Three great papers (cladistics; paraphyly)

[Ken Kinman]

Brian,
     Well, I don't agree with Ernst all the time either.  :-)    In fact, in
that 1998 paper (in a footnote on page 9721), Mayr says "Paraphyly does not
occur in Darwinian classification."   EGAD!!!   I guess that means I'm not a
Darwinian either.  Sorry Ernst, but the *inexplicit* dumping of paraphyly
and holophyly into monophyly is almost as bad as the strict cladists dumping
paraphyly and polyphyly together as non-monophyly.  Paraphyly must be
explicitly separate, not dumped in with polyphyly (strict cladism) or dumped
in with holophyly (strict eclecticism).
      That said, I think the rest of Mayr's paper is a wonderful overview
and full of insight.  His criticisms of Woesian ideas are mild and
relatively charitable (at least compared to mine).  Woese's contributions in
the 1970's were a wonderful expansion of our knowledge of prokaryotic
diversity, but it is becoming increasingly clear that those ideas were
carried to extremes during the 1980's and 90's in ways that that may not be
disentangled for many years.
      In addition to the criticisms made by Mayr in 1990 and 1998, I believe
Woese's ideas have thwarted an understanding of the phylogeny and evolution
of eubacteria in particular.  And I strongly believe that one aspect of that
damage comes from the widespread cladistic error of rooting Eubacterial
phylogenies using Metabacteria (a.k.a. "Archaea") as the outgroup.  This has
profound implications for the structure of the true "Tree of Life" at the
broadest levels.  Woese himself seems to admit on occasion that Eubacteria
came first (which makes Metabacteria its exgroup, and Mayr's criticism of
the term "Archaea" is right on target).  The more derived an exgroup it
turns out to be, the more distortions Three Domain Trees will be seen to
have had (so much so that the Three Domain classification will almost
certainly not survive).
     I don't blame Mayr for not getting into all this, because it will take
more whole genome sequences to clarify the situation and sort out the whole
mess (and show how just how badly circular reasoning has perpetuated it).
Until then, I continue to strongly urge bacteriologists NOT to use
Metabacteria (a.k.a. "archaea" or "archaebacteria") as an outgroup to
Eubacteria, because using an exgroup (which is effectively an ingroup) as an
outgroup is cladistic suicide (this is one of the worst mistakes one can
make in a cladistic analysis).  Until we discover how to root the tree of
life, it is best to use unrooted trees to analyze the broadest
interrelationships of prokaryotes.  But at least Mayr's rather mild
criticisms of Woese's ideas has undoubtedly helped to at least mitigate some
of the damage.
             ----- Ken Kinman
******************************************
>From: "B.J.Tindall" <bti at DSMZ.DE>
>Reply-To: "B.J.Tindall" <bti at DSMZ.DE>
>To: TAXACOM at USOBI.ORG
>Subject: Re: Three great papers (cladistics; paraphyly)
>Date: Wed, 16 Jan 2002 14:20:37 +0100
>
>Ken
>two problems here -
>a) if you link this into the current debate on cladistics you won't find
>many bacteriologist who use cladistic methods so there is a tendancy to say
>clear 3 groups - Archaea/Archaebacteria, Eukarya and Bacteria/Eubcatreia
>(Metabacteria being rarely used).
>b) Ernst Mayr is fairly negative about certain aspects of bacterial
>taxonomy - most of the arguments about the diversity of plants and animals
>rests on morphological criteria, and if your objects do not have very
>distinctive morphologies then they are "not very diverse". Of course if the
>diversity is at a different level then this type of argument ignores that.
>
>.......but you know that I do not always agree with you Ken ;-)
>
>Brian
>
>Ken Kinman wrote:
> >    (3)  Having read papers by those two younger guys (one a botanist and
> >one a zoologist), you might want to look at it from a bacteriological
> >perspective from someone who is better known:
> >    Ernst Mayr. 1998.  "Two Empires or Three" (Proc. Natl. Acad. Sci.,
> >95:9720-9723).  Since Ernst named me in his acknowledgments, I guess that
> >makes me bias, but I think it's a great paper.
> >            --------Ken Kinman


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