Reptilia

Because Reptilia is not a clade, your counter argument falls apart: we do not expect a nested hierarchy in this group.

A Disclaimer for Behe? 2009

You attempted to use Reptilia and Aves as an counter example but you failed because Reptilia is not a clade.

A Disclaimer for Behe? 2009

In cladistics, Aves is nested in Reptilia through Diapsida.

A Disclaimer for Behe? 2009

You attempted to use Reptilia and Aves as an counter example but you failed because Reptilia is not a clade.

A Disclaimer for Behe? 2009

'Reptilia' -- the class which exhibits the largest proportion of entirely extinct forms of any one type, -- that of the 'Crocodilia', has persisted from at least the commencement of the Mesozoic epoch up to the present time with so much constancy, that the amount of change which it exhibits may fairly, in relation to the time which has elapsed, be called insignificant.

Lectures and Essays Thomas Henry Huxley 1860

Basal synapsids (things like caseids, ophiacodontids and sphenacodontids) looked superficially reptile-like, and for this reason non-mammalian synapsids have traditionally been dubbed ‘mammal-like reptiles’, and even classified within Reptilia.

Archive 2006-05-01 Darren Naish 2006

It was properly defined as Reptilia + an obscure fossil group called Mesosauridae.

Down with phyla! (episode II) - The Panda's Thumb 2005

Dr. Andrew Smith, in his excellent work on "Reptilia," gives the following interesting account of the power of the serpent, and of other animals, to fascinate their prey.

The Atlantic Monthly, Volume 05, No. 32, June, 1860 Various

They just no longer fit into the class "Reptilia".

freshnews.org - most clicked links 2010

The latter band was so impressed by the singer when the musicians first saw her that they recruited her to duet with singer Julian Casablancas on "Modern Girls and Old Fashion Men," the B-side to the group's "Reptilia" single.

SFGate: Top News Stories 2009