BIO 554/754
Lecture Notes 1
Introduction to Birds 

An updated version of these notes can be accessed from a new "Avian Biology' page



A 75-million-year-old meat-eating dinosaur (Bambiraptor feinbergi) has a number of features that look more bird-like
than dinosaur-like, providing evidence that birds may have evolved from dinosaurs.


In support of the 'theropod hypothesis':
  • bone morphology
    • theropod foot (3 digits; but see 'Bird embryos have 5 fingers' below) - very similar to that of modern birds
    • carpal bone in the wrist called the semilunate - present only in theropods & early birds like Archaeopteryx
  • shoulder sockets of some theropods & those of modern birds are similar (allowing them to tuck 'arms' or wings close to the body)
  • theropods (some such as Oviraptor) & birds - eggs in nests that were (are) incubated (or at least protected)
Evidence against the 'theropod hypothesis':
  • How could animals designed by evolution for running give rise to flying animals (but see information about Microraptor zhaoianu below) ?
  • How could complex structures like feathers evolve before becoming useful for flight?
    • feathers of 'non-fliers' like Ostriches & Kiwis have become more hair-like 
[The 'feather' question may have been answered. Current evidence indicates that dinosaurs may well have evolved feathers for insulation (see 'Warm and Fluffy' below).]
In support of the 'thecodont hypothesis':
  • it is difficult to see how 'ground-runners' could give rise to flying animals; gliding seems (to some) more reasonable & some tree-dwelling thecodonts (like Megalancosaurus below) have been reported
    • bird bodies are flattened from top to bottom; theropods were flattened from side to side (not good for flying)
  • feathers more likely evolved as stabilizers in gliding species rather than for insulation in running species
Evidence against the 'thecodont hypothesis':
  • currently no supporting fossil evidence (no feathered thecodont has been found)


The bird-like head of Megalancosaurus. The 
posteroventral position of the foramen magnum is 
similar to that of birds and unlike the posterior 
orientation typical of theropods. Note the beak-like 
snout and the exceptionally large, bird-like orbits. 
The articulated left manus exhibits several 
scansorial adaptations, including semi-opposable, sharp-
clawed digits and well-developed flexor tubercles.
The small Late Triassic thecodont Megalancosaurus preonensis is an especially bird-like archosaurian reptile that may provide valuable insight into the morphology of protoavians. Megalancosaurus exhibits a suite of arboreal characteristics, including long limbs with opposable digits, sharp, mobile claws, tarsi and pedes similar to those of arboreal mammals, and a long, possibly prehensile tail. The strap-like scapula is more bird-like than that of any other known archosaur. The anterior limbs, without manus, are, like those of Archaeopteryx and other volant birds, longer than the hindlimbs minus pedes—a condition never exhibited by theropods. The exceptionally light, bird-like head was positioned on a long mobile neck composed of six or seven elongate cervical vertebrae. The skull has a number of very bird-like features, including a posteroventrally positioned foramen magnum, relatively large orbits, and a tapered beak-like snout with small isodont teeth set in sockets. Examination of the specimens indicates the likelihood that Megalancosaurus was a patagial glider. These attributes include long anterior limbs with only partially extendable elbow, long and mobile rudder-like tail, notarium formed by 4 dorsal vertebrae, and a skeleton lightened by excavation of nearly every axial element. Though probably not the avian ancestor, Megalancosaurus represents a chronologically and biophysically plausible model for a gliding stage through which birds must have passed. -- From Geist and Feduccia (2000).

Possible scenario for the origin of birds from dinosaurs and the consequent evolution of flight (After Padian 1996.)

