More on the 'cladistics' of sequences

[John Grehan]

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From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On Behalf Of pierre deleporte
Sent: Thursday, June 10, 2004 1:16 PM
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Subject: Re: [TAXACOM] More on the 'cladistics' of sequences

Clear enough = uniform character state in all outgroups. Lucky if you find 
many of such characters. 

So far much more lucky for the orangutan than the chimpanzee

Risky if you discard other ones.

Agreed.


>Yes there are three characters that may be apomorphic with respect to
>humans and orangutans, but also have representation in outgroup species.

Thus they can be either convergent, or synapomorphies at a deeper node. No 
other way. And unfortunately it's not written on the characters. Better 
enlarge your analysis.

Yes they do require further consideration.

>One involves thick dental enamel which is found in a couple of monkeys,

I heard of a problem of the nature of the enamel. Why would one retain 
thickness, if it's not the same enamel? How do you code: thick enamel of 
kind 1, and thick enamel of kind 2?  Unless we assume that there is a 
homologous physiological mechanism controlling for thickness of enamel, 
identical even for different kinds of enamel... Anyway you can hardly 
consider enamel thickness and ignore enamel structure. It thickness groups 
Homo with Pongo, but structure groups Homo with Pan... Matter to think about...

There are different kinds of enamel deposition in terms of rates for example, but these are not inconsistent with the model of thick enamel being unique to humans and orangutans. One could incorporate the different enamel rates as a multi-state character. In the orangutan and humans the molars have both thick dental enamel and low cusped teeth (also apmorphic) whereas in the monkey case the teeth are high cusped (along with all other extant primates except humans and orangutans - the implication here being that fossil taxa with these two features are also part of the human lineage).

>what they do follows from the assumptions about the
>characters in the first place so if the characters are not already
>limited to apomorphic features then the result may be just a 'cladistic'
>analysis of phenetic characters.

But you use only thick enamel to tend to support the rooting of Homo with 
Pongo as a monophyletic group, right?

It's one of the proposed synapomorphies

Well, the programs do just that.

My understanding is that the programs will recognize a level of congruence of this character with others showing the same relationship.

People put characters in the analysis. Like you. These characters have 
different states. Like yours. Outgroups are labelled a priori, like you do. 
Hence putative polarity of characters relative to outgroups is fixed a 
priori, with some possible ambiguities, like for your own characters. The 
program optimizes the solution considering all the states of affairs 
according to cladistic rules. Like you do, like you just stated it above.

Only it seems that some people do not polarize the characters a priori as they leave them unordered in the analysis.

John Grehan


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 66
Télécopie : 02 99 61 81 88