Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. 2008. J. W. Brown et al. BMC Biology 6:6 (open access)
From the press release:
A new analysis offers the strongest molecular evidence yet for an ancient origin of modern birds, suggesting that modern birds arose more than 100 million years ago, not 60 million years ago, as fossils suggest.
"Scientists typically use two sources of information to date biological events: the fossil record, which contains physical remains of ancient organisms, and molecular genetic data," said graduate student Joseph Brown, who is first author on the paper. In the case of modern birds, however, the two approaches have yielded conflicting results, at times leading to heated debates between paleontologists and molecular biologists. Molecular biologists have asserted that the fossil record must be incomplete, while paleontologists have countered that the genetic data must be suspect.
"What my colleagues and I did was apply all of these new methods to the problem of the origin of modern birds, with each method making different assumptions about how mutation rate changes across the tree," Brown said. He hoped the analysis would narrow the gap between fossil and molecular data, but in fact it only reinforced the rock-clock split by underscoring the finding that modern birds arose more than 100 million years ago.