[Taxacom] FW: Character weighting

[Jason Mate]

> 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. 

Weighing them all the same is no any more objective than giving them different weights. The problem comes with the weights you assign as these will obviously influence the ensuing phylogeny. How do you justify a weight of 5x versus 2x or 10x? Accusations of data massaging will surely follow any study that applies relative weights in this manner.

> 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.

That´s different. Farris was a big supporter of this and as I mentioned before they all use some measure of internal congruence. Reweighing after the analysis using internal measure is objective but it only
serves to weed out the minor phylogenies: i.e. to reduce the number of possibilities and therefore improve the resolution of your consensus tree (mjority consensus will practically do the same so I guess reweighing has given way to the less "dangerous" sounding MC. In any case it never (that I know of,
treading on thin ice here) results in a novel topology.

> 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.

Never have used a phylogeny to derive an automatic classification. In fact I have just read a paper on Furnariides (Moyle et al, 2009) in which they create two new tribes based on a phylogeny derived from a (admitedly large) molecular dataset. Neither tribe is morphologically defined and they are embeded in a rapidly evolving and species-diverse group. No idea about these birds (most birds for that matter) but I have always disliked blind application of phylogenies in this manner. I do think that there is a certain art in the classification (applying the phylogeny) but the actual process of generating the phylogeny should be as transparent as possible.

> Note that when you add comments about 3rd codon positions and problems with that, you are correct but off subject. 

Apologies, they were directed at a different post and in the spirit of economy I appended them to the same email.

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> 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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