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RE: Turtles and Crocodylians are not Reptiles - no? What are they?

Robert Takata wrote:

> Well, actually almost by definition in phylogenetic context "closer"
> *necessarily* means that... E.g. branch-based taxon definition use
> "closer to A than to B" formula.

Yes - for stem-based clades the "Closer to A than to B" formula has often been 
used.  But I've noticed that this formula has tended to go out of vogue lately, 
and replaced by alternate definitions for stem-based clades, such as "Sharing a 
more recent common ancestor with A than with B", "A and all taxa sharing a more 
recent common ancestor with it than with B", or "The most-inclusive clade 
containing A but not B".  I don't know if this reflects a conscious effort; but 
it's apparent nonetheless.  I think the "Closer to A than to B" definition was 
ambiguous, given that although it implied shared ancestry, it was not explicit.

Mike Keesey wrote:

> That seems like a very unstable metric to me, since it relies on which taxa 
> are used in the topology in question. For example, look at this topology: 
> ((Archaeopteryx, Passer), (Troodon, (Microraptor,(Unenlagia, (Velociraptor, 
> Deinonychus))))). Here there are two steps from Archaeopteryx to Passer, but 
> seven from Archaeopteryx to Deinonychus. Obviously, I've skewed the taxon 
> list to get this result, but, still, the numbers are going to vary from 
> topology to topology, especially considering that we only know a fraction of 
> the actual taxa. 

Yes, I take your point, which is a good one.  There is a context here; with 
your topology birds are represented by 2 taxa, and Deinonychosauria is 
represented by 5 taxa, so this phylogenetic analysis wouldn't be examining the 
interrelationships of birds.  


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