[Taxacom] quote of the week

[John Grehan]

-----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