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Re: amniotes philogeny
You raise some good questions and I'd be interested in an answer too,
since I've been searching for some time for some reassurance that
the exclusion of basal amniotes from the Reptilia makes scientific
sense and wasn't just to "save" mammals from being placed in
the "Reptilian" clade. (Of course it were up to me "reptile/Reptilia"
would be chucked out as a taxonomic term altogether...)