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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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