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

Richard Jensen rjensen at saintmarys.edu
Thu Nov 15 10:19:03 CST 2012


I can't believe that a UPGMA analysis takes too much computation time - 
   are they running it on an 8086 PC?

Dick J

On 11/15/2012 10:51 AM, Ashley Nicholas wrote:
> Thanks for the insight Dan,
>
> Sadly I do know of some labs that still routinely using phenetics particularly Nearest Neighbor. When I queried this, I was told by a colleague  that UPGMA, although the preferred method, took too much computation time!!!! Which I found disturbing given that science is all about maximizing and not minimizing the uncertainty of results. I must say though that these labs also routinely run Maximum Likelihood and Bayesian Analyses using the same gene sequences. I guess they do this to assess if there is any congruence in the results of all three analytical methods?
>
> Regards
> Ashley
> ---------------------------------------------------
> Ashley Nicholas (PhD)
> Associate Professor & Curator Ward Herbarium
> School of Life Science,  Westville Campus
> University of KwaZulu-Natal,
> Private Bag X54001,
> Durban, 4000, South Africa
> Tel.:+27-31-260 7719 Fax.: +27-31-260 2029
> http://lifesciences.ukzn.ac.za/Staff/Biodiversity/biodiv_evo_staff/Durban/nicholasa.aspx
> nicholasa at ukzn.ac.za<mailto:nicholasa at ukzn.ac.za>
> ----------------------------------------------------
> Empirical scientists do not deal with the truth, we deal with hypotheses. At their best these hypotheses are insightful and predictive, however, nonetheless experience has shown that they are often only a poor approximation of reality and therefor the truth. - Ashley Nicholas
> --------------------------------------------------------------------
>
> From: daniel.lahr at gmail.com [mailto:daniel.lahr at gmail.com] On Behalf Of Dan Lahr
> Sent: 14 November 2012 19:46
> To: Ashley Nicholas
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] FW: cladistic analysis for morphological characters -- UPGMA is not cladistics
>
> 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<mailto: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> [mailto: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<mailto: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
>>
>> _______________________________________________
>>
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu<mailto:Taxacom at mailman.nhm.ku.edu>
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>
>> The Taxacom archive going back to 1992 may be searched with either of
>> these methods:
>>
>> (1) by visiting http://taxacom.markmail.org
>>
>> (2) a Google search specified as:  site:
>> mailman.nhm.ku.edu/pipermail/taxacom<http://mailman.nhm.ku.edu/pipermail/taxacom>  your search terms here
>>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu<mailto:Taxacom at mailman.nhm.ku.edu>
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom<http://mailman.nhm.ku.edu/pipermail/taxacom>  your search terms here
> ======= Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer =======
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu<mailto:Taxacom at mailman.nhm.ku.edu>
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom<http://mailman.nhm.ku.edu/pipermail/taxacom>  your search terms here
>
>
>
> --
> ___________________
> Daniel J. G. Lahr, PhD
> Dept of Zoology, Univ. of Sao Paulo, Brazil
> ======= Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer =======
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here

-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674





More information about the Taxacom mailing list