3TA (was Human and ape phylogeny)
pierre.deleporte at UNIV-RENNES1.FR
Mon Apr 7 19:26:11 CDT 2003
Hi René, David, and taxacomers
I think this thread has no more connexion with the Human-apes thread, hence
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."
>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
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
- evolutionary models
>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
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
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
"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
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
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
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
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 ! :-)
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