[Taxacom] (no subject)

[Richard Zander]

Lots of conceptual leaps, Alexander, where you support phylogenetic for
all the good it has done, yet doggedly duck the elephant in the room. 

" it just so happens that in higher taxa what we observe is a
bifurcating tree of life, and this is best described with a strictly
cladistic system." Really? The software gives a bifurcating tree of
life. Parsimony comes out of cluster analysis which represents
clustering most atomistically as "these two are more close to each other
than either is to a third" which can be in a great leap of logic
extended to evolution of lineages. But then, what about a pectinate tree
with the ancestor surviving to the present? That seems to be a
bifurcating tree, yet the pleisiomorphic ancestor of all but one
exemplar is much the same (except for gradual accumulation of minor
molecular changes used for tracking the gradual peripheral speciation of
daughter species). This isn't exactly what one envisions by a
bifurcating tree of life. It is more like a bush, isn't it, yet if we
estimate the number of surviving ancestors in any published tree by the
number of identical taxa (particularly species) separated by other taxa
on a molecular tree (heterophyletic), then we should expect oh maybe 10
percent of the exemplars in most cladograms that actually include
duplicate exemplars of widespread taxa to represent surviving ancestors
and therefore make "bifurcation" not the correct interpretation but
polytomy of taxa based on expressed traits. Since all but one exemplar
may be an ancestor of another exemplar, one does not even have to
postulate a nodal ancestor different from all the exemplars for these
apparently branching lineages, which is certainly more parsimonious than
"parsimony."

I think that your focusing on successes of sister-group analysis does
not imply that only sister-group analysis is now the correct means of
generating classifications. Monophyly means phylogenetic monophyly, or
holophyly, not evolutionary monophyly. Success in testing means getting
the same answers with different data and different methods. If you get
the same sister-groups consiliently, well that's great. Sister-group
analysis is no problem. (Well, repeatability is a problem when the only
assurance of repeatability is everyone agreeing to weight all traits
alike.)

It is the creation of a special-purpose classification that restricts
the evolutionary content of classification to only sister-groups that I
object to. Phylogenetics does generate, are profess to approach, an
"accurate model of nature" in respect to phylogeny, but much evidence of
ancestor-descendant evolution is ignored and the whole truth is not
represented.

The evidence for higher-level taxa are the autophyletic taxa that have
been given high rank in the past to flag comparatively (at a particular
taxonomic level) major innovations in evolution that are not
phylogenetically informative. Phylogeneticists may not be interested in
such traits, but evolutionists, ecologists, biodiversity specialists,
teachers, governmental agencies, and so on really are, since they expect
a classification to reflect what we know about evolution not just what
we know about phylogenetics.

Yes, I understand Scrophulariaceae was a mish-mash, and splitting and
moving taxa about was called for. Certainly molecular analysis reveals
where one taxon should be reassociated with other taxa. It is the LOSS
of evolutionary information about ancestor-descendant relationships in
classification due to enforcement of holophyly as the only way to form a
taxon that is now crippling classification.

Regarding "it is about building the model that best describes what goes
on/happened in nature." I agree. 

*****************************
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
Non-post deliveries to:
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
Alexander.Schmidt-Lebuhn at biologie.uni-goettingen.de
Sent: Friday, April 03, 2009 9:22 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] (no subject)

Monophyly, on the other hand, is a clear, testable criterion. The
testability then leads to the second point. It makes systematics a
hypothesis-testing endeavor, i.e., real, hard science, and thus takes it
above the purely descriptive level.
Thirdly, what is a system (or scientific knowledge in general) meant to
be? An as accurate model of nature as possible. And it just so happens
that in higher taxa what we observe is a bifurcating tree of life, and
this is best described with a strictly cladistic system.

(Where "strict cladists" really go to far IMO is when they try to apply
monophyly to the recognition of systems that are, by their very
definition, not bifurcating but reticulating, such as species. I have
even once seen a presentation where a master's student, apparently
brainwashed by cladomania, was apologetic for recognizing paraphyletic
SUBspecies...)

On the other hand, there are hardly any convincing arguments for
paraphyletic higher-level taxa. It all seems to boil down to "I (or the
end-user) like the names and system I'm used to better". But science is
not about what you find comfortable, it is about building the model that
best describes what goes on/happened in nature. And if the current model
is suboptimal, yes, then sciences is anti-(taxonomic) stability, that is
how it should be!