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

Richard Zander Richard.Zander at mobot.org
Tue Nov 13 09:52:36 CST 2012


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
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-----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
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>
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