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

John Grehan calabar.john at gmail.com
Wed Nov 14 11:21:15 CST 2012


'causal' being another word for a story.

John Grehan

On Thu, Nov 15, 2012 at 4:02 AM, Richard Jensen <rjensen at saintmarys.edu>wrote:

> 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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