Darwin (was: Phylogenetic evidence)

[pierre deleporte]

At 16:15 25/07/2002 +0200, you wrote:
>From: Richard Jensen
>If I take this literally, then you are arguing that there can exist a
>clade in which the objects have absolutely nothing in common ("...members
>do not share any character state in common...").  If that's the case, then
>the "clade" does not exist - it cannot be supported by any evidence and,
>in my mind, consists of two mutually exclusive classes of unknown affinity.
>Can you provide an example of such a clade?
>===========
>Um, am I wrong here? What about the character matrix (+ = apomorphy)
>    1 2 3 4 5 6 7 8
>A  - + + + + + + +
>B  + - + + + + + +
>C  + + - + - - + +
>D  + + + - - - - -
>
>... does not it result in a cladogram (((AB)C)D) ? If yes (and perhaps I
>am missing something here), then we have a clade ABCD where the species do
>not share any single common character state.
 >Ooops, mea culpa - the cladogram in my previous mail is not indeed
parsimonious;
 >Zdenek

It happens that I just discussed a similar example off list. Interestingly,
it seems that the "reversals" problem is a classic in the class / cluster
debate.

A way to deal with this problem is to consider the "three taxon analysis"
(3TA) debate in the recent literature.

Nelson (1996, "Nullius in verba") wrote :

"Several years ago, J.S. Farris and I agreed to disagree over the
interpretation of a data matrix for taxa ABCD, with a trio of hypothetical
characters conflicting in all possible combinations of 2 of 3 taxa BCD:

Matrix 1:

O  000
A  000
B  110
C  101
D  011

With inclusion of an all-zero outgroup (O) in the data matrix, Hennig 86
yield six trees : three with a basal trichotomy, AB(CD), AC(BD), AD(BC),
and three resolved tres, A(B(CD)), A(C(BD)), A(D(BC)), all with length 5,
ci 60, ri 33. The strict consensus of the trees is uninformative.To me,
however, it seemed that the trio of characters might be seen to associate
taxa ABCD, such that only the resolved trees, and their informative strict
consensus A(BCD), are relevant. Farris stated that such should simply not
be don. The reason was that his optimization criteria produce no
unequivocal synapomorphy for the group BCD."

The following debates are quite interesting regarding the point at stake.
It appears that Nelson resolves the phylogeny A(BCD) using his "three taxon
analysis" (3TA) procedure.
It appears that this procedure is indifferent to topographic contiguity =
homology by descent, and also to reversals as possible synapomorphies.
It appears that a modified (improved ?) version of it (m3TA) leads to plain
classic phenetic clustering (by overall similarity based on all occurences
of traits considered separately two by two, absence excluded).

To the objection: "why should all these characters partly point to group
(BCD) if there is no such a group ?", it was answered: "why can't we find
the slightest unambiguous synapomorphy if such a group really exists ?"

The conclusion is that standard cladistic phylogenetic analysis, quite
logically, finds no resolution without some non ambiguous synapomorphies,
and that competing so-called "cladistic approaches" find such "cluster
resolutions" only when... they inadvertently "rediscover" and apply
phenetic methods.

The charge of clustering on similarity instead of defining classes can be
addressed to 3TA, and to m3TA = phenetics, not to standard cladistic
parsimony analysis. Reversals is not a problem, and the "classic" examples
in this debate merely do not contain cladistic resolution.

For nomenclatural purposes, opting for naming a group (BCD) in this case
would be applying "locally" a phenetic clustering, forcing taxonomic
resolution, possibly in an otherwise classic phylogenetic system. No
problem for me, a cladist without a resolved cladogram should not object
for alternative expedients... provided that warnings should be clearly
posted: "This is a local phenetic clustering, not to be taken as resolved
phylogeny". Maybe a "reasoned eclecticism" is possible this way, with clear
priority rules for methods and criteria... (should please to Ken, some way...).

If this can help...

(The whole "3TA" debate can be followed mainly in Cladistics and Systematic
Biology of the ten last years, notably papers by Nelson, Platnick,
Scotland, Carine, Williams, Farris, Kluge, de Laet, Smet, Deleporte, and
others... sorry for those I don't remember now...).

Pierre