[Taxacom] Why character-tracking doesn't happen?

[Steve Manning]

I submit the following thoughts:

First, the easier one.  To answer the question at the end of your 
post, I don't know what people think but doubt that further 
investigation is usually completely infeasible.  One type of 
investigation that might be feasible is to determine the likely 
climatic conditions at the time taxa supposedly diverged, or to even 
determine under present conditions whether a particular character is 
likely to be "strongly selected", such as apparently is the case in 
the famous Hawaiian tarweeds and their relatives with major 
environmental changes over a small geographical area.  If so, that 
would skew or alter what might otherwise be the most parsimonious 
cladograms.  Of course if the gene controlling a particular 
morphological character has been sequenced, all the better.

Second, it seems to me that probability needs to be put front and 
center both with character tracking and with phylogenetic 
hypotheses.  For example if parsimony is the guiding principle, then 
the most probable tree could not only be determined but be 
accompanied by an analysis and statement of the probability that it 
is the correct one, within stated parameters.  Similar probabilities 
could be stated for the second, third and however many more trees the 
researcher wanted to analyze.  I think in most cases, especially at 
lower taxonomic levels, the probability of even the most probable 
trees representing the exact evolutionary history is less than 0.5, 
meaning it probably didn't happen exactly that way.  Maybe one could 
put forth how many trees one must consider before the probability 
that any one of them is completely correct reaches over 0.5; then one 
could say that probably it happened as indicated in one of the 
following (1000 or more?) ways.  Sort of like, but harder than, 
predicting in advance which team will win an athletic 
tournament.  Such analyses improve perspective I think.  Evolutionary 
history may match the most parsimonious tree about as often as the 
team ranked number one before a tournament actually wins the tournament.

Then character tracking could be one of the factors that affects 
those probabilities.  There too, probability analysis seems in 
order.  What are the probabilities, for a single character, that it 
reached its present distribution by path x? y? or z? etc.  How 
different is path x from each traditional cladogram or morphological 
analysis or combination thereof?  etc.  The math will get complicated!

Steve

At 10:53 PM 9/11/2008, Bob Mesibov wrote:
>There were no serious nibbles at the bait I dangled here recently on
>character-tracking, i.e. investigating apparent homoplasy as a way to
>evaluate the plausibility of a phylogenetic hypothesis.
>
>I'm now aware that there are two philosophical objections to what I
>suggested. First, some cladists don't think of trees as history.
>Homoplasy is just a nuisance in their attempts to build a robust
>classification. This classification *reflects* history but isn't the
>same as history, so character-tracking would be meaningless.
>
>Second, some people accept homoplasy as an explanation for character or
>gene-history incongruence when *building* trees, but not as an
>explanation for *understanding* what happens in the tree they built.
>
>It works like this. A tree is built on an optimality criterion, say
>parsimony. Within this tree there's incongruence: not all the
>morphological characters, or all the sequences in a multi-locus gene
>set, will give the same tree when analysed separately. This incongruence
>is explained *after the fact* as due to homoplasy.
>
>The 'after-the-fact'er' stands by the phylogenetic hypothesis as simply
>the best available under the optimality criterion used in the analysis.
>It may or may not reflect historical reality. There is therefore no
>reason to track characters through the tree. My earlier, imagined, inner
>conversation - 'Hmmm. If this tree is correct, then this character must
>have had this interesting history...' - never happens. Optimality slays
>homoplasy, but there's no corpse.
>
>I think the same loss of information occurs when people build supertrees
>from separate phylogenetic hypotheses, or combine data before analysis
>using 'total evidence'. [Which is no such thing. It's short for 'data I
>can code and treat as equivalent and independent', and excludes relevant
>data that can't be coded in that manner.] Both methods give consensus
>trees in which the entities being 'treed' are nearly indefinable
>(Richard Zander says combining apples and oranges and lemons gives you
>fruit salad), and in which homoplasy is an explanation at a level deeper
>than the one at which the analysis operates.
>
>Do people working at this higher level think something like: 'The genes
>and/or morphological characters disagree. I don't know why and it's not
>feasible to investigate. All I know is that this is a pretty good tree
>based on sound methodology'??
>--
>Dr Robert Mesibov
>Honorary Research Associate
>Queen Victoria Museum and Art Gallery and
>School of Zoology, University of Tasmania
>Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
>(03) 64371195; 61 3 64371195
>http://www.qvmag.tas.gov.au/mesibov.html
>
>
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Dr. Steve Manning
Arkansas State University--Beebe
Mathematics and Science
Professor of Biology
P.O. Box 1000
Beebe, AR  72012
Phone: 501-882-8203
Fax: 501-882-4437