3TA (was Human and ape phylogeny)

[Richard Jensen]

I can't help but think that phenetics is getting a bad rap here.  Phenetic
analyses make no reference to apomorphic, plesiomorphic, synapomorphic, etc.
with respect to characters.  Characters provide the information by which the
analysis is conducted and a phenetic analysis will lead to a classification.
And, it is a testable hypopthesis of relationships.

Sokal and Sneath never intended for phenetic analyses to be interpreted as
phylogenetic or evolutionary classifications.  Colless noted that, with certain
assumptions, phenetic analyses would be expected to be good approxamations to
such releationships and it has been suggested that in situations in which there
is little homoplasy, phenetic analyses and cladistic analyses may yield the same
"solution."  And, despite the appearance of phenograms as trees, they cannot be
interpreted as rooted trees.  They represent sets and subsets in a nested
fashion.

Further, don't criticize phenetics for the many options available for conducting
phenetic analyses.  Unless I have missed something important over the last 20
years, there are a variety of approaches for conducting cladistic analyses and
they typically yield different results for a single data matrix.  In other
words, both approaches yield results that are dependent on a set of choices made
by the investigator.  The fundamental question is whether or not the choices
made can be justified (e.g., including or ignoring negative matches when
calculating association coefficients).

Dick

pierre deleporte wrote:

