[Taxacom] FW: cladistic analysis for morphological characters -- UPGMA is not cladistics

Kirk Fitzhugh kfitzhugh at nhm.org
Tue Nov 13 16:30:49 CST 2012


Richard,

I do hope you're referring to my view that a 'tree' sensu a cladogram, not any phenetic contraption, implies a specifiable set of explanatory hypotheses. For that reason, too much emphasis is placed on branching diagrams, when our real interest as scientists is causal understanding. A cladogram is merely a profoundly vague representation of equally vague causal accountings (assuming the name of the game in science is causal understanding).

Kirk

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Natural History Museum of Los Angeles County
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________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Richard Zander [Richard.Zander at mobot.org]
Sent: Tuesday, November 13, 2012 10:38 AM
To: Ashley Nicholas; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] FW: cladistic analysis for morphological characters      -- UPGMA is not cladistics

Ah, yes, youth should question the decisions of their elders.



Re phenograms and hypotheses, I agree with Fitzhugh, who, on Taxacom,
has doggedly pointed out that a tree is not a causal explanation.  The
neat and well supported cladograms show nesting, which is not a process
in nature (pace birds). The phenograms/cladograms/phylograms need a
process-based explanation. A phenogram is the truth only in that it is a
nested set generated by data selected to generate a nested set. A
phenogram is a phenogram, that's the truth. Basing a classification on a
dendrogram that truly represents the nesting information in the data
means a classification based on truth, but only on a methodological
basis. The causal origin of the nesting shown by the dendrogram may be
serial macroevolutionary transformation at the taxon level, we hope.
Figuring out the latter is difficult. Process-based truth is a rarely
obtained commodity in science.



Nesting does not happen in nature (there's a scowling sparrow pecking at
my window). Serial transformations do, according to theory. I don't see
much in the literature about serial macroevolution of taxa, but I do see
lots of "answers" about nesting. The question seems to be missing for
those answers. I suggest it is "What are the serial macroevolutionary
transformations that involve these taxa, and how might such help
classification?"



Probably not affect classical classifications much, since Linnaean
classification uses names to distinguish and to group, but not to
reflect wildly varying theories of evolution, which should be discussed,
not cast in nomenclatural stone.



____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/
<http://www.mobot.org/plantscience/resbot/>  and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
<http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
<http://www.mobot.org/plantscience/resbot/21EvSy.htm>
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

________________________________

From: Ashley Nicholas [mailto:Nicholasa at ukzn.ac.za]
Sent: Tuesday, November 13, 2012 12:04 PM
To: Richard Zander; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] FW: cladistic analysis for morphological
characters -- UPGMA is not cladistics



I agree. Classifications are hierarchical, cladograms are not. However,
both convey different information and perspectives on biodiversity --
which need not be in conflict.

Richard, I am interested that you say that phenograms cannot be equated
to a hypothesis -- I hope you are not asserting that they are the truth?
Surely, in the end, all the results of any analyses can be used to
induce hypotheses or can be interpreted as a hypothesis? Or they can
also be discarded as unhelpful or empirically questionable.

I am not sure what your end paragraph is about. What questions are we
talking about? I think we, as a generation, have a better understanding
and insight into what is happening and what has happened in the past
regarding our universe and the phenomena that manifest within what we
perceive as reality. But, in the end, I still agree with Popper, and
some of his predecessors, that all knowledge has some degree of
uncertainty. Scientific consensus does not make something true.
Newtonian determinism was replaced by Einstein and Relativity. I wonder
how many of our most treasure hypotheses, especially those that are
powerfully predictive, will still be up held by empirical scientists in
300 years time?

Ashley
________________________________________
From: Richard Zander [Richard.Zander at mobot.org]
Sent: 13 November 2012 17:52
To: Ashley Nicholas; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] FW: cladistic analysis for morphological
characters -- UPGMA is not cladistics

The resulting phenogram is not a hypothesis, it is the result of an
analysis of properties of nesting in a data set limited to data
informative of those properties. Evolution is not nesting, but nesting
can be informative if you think about it.

Phylogenetics leaps from nesting to classification without explaining
the nesting in terms of serial macroevolutionary transformations of
taxa.

Classification is nesting, evolution is not nesting.

Hey, I think after years and years we are slowly, slowly converging on
agreeing what the question is for all those answers in the literature.

____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
UPS and FedExpr - MBG, 4344 Shaw Blvd, St. Louis 63110 USA

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Ashley Nicholas
Sent: Tuesday, November 13, 2012 6:01 AM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] FW: cladistic analysis for morphological characters
-- UPGMA is not cladistics

John you are right,

UPGMA is a phenetics method and is not eplicitly evolutionary. It only
measures similarity, and similarity is not always a good indicator of
descent from a common ancestor. This is especially true in flowering
plants where convergent evolution/homoplasy is rife.

Analogous (rather than homologous) base pair sequences are probably less
common than in morphology -- so maybe molecular systematists can get
away with approximating it to an evolutionary tree. However, in the end
it is not an explicit evolutionary tree -- and this needs to be
acknowledged rather than ignored (which is what usually happens).
However, no matter what, the resulting phenogram is a hypothesis. This
hypothesis is as valid as any other hypothesis (until falsified) -- and
probably carries some interesting insightes and may generate some
interesting questions for further explorations.

The text books say a minum of 60 characters is needed but I would think
the number of characters needed would depend on the size of the group
being analysed. Some statistician has probably established this??

Regards
Ashley

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
Sent: 10 November 2012 17:08
To: Sami Rabei
Cc: TAXACOM
Subject: Re: [Taxacom] cladistic analysis for morphological characters

In my opinion its ok to make a cladistic analysis for any number of
characters. It just depends where those characters are clustered within
the group analyzed as to the result. I suspect that unless the
characters are dispersed throughout the 44 species, there will be some
clades that have some measure of good support, others that do not, and
others that whose relationships are unresolved.

I'm a bit out of touch with all methods, but I recall UPGMA is a
phenetic method?

John Grehan

On Sat, Nov 10, 2012 at 6:45 AM, Sami Rabei <samirabei at mans.edu.eg>
wrote:

> Dear All
>
> I have 81 morphological characters for 44 species. it is right to make
> a cladistic analysis for them. If it is ok which program I can use
> it.On the other hand I did UPGMA .
>
> Many Thanks in advance
>
> All the best.
>
> Sami Rabei
>
> http://mansoura.academia.edu/SamiRabei
>
> ----------------------------------
> With my Best Wishes
> Sami Hussein Rabei, Ph.D.
> Botany Department
> Faculty of Science,
> Damietta University
> New Damietta , Post Box 34517
> Damietta
> Egypt .
>
> Tel. Mobile: 002 0127 3601618
> Tel. Work: 002 057 2403981
> Tel. Home: 002 057 2403108
> Fax: 002 057 2403868
>
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