sexuality & Trees of Life

B. J. Tindall bti at DSMZ.DE
Fri Nov 17 09:42:47 CST 2000


Ken Kinman wrote

At 17:23 16.11.99 PST, you wrote:
>Brian,
>     I think you should perhaps read the last sentence which you wrote,
>about ignoring one aspect of diversity in favor of another.  When you said
>sexual reproduction is limited to a "small section of organisms", this is
>precisely what you were doing, and the main reason I challenged the
>statement.

Sorry, did not want to cause offence (seem to have managed that!!). Of
course eukaryotes are important I do not deny that, but the view is often
presented that (described) prokaryotic species account for about 1% of all
described species, and are, therefore unimportant (not my words). However,
and I hate the "numbers game", what happens if we find that described
prokaryotic species eventually make up 50% of all described species and
that Metazoan and Metaphytan species account for 20% of all described
species? The rest being protists etc. which I have assumed may eventually
loose their tag as being either "animal" or "plant". Once again sorry if I
annoyed anyone, this was not my intention.

>     And I am certainly not one to underestimate the diversity of
>prokaryotes.  I named Order Verrucomicrobiales in 1994 ("officially" named
>by others in 1995), and I named Class Verrucomicrobea in 1994 (there is
>still apparently no "official" name for this class, but Phylum
>Verrucomicrobia was named about 1998, which I think was overdoing it to call
>it a separate phylum).  I named the very distinctive Family Synergistaceae
>in 1996, when I saw NCBI wrongly classifying Synergistes in Family
>Clostridiaceae (which are totally unrelated), and it took over a year to get
>them to finally change that.  I went further and named Order Synergistales
>in 1998, but I've heard talk some think it should have its own phylum
>too---I don't mind recognizing diversity, but there is such a thing as going
>overboard.

Valid publication of names is required as laid down by the Bacteriological
Code, which can only carried out via the International Journal of
Systematic Bacteriology. As for the NCBI, my contacts suggest that they are
trying to do a difficult job in maintaining the database and they probably
do not have the same taxonomic background as we do.

>     I don't think anyone has yet followed my lead in recognizing the very
>distinctive Order Thermodesulfobacteriales (which I also named in 1994).
>And while we are on that subject, I wish Woese set the record straight:
>Ether-linked lipids (even the branched-chained types) are not restricted to
>Metabacteria (= "Archaea")--- they are found in the eubacterial order just
>mentioned, plus Orders Thermotogales and Aquificales as well.  Ignoring
>evidence of intermediacy between Eubacteria and Metabacteria is something
>Woese appears to be good at.  And even the rRNA distances between these
>so-called Domains continues to shrink.

Have to pull you up on your ether lipids - Archaea are unique in producing
isoprenoid side chains, whereas Thermodesulfobacterium, Thermotoga and
Aquifex produce either straight chain or terminally branched side chains.
Similarly some clostridia also produce alkenyl ethers (again straight
chain). My guess is that Archaea use the addition of branched C5 (isoprene)
units for chain elongation, whereas the others are using C2 addition.
Although the biochemical pathways are not fully elucidated it does look as
if there are some fundamental differences somewhere. Most people, including
above quoted scientist get this wrong, even seen articles talking about
fatty acids in Archaea (haven't found them yet in significant quantities).
You won't find me saying ether lipids are unique to Archaea, but I would
say isoprenoid ether linked lipids are unique to Archaea (which is still
correct). One can even further qualify this based on di- and tetraethers,
and even on the rather interesting "limited" range of chain lengths.
As for shrinking differences between "Domains" there are so many
"microorganisms" to be discovered that there are bound to be changes.

>     So please don't dismiss me as a zoologist who doesn't appreciate the
>diversity of prokaryotes.  In fact, I believe it is Woese himself who
>trivializes Eubacteria at the expense of "Archaea", and is badly misrooting
>them in the process.  And for of those of you who saw that PBS show last
>week, they were so surprised that the Thermotoga genome was so much like
>those of "Archaea".  Well, I have news for them.  I clearly showed this
>relationship in my 1994 book (5 years ago!!), where I showed Togobacteracea
>giving rise to Metabacteria (i.e. "Archaea").  I sent Woese a copy of my
>bacterial classification in 1994---there was no need for him and his
>colleagues to be surprised at such genomic similarities.

Despite being in Germany we saw a video. Oh dear, yes there are lots of
problems, not just rooting trees etc. Some of the historical "facts" were
also incorrect. We had a workshop here last week which looked at problems
in sequence analysis- we still need to learn quite a bit. What about giving
me the references to the work you quote.

>      Getting back to the main point, I would quote your last statement:
>"Accepting one aspect of diversity does not mean that the other should be
>ignored."  I think this advice should be directed at Carl Woese, who bases
>his so-called Tree of Life solely on rRNA distances.

Of course the opposing camps are Woese amd Mayr and both are probably
guilty of similar problems. Of course my statement is general and not
directed at anyone in particular - again no direct attack intended, just
highlighting a general problem.

And your own statement
>that sexual reproduction is restricted to a "small section of organisms"
>clearly reflects Woese's very restricted view of diversity.  And I don't
>think entomologists probably cared much for that remark about the colours of
>butterfly wings (even if some lay people probably still have that
>misconception about taxonomy).

Covered that one above, and I agree we do not get anywhere by taking up
extreme positions. Actually if butterfly taxonomy does find the colour and
shape of the wings to be important criteria, and there is correlation with
other data (see another e-mail on this point), then I certainly do not
object, but one should not apply this standard to all organisms.

>     I already fully appreciate the diversity of prokaryotes, and far from
>sweeping it under the carpet, I have named new orders and classes of
>bacteria (and not just those named above).  However, if microbiologists want
>zoologists and botanists in general to appreciate prokaryotic diversity more
>fully, I wouldn't suggest doing it by trivializing Metazoa and Metaphyta as
>a "small section of organisms".  There are a lot more yardsticks than just
>the rRNA gene.  I've personally studied hundreds of bacterial rRNA
>sequences, and they are important.  But I certainly don't believe in this
>extreme Woesian pendulum swing, and calling Metazoa and Metaphyta little
>"twigs" on the tree of life just because their rRNA sequence is stabilized.
>That perspective is more extreme than the one it was supposed to correct.

What evidence do you have that the rRNA sequences have stabilised in
Metazoa and Metaphyta, whereas you would imply that this is not the case in
prokaryotes? This is an important point.

Hope I have clarified a few points and raised a few new ones
Brian Tindall

>                       ---------Ken Kinman
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