New species of dromaeosaurid dinosaur may give insights into the evolution of flight (Xu et al. 2000) -- Microraptor zhaoianus, the smallest non-avian dinosaur yet discovered, was a bipedal dinosaur that may have been adapted to live in trees. A small section of fuzz, possibly a precursor to feathers, was also found on the specimen. Although it lived some 20 million years after Archaeopteryx, Microraptor is one of the most-bird like dinosaurs known. "(Microraptor) shows a number of modifications to the hips, tail and teeth which are in some ways intermediate between those of advanced meat-eating dinosaurs and birds. "It might represent the most bird-like dinosaur," Xu said. In addition to being birdlike, Microraptor possessed foot adaptations, including an extended toe, that may have allowed it to grasp the branches of trees. If correct, that would make Microraptor the first known arboreal, or tree dwelling, dinosaur. This tree-dwelling feature may also provide support for the hypothesis that flight evolved from trees, rather from the ground. But, for flight to originate, many scientists say, the animal has to be small, and until now feathered dinosaurs discovered by paleontologists have been too large to fly. Microraptor closes this size gap. The find "further shortens the morphological gaps between dinosaurs and birds," Xu said.
    Some disagree with Xu et al.'s (2000)  interpretation of this specimen, including Larry Martin, a University of Kansas paleontologist. "It (Microraptor) may still be a bit too big for the origination of flight," he said. Martin also pointed out that the extended toe and other adaptations of the foot do not clearly show that Microraptor was suited for an arboreal life. Paleontologist Cathy Forster is also skeptical about the idea of the tree-dwelling hypothesis. "I think they're kind of going out on a limb on that one (tree-dwelling)," she said. However, despite this disagreement, Microraptor is still considered a vital link in the evolution of avian flight.
Cover of The Auk - January 2002
Microraptor zhaoianus
Painting by Louis V. Rey


Another possible scenario for the origin of birds.



Rahonavis ostromi
(Drawing by T. Michael Keesey)
Somewhere between dromaeosaurids & birds


(Drawing by T. Michael Keesey)

The avian nature of the brain and inner ear of Archaeopteryx  (Alonso et al. 2004) - Archaeopteryx, the earliest known flying bird from the Late Jurassic period, exhibits many shared primitive characters with more basal coelurosaurian dinosaurs (the clade including all theropods more bird-like than Allosaurus), such as teeth, a long bony tail and pinnate feathers. However, Archaeopteryx possessed asymmetrical flight feathers on its wings and tail, together with a wing feather arrangement shared with modern birds. This suggests some degree of powered flight capability but, until now, little was understood about the extent to which its brain and special senses were adapted for flight. Alonso et al. (2004) investigated this problem by computed tomography scanning and three-dimensional reconstruction of the braincase of the London specimen of Archaeopteryx. A reconstruction of the braincase and endocasts of the brain and inner ear suggest that Archaeopteryx closely resembled modern birds in the dominance of the sense of vision and in the possession of expanded auditory and spatial sensory perception in the ear. Alonso et al. (2004) concluded that Archaeopteryx had acquired the derived neurological and structural adaptations necessary for flight. An enlarged forebrain suggests that it had also developed enhanced somatosensory integration with these special senses demanded by a lifestyle involving flying ability.

BBC Video: Short interview with one of the authors, Dr. Milner


Evolution of Feathers -- The evolutionary transition series of feather morphologies predicted by the developmental theory of feather evolution (Prum 1999 ). The model hypothesizes the origin and diversification of feathers proceeded through a series derived evolutionary novelties in developmental mechanisms within the tubular feather germ and follicle. Stage I—The origin of an undifferentiated tubular collar and feather germ yielded the first feather, a hollow cylinder. Stage II—The origin of differentiated barb ridges resulted in a mature feather with a tuft of unbranched barbs and a basal calamus emerging from a superficial sheath. Stage IIIa—The origin of helical displacement of barb ridges and the new barb locus resulted in a pinnate feather with an indeterminate number of unbranched barbs fused to a central rachis. Stage IIIb—The origin of peripheral barbule plates within barb ridges yielded a feather with numerous branched barbs attached to a basal calamus. There is insufficient information to establish a sequence for Stage IIIa and Stage IIIb, but both those stages are required in the next stage. Stages IIIa+IIIb—The origin of a feather with both a rachis and barbs with barbules created a bipinnate, open pennaceous structure. Stage IV—The origin of differentiated proximal and distal barbules created the first closed, pennaceous vane. Distal barbules grew terminally hooked pennulae to attach to the simpler, grooved proximal barbules of the adjacent barb. Stage Va—Lateral displacement of the new barb locus by differential new barb ridge addition to each side of the follicle led to the growth of a closed pennaceous feather with an asymmetrical vane resembling modern rectrices and remiges. Stage Vb—Division and lateral displacement of the new barb loci yielded opposing, anteriorly and posteriorly oriented patterns of helical displacement producing a main feather and an afterfeather with a single calamus. The afterfeather could have evolved at any time following Stage IIIb, but likely occurred after Stage IV based on modern afterfeather morphology. See Prum (1999)  for details of additional stages in the evolution of feather diversity (Stages Vc–f).



