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Re: final thoughts
I was not talking about the "defined" holophyletic groups. I am
talking about taxa like Lophotrochozoa (invertebrate superphylum), which is
almost certainly paraphyletic (its proposed synapomorphies are actually
symplesiomorphies). It gave rise to Ecdysozoa (another superphylum), which
I would agree is probably holophyletic (but deeply nested within
The most damaging paraphyletic group, which is widely regarded as
holophyletic, is Domain Bacteria (eubacteria). Far from being sister group
to the "Archaea"-Eukaryota clade, the actual sister group of the latter
clade is deeply nested within the eubacteria.
Unfortunately, because of the undue influence of Carl Woese,
bacteriologists continue to use members of "Archaea" as outgroups to
eubacteria, which is sort of like using birds as an outgroup to
reptiles---in which case reptile phylogenies would be totally distorted,
having dinosaurs as the most basal reptiles instead of mesosaurs or
pelycosaurs (or primitive anapsids for the "cladistic" Reptilia sensu
In the same way, eubacterial phylogenies are highly distorted because
they are erroneously believed to be holophyletic (or at least treated as
such by misrooting them with an "Archaea" outgroup). There are many other
cases of paraphyletic groups being treated as if they are holophyletic. The
rush to cladify is creating all kinds of problems that are not yet readily
apparent, but will cause all kinds of confusion in the years to come.
Cladistic analysis is a very powerful tool, and like any powerful tool, it
can be very destructive when used improperly. In many cases, I believe
strictly cladistic classifications (especially at higher taxonomic levels)
will continue to generate more such problems, and it's just one more reason
for eclecticists to dislike them.
P.S. By the way, I usually do not use the name "Archaea" or
"Archaebacteria" (eubacteria are far more archaic), so I use the term
Metabacteria (proposed by Japanese biologists in 1979, but ignored by Woese
and therefore almost everyone else). But to maintain continuity and
minimize confusion, I divide Phylum Metabacteria into Classes Crenarchaea
and Euryarchaea (and maybe these classes will be renamed when people realize
they are deeply nested within eubacteria, and are therefore not "archaic").
Woese's attempt to cladify life into three Domains is going to fall flat on
its face, and this is something all cladists should be concerned about. The
paraphyly of Lophotrochozoa will likewise cause years of problems for
invertebrate zoologists, until it is recognized that its purported holophyly
was based on symplesiomorphies. So it goes.
> And of course, there are other purported holophyletic taxa proposed by
cladists that are probably really paraphyletic (and they are more
problematic when they go unrecognized).
First, if they are defined as "holophyletic", they cannot be paraphyletic.
There is no way to make "the common ancestor of all living mammals and all
of its descendants" paraphyletic.
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