However, back to rooting, this isn't a problem. In these analyses, birds
were not the only taxa in the matrix, so were oviraptorosaurs and
troodonts and ornithomimes. To root a taxon in a cladistic matrix, you
have to explicitly tell it that taxon is the outgroup, and this is only
done if the group appears at the base or is not a member of the groups
studied to begin with. so a non-maniraptoran would be chose, e.g.,
ornithomimes, and the rest "fall as they may." It would be very unwise,
and unpracticed to my knowledge, for the taxa to be rooted on birds.
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Jaime A. Headden