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

[Jim Whitfield]

Hi Derek (and others),
        The Nixon and Carpenter (1993) paper presents (well) the
strict cladistic perspective after more modern parsimony algorithms
were developed.
        The move towards depending upon outgroup analysis rather than
a priori polarization dates back much farther, however, partly to
papers by Farris, partly to the early 1980's arguments about outgroup
analysis by Watrous and (Quentin) Wheeler, Donoghue and the
Maddisons, among others, and finally to the following paper, which I
think at the time was pretty influential, if today often forgotten:

Meacham, C. A. 1984.  The role of hypothesized direction of
characters in the estimation of evolutionary history.  Taxon 33:
26-38.

Chris (Meacham) examined a number of real data sets and concluded
that polarity per se is very seldom the cause of character conflict
(character ordering can be however).  He suggested that obtaining the
minimum-length unrooted tree and then rooting by outgroup (what now
happens in most computer analyses) is likely to produce virtually
identical results anyway, and avoids the need to make a number of
possibly spurious directionality assumptions up front.

This is obviously an old paper, and tons more (and larger) studies
would be available for analysis now.  it would be interesting, as you
suggest, to see the comparison done with the tools we have now!

                                                        Cheers, Jim


>From: Derek Sikes <dsikes at UCALGARY.CA>
>Subject:      Re: Character Polarity (from Molecular taxonomy: on way out?)
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>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
>
>++++++++++++++++++++++++++++++++++++++++++++++
>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
>++++++++++++++++++++++++++++++++++++++++++++++


--
James B. Whitfield
Professor
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