@article{doi101086407902, author = "Ostrom, John H.", title = "Archaeopteryx and the Origin of Flight", year = "1974", journal = "The Quarterly Review of Biology", abstract = {Reexamination of the specimens of Archaeopteryx, which constitute the only direct evidence pertaining to the habits and mode of life of the earliest stages of avian evolution, indicates that neither the highly favored arboreal theory nor the much critized cursorial theory offers adequate explanation for the origin of avian flight. The osteology of Archaeopteryx, in virtually every detail, is indistinguishable from that of contempraneous and succeeding coelurosaurian dinosaurs-especially in the details of the manus, forelimbs, and pectoral arch. It is proposed that these conditions reflect a highly predaceous mode of life for Archaeopteryx, rather than being arboreal adaptations. Plumage, in the form of contour feathers, is believed to have arisen in response to the need for controlling heat loss (and gain) and was secondarily modified on the fore limbs to enhance the prey-catching function of the hands. Enlargement of the primordial "primaries" and "secondaries" transformed the forelimbs of "proto-Archaeopteryx" into large, continous, trapping surfaces-natural insect nets-activated by powerful ventral adductor muscles (the pectoralis group). These adaptations were admirably preadaptive for active, flapping flight. The primordial insulative function of contour feathers and the predatory hypothesis for the enlargement of the remiges seem to account for the otherwise paradoxical presence in Archaeopteryx on essentially modern "flight" feathers in the absence of virtually all of the skeletal specializations that are associated with (or required for?) modern bird flight, whereas those skeletal specializations that are present in Archaeopteryx are the same, or nearly the same, as those that are preserved in various (presumed) predaceous coelurosaurian dinosaurs.}, url = "https://doi.org/10.1086/407902", doi = "10.1086/407902", openalex = "W2085277132" } @article{ostrom1974archeopteryx9, author = "Ostrom, J. H", title = "Archeopteryx and the origin of flight", year = "1974", journal = "Quarterly Review of Biology, v. 49, p. 27-47", note = "talkorigins\_source = {true}; raw\_reference = {Ostrom, J. H., 1974, Archeopteryx and the origin of flight: Quarterly Review of Biology, v. 49, p. 27-47.}" } @article{regal1975the12, author = "Regal, P. J", title = "The evolutionary origin of feathers", year = "1975", journal = "Quarterly Review of Biology, v. 50, p. 35-66", note = "talkorigins\_source = {true}; raw\_reference = {Regal, P. J., 1975, The evolutionary origin of feathers: Quarterly Review of Biology, v. 50, p. 35-66.}" } @article{doi101111j109583121976tb00244x, author = "Ostrom, John H.", title = "Archaeopteryx and the origin of birds", year = "1976", journal = "Biological Journal of the Linnean Society", abstract = "The question of the origin of birds can be equated with the origin of Archaeopteryx, the oldest known bird. Analysis of the five presently known skeletal specimens of Archaeopteryx. and comparison with the skeletal anatomy of the several reptilian groups that have been proposed as possible ancestors of birds (Ornithopoda, Theropoda, Hseudosuchla and Sphenosuchidac), confirm the conclusions (long rejected by most subsequent workers) of Heilmann (1926), Lowe (1935, 1944) and Holmgren (1955), namely, that the skeletal anatomy of Archaeopteryx is extraordinarily similar to that of contemporaneous and succeeding coelurosaurian dinosaurs. Rejection of these similarities as adaptive structures only (parallel or convergent similarities), and therefore of no phylogenetic importance, is here considered invalid. Heilmann was the first to identify the only evidence that has been cited so far for dismissing coelurosaurian-avian ancestral–descendant relationships, the supposed absence of clavicles in all theropods, and on that basis suggested a common Archaeopteryx–dinosaur ancestry among pseudosuchian reptiles. That evidence is negative and thus inconclusive, and is now known to be