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(Responding to a question from Matt Troutman that was posted to the list)

Sorry to say, but no, tinamous were not included in the analysis.   This
paper was written by people that are much more familiar with molecular
biology than they are with paleontology, and their conclusions and
interpretations are based on molecular evolution data, and do not address
the skeletal data. (Skeletons? aren't those just frames for holding the
interesting parts?)
   What I found interesting was the fact that in this study, ratites appear
to have diverged from the rest of the neornithines in the mid to late
cretaceous, and thus could have been contemporary with enantiornithines,
feathered theropods, and paleognaths, although I know of no fossil evidence
to support this.   One interpretation of the molecular results (he said,
going out on a limb) would be that by the mid-cretaceous, the warm-blooded,
feathered body plan had conferred enough of a selective advantage to allow a
fairly large adaptive radiation of forms to take place among the feathered
dino and bird taxa.   As evidence of this we have the recent plethora of
feathered fossils to examine.   Part of this hypothetical radiation may have
included physiological changes controlled by altered gene expression, with
different groups using different sets of genes to achieve similar final
results.   I was thinking that it was possible that Neornithes used one set
of genes for sex determination, Enantiornithes may have used another set of
genes for sex determination, and perhaps ratites were somewhere in between.
There is no reason to think that ratites would be closer to enantiornithes
than they are to neornithes, but they may have used the same or similar
genes for sex determination, with neornithes being the derived condition.
What is missing is an analysis of these same genes in several other taxa
(tinamous, crocodilians, taxon of your choice here), to see if the gene
mapping data reflects the physical data of the fossils.   Remember, the
interpretation is based on molecular evolution data, and does not address
the skeletal data, which may not support the hypothesis.   The real purpose
of all this is to form a testable hypothesis- in this case molecular
evolutionary techniques could be used to generate a cladogram which could be
compared with cladograms generated by traditional paleo methods.