[Taxacom] Rational holophyly and ideological extinction

Tue Mar 17 08:59:47 CDT 2009

Curtis Clark has cogent arguments. My replies follow snips of his
comments:

Curtis wrote: 1. First, ancestors. There are organisms alive today that
are ancestors of other living organisms but the cases where the ancestor
is generally considered to be of a separate species from the descendant
are extremely rare.

Reply:
It is uncommon for sister-group relationships of species to be well
supported in detail (general clustering of species is well supported) as
an advance or new knowledge over what is obvious from omnispection,
although gene trees may be quite detailed. Molecular trees demonstrate
only genetic continuity, not necessarily speciation events unless one
invokes uniform gradualist speciation and the biological species
concept, in which case anagenetic change in both sister groups then
generate different species. Second, molecular paraphyly of species is
not extremely rare since many cladograms in the literature with lots of
exemplars of the same species demonstrate ancestor-descendant
relationships. This goes for higher taxa as well, of course, but
knowledge is presently somewhat limited by the general lack of multiple
exemplars of the same taxon in any one study.

2. Second, it is well-established that some species are ancestors of
other species. If one assumes that species are real, this has some
evolutionary meaning (if species are not real, it's religion), but it is
not possible to interpret all of evolutionary history as a nested set of
peripatric speciations.

Reply: One of the points I commonly make on Taxacom is that given the
data we have, including that of DNA, we cannot resolve many sister-group
relationships reliably and it is even more difficult to resolve
ancestor-descendant relationships though many are obvious as
paraphyletic-autophyletic pairs. We must be satisfied with partial
cladograms and partial taxon trees. Resolution itself is not support, as
is well known, since totally random data sets commonly produce well
resolved parsimony trees. I think that eliminating ancestor-descendant
relationships from classification when they are known or are well
supported as paraphyly-autophyly relationships is no solution. 

3. Third, it is generally impossible to say with any certainty that any
given fossil is the ancestor of an organism alive today (although it is
quite credible to say that it is a relative).

Reply: This seems a quibble. Of course fossils may represent extinct
lines. One can say that dinosaurs are the ancestors of birds but cannot
say that Tyranosaurus is the ancestor of anything alive today. I think
that it is okay to say that a paraphyletic species (e.g. brown bear) is
the ancestor of its autophyletic descendant (polar bear) given what we
know even though any given brown bear fossil may not be the ancestor of
anything alive today.

4. Fourth, higher taxa can be ancestral to other higher taxa only if
they are paraphyletic. Ancestor-descendant relationships are thus an
artifact of the way a taxonomist chooses to draw up the taxa. One could
argue that in the case of two lineages, one derived from an ancestral
species and another from one of its peripatric descendants, the former
is irreducibly paraphyletic, but I see that as equivalent to saying that
I am irreducibly paraphyletic: not of much use except as a straw man.

Reply: ". . . an artifact of the way a taxonomist chooses to draw up the
taxa" seems a criticism dependant on cladists' use of holophyly to
delimit taxa under the assumption that it is more scientific. Nonsense.
Holophyly is dependant on the cladist's choice of character weighting,
sampling, and other assumptions and biases, and particularly on attitude
about phylogenetic monophyly versus evolutionary monophyly. It's
circular. I'm afraid I don't understand the irreducible paraphyly bit,
and how this might support ignoring ancestor-descendant relationships in
classification. Please explain.

5. We all know that there are ancestors in evolution. But history has
shown that they are devilishly hard to pinpoint, much less to develop
testable hypotheses about.

Reply: Cladists write the histories nowadays. There are many techniques
for pinpointing ancestors, mostly involving that old field
biosystematics, now fallen into shadow. Chromosome numbers, crossing
experiments, and biogeography come immediately to mind: of two closely
related species, the tetraploid may be hypothesized as derived from the
diploid, particularly if it is local and the diploid is widespread, and
particularly if one can generate an identical tetraploid from the
diploid experimentally with colchicine or whatnot. This is pinpointing,
since science, like Obama, does not let perfection drive out the good.
In addition, in my opinion, any paraphyly or even polyphyly of
traditional groups on a molecular tree is evidence of a shared ancestor
(at some taxonomic level) deep in the tree. They are not "devilishly
hard to pinpoint", but are obvious as the "massive homoplasy" that
cladists vigorously suppress by insisting on strict holophyly and
backing it up by making new combinations and new names that change
nomenclature such that only sister-group relationships are recognized.
This is ideological extinction of a major class of evolutionary
information in classification. The only way to corroborate splitting
molecularly paraphyletic or polyphyletic lineages (which may be
evolutionarily monophyletic because they share a deep ancestor) is to
demonstrate that the products of the split (separate lineages) are
significantly better circumscribed by new circumscriptions by expressed
traits than they were previously. This is because splitting in any way
of a large taxon into smaller taxa will commonly result in some kind of
description for each of the smaller taxa, which is a problem in
statistics called multiple comparisons). That new description must be
better than any previous description for a larger (or smaller) grouping
at that rank to be corroborative.

6. For a cladist to say that ancestors are unimportant is perhaps
arrogant, but for a cladist to say that our time is better spent looking
at sister-group relationships is a nod to reality.

Reply: I stipulate and asseverate that phylogenetic analysis resulting
in clarified sister-group relationships is a good thing, an advance, a
revelation of exciting details (as hypotheses) about evolution (using a
non-ultrametric clustering method based on a simple model of evolution
called parsimony), and a good use of time. I also think that wrenching
all ancestor-descendant information from classifications as a blood
sacrifice in honor of this advance, and relegating the study of
ancestor-descendant relationships to the same intellectual level as
voodoo and metaphysics (pace voodoo doctors and metaphysicians among us)
is a kind of latter-day Lysenkoism. Mine is not an extreme position,
since (as I repeat from elsewhere) classifications and taxonomic
treatments following strict phylogenetic monophyly have damaged
evolution more strongly than creationism or intelligent design will ever
do.

*****************************
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
*****************************

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
Sent: Monday, March 16, 2009 10:40 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Rational holophyly and deological extinction