[Taxacom] quote of the week

Pierre Deleporte pierre.deleporte at univ-rennes1.fr
Tue Mar 25 12:51:53 CDT 2008


This is the illustration of what I tried to prevent by my tentative 
explanation of the John Grehanian version of 'cladistics'

not only the author has a personal notion of 'phenetic' (...applied to 
characters, no less), but he has also a personal notion of 'cladistic' 
(see my previous post: approximately clique + homoplasy-free +  polarize 
a priori + treat by hand + don't consider numbers, with some doubt about 
the outgroup criterion for rooting, but the last post is definitely not 
encouraging...)

please note also (below) that the Grehanian method seems completely 
hermetic to understanding the part of topological constraint an unrooted 
topology imposes on any conceivable rooting, despite the splendid 
efforts of Brian O'Meara at expliciting this extremely basic logical 
point, and nicely providing molecular data to chew on (for anybody 
really wanting to chew)
(by the way, all these notions belong to introductory lectures in 
phylogeny inference)

it ends up that anything unlike the Grehanian ways can be rejected as 
not being 'solid cladistic foundation' (without defining these words), 
and qualified of 'overall similarity' (without verifying the relevance 
or the ineptia of the assertion, as illustrated below)
hence, anything unlike the (still not formalized) Grehanian method in 
'non-cladistic', and bad; and only John Grehan can judge by applying 
unformalized Grehanian criteria

just an attempt at improving mutual communication in this dreadful world...
(perhaps a great step toward improved communication could be the early 
identification of fake discussion)

Pierre


John Grehan wrote:
>  
>
> -----Original Message-----
> From: Brian O'Meara [mailto:omeara.brian at gmail.com] 
> Sent: Monday, March 24, 2008 3:40 PM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] quote of the week
>
> On Mar 21, 2008, at 6:31 PM, John Grehan wrote:
>   
>> Here's where I will probably show even more ignorance than usual.  
>> If one only has to align five taxa (orang, chimp, bonobo, gorilla,
>> human) is suggested below what is the point if there is no outgroup 
>> for analysis? I have seen quite a few analyses that treat the 
>> orangutan as the outgroup which means, of course, that the analysis 
>> contributes nothing to the orangutan question. In other analyses only 
>> one or two species of gibbon or monkey are used. If that were done in 
>> morphology one would be laughed out of the room (I take that back, 
>> evidently that is no longer the case).
>>
>>     
>
>   
>>> Yes, it would be better to have an outgroup, but even without it,
>>>       
> there is information about the groupings.
>
> Yes - purely non-cladistic by my admittedly limited understanding.
>
>   
>>> If orang were sister to human, the unrooted tree would have a
>>>       
> bipartition between
> (human,orang) and (chimp, bonobo, gorilla). 
>
> If that were the real representation, and in the absence of a solid
> cladistic foundation that whole contention is open to question.
>
>   
>>> Of course, this bipartition is consistent with several rooted trees,
>>>       
> such as human sister to everything else, but not with any rooted trees
> having a (human, chimp, bonobo) clade, and so it would be evidence
> against the standard view of great ape relationships. 
>
> By "standard" what are you referring to?
>
>   
>>> If the true rooted tree has a (human, chimp, bonobo) clade, this would
>>>       
> show up in the unrooted tree as a >>bipartition between (gorilla, orang)
> and (human, chimp, bonobo). Thus, the unrooted tree provides some
>   
>>> information about whether a particular clade is possible under any
>>>       
> rooting of the tree.  
>
> Seems to me that if it is not cladistic it may not mean anything other
> than a measure of overall similarity.
>
>   
>>> It's actually also possible (but probably not a good idea, in
>>> general) to get a rooted tree back from a tree search with no
>>>       
> outgroups specified by using UPGMA, a >>likelihood search with molecular
> clock enforced, or with some of the search options in BEAST.
>
> In other words, non-cladistic measures of relationship trump cladistic
> morphology?
>
> John Grehan
>
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>   

-- 
Pierre Deleporte
Université de Rennes 1
CNRS UMR 6552 
Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88






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