# [Taxacom] cladistics (was: clique analysis in textbooks)

John Grehan jgrehan at sciencebuff.org
Fri Aug 19 07:23:33 CDT 2011

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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 Sergio Vargas

> I'm not sure one could/should call Maximum Parsimony (MP), or Maximum
> Likelihood (ML) and derivatives, clustering procedures.

When rooted, they cluster taxa together so that is what I was referring to.

>>>Don't understand what is meant about how the retained data set will
>>> mechanically change without biological reasons with respect to larger or
>>>>narrower ingroup.

> say you want to evaluate the relationships of the following taxa,
> ((Chimp,Human,Gorilla,Orang),Monkeys=Outgroup).

> What Pierre is pointing out is that if you constraint your data matrix
> in a way that only characters that appear to be "shared derived" in the
> ingroup are used for the analysis, the data matrix (lets call it A) you
> end up using is (necessarily) a proper subset of a bigger matrix (lets
> call it B) composed by the characters matching your pre-selection
> criterion + the character not matching it. After the analysis of matrix
> A you find ((((Orang,Human),Gorilla),Chimp),Outgroup) as the MP tree, so
> far so good.

Yes, I understand that

> But say you now want to evaluate the relationships of
> ((Chimp,Human,Gorilla,Orang,Monkeys),Whatever_appropriate_taxa=Outgroup).
> It is very likely that applying the same pre-selection method, viz. only
> shared derived characters in the ingroup will be included, you will end
> up having a matrix (say C) that is either very similar to B or is B
> itself, but either way must include A too because the way you pre-select
> your characters. After the analysis, you find that the new MP topology
> is (((((Chimp,Human),Gorilla),Orang),Monkeys),Outgroup). This happens
> simply because of your pre-selection criterion, has no biological basis,
> and would not have happened if you had included all characters from the
> very beginning. I would add is sufficient to reject the pre-selection
> criterion ad portas and refute the results obtained using it as
> logically inconsistent.

By this logic one would have to argue that no phylogenetic analysis is effective unless all life is done in one go. My view is that comparing a larger ingroup by including gibbons or monkeys would not change anything at all with respect to the original relationship, but if there are some additional characters that have unique states within the ingroup that link, for example, some gibbons or monkeys with one or more of the large bodied hominoids, and that if there were a sufficient number of them, it might undo the monophyly of one ore other monkey groups

>>Where this is done to include all characters, whether or not they are
>> restricted to the ingroup, to my mind results in an analysis of overall
>> similarity rather than >cladistic derivation.

> I think the use of "overall similarity" here is misleading because it
> sound as if MP and NJ are exactly the same, and they are not (see also
> above).

I mean overall similarity in that the measure of similarity encompasses both uniquely shared and non-uniquely shared similarities.

John Grehan

--
Sergio Vargas R., M.Sc.
Dept. of Earth&  Environmental Sciences
Palaeontology&  Geobiology
Ludwig-Maximilians-Universität München
Richard-Wagner-Str. 10
80333 München
Germany
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sevra at marinemolecularevolution.org

check my webpage:
http://www.marinemolecularevolution.org

check my research ID:
http://www.researcherid.com/rid/A-5678-2011

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