Three item data

[David Williams]

Rene Zarageta-Bagils makes the non unreasonable point that 'Farris
optimization' is flawed. This much has been evident for some time. Pierre
Delaporte counters this by saying that it is "not 'flawed', it just fits a
particular model of evolution". Alternatively, one might be led to suspect
that, perhaps, the model of evolution is flawed. Three-item statements
represent a different aspect of data by specifying precisely the
relationships implied by the data. But not according to Delaporte. He
retreats to safety with the idea that the analysis of three-item data is
"non-evolutionary, i.e. fitting no conceivable evolutionary process, and
thus non-phylogenetic at all." One wonders quite what Delaporte imagines
are "conceivable evolutionary processes", one wonders quite where
Delaporte's special knowledge comes from, quite how he knows what is and is
not a "conceivable evolutionary process" (a past generation of
palaeontologists comes to mind). To suggest that the analysis of three-item
data is 'non-evolutionary' springs from the mind of Delaporte only; no one
who has ever written on the subject of three-item data has suggested what
is and is not to be regarded as "conceivable evolutionary processes".
Oddly, Delaporte connects three-item data and its analysis with phenetics.
How that equation is made, again, seems only to be in the mind of Delaporte
(if a 'method' offers no "conceivable evolutionary process" that Delaporte
imagines then, of course, his reasoning goes, it must be phenetic). This
betrays a misunderstanding of both cladistics and phenetics. One might ask,
as well, for a quick examination of any data matrix of binary characters.
Are those data phenetic? Do they specify any relationships? It might be a
bitter pill for Delaporte (and others) to swallow but matrices of binary
characters are indeed inherently phenetic (without any meaning). It might
come as a surprise to him that three-item data does have meaning, by
including precise statement of relationships (what, after all, are the
products of evolution?). It might also come as a surprise to him, should he
wish to consider the problem, that much of what we do today that
masquerades under the name of 'phylogenetics' is phenetics with some added
"conceivable evolution process" (mathematics not biology). Rene's point is
well made but remains unanswered -- perhaps because there is no answer
beyond the cladistic idea of relationships.

"Farris optimization, or Wagner trees, or standard parsimony analysis, is=20
not "flawed", it just fits a particular model of evolution. You can allow=20
character reversals, and thus reversals can tend to "support" a clade, for=
=20
instance apomorphic reversal to "loss of tail" can support a clade. If this=
=20
agrees with your model of character evolution, it's OK. If not, use PAUP=20
"stepmatrix" tool and weight character step costs against reverals, and so=
=20
on for an illimited series of models with possible differential charcter=20
steps weighting...
All depends on your model of character evolution.
But if you really like phenetics, use three-taxon analysis in its last=20
versions : its a true, and unexpected, rediscovery of phenetics, by people=
=20
initially dealing with "parsimony" in the "cladistic" school. 3TA=20
implements no implicit or explicit notion of character evolution. Even the=
=20
basic notion of homology by descent between similar character states is=20
broken down by the splitting of characters into separate "three taxon=20
statements" treated independently. Different states of a same character and=
=20
different occurences of a same character state are split into peaces with=20
no return.


Phenetics did not care with evolution either, it was "overall similarity=20
for overall similarity's sake", just so. Like 3TA is 3TA for 3TA's sake.=20
Just so.
3TA has obviously no "flaw", and cannot have any flaw, merely because it=20
has no model to implement, and thus provides no handle to evaluate its=20
adequacy.


David M. Williams
Department of Botany
The Natural History Museum
Cromwell Road
London SW7 5BD
UK

Voice           +44 (0)20 7942 5114
Fax             +44 (0)20 7942 5529
email           d.m.williams at nhm.ac.uk
                 DMyWilliams at aol.com

Museum web page http://www.nhm.ac.uk