Warm and fluffy -- A Chinese fossil shows that primitive feathers covered a small predatory dinosaur from head to tail (Ji et al. 2001). Palaeontologists have found feathers and feather-like structures on several other Chinese dinosaurs, but only on parts of their bodies. This fossil is the first to show feathers over the whole animal, showing that dinosaurs may well have evolved feathers for insulation before they were used for flight. "This is the specimen we've been waiting for," said Ji Qiang of the Chinese Academy of Geological Sciences. About a half-meter long, the fossil was a juvenile dromaeosaur, a close relative of Velociraptor and a member of the theropod family. Downy fibres covered its head and tail, and tufts of filaments that resemble primitive feathers sprouted from other parts of the body. Branched structures like modern feathers grew on the backs of the animal's arms. The long rigid tail and other skeletal features mark the fossil as a dinosaur rather than a bird. The Chinese-American team verified that the top and bottom slabs which sandwiched the bones matched exactly to assure it was not a fake. The 130-million-year old fossil "shows us that advanced theropod dinosaurs may have looked more like weird birds than giant lizards," says Mark Norell, a palaeontologist at the American Museum of Natural History in New York. -- Jeff Hecht, New Scientist

Photo: Mack Blison, American Museum of Natural History

Blue Whistling-Thrush (Myiophonus caerulea)
© Dr. Bakshi Jehangir -

Transmission electron micrographs of the spongy medullary keratin 
of the UV-colored feather barbs of Myiophonus caeruleus
Left panel: cross-section of a UV-colored feather barb ramus 
showing the solid keratin of the barb cortex at the periphery, three adjacent medullary cells with spongy keratin matrix and cell walls, 
and melanosomes around the large vacuole at the center of the 
barb ramus. Right panel: close-up of the spongy medullary 
matrix of keratin bars and air vacuoles. Scale bar equals 500 nm. Abbreviations: c = barb cortex; cw = cell wall, k = spongy 
medullary keratin, m = melanosome, and v = air-filled vacuole. 

Avian Plumage Color (Prum et al. 2003) -- The colors of avian plumage are produced by chemical pigments (e.g., melanin or carotenoids) or by nanometer-scale biological structures that differentially scatter, or reflect, wavelengths of light. No exclusively blue or UV-colored pigments are known in vertebrates, but various carotenoid pigments in bird feathers produce UV wavelengths in combination with human-visible yellow, orange, or red colors. Ultraviolet structural colors of feathers can be produced by two types of structures. Primarily iridescent colors are produced by arrays of melanin granules in feather barbules. Those structural colors are created by coherent scattering, or constructive interference, of light waves scattered from the layers of melanin granules in barbules. A few species of hummingbirds and European Starlings are known to produce UV hues with coherently scattering melanin arrays in feather barbules.
   The most commonly distributed UV hues, however, are structural colors produced by light scattering from the spongy medullary layer of feather barbs. To date, primarily UV hues have been documented in the feather barbs of Chalcopsitta cockatoos (Psittacidae) and Myiophonus thrushes (Turdidae). Extensively UV hues with a peak reflectance in the human-visible blue range have been observed in feather barbs of Blue Tits (Parus caeruleus), Bluethroats (Luscinia svecica), and Blue Grosbeak. In addition, Prum et al. (2003) have found extensive UV reflectance from apparently blue feather barbs in many families and orders of birds including motmots (Momotidae), manakins (Pipridae), cotingas (Cotingidae), fairy wrens (Maluridae), bluebirds (Sialia), buntings and others. The structural UV hues of feather barbs, like other barb structural colors, are produced by the keratin air matrix of the spongy medullary layer of the barb ramus. However, the precise physical mechanism by which the human-visible and UV barb colors are produced remains controversial. Analysis of the spongy medullary keratin of UV-colored feather barbs of Myiophonus caerulea by Prum et al. (2003) demonstrated that, in this species, color-producing tissue is substantially nanostructured at the appropriate spatial scale to produce the observed ultraviolet hues by coherent scattering, or constructive interference. 

Golden Eagle skull


Bee Hummingbird


Despite such variation, all living birds exhibit a remarkable similarity because of their (or their ancestor's) adaptations for flight. The success of birds, as a group, is in large part due to this ability to fly! Flight is, however, demanding and the bird body shows several modifications for this mode of locomotion:

A European Starling in a wind tunnel with an airflow of
9 m/s visualized using the smoke-wire technique.
The skeleton of birds shows numerous modifications for the demands of flight:

Schematic cross-section through a bird bone.
A - periosteal surface, B - lamellar cortical layer,
C - endiosteal surface, D - trabecular layer,
E - pores/pneumatic openings/blood vessel openings
(From: Davis 1998).

