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Multiple losses of flight in ratites?

John Harshman, Edward L. Braun, Michael J. Braun, et al. (2008).  Phylogenomic 
evidence for multiple losses of flight in ratite birds.  Proc. Natl. Acad. Sci. 
Published online before print September 2, 2008, doi: 10.1073/pnas.0803242105 

Abstract: "Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, 
flightless birds that have long fascinated biologists. Their current 
distribution on isolated southern land masses is believed to reflect the 
breakup of the paleocontinent of Gondwana. The prevailing view is that ratites 
are monophyletic, with the flighted tinamous as their sister group, suggesting 
a single loss of flight in the common ancestry of ratites. However, 
phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal 
that unequivocally places tinamous within ratites, making ratites polyphyletic 
and suggesting multiple losses of flight. Phenomena that can mislead 
phylogenetic analyses, including long branch attraction, base compositional 
bias, discordance between gene trees and species trees, and sequence alignment 
errors, have been eliminated as explanations for this result. The most 
plausible hypothesis requires at least three losses of flight and explains the 
many morphological
 and behavioral similarities among ratites by parallel or convergent evolution. 
Finally, this phylogeny demands fundamental reconsideration of proposals that 
relate ratite evolution to continental drift."

Although all the included trees put tinamous inside ratites, there are 
differences as to the identity of the exact sister group of tinamous (either 
rheas, or a kiwi+emu+cassowary clade).  Also, the authors explicitly favor 
multiple losses of flight over a single regain of flight:

"Evolution of Flightlessness. Any topology that nests the volant tinamous 
within the flightless ratites requires either multiple losses of flight or a 
loss of flight in the ancestral paleognath and a regain in tinamous. Although 
loss and regain is more parsimonious if both transitions are equally probable, 
multiple losses of flight are more likely. Flight has been lost in members of 
18 extant bird families, many more times in extinct groups, and hundreds of 
times in the family Rallidae alone (21, 54, 56). Thus, the loss of flight is 
much more probable than gain. Given the position of tinamous in either optimal 
tree based on the complete dataset (Fig. 1, Fig. S1A), flight must have been 
lost independently at least three times, in ostriches, rheas, and Australasian 
ratites. A scenario in which tinamous regained flight would be even more 
interesting, but there are no examples of avian lineages that have lost and 
regained flight."

Although the authors are probably correct in their reasoning, it does seem a 
little circular.  If there were birds that regained flight from a flightless 
ancestor, would we necessarily recognize them as such?  Or would we just assume 
that if a given lineage of birds includes more than one flightless species 
separated by at least one flighted species then it's always the result of 
multiple losses of flight?  As mentioned previously on this list, phasmids 
appear to have regained flight more than once from a flightless condition... 
But things might be very different in birds:




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