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

Richard Jensen rjensen at saintmarys.edu
Wed Nov 14 09:02:54 CST 2012


Kirk,

Don't the branching patterns we see in cladograms (or the nested sets we 
see in phenograms) imply a cause?  These groups exist for a reason - we 
have identified characters and examined the distributions of characters 
to determine if there are patterns.  We could argue that these patterns 
are just chance consequences of developmental processes, but I would 
like to believe that these patterns have a causal basis.  Our 
recognition of, say, Spermatophyta (the seed plants) is based on our 
understanding that these plants share an evolutionary history reflected 
in their reproductive (and other) structures.  By examining the fossil 
record and using the tools of evo-devo, botanists are constructing 
causal explanations for the patterns we see.

Dick J


On 11/13/2012 5:30 PM, Kirk Fitzhugh wrote:
> 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
> 900 Exposition Blvd
> Los Angeles CA 90007
> Phone: 213-763-3233
> FAX: 213-746-2999
> e-mail: kfitzhug at nhm.org
> http://www.nhm.org/site/research-collections/polychaetous-annelids
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> ________________________________________
> 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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-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674





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