Character Polarity (from Molecular taxonomy: on way out?)

[Derek Sikes]

This Nixon & Carpenter paper is certainly cited as the 'key' paper  
justifying 1) not polarizing before analysis, 2) searching on  
unrooted trees, 3) rooting after the shortest tree is found which  
subsequently provides directionality, aka polarity, to the evolution  
of (many of) the characters.

However, I wonder if anyone, on either side of the debate (and so far  
it seems that Grehan is alone on his side), can point to a paper that  
shows a thorough comparison of 'a priori' polarization to 'a  
posteriori' polarization (a la Nixon & Carpenter '93). I would like  
to see a paper that takes, say, a dozen or more published, empirical  
datasets that have been analyzed in the 'old style' of 'a priori'  
polarization and that reanalyzes them in the new, unrooted, Nixon &  
Carpenter method, with rooting providing polarization after the fact.

 From theory we would expect the following:

1) if the hand-polarization was done in strict accordance to the  
rules used for outgroup polarization and combined with thorough  
application of an optimality criterion like parsimony, the results  
should be the same

2) if the hand-polarization was done using a variety of methods  
(ontogeny, fossils, etc) including intuition but parsimony was still  
rigorously applied the results could very well be different

3) if the hand-polarization was done in strict accordance to the  
rules of outgroup polarization but the parsimony criterion was not  
rigorously applied (eg shortest trees were not found) the results  
could very well be different


I hope such a paper exists. Nixon & Carpenter don't really  
demonstrate the difference using empirical datasets, but I'm not  
aware of such a paper. If anyone knows of one I would love to hear of  
it. We have theory and that is comforting, but honest demonstration  
that the theory is correct would be even more comforting!

It seems that Grehan is not really that worried about his dataset  
having characters that are plesiomorphic for his ingroup as long as  
they are coded such that they CANNOT be mistaken for apomorphies -  
he's worried about a method that allows these characters states to be  
mistaken for apomorphies of his ingroup, and thus keeps repeating,  
and repeating, and repeating that, in his opinion, the best way (only  
way?) is to eliminate these characters before analysis to prevent  
this mistake from happening.

What he fails to realize is that, especially for large complex  
datasets, and this was driven home by Wiley '81 and Paterson '82 that  
looking at characters in isolation can only get one so far- doing so  
provides only *hypotheses* of homology and if one chooses, polarity.  
These hypotheses are tested via congruence with other characters -  
the more additional characters, the better the the test. If one  
eliminates all possible homoplasy or characters that map such that  
one's favorite characters' polarities are reversed, one weakens the  
tests and biases the results towards what one imagined they should  
be. This is, of course, poor scientific practice but strongly and  
repeatedly advocated by Grehan.

Let's throw out polarity altogether and simply talk about unrooted  
trees. If John is so worried that polarity mistakes are leading to  
the wrong tree then let's forget about polarity and just look at  
unrooted trees. In such trees each character (if morphology) will  
change once or more. Without a root it won't be obvious which state  
is the derived state and which the ancestral but it will be obvious  
*where* on the tree the change takes place. Such an unrooted network  
showing the smallest number of evolutionary changes for any ape  
dataset I know of still joins the African apes, including Homo,  
together. And polarity has nothing to do with it! [<- note: this last  
statement is *very* important]

I expect John will say unrooted trees are not "cladistic", and, as  
usual, he will be wrong. He will also probably repeat something about  
how important it is to limit one's dataset to characters whose states  
are only derived for the ingroup (not understanding that one's  
ingroup could be someone else's outgroup!).


(I have got to stop posting on this issue - I've got work to do! -  
but if anyone knows of such a paper as described above, please inform  
us...)

Cheers,
Derek


Patterson, C. 1982. Morphological characters and homology. Pp. 21–74,  
In Problems of Phylogenetic Reconstruction. (K.A. Joysey and A.E.  
Friday, eds.). Systematics Association Special Volume. London,  
Academic Press


On 20-Jul-05, at 7:48 AM, Hume Douglas wrote:

> To me the question of a priori character polarization was answered  
> effectively in this paper:
>
> Nixon, K.C. and Carpenter, J.M. 1993. On outgroups. Cladistics 9:  
> 413-426
>
> In this paper Nixon and Carpenter make it clear that the function  
> of outgroups is to choose the root of the tree. Before that, the  
> tree is chosen using an algorithm without reference to character  
> polarity. There is no need to consider the polarity of characters  
> before the analysis. For many characters the outgroup does not  
> provide any clues about polarization in any case.
>
> Hume Douglas           Carleton University, Ottawa, ON, CANADA

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Derek S. Sikes, Assistant Professor
Division of Zoology
Department of Biological Sciences
University of Calgary
2500 University Drive NW
Calgary, Alberta, Canada, T2N 1N4

dsikes at ucalgary.ca
http://homepages.ucalgary.ca/~dsikes/sikes_lab.htm

phone: 403-210-9819
FAX:  403-289-9311

"Remember that Truth alone is the matter you are in Search after; and  
if you have been mistaken, let no Vanity reduce you to persist in  
your mistake." Henry Baker, London, 1785

Entomological Society of Alberta:
http://www.biology.ualberta.ca/courses.hp/esa/esa.htm
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