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BTW, how does PAUP differentiate massive convergence versus homology? Or
does it take human intervention (weighin characters, etc>) to note the key
Erm... huh? PAUP* does cladistics. This means that it will give you those
distributions of character states across trees ( = it will give you those
trees) that can be explained with the fewest assumptions of convergence ( =
the most parsimonious ones). It tries to distribute all characters so that
each state change happens once, and balances them against one another so
that the fewest additional changes must be assumed. If... I hope this
sentence isn't too long... :-/ if there are enough characters the most
parsimonious distribution of which contradicts the assumption that the
character change in question happened only once, the character change in
question will be shown as having happened several times convergently.
If you don't trust the result because the character is related to
(say) burrowing, then add more characters (see "enough" above) and/or more
taxa to test your distrust. More taxa, especially more basal taxa, help
because if the basal taxa of two clades retain plesiomorphies that the
derived ones lack, the corresponding apomorphies can no longer come out as
synapomorphies of the two clades.
Something tells me I should use PowerPoint to explain this...
The answer will not only affect the mesosaur question, but another one
that recently came up about "worm lizaards" and "legless lizards", which
are all definitely lizards, but are they all related? Or does burrowing
Which ones do you mean, amphisbaenians and anguids? They seem to be rather
distantly related... yes, burrowing does impose a lot of convergence.