Three great papers (cladistics; paraphyly)

[B.J.Tindall]

Hi Ken,
A number of comments:
a) it is now accepted by those developing these concepts further that you
can't root the ribosomal gene tree using just the ribosoaml gene sequences.
In fact I am not sure how you actually locate the "first organisms" anyway.
b) sometimes I get the impression that the exchanges between Mayr and Woese
are based on Woese writing down his ideas and Mayr writing down his ideas
in exchange, but when you compare the two publications they are talking
about slightly different things!! ;_)
c) can't argue with your point on rooting the tree, and same goes for you
raising the point on circular arguments. Genomics has indicated the
complexity of biological systems and the fact that we have to go back to
understanding organisms at as many levels as possible. As a sideline I find
it interesting that the DOE call for proposals mentions a nice long list of
disciplines, but not systematics - a lot of problems arise because of the
failure to appreciate the significance of systematics in modern biology
(particularly in bacteriology).
c) the nice long exchanges on cladistics and paraphyly etc. during the last
days suggest that there is a lot left to look at in more detail and perhaps
neither one system nor the other has the ultimate answer, perhaps there is
a third alternative somewhere waiting to be discovered. I agree with at
least one point it is important to look at alternative arguments and
evaluated them for yourself.
Brian
P.S. as a matter of interest I am informed that yet another paper on yet
another alternative classification of prokaryotes is to appear soon from
Cavalier-Smith.

At 22:28 16.1.2002 -0600, Ken Kinman wrote:
>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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