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

Tue Nov 13 07:45:55 CST 2012

Ashley's comments are clearly reminiscent of what Sneath & Sokal wrote 
in their seminal texts (Sokal & Sneath 1963; Sneath & Sokal, 1973) on 
numerical taxonomy.  They referred to the 60 character minimum as well 
as to the "matches asymptote" - as the number of characters increases, 
the measure of similarity (or dissimilarity) among OTUs is likely to 
stabilize.  They were also explicit in stating that, while phenograms 
are not intended to reflect evolutionary history, they will, in many 
cases, be a good first approximation of such.

UPGMA phenograms are based on (dis)similarity matrices, and there are a 
number of choices for determining  pairwise OTU relationships.  If one 
wishes to use a UPGMA phenogram as an approximation of evolutionary 
relationships, then one can choose a measure that is consistent with the 
kinds of data and a clustering algorithm appropriate both for the 
similarity measure used and the relative numbers of OTUs in different 
subsets of the "ingroup". Colless, Estabrook and others discussed 
various approaches that may yield good approximations.

Cheers,

Dick J

On 11/13/2012 7:01 AM, Ashley Nicholas 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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-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674