[Taxacom] PhyloCode & ICZN to "duke it out"?

Fri Oct 5 11:17:30 CDT 2007

One way to look at paraphyly is that there is a clear difference between
evolution of expressed traits and of genealogies of non-coding molecular
traits. 

A single phylogenetically complex ancestor may have sent off through
parallel evolution a number of new lineages with different expressed
traits, and these lineages may align nicely with molecular lineages, but
all may be generated by one morphologically and bio-role stable (through
stabilizing selection) species. Paraphyly, especially when one or more
species cannot be rejected as surviving ancestors, then reflects
possible evolution of expressed traits, unless falsified. It's the null
hypothesis, sure, but support for the alternative hypothesis of
monophyly must come from evaluation of expressed traits, not DNA. 

I can't see molecular systematics falsifying the above, though the
end-run is clear: just redefine evolution as changes in non-coding
traits, and presto the paraphyly problem goes away because DNA always
changes with lineage splits but not necessarily evolution of expressed
traits.

Remember expressed traits? Morphology and biorole? These used to be
important in taxonomy because they were important in evolution. 

******************************
Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
For FedEx and UPS use:
Missouri Botanical Garden
4344 Shaw Blvd.
St. Louis, MO 63110
******************************
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Ken Kinman
> Sent: Friday, October 05, 2007 9:50 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] PhyloCode & ICZN to "duke it out"?
> 
> >From: "Richard Pyle" Date: Thu, 4 Oct 2007
> 
> >2) Another common criticism of Phylocode is that it will lead to a
> >proliferation of names because every node could presumably be named.
But
> >in
> >practice, this won't happen because: a) not every node will be named
--
> >only
> >those for which a name assists in communicating ideas about inferred
> >phylogenetic rlationships; and b) many names, though perhaps
technically
> >"valid" in the Phylocode context, will not be used because they have
> little
> >or no communicative value.
> >
> *****************************
> Hi Richard,
>      I am not nearly as optimistic about this or other problems that
have
> been discussed.  I regularly read debates among PhyloCoders
themselves,
> and
> they have already proposed a dizzying array of clade names for just
the
> dinosaurs, some of which are synonymous as different authors rush to
gain
> priority for their own taxon names.  It isn't pretty even among
> PhyloCoders,
> and it would (will?) be even uglier once they start attacking us
instead
> of
> each other.  I've even heard a number of proponents of strict cladism
say
> they look forward to the day when the proponents of paraphyly have
"died
> off".  I guess they don't realize how many of us there really are.
> 
>      And I think the term "monophilia" is far too kind (after all I
love
> clades too).  I still think the term "paraphylophobia" more accurately
> captures the main shortcomings of strict cladism and the great harm it
> will
> do to nomenclature and our ability to communicate (not just with each
> other,
> but with people outside of professional biology).
> 
>      To take just one minor problem you brought up.  Since genus
Gomphosus
> is pretty clearly cladistically embedded within genus  Thalassoma,
strict
> cladists WILL insist on "correcting" this paraphyly "problem".  But
it's
> not
> as simple as changing to Thalassoma varium, because Gomphosus has
> priority,
> so ALL the Thalassoma species would actually be dumped into Gomphosus
(and
> many of the specific endings will change as well).
> 
>      Wouldn't it be simpler if PhyloCode just allowed paraphyly the
way
> they
> allow use of ranks.  But that isn't going to happen, because their
idea of
> communication is extremely strictly formulated and legalistic (far
more
> than
> ours).  Anyway, I will simply keep Gomphosus and Thalassoma as
separate
> genera, but will mark Thalassoma as a paraphyletic mother group
(something
> like this):
> 
>    4  Thalassoma%
>   _a_ Gomphosus
> 
>       There is also the question of Halichoeres maculipinna, which
doesn't
> belong to Halichoeres at all.  I would simply place it as the
basalmost
> species of Thalassoma, but I suspect PhyloCoders will insist on
creating a
> new genus for it.  Take my approach and you only shift one species
> (maculipinna) to Thalassoma, while strict cladists will definitely
LUMP
> all
> Thalassoma species into Gomphosus (unless they suppress the latter
name),
> and probably SPLIT maculipinna off as a new genus.  Lots of name
changes
> that I believe to be unnecessary and avoidable.
> 
>     Multiply such unnecessary lumping and splitting a thousand times
(just
> among genera) and it will cause much confusion and anger beyond our
> profession.  All because strict cladists (and PhyloCoders in
particular)
> want to split hairs and create a nomenclatural legal society with
> ultimately
> millions of strictly defined names (including ours, which are admitted
> loosely defined, but that sure beats a straight-jacket).
> 
>      And it doesn't stop at generic names.  Will clade Aves be
restricted
> to
> crown group birds (thus a senior synonym of perfectly good name
> Neornithes)?
>   Probably!!!  Likewise Amphibia, Reptilia, Tetrapoda, and many others
> will
> be redefined as crown clades that are a far cry from their normal
content
> (especially if you include fossil taxa).  Zoologists face a huge mess
at
> EVERY taxonomic level as this spreads from its epicenter (in
herpetology).
> Most botanists on the other hand will likely watch it all play out
from a
> safe distance and learn a valuable lesson from our turmoil.  I once
hoped
> strict cladism (and the even stricter PhyloCode) could be kept in
their
> own
> sandbox, but no more.  Too many of them are already taking sand from
our
> box
> AND adding insult to injury by throwing it back into our faces.
>     -----Ken Kinman
> 
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