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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 Lophotrochozoa).
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 stricto).
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.
-----Ken Kinman
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.
kinman@hotmail.com writes:
> 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).

NJPharris@aol.com responded:
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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