Transition/transversion=?

Mark Siddall mes at zoo.toronto.edu
Fri Aug 25 08:04:49 EST 1995


In article <41k2rc$ig9 at mserv1.dl.ac.uk> "JAMES O. MCINERNEY" <James.Mcinerney at UCG.IE> writes:
>
>
>Well, we haven't had this kind of answer on this group for a while.  I know
>that prejudices do exist and some people prefer parsimony methods and some
>people prefer distance based methods.  However I feel that when somebody
>asks a question in this way that they should receive the pros and cons of
>both. 

Fair enough.  But they should not be given poor information and misrepresentations.
My response certainly was philosophically biased but it was not a
misrepresentation.  Your is, as I will point out.

>
>Briefly, the argument against parsimony is that the first thing you do is take
>the majority of the characters in your data set and throw them out.  Also there

Misrepresenation #1.  We do not throw any characters out.  I presume
that what you are referring to is that characters that are invariant
or that are different for only one taxon are phylogenetically 
uninformative.  This does not mean we throw them out.  Go ahead and leave them
in for all I care.  It will not change the answer.  The point is that
if a charater has not changed... there has been NO evolution!  If you'd
care to re-define evolution then go ahead.  Until then, evolution is
about change (no?) and phylogeny reconstruction, is as well.

>is no statistical framework built into the parsimony procedure, so should you
>accept the most parsimonious tree as the one and only, with no idea of how good
>or bad this tree really is (what about multiple equally parsimonious trees?)?

I'm not sure that this was a complete sentence but I think I get your
drift. No there is not a statistical framework built in.  But then
we hold that the phylogenetic history of a set of taxa is a historical 
singularity, not a population that can be sampled.  That is, it occurred once.

I have said much more on this elsewhere.

>
>The argument against distance based methods (in addition to the ones mentioned
>above by M. Siddall) is that you use some characters in a negative way (an
>analogy: mushrooms, E. coli and the oak tree are joined together by virtue of
>not possessing vertebrae), with cladistic methods, organisms are put together
>only if they share characters that have arisen relatively recently
>(shared-derived characters).

Misrepresentation #2.  We do not only concern ourselves with changes that are
relatively recent.  We do concern ourselves with changes however.
That is, we concern ourselves with evolution.  That jellyfish, ants
and Parmecium spp. lack a backbone has nothing to do with evolution.
That is, nothing has happened to give them each this characteristic...
more to the point... the only reference point for the question is
that vertebrates have  had some thing happen in their 
history.  Again... this is about evolution... about change.
In so far as change is concerned... whether those changes are recent or
ancient does not matter.

>
>Now for my humble opinion...A distance method can be very good (as we see from
>simulation studies) at retrieving the correct tree, especially if one chooses

Oh?  And how do you know when you have the correct tree?

>the proper correction for multiple hits.  When a good tree building method like
>the neighbor joining method is used then the chances of retrieving the correct

Neighbor Joining is NOT a good tree building method.  If you change the order of
input of taxa, you change the tree.  Ummm... sound like a problem?
If you replicate a taxon you change the tree elsewhere.  
There are manmy other problems.

>tree are pretty o.k.

Again I ask how you know when you got the correct tree?????
Does the hand of Providence come down and put a gold star on your 
work?

>
>Parsimony is really neat for examining how evolution has occurred, which

Agreed.

>characters are leading to confusion and instability, what is the general mode
>of evolution (transformation from one character state to another).
>

IE EVOLUTION and PHYLOGENY.

>
>The philosophy of the investigator is personal, but as a bench scientist who
>cares more about the result and the hypotheses I can make from my data than
>any philosophical do's and don'ts, my advice is to use both.  Agreement is good,

Agrement between two or more bogus methods means diddly.

Mark
-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062



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