frequent number of trees of one sort, and a smaller number of the other two possible resolved trees, and these two are about equal frequency, which is to be expected for this scenario. Thus, the single species tree is prefered over the undifferentiated and unanalyzable molecular ancestor.

So, for the sempiternal orang/man/chimp/gorilla question, there are several possibilities. One might wonder why the morphological traits of man/orang evolved twice if ((man, chimp) gorilla) orang. Or why the molecular traits of gorilla/chimp evolved twice if ((man, orang) chimp) gorilla. Or maybe some exotic scenario presents itself to the Taxacomers' perfervid imagination: balanced selection for man/organ ancestor followed by wrong gene history. Anybody? (Nothing involving sheep, though.) 

Right now I repeat my take on this, Grehan is right for wrong reasons. Molecular history shared by of a vast majority of gene sequences is correct but the traits shared by man and orang were salted away epigenetically in the ancestors of chimp and gorilla. Is there evidence for this? There is a lot of cases in the literature that major traits and trait complexes are conserved for hundreds of thousands of years, then apparently reactivated. I can give examples if anyone wants to investigate. Morphology is the interface with selection, and we cannot ignore it.

_______________________
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org


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