A modern interpretation of bird evolution, based on molecular data
(ED Jarvis et al. 2014. Science, 346:1320)

    The historical understanding of the evolutionary origin of taxonomic orders of moderns birds was based on a fossil record that identified bird-like forms as far back as 100 MYBP. In particular, the occurrence of flightless Ratite forms on the three continents of Gondwanaland (Ostriches in Africa, Rheas in South America, and Emus in Australia) suggested a common origin before the breakup of the super-continent. Given this timing, early molecular studies of birds then suggested that the "Molecular Clock" in birds ran unaccountably "slow", in contrast to mammals and other vertebrates classes. That is, for example, the molecular differences between Galliformes (Chickens and relatives) from Anseriformes (Ducks and relatives) was substantially less than for a pair of mammalian orders that had diverged 100 MYBP. The seeming rate inconsistency of the Molecular Clock was used as an argument against its general use.

    Modern studies of the molecular evolution of bird orders shows instead that the Ratites separated from other bird orders long before the general Adaptive Radiation of modern bird orders 65 MYBP. Note that, even though the ancestors of chickens and ducks had already separated from other birds 90 MYBP, the divergence of these two orders occurs simultaneously with the main radiation. This suggests the hypothesis that the sudden diversity of birds was connected with the disappearance of the (other) Dinosaur orders at the K-T (Cretaceous - Tertiary) Boundary, possibly by the clearing of old adaptive niches and creation of new ones.

    This history demonstrates the increasing success of molecular data in establishing a reliable, dated phylogenetic history for groups of organisms, which can then be used to explain that morphological evolution, rather than the tail-chasing process of beginning with morphology to create a phylogenetic scheme, and then using the scheme to explain morphology.