[Fwd: Re: Probabilities on Phylogenetic Trees]

Richard Zander bryo at COMMTECH.NET
Tue Sep 16 07:53:36 CDT 1997


Tom DiBenedetto wrote:
>
> Richard Zander wrote:
>
> >> >Maximum parsimony, which is a belief-oriented analysis....
>
> >> What do you mean "belief-oriented'?
>
> >Just in the sense that there is no sampling during phylogenetic
> >time...no information at each node of the Markov process,
>
> It wont be hard for me to play dumb here,,,,I dont really know what
> this means.
> A parsimony analysis deals simply with the distribution of character
> states (the
> groupings implied by the state-distributions of each character), and
> chooses the
> pattern which is most consistent with all of those groupings. It
> makes no reference
> to process.

Sure it does. You state below that there is no process other than
descent...that's the process, and it is modeled simply and with a lot of
assumptions when the model's pattern is imposed on the data.
 >
> >Excellent, but what is the method reconstructing?
>
> It is reconstructing the phylogeny under the assumption that the
> phylogeny can
> be inferred through examination of character-state distributions, and
> that there is no process, other than descent, which can pattern
> character distributions throughout the various character systems
> which one can investigate. That is why cladists emphasize "total
> evidence", looking to as many character systems as possible, rather
> than relying exclusively on one (very problematical) source of
> evidence (as do the statistical phylogeneticists with their reliance
> on sequence characters only).

Good. One of my queries on this thread was IF statistical phylogenetic
analysis was valid, if if if, then can one assign posterior
probabilities to the results of maximum parsimony analysis, as is done
in maximum likelihood analysis. What assumptions must be made (rate of
evol? what?).
>
> > A phylogenetic tree
> >believed to be based on slow and even evolutionary processes,
>
> parsimony makes no such assumption

> > I'm thinking that if a phylogenetic result is supposed to have a
> >probabilistic basis, then the probability (given all those mathematical
> >figures, there has to be a pony somewhere) that the resultant tree is
> >the true should be calculable.
>
> I dont see that. The probabilistic basis you refer to is a question
> of the extent to which the result fufills the demands of the method
> from which it is drawn. The ultimate truth of the result would
> entail, in addition, the question of the reliability of the method
> itself. Since we can never know the ultimate truth of historical
> reconstructions, the ultimate reliability of the method is
> unknowable; our only recourse is to use methods which are consistent
> with those notions we are prepared to accept as assumptions.
> A parsimony analysis will yield a result which is most consistent
> with the notions that life evolved, and that characters which are
> determined (to the best of our biological knowledge) to be the same,
> in different taxa (homologous) are present by descent, I dont know of
> a better way of approaching the "truth" within the framework of
> evolutionary biology.

This sounds as if the pattern developed in a maximum parsimonious
cladogram is judged to approximate expected evolutionary relationships
on the basis of "like produces like." Well, heck, that sounds great. Do
you agree than that maximum parsimony is best viewed as a clustering
method that incorporates a phylogenetic element? My word "expected"
above, however, emphasizes my take that more theory is imposed on the
data than squeezed out.

>
> > I've figured that if a tree with an extra
> >step is half as probable, then in the case of a three terminal taxon
> >tree (two taxa of which share an advanced character), which has three
> >possible topologies, the shortest tree should have a probability of .5,
> >and each of the two (1-step) longer trees, should have a probability of
> >.25.
>
> But the question of whether this is the true tree is not at all
> addressed by this. What is the probability that the apomorphy you
> identify is really the result of an evolutionary transformation event
> that actually occurred in the ancestor of the those two taxa? How can
> such a queston be answered?
snip
> To assert that a model derived phylogeny is the "best estimate" of
> the REAL phylogeny, and that is the end of the story, is absurd, for
> it assumes that the model is an accurate mirror of evolutionary
> processes, when in fact the model remains *untested* in the very
> domain in which it is supposedly revealing the truth.

Ah. Clearly you *don't* see theory imposed on data to wrench it into a
pattern as I see happening. How you can say a step longer is an ad hoc
explanation is beyond me. I can see where trees very much different from
phenetic and max parsimony analysis can be seen as doubtful explanations
because they are so very different from "like makes like." But any trees
similar to phenetic cluster-produced trees and/or to max parsimony trees
can't possibly be called doubtful because their explanations are somehow
"ad hoc." All these trees reflect considerable natural selection.
  The reason scientists like simple/razor explanations is that these can
be tested right away, most easily. Systematics cannot test its simplest
explanations (other than by total evidence), and therefore we emphasize,
wrongly, simplicity as an end in itself. My point is that we are not
reconstructing anything, we are imposing theory on data. To the extent
that the theory is assumed to be generally right, that's great.

snip

> Given the results of process modelling to date, I sense that there
> should probably be an expectation that the model will be different in
> just about every different taxon (and for every different sequence).

I should hope so.

--

*******************************************************
Richard H. Zander, Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA bryo at commtech.net
*******************************************************




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