[Taxacom] The difference

Sun Oct 28 04:08:27 CDT 2007

As I said before, I'm completely with you (and Don Colless) regarding the
folly of combining morphological and molecular characters as though they
were 1:1 equivalents in terms of their phylogentically informative value. As
I said in my first post, I'm not optimistic that we will ever have a
satisfactor way fo quantitatively weighting them appropriatly, so I agree
with Don that it's probably more useful to think of them as parallel means
of intrpreting evolutioanry affinities. 

But the conclusion I've come to after thinking about this sort of stuff is
that we have a much more fundamental problem going on here, which is that I
believe we don't yet quite understand evolution and phylogenies as well as
we think we do. And I certainly don't think we've come to grips yet about
how best to characterize our interpretations of those phylogenies (whether
through nomenclature, or cladograms, or whatever).

In comparison to the epiphany of seeing morphology as an extension of genome
(and of seeing the moon as a sphere in space rather than a disk in the sky),
I don't think we've quite yet had the epiphany that bridges the gap between
individual reproductive events (organismal time scales) and the process of
speciation (evolutionary time scales). This comes back to my earlier
ramblings about all life on earth being an extremely smooth and unbroken
chain of information flow across some 4 billion years.  That's a lot for us
mere taxonomists to get our heads around.

Aloha,
Rich

________________________________

	From: Richard Zander [mailto:Richard.Zander at mobot.org] 
	Sent: Saturday, October 27, 2007 10:49 AM
	To: Richard Pyle; taxacom at mailman.nhm.ku.edu
	Subject: RE: [Taxacom] The difference

	Rich:  Thanks for the follow up. I do think that the author of every
paper that analyzes a combined morphology and molecular data set does make a
decision on the number of apomorphic shared DNA bases implied by a shared
apomorphic morphological trait, namely one. This could be wrong by two
orders of magnitude. Even if a shared morphological trait were recognized as
a surrogate for, say,only  10 shared molecular traits, the fabric of modern
phylogenetic classification would necessarily change. 

	1. Combined data sets would suddenly not swamp the morphological
component, 
	and if the data sets were not combined, then
	2. morphological data sets would suddenly have high bootstraps and
maybe statistically certain BPPs on branch arrangements. 

	(Remember when "optimality alone" of morphological data sets was in
vogue as justification for using cladograms in classification? Maybe we are
back to puzzling over morphological cladograms.)

________________________________

	From: Richard Pyle [mailto:deepreef at bishopmuseum.org]
	Sent: Fri 10/26/2007 6:21 PM
	To: Richard Zander; taxacom at mailman.nhm.ku.edu
	Subject: RE: [Taxacom] The difference

	I agree -- and the point of my message was to emphasize my agreement
(though
	maybe I didn't articulate it well). And, I'm not so sure there is a
large
	literature concerning this issue. 

	My point was (like your point), that despite the fact that it should
be
	"obvious", very few people seem to treat it as such -- as your post
	underscored.

	Aloha,
	RIch

	> -----Original Message-----
	> From: Richard Zander [mailto:Richard.Zander at mobot.org]
	> Sent: Friday, October 26, 2007 12:15 PM
	> To: Richard Pyle; taxacom at mailman.nhm.ku.edu
	> Subject: RE: [Taxacom] The difference
	>
	> Well, sure, Rich, I appreciate that I did not include an
	> acknowledgement that there is doubtless a large literature
	> glancing off this obvious fact. There is, however, no action.
	> If morphological traits are surrogates for more than one
	> molecular trait, there is certainly no mention, hint, or
	> quibble about this in actual phylogenetic analyses of combined
data.
	>
	> R.
	>
	> ******************************
	> 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
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	> ******************************
	>
	> > -----Original Message-----
	> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
	> > bounces at mailman.nhm.ku.edu] On Behalf Of Richard Pyle
	> > Sent: Friday, October 26, 2007 4:31 PM
	> > To: taxacom at mailman.nhm.ku.edu
	> > Subject: Re: [Taxacom] The difference
	> > place
	> > to use the word "epiphany" for something so obvious that any
	> high-school
	> > student with a grade of "C" or better in introductory biology
should
	> know,
	> > but I think it representes a fundamental cognition of
	> something we all
	> > know to be factually true, but haven't quite itegrated it into
our
	> > mental abstraction of biodiversity to the point where it shapes
our
	> perspective
	> > of
	> > the world around us. I know that sounds largely like
	> gobble-dee-gook,
	> but
	> > there is something real in there about interpreting the
	> world in a new
	> way
	> > after putting an otherwise obvious fact into proper context
	> (I had a
	> > similar experience late one night the first time I saw the moon
as a
	> 3-dimentional
	> > object floating in space, rather than a big disk).
	> >
	> > Aloha,
	> > Rich
	> >
	> >
	> >
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