> Hi René, David, and taxacomers
>
> I think this thread has no more connexion with the Human-apes thread, hence
> my re-naming.
>
> I will not comment all the points made by René (although I disagree with
> all of them in the slightest details). I just try to point at the core of
> the question on two points: semantics, and models.
>
> - semantics :
>
> At 11:56 05/04/2003 +0200, René Zaragüeta Bagils wrote :
> >(...)
> >it is logically inconsistent to optimize "reversals" because they cannot
> >be "apomorphic", by definition (except in phenetics...)
> >(...)
> >Pierre Deleporte wrote:
> >"But if you really like phenetics, use three-taxon analysis in its last
> >versions [...] This makes the method non-evolutionary, i.e. fitting no
> >conceivable evolutionary process, and thus non-phylogenetic at all."
> >Re:
> >What do you mean by "last versions"? I do not agree with "modified
> >three-taxon analysis" because it is as phenetic as standard parsimony (it
> >optimizes absences). It seems to me that it is you who like phenetics
> >(e.g. when you say that "apomorphic reversal to 'loss of tail' can support
> >a clade")
>
> Yes I mean "modified 3TA", which has been demonstrated as being pure
> phenetics (i.e. clustering on the basis of overall similarity, and not
> optimizing homology by descent).
>
> A basic misconception in the three-taxon-analysis school is to consider
> that "phenetics" means: "grouping (sometimes) on the basis of the absence
> of a feature". This is ignoring the current definition of phenetics (=
> grouping on the basis of overall similarity, as repeatedly stated on this
> list), and also ignoring that phenetic methods can implement an illimited
> variety of similarity or distance measures, including methods which group
> on the basis of the overall co-occurence of presence of features, to the
> exclusion of the co-occurrence of absence. You then get a phenetic
> clustering on the basis of overal similarity of presence of features only
> (would then 3TA proponents call it "non-phenetic"?).
> This very peculiar acception of "phenetics" in 3TA jargon makes their
> comments on the topic very difficult to understand for the naive outsider.
> A complete dialogue of the deaf in fact.
>
> René also wrote:
> >Optimizing instances and non-instances of characters at the same time is
> >simply phenetic (just so).
>
> No, phenetics is not better defined as "just so". Sorry if my last post
> could suggest this. Applied to molecular data under the character evolution
> model of "molecular clock", a phenetic clustering is clearly phylogenetic,
> the evolutionary model justifying the approach is explicit (whether the
> model is biologically realistic in this or that case is debatable of
> course, and molecularists have developed methods to test for this in the
> structure of the data matrix).
>
> But applied to morphological data, phenetics is "just so" (because there is
> no model of "morphological clock" justifying the use of the method for
> phylogeny inference on such data). Notably, the phenetic school of
> systematics in the seventies presented itself as biologically "just so"
> (they did not pretend to infer phylogenies). Its explicit goal was stable
> classification/nomenclature, but not biologically meaningful systematics.
>
> See also recent posts, like David Orlovich, or B.J. Tindall :
> " It is difficult to see how a data set can be phenetic. It may be handled
> in a phenetic way (overall similarity)."
> and Peter Hovenkamp for his comment on the notion of phylogenetic
> (transforming) characters.
>
> - evolutionary models
>
> René wrote:
> >However, how can absences evolve (=transform, I guess you should say) in
> >your model? What do you mean by the evolution of the "lack of a tail"? How
> >can, for instance, natural selection work on the absence of something?
>
> Very simply: evolution acts on absence by selecting against corresponding
> presence. Selection acts in selecting in a population between the
> descendants of individuals with no tail (ancestral state) and of mutants
> with a tail (new feature), on the basis of differential fitness
> (differential number of reproductive decendants from the two types of
> individuals with/without a tail according to their differential adaptation
> to the environment), or possibly on the basis of mere genetic drift (=
> chance alone) in small populations.
> "Evolutionary transformation" is not magics.  Biology is meaningful.
> Considering population biology, population genetics, genetics of the
> development, can give useful insights into how evolution can proceed.
> Artificial selection too (Darwin's pigeons to start with). Provided people
> take an interest in such matters, of course.
>
> >How can you distinguish between the 'transformation' of the absence of a
> >tail to the presence of a tail and the 'transformation' of the absence of
> >a leg to the presence of a
> >tail?
>
> Humm... I'm no specialist, but in my humble opinion it seems that they do
> not fit exactly in the same place on otherwise similar squeletons. This
> remark is as old as the "principe des connections" of Geoffroy
> Saint-Hilaire, and basic to all homology assessment in morphology, with an
> obvious equivalent in molecular studies (sequence alignment and secondary
> structure). Centuries of comparative anatomy make sense, and modern
> molecular biology too. Provided people take an interest in such matters, of
> course.
>
> OK you question my model, fine, but may I question yours ? I fear not.
>
> In my view, the basic problem with 3TA is the absence of an explicit model
> of character evolution. All biological evolutionary consideration is
> absent, as if "replaced" by general notions of "hierarchy" and
> "relationship", which are certainly not biological in themselves.
>
> Thanks also to David Williams for his comments, which help illustrating the
> point.
> David wrote:
>
> "One wonders quite what Deleporte imagines are "conceivable evolutionary
> processes", one wonders quite where Deleporte's special knowledge comes
> from, quite how he knows what is and is not a "conceivable evolutionary
> process"."
>
> OK David, so much for me, I certainly made an infortunate tactical error in
> stating "no conceivable", I should have written instead "no explicit
> evolutionary model in 3TA" .
>
> So, once a proponent of 3TA, just one, anyone (but at least one !), will
> have explicitly stated what model of character evolution he is
> implementing, the question of this model being "conceivable" or not for a
> contemporaneous biologist will only be raised. I infortunately jumped over
> this obligatory stage of the discussion, and anticipated the conclusions
> according to my own inability, despite my sincere efforts, of conceiving a
> biological model of character evolution fitting 3TA procedures. Sorry David.
>
> The problem is that this discussion is impossible at the present time,
> because not a single proponent of 3TA, and symptomatically neither David
> nor René in their last posts on this list, ever stated what notion of
> biological evolution, of character transformation, was implemented in this
> approach.
> Norman Platnick was the only one I know who tempted something this way
> (trying to justify 3TA as an improved implementation of evolutionary
> homology optimization, and whose attempts were rebutted in the nineties, by
> myself among others). Platnick's papers were notably separated from
> Nelson's ones at this time of the debate, Nelson never arguing optimization
> of evolutionary character homology (but only "more precise use of
> parsimony" and "relationships" instead, which is not biological in itself).
>
> So, I can just reiterate the question: dear David or René, what conception
> of the evolutionary process, or what biological conception of the
> similarities and differences of characters in taxa are you implementing,
> when you perform 3TA ? Or more simply (like I already asked David five
> years ago): "Why do you do that rather than something else", as
> phylogeneticians ?
>
> Note that I consider that you are, as I do, trying to infer a phylogeny
> from a data matrix of terminal taxa and characters. If not, forget all what
> I said, my comments do not concern non-phylogenetic approaches.
>
> But please, don't just answer "relationship", or "hierarchy", not even
> "precise statement of relationships" or "cladistic idea of relationships"
> (like in last post by David),  I think I really know this by heart since
> the time, and I'd rather like to read something, anything biologically
> meaningful instead.
> Similar or different traits are present in different taxa: how do you
> figure out this may the h...ll come from, biologically speaking ? People
> who have no answer to this question cannot logically infer a phylogeny from
> a data matrix. Inferring the history of evolution (phylogeny) requires the
> explicit implementation of some notion of evolution as a process. If not,
> then "anything goes"... not for me, thanks.
>
> best and cheers (David, I pay the beers !   :-)
> Pierre
>
> Pierre Deleporte
> CNRS UMR 6552 - Station Biologique de Paimpont
> F-35380 Paimpont   FRANCE
> Téléphone : 02 99 61 81 66
> Télécopie : 02 99 61 81 88

--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen