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[B. J. Tindall]

Some time ago I became interested in different ways of evaluating data for
taxonomic purposes. As a microbiologist (dealing with Bacteria and Archaea)
I began to look at various methods in use in botany and zoology and soon
found myself up against the problem of terms which people are using in
different ways, so I sat down and tried to get down to the bare bones of
what some of the various terms mean. I don't want to cause offence, but it
seems to me that there are three terms which cause some confusion:
1. Phenetic - evaluation based on overall similarity (trouble is that the
term seems to have picked a more limited definition of being only
phenotypic data in prokaryotes). Seems to me that this is the "melting pot"
method, in which all data is reduced to a set of similarity values.
2. Cladistic - I located the term clade, but I could not work out who first
used the adjective "cladistic" in its present meaning. Seems that this
method is based on the sorting and weighting of individual characters.
3. Phylogenetic - this appears to be a term which is difficult to nail
down. In  a Hennigian sense I would assume that it is equivalent to
cladistic methods. However, the main problem is that in this sense it
appears to be automatically linked to evolutionary history. That sub-branch
of cladistics which goes under the name "transformed" or "pattern
cladistics" seems to try to uncouple itself from evolutionary history,
although evolution still has a part to play. Then, of course there are all
those people doing sequence alignments of genes and proteins who also count
themselves under the heading "phylogenetic", but their work usually boils
down to similarity matricies and the underlying theory looks very much
"phenetic".

I would suggest that if you reduce these three terms to their basic
elements phenetic evaluation makes use of data transformed into similarity
values which are used to generate a "dendrogram = phenogram", whereas
cladistic evalution sorts through the individual characters and tries to
make sense of their distribution in order to create a "dendrogram =
cladogram". I would then suggest that both types of evaluation can be used
to investigate aspects of phylogeny, although without adding some form of
evolutionary theory on top neither type of method is inherently
"phylogenetic". Thus I can sort organisms into groups by overall
similarity, or based on character sets, but neither the resulting
phenogram, nor the resulting cladogram is the "phylogenetic tree" unless I
start to try to explain the resulting dendrogram in terms of evolution.
This links into the last paragraph of what John Trueman wrote under the
subject "reweighting characters, few and many" on testing the results
against a hypothesis. I guess I am treading on dangerous ground, but
comments would be helpful.
Brian Tindall
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