Bird embryos have 5 fingers -- The developmental origin of digits in the wings of birds has been hotly debated for more than a century. Larsson and Wagner (2002) have shown unequivocally that five digits are present during the early development of chickens. The earliest stage of digits is a condensation of mesenchymal cells and digit I is, thus, transiently present during development. This establishes that three digits in the wings of birds are digits II–IV. However, theropod dinosaurs are assumed to have had digits I–III. Feduccia & Nowicki (2002) claim that for this reason, a descent of birds from theropods is impossible and that instead, birds are descended from archosaurs other than dinosaurs (e.g., thecodonts). Galis et al. (2002) believe it improbable that the multitude of shared characters between theropods and birds are the result of convergence. That leaves three possible scenarios: (1) birds descending from archosaurs other than dinosaurs, which cannot satisfactorily explain the many similarities between birds and theropods; (2) the 'frame shift hypothesis' [theropod ancestors of birds initially had digits I–III and, before the origin of birds, a shift occurred such that digits II–IV developed with identities I–III; Wagner and Gauthier (1999)] for which there is as yet no adaptive significance that would overcome the evolutionary constraint; and (3) birds descending from theropods with digits II–IV, which is the most parsimonious evolutionary transition scenario but for which there is as yet no fossil evidence.
Developmental stages of chick wings in dorsal view. (a) Adult wing with three ossified digits. (b) Stage 35 embryo with four chondrified digits. (c) Stage 29 embryo with five mesenchymal digits (From: Galis et al. 2002).

Sword-billed Hummingbird (Ensifera ensifera) skeleton
(Used with permission of Dennis Paulson, Director, Slater Museum of Natural History)

Rhea (Rhea americana) skeleton


The muscles of birds have also been modified by natural selection to meet the demands of flight:

Tendon of the supracoracoideus passing through the
foramen triosseum and inserting on the humerus
(From: Degernes and  Feduccia 2001).

Migration & muscle damage -- Exercise-induced muscle damage is often a consequence of strenuous exercise.  In birds, the high intensity and long duration of migratory flights could result in significant muscle damage, possibly due to metabolic factors (e.g., elevated temperature, lowered pH, & ionic shifts). Because exercise-induced muscle damage is characterized by leakage of  muscle-specific proteins into the blood plasma (e.g. creatine kinase), Guglielmo et al. (2001) used plasma creatine kinase (CK) activity as an indicator of muscle damage to determine if the high intensity, long-duration flights of two migratory shorebirds cause damage that must be repaired during stopover. They found that plasma CK activity was significantly higher in migrating Western Sandpipers (a non-synchronous, short-hop migrant) than in non-migrants. Similarly, for Bar-tailed Godwits (a synchronous, long-jump migrant), plasma CK activity was highest immediately after arrival from a 4000–5000 km flight from West Africa to The Netherlands, and declined before departure for arctic breeding areas. Juvenile Western Sandpipers making their first southward migration had higher plasma CK activity than adults. These results indicate that muscle damage does occurs during migration, and that it is exacerbated in young, relatively untrained birds. However,  increases in plasma CK activity were relatively small, suggesting limited muscle damage. Thus, avian flight muscles appear to be superbly adapted to high intensity exercise, and likely possess morphological, physiological and biochemical mechanisms to prevent damage (e.g. antioxidants). 
Western Sandpipers

Tendons extend from the muscles to permit the flexing of toes.
Dorsoplantar (center) and lateral (right) views of the intertarsal joint: ct, cranial tibial tendon;
fl, fibularis longus tendon; lde, long digital extensor tendon; g, gastrocnemius tendon; and t, tibial cartilage
(center & right images from: Linn et al. 2003).