false. With the exception of fused clavicles and unique ischial morphology, virtually every skeletal feature of Archaeopteryx is known in several contemporaneous or near-contemporary coelurosaurian dinosaurs and many of these conditions are unrelated, specialized features (the detailed morphology of the manus, metacarpus, carpus, humerus, scapulocoracoid, pes, metatarsus, tarsus, femur, pubis, ilium, skull and mandibles). The presence of so many derived characters in common clearly establishes that the closest ancestral affinities ot Archaeopteryx are with coelurosaurian theropods. There is no contrary evidence and any other explanation is illogical. All available evidence indicates unequivocally that Archaeopteryx evolved from a small coelurosaurian dinosaur and that modern birds are surviving dinosaurian descendants. Stated simply, avian phylogeny was: Pseudosuchia Coelurosauria Archaeopteryx higher birds. The question of the origin of birds can be equated with the question of the origin of Archaeopteryx. This last question evokes two possible answers, depending upon how one views the importance of “primitive versus derived characters” in assessing phylogenetic relationships. One possible answer is: Archaeopteryx is a direct descendant of some unknown, but presumably Euparkeria-like pseudosuchian. This answer is predicated on the belief that Archaeopteryx only parallels or converges with various coelurosaurs in certain skeletal similarities. This is the view now held by the majority of biologists– a view that I find unacceptable. The second possible answer is: Archaeopteryx is directly descendant from a small unknown Ornitholestes-like coelurosaurian dinosaur. This answer assumes that skeletal similarities between coelurosaurs and Archaeopteryx are derived from a common ancestor, itself a coelurosaur. This is the view advocated here. There is no evidence to support an ornithischian ancestry of birds. The pubis of Archaeopteryx apparently was not reflected backward as in ornithischians and modern birds, and in any case, the ornithischian pubis is only superficially like that of living birds. Nor is the so-called ornithopod foot like that of birds. Evidence of close theropod–Archaeopteryx relationships, however, is abundant: the presence of the same, multiple, specialized adaptations in both Archaeopteryx and various coelurosaurs (tridactyl manus, metacarpus and carpus morphology, forelimb and pectoral girdle structure, four-toed pes, reversed hallux, metatarsal morphology, mesotarsal joint, hindlimb construction, pelvic form, plus elongated forelimbs, bipedal posture, vertebral structure and formula, and basic cranial morphology). The presence in Archaeopteryx, coelurosaurs and pseudosuchians of several primitive characters in common (thecodont dentition, sclerotic ring, possibly amphicoelous vertebrae, long caudal series, gastralia, pubic symphysis, short coracoids) indicates only a probable common ancestry. It does not establish that the Coelurosauria could not have given rise to Archaeopteryx–and higher birds. There is no evidence (outside of Lagosuchus and Lagerpeton) of shared derived characters to suggest a close evolutionary relationship between classic pseudosuchians and Archaeopteryx. Similarly, there is no clear-cut evidence in the form of shared derived characters to link Archaeopteryx with Sphenosuchus. The absence of clavicles in theropods (now known to be false), once considered as conclusive evidence against a coelurosaurian ancestry of birds, is no more significant than is the absence of a sternum in all known pseudosuchians as evidence against a pseudosuchian ancestry of all other archosaurs. The absence of any known “ideal” coelurosaurian pre-Archaeopteryx is only negative and inconclusive evidence, especially in view of our meagre and exceedingly deficient knowledge about Early and Middle Jurassic terrestrial vertebrates. All available evidence indicates that the immediate ancestor of Archaeopteryx was a small coelurosaurian dinosaur and that the phylogeny of avian ancestry was: Pseudosuchia–Coelurosauria–Archaeopteryx:– higher