[Taxacom] Character weighting

[Peter Stevens]

Of course the historical irony here is that phenetics developed in  
part as a response to the a priori/a posteriori weighting of  
systematists interested in evolution in the first half of the last  
century What goes around, comes around, although it is often the  
changing context that makes things interesting.

p.
On Aug 19, 2009, at 5:11 PM, Richard Zander wrote:

> When phylogeneticists weight all traits alike, is this objective?  
> It's commonly accepted as "wrong" but we kick clods sheepishly and  
> glance about furtively when we admit this. I say "we" since the  
> Laplacian (I think it was who said when nothing is known about  
> weighting, equal weighting is better in some way) fault is everyones.
>
> I have a paragraph I wrote in an early, early paper:
> "Weighting highly those characters with best fit as determined  
> after the parsimony analysis, may be done in various ways: Ladiges  
> et al. 1989 used the consistency index (c) over the patristic unit  
> character length (Farris 1969) and also the product of character  
> consistency and character retention index as was determined in  
> Hennig86 (Farris 1989). Inasmuch as all characters theoretically  
> have different phylogenetic importance (as per discussion by Farris  
> 1983: 11), equal weighting prior to the exact algorithm is  
> equivalent to arbitrary weighting (Swofford & Olsen 1990: 464).  
> Thus, the more the characters are (reasonably) weighted  
> differently, the less arbitrary is their weighting; Kluge and  
> Farris (1969) recommended weighting by degree of variability of a  
> character within OTU's, this being an estimate of the rate of  
> evolution of that character. No method now exists to recommend the  
> best weighting by character fit (Farris' 1969 example works for an  
> artificial data set with a known random element)."
>
> I can give references if asked. So there are objective (as opposed  
> to certain or true) methods of weighting on the basis of  
> evolutionary theory. Convergence is an evolutionary theory. So: In  
> one paper I increased weighting of morphological traits NOT  
> associated with convergence of a particular plant organ to force  
> convergence-related traits high in the tree. All attempts at  
> recovering a one-time historical event are heuristic, and one  
> should not confuse "objectivity" in this context with objectivity  
> in analyzing a universal in physics.
>
> We all get funny results, and those call for considered and  
> reasoned judgment, which can be called "subjective" by those  
> promoting automatic classification or automatic evolutionary  
> relationships, but is the basis for true advances in the field.
>
> Note that when you add comments about 3rd codon positions and  
> problems with that, you are correct but off subject.
>
> *****************************
> Richard H. Zander
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>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom- 
> bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> Sent: Wednesday, August 19, 2009 4:13 PM
> To: Taxacom
> Subject: [Taxacom] Character weighting
>
>
> I´ll ask you if you tell me how you arrive at it. Thanks to Pierre  
> for succintly putting an end to "molecular data is phenetic"  
> mantra. I will get into hot water with many but how do you weigh  
> your characters objectively? I can see objectiveness in weighing  
> based on codon position or transitions vs transversions or  
> according to the aminoacid encoded. I can also see the  
> objectiveness of character reweighting according to some measure of  
> internal congruence (the idea being that you encourage the signal;  
> of course doing this between datasets encourages the selection of  
> an "average" phylogeny which might not be the species tree). But  
> even these can arrive at "funny" results. In the case of extreme  
> weighting (i.e. effectively 0 weight to 3rd codons) you can loose  
> all resolution.
>
>
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