Summary - Avian Anatomical Adaptations for Flight:

Avian personalities -- Personalities are general properties of humans and other animals. Different personality traits are phenotypically correlated, and heritabilities of personality traits have been reported in humans and various animals.  In Great Tits,  consistent heritable differences have been  found in relation  to exploration, which is correlated  with various  other  personality traits. van Oers et al. (2004) examined  whether or  not risk-taking behavior is part of these avian personalities. They found that (1) risk-taking behavior is repeatable and correlated with exploratory behavior in wild-caught hand-reared birds, (2) in a bi-directional selection experiment on ‘fast’ and ‘slow’ early exploratory behavior, bird lines tend to differ in risk-taking behavior,  and  (3)  within-nest  variation  of  risk-taking  behavior  is  smaller  than  between-nest  variation.  To show that risk-taking behavior has a genetic component in a natural bird population, van Oers et al. (2004) bred Great Tits in the lab and artificially selected ‘high’ and ‘low’ risk-taking behavior for two generations. They found a realized heritability of 19.3% for risk-taking behavior. With these results, the authors show that risk-taking behavior is linked to exploratory behavior, and provide evidence for the existence of avian personalities.        Risk-taking  behavior was also found to be correlated with other  aspects  of  avian  personality.  Novelty,  exploration and risk-taking behaviors seem to be traits of the personality  concept,  which  is  in  line  with  the  results  of  other studies   on   personalities. Risk-taking behavior is known to influence life-history decisions, and evidence is also accumulating  that  other  personality  traits  affect  reproduction,  survival  and  dispersal.  In sum, birds have genetically determined personalities that can be observed in a variety of ecological circumstances. 

Lecture Notes:

II - Bird Flight I

III - Bird Flight II


Alonso, P. D., A. C. Milner, R. A. Ketcham, M. J. Cookson & T. B. Rowe. 2004. The avian nature of the brain and inner ear of Archaeopteryx. Nature 430: 666 - 669.

Davis, P. G. 1998. The bioerosion of bird bones. Int. J. Osteoarcheology 7:388-401.

Degernes, L. A. and A. Feduccia. 2001. Tenectomy of the Supracoracoideus Muscle to Deflight Pigeons (Columba livia) and Cockatiels (Nymphicus hollandicus). Journal of Avian Medicine and Surgery 15: 10–16.

Feduccia, A. and J. Nowicki. 2002. The hand of birds revealed by early ostrich embryos. Naturwissenschaften 89: 391–393.

Geist, N. R. and A. Feduccia.  2000. Gravity-defying Behaviors: Identifying Models for Protoaves. American Zoologist 40: 664-675.

Galis, F., M. Kundrát, and B. Sinervo. 2002. An old controversy solved: bird embryos have five fingers. Trends in Ecology and Evolution 18:7-9.

Guglielmo1, C. G., T. Piersma, and T. D. Williams. 2001. A sport-physiological perspective on bird migration: evidence for flight-induced muscle damage. Journal of Experimental Biology 204: 2683-2690.

Ji, Q., M. A. Norell, K.-Q. Gao, S.-A. Ji, and D. Ren. 2001. The distribution of integumentary structures in a feathered dinosaur. Nature 410: 1084-1088.

Larsson, H.C.E. and G.P. Wagner. 2002. Pentadactyl ground state of the avian wing. J. Exp. Zool. (Mol. Dev. Evol.) 294: 146–151.

Linn, K. A., A. S. Templer, J. R. Paul-Murphy, R. T. O'Brien, B. K. Hartup, & J. A. Langenberg. 2003. Ultrasonographic imaging of the Sandhill Crane (Grus canadensis) intertarsal joint. Journal of Zoo and Wildlife Medicine 34: 144-152.

Padian, K. 1996. Early bird in slow motion. Nature 382:500-401.

Prum, R. O. 1999. Development and evolutionary origin of feathers: Journal of Experimental Zoology 285: 291–306.

Prum, R. O., S. Andersson, and R.H. Torres. 2003. Coherent scattering of ultraviolet light by avian feather barbs. Auk 120:163-170.

van Oers, K.,  P.J. Drent, P. De Goede and A.J. van Noordwijk. 2004. Realized heritability and repeatability of risk-taking behaviour in relation to avian personalities. Proceedings of the Royal Society of London, Series B 271: 65-73.

Wagner, G. P. and J.A. Gauthier. 1999. A solution to the problem of the homology of the digits in the avian hand. Proc. Natl Acad. Sci. USA 96: 5111–5116.

Xu, X., Z. Zhou, and X. Wang. 2000. The smallest known non-avian theropod dinosaur. Nature 408: 705 - 708.

Useful links:

BBC's Birds

Bird Evolution

Bird Evolution: A Theropod Legacy

Guinness Book of Records - Birds

Introduction to Birds

The Evolutionary History of Birds

The Origin and Early Evolution of Birds

The Life of Birds

Trying to Understand the Other Side: An Attempt to Explain Systematic Ornithology's Take on the Origins of Birds

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