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

Dan Lahr dlahr at ib.usp.br
Wed Nov 14 11:46:18 CST 2012


Hi Ashley,

"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."

It is most certainly not.  There are only 4 options for a site (ATCG), 5 if
you count indels, and convergent hits are highly likely.  Molecular
systematists or anyone that cares about molecular evolution cannot get away
with that, and that is why probabilistic methods are used instead of
similarity methods.  These assume a model of evolution to infer how many
substitutions actually took place in a specific site, even though what you
may see in modern terminals are the same base pairs for a given site.  One
of the trickiest parts is to flesh apart homology from convergence in
molecular sequences, and a lot of money and intellect is poured into that
very issue.

I am not following this thread, so not sure if this is what you meant, in
which case I apologize. I just wanted to clarify that molecular
systematists do NOT rely on similarity methods of historical
reconstruction.  If you do see such a case in a paper newer than 1990´s,
then it is a glaring omission from the reviewers and editor.

Kind regards,

Dan

On Tue, Nov 13, 2012 at 10:01 AM, Ashley Nicholas <Nicholasa at ukzn.ac.za>wrote:

> 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 .
> >
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-- 
___________________
Daniel J. G. Lahr, PhD
Dept of Zoology, Univ. of Sao Paulo, Brazil



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