THE traditional classification of reptiles is based on a single key ch
aracter, the presence and style of fenestration in the temporal region
of the skull. Snakes, lizards, crocodiles, dinosaurs and others are '
diapsids', in that they have (at least primitively) two holes in the t
emporal region. Reptiles in which the skull is completely roofed, with
no temporal fenestration, are the 'anapsids'. These include many Pala
eozoic forms such as captorhinomorphs, procolophonids and pareiasaurs,
but also include Testudines (turtles and tortoises). Consistent with
this assumption, recent analyses of the affinities of Testudines have
included Palaeozoic tars only, placing them as akin to captorhinomorph
s(1) or procolophonids(2) or nested within pareiasaurs(3,4). Here we a
dopt a broader perspective, adding a range of Mesozoic and extant taxa
to the analysis. Our result robustly supports the diapsid affinities
of turtles, and so requires reassessment of the use of turtles as 'pri
mitive' reptiles in phylogenetic reconstruction. More generally, it il
lustrates the difficulties of treating groups, such as the Testudines,
that have extant members with peculiar morphologies that mask phyloge
netic affinity; the hazards of relying on key characters such as tempo
ral fenestration, which may mislead; the problems of outgroup choice f
or wide-ranging, inclusive analyses that include data from Recent and
extinct groups; and the difficulties of judging the value of parsimony
when applied to such inclusive analyses.