The possibility that dinosaurs were the ancestors of birds was first suggested in 1868 by 
Thomas Henry Huxley.
 After the work of 
Gerhard Heilmann  in the early 20th century, the theory of birds as dinosaur descendants  was abandoned in favor of the idea of their being descendants of  generalized 
thecodonts, with the key piece of evidence being the supposed lack of 
clavicles in dinosaurs.
 However, as later discoveries showed, clavicles (or a single fused 
wishbone, which derived from separate clavicles) were not actually absent;
 they had been found as early as 1924 in 
Oviraptor, but misidentified as an 
interclavicle.
 In the 1970s, 
John Ostrom revived the dinosaur–bird theory,
 which gained momentum in the coming decades with the advent of cladistic analysis,
 and a great increase in the discovery of small theropods and early birds.
 Of particular note have been the fossils of the 
Yixian Formation, where a variety of theropods and early birds have been found, often with feathers of some type.
  Birds share over a hundred distinct anatomical features with theropod  dinosaurs, which are now generally accepted to have been their closest  ancient relatives.
 They are most closely allied with 
maniraptoran coelurosaurs.
 A minority of scientists, most notably 
Alan Feduccia and 
Larry Martin, have proposed other evolutionary paths, including revised versions of Heilmann's basal archosaur proposal,
 or that maniraptoran theropods are the ancestors of birds but themselves are not dinosaurs, only 
convergent with dinosaurs.
Feathers
Archaeopteryx, the first good example of a "feathered dinosaur", was discovered in 1861. The initial specimen was found in the 
Solnhofen limestone in southern Germany, which is a 
lagerstätte, a rare and remarkable geological formation known for its superbly detailed fossils. 
Archaeopteryx is a 
transitional fossil,  with features clearly intermediate between those of modern reptiles and  birds. Brought to light just two years after Darwin's seminal 
The Origin of Species, its discovery spurred the nascent debate between proponents of 
evolutionary biology and 
creationism.  This early bird is so dinosaur-like that, without a clear impression of  feathers in the surrounding rock, at least one specimen was mistaken  for 
Compsognathus.
Since the 1990s, a number of additional 
feathered dinosaurs  have been found, providing even stronger evidence of the close  relationship between dinosaurs and modern birds. Most of these specimens  were unearthed in the 
lagerstätte of the Yixian Formation, 
Liaoning, northeastern 
China,  which was part of an island continent during the Cretaceous. Though  feathers have been found in only a few locations, it is possible that  non-avian dinosaurs elsewhere in the world were also feathered. The lack  of widespread fossil evidence for feathered non-avian dinosaurs may be  because delicate features like skin and feathers are not often preserved  by fossilization and thus are absent from the fossil record. To this  point, protofeathers (thin, filament-like structures) are known from  dinosaurs at the base of Coelurosauria, such as 
compsognathids like 
Sinosauropteryx and 
tyrannosauroids (
Dilong),
  but barbed feathers are known only among the coelurosaur subgroup  Maniraptora, which includes oviraptorosaurs, troodontids,  dromaeosaurids, and birds.
  The description of feathered dinosaurs has not been without  controversy; perhaps the most vocal critics have been Alan Feduccia and  Theagarten Lingham-Soliar, who have proposed that protofeathers are the  result of the decomposition of collagenous fiber that underlaid the  dinosaurs' integument,
 and that maniraptoran dinosaurs with barbed feathers were not actually dinosaurs, but 
convergent with dinosaurs.
  However, their views have for the most part not been accepted by other  researchers, to the point that the question of the scientific nature of  Feduccia's proposals has been raised.
Skeleton
Because feathers are often associated with birds, feathered dinosaurs are often touted as the 
missing link  between birds and dinosaurs. However, the multiple skeletal features  also shared by the two groups represent another important line of  evidence for 
paleontologists. Areas of the skeleton with important similarities include the neck, 
pubis, 
wrist (semi-lunate 
carpal), arm and 
pectoral girdle, furcula (wishbone), and 
breast bone. Comparison of bird and dinosaur skeletons through 
cladistic analysis strengthens the case for the link.
Soft anatomy
Large meat-eating dinosaurs had a complex system of air sacs similar  to those found in modern birds, according to an investigation which was  led by Patrick O'Connor of 
Ohio University.  The lungs of theropod dinosaurs (carnivores that walked on two legs and  had bird-like feet) likely pumped air into hollow sacs in their 
skeletons,  as is the case in birds. "What was once formally considered unique to  birds was present in some form in the ancestors of birds", O'Connor  said.
 In a 2008 paper published in the online journal 
PLoS ONE, scientists described 
Aerosteon riocoloradensis, the skeleton of which supplies the strongest evidence to date of a dinosaur with a bird-like breathing system. 
CT-scanning revealed the evidence of air sacs within the body cavity of the 
Aerosteon skeleton.
Another piece of evidence that birds and dinosaurs are closely related is the use by both of 
gizzard  stones. These stones are swallowed by animals to aid digestion and  break down food and hard fibers once they enter the stomach. When found  in association with fossils, gizzard stones are called 
gastroliths.
Reproductive biology
A discovery of features in a 
Tyrannosaurus rex skeleton  recently provided more evidence that dinosaurs and birds evolved from a  common ancestor and, for the first time, allowed paleontologists to  establish the sex of a dinosaur. When laying eggs, female birds grow a  special type of bone between the hard outer bone and the 
marrow of their limbs. This 
medullary bone, which is rich in 
calcium,  is used to make eggshells. The presence of endosteally derived bone  tissues lining the interior marrow cavities of portions of the 
Tyrannosaurus rex specimen's hind limb suggested that 
T. rex used similar reproductive strategies, and revealed the specimen to be female.
 Further research has found medullary bone in the theropod 
Allosaurus and the ornithopod 
Tenontosaurus. Because the line of dinosaurs that includes 
Allosaurus and 
Tyrannosaurus diverged from the line that led to 
Tenontosaurus  very early in the evolution of dinosaurs, this suggests that dinosaurs  in general produced medullary tissue. Medullary bone has been found in  specimens of sub-adult size, which suggests that dinosaurs reached  sexual maturity rather quickly for such large animals.
Behavioral evidence
A recently discovered 
troodont fossil demonstrates that some dinosaurs slept with their heads tucked under their arms.
 This behavior, which may have helped to keep the head warm, is also characteristic of modern birds.
      
 
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