Bird origins have been debated ever since Darwin published his "Origin of Species," and was subsequently challenged on the topic by Sir Richard Owen, who pointed out the lack of transitional fossil forms in the evolution of the highly derived avian body plan. Indeed, Owen likely carefully selected birds to make his point due to their many unique traits and physiological features such as flight, feathers, bipedality, and a remarkable respiratory system in which the lungs are connected to and ventilated by a complex system of air sacs that pneumatize the skeleton. Within two years of this debate, the discovery of the first specimens of Archaeopteryx provided conclusive evidence of avian evolution in the fossil record and became the focal point for research and deliberation on the topic for more than a century. While the fossils of Archaeopteryx provided incontrovertible evidence for a reptilian origin for birds, opinions varied as to which group of reptiles birds may have originated from.
Following the discovery of the small nonavian theropod Compsognathus in the same limestone deposits as Archaeopteryx, Huxley (1868) pre-sciently proposed an evolutionary relationships between birds and nonavian theropods based on shared traits such as three principal, weight-bearing toes in the foot (confirmed by foot-prints), a tall ascending process of the astragalus, and hollow bones. Other contemporary evolutionary biologists such as Cope favored an evolutionary relationship between birds and ornithopod dinosaurs such as hadrosaurs, based again on a three-toed foot and a retroverted pubic shaft. While a variety of ancestors or sister taxa were proposed for birds, a broad consensus that they were related to dinosaurs prevailed until the publication of the English edition of Heilmann's (1926) "Origin of Birds." Heilmann's book presented a detailed study of neontological, embryological, and fossil evidence, all of which pointed to a theropod ancestry for birds. Nevertheless, based on the prevailing assumption of the time that dinosaurs ancestors had lost their clavicles, their reappearance in birds would violate Dollo's (1893) law of irreversibility. Heilmann therefore concluded that the similarities between birds and theropods were due to convergence, and that birds were derived from more basal archosaurs that still retain clavicles.
Due to the thoroughness of his book, Heilmann's (1926) hypothesis held sway for the next four decades until the discovery and description of the mid-sized dromaeosaurid theropod Deinonychusby Ostrom (1969). Ostrom's detailed study of the skeletal anatomy of Deinonychus led him to recognize derived characters shared between it and the basal bird Archaeopteryx (Ostrom, 1976), and to the discovery of a misiden-tified specimen of Archaeopteryx (Ostrom, 1970).
Among the new traits that Ostrom mustered to revive a theropod ancestry for birds are the presence of a half-moon-shaped wrist bone that allows the hand to adduct against the forearm as in the wing-folding mechanism of living birds, and a three-fingered hand with characteristic proportions between the three metacarpals and phalanges. Following Ostrom's work, progressively more evidence has been amassed to support this hypothesis of avian origins, as a plethora of new fossil discoveries continue to blur the morphological distinction between birds and their closest thero-pod relatives.
Over the past three decades, widespread adoption of cladistic methodology for establishing and testing proposed evolutionary relationships has provided the conceptual framework for deciphering the origin and evolutionary history of birds. Gauthier (1986) was the first to apply an explicit cladistic parsimony analysis of theropod relationships to the question of bird origins. In doing so, he provided the first rigorous test of the hypothesis of theropod ancestry and set the stage for evaluating the evolutionary history of avian anatomy, physiology, and behavior in a quantitative framework. Subsequent decades have seen a remarkable surge in the discovery of new ther-opods, including fossil stem birds, with each discovery spawning novel systematic analyses (for reviews see Weishampel et al., 2004; Norell & Xu, 2005; Benton, 2008) and further supporting the hypothesis that birds are theropod dinosaurs.
To date, profound advances have been made in teasing out the evolution of the avian body plan as well as correlated physiological features and life history parameters of modern birds. Likewise, our knowledge of these traits in modern birds and their anatomical correlates has been used to yield insight into the biology of nonavian theropod dinosaurs and to infer whether particular avian traits originated before or after the origin of the avian lineage itself. Here we provide a general overview of the stepwise acquisition of the avian body-plan throughout the theropod family tree and discuss how the physiology of modern birds is being used to reconstruct aspects of dinosaur biology.
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