birds. Ornithopod-Archaeopteryx ancestral-descendant affinities may be dismissed because of the false “avian” organization of the pelvis in the Berlin specimen of Archaeopteryx and the merely superficially bird-like construction of the ornithisehian pelvis. The suite of specialized characters unique to ornithischians (e.g., predentary, tooth morphology), that occur even in Triassic representatives, is further evidence for dismissing close affinity between ornithopods and Archaeopteryx. The supposed close relationship between birds and pseudosuchians is judged to be remote at best, due to the completely primitive nature of the few anatomical features which pseudosuchians have in common with Archaeopteryx. Sphenosuchus, a primitive and early archosaur, is also a potential avian ancestor, but existing evidence consists of primitive archosaurian features plus a few similarities with certain modern birds. These similarities, which are present in two groups that are separated from each other by more than 200 million years, and which cannot be demonstrated in Archaeopteryx, are considered irrelevant to the origins of Archaeopteryx and subsequent birds.", url = "https://doi.org/10.1111/j.1095-8312.1976.tb00244.x", doi = "10.1111/j.1095-8312.1976.tb00244.x", openalex = "W2090677329", references = "doi101002jmor1051140102, doi10103714088000, doi101038248168a0, doi101086407902, doi101098rstb19610007, doi101098rstb19650003, doi101111j146979981913tb06148x, doi101139e72031, doi101146annurevea03050175000415, doi101146annureven10010165000525, doi10129879781933789439, doi1023071292217, doi1023071441916, doi104095101672, doi104095105003, doi105281zenodo1040385, doi105479si03629236110i, doi105962bhltitle59991, doi105962bhltitle68064, doi107312simp92414, gilmore1924a, openalexw1879660213, openalexw3146596760, openalexw607142922, ostrom2019osteology, ostrom2020stratigraphy, russell1969a, walker1964triassic" } @misc{olson1979flight8, author = "Olson, S. L. and Feduccia, A", title = "Flight capability and the pectoral girdle of Archeopteryx", year = "1979", howpublished = "Nature, v. 278, p. 247-248", note = "talkorigins\_source = {true}; raw\_reference = {Olson, S. L., and Feduccia, A., 1979, Flight capability and the pectoral girdle of Archeopteryx: Nature, v. 278, p. 247-248.}" } @misc{ostrom1979bird10, author = "Ostrom, J. H", title = "Bird flight", year = "1979", howpublished = "How did it begin?: American Scientist, v. 67, p. 45-56", note = "talkorigins\_source = {true}; raw\_reference = {Ostrom, J. H., 1979, Bird flight: How did it begin?: American Scientist, v. 67, p. 45-56.}" } @misc{caple1983the2, author = "Caple, G. R. and Balda, R. P. and Willis, W. R", title = "The physics of leaping animals and the evolution of preflight", year = "1983", howpublished = "American Naturalist, v. 121, p. 455-476", note = "talkorigins\_source = {true}; raw\_reference = {Caple, G. R., Balda, R. P., and Willis, W. R., 1983, The physics of leaping animals and the evolution of preflight: American Naturalist, v. 121, p. 455-476.}" } @misc{lewin1983how4, author = "Lewin, R", title = "How did vertebrates take to the air?", year = "1983", howpublished = "Science, v. 221, p. 38- 39", note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1983, How did vertebrates take to the air?: Science, v. 221, p. 38- 39.}" } @book{martin1984the6, author = "Martin, L. D", title = "The Origin of Birds and Avian Flight, in Johnston, R. F., ed., Current Ornithology", year = "1984", publisher = "London, Plenum Press, p. 105-129", note = "talkorigins\_source = {true}; raw\_reference = {Martin, L. D., 1984, The Origin of Birds and Avian Flight, in Johnston, R. F., ed., Current Ornithology: London, Plenum Press, p. 105-129.}" } @misc{reitschel1984feathers13, author = "Reitschel, S", title = "Feathers and Wings of Archeopteryx, and the Question of Her Flight Ability, in Hecht, M. K., Ostrom, J. H., Viohl, G., and Wellnhofer, P., eds., The Beginnings of Birds", year = "1984", howpublished = "Eichstatt, Fruende des Jura- Museums, p. 249-260", note = "talkorigins\_source = {true}; raw\_reference = {Reitschel, S., 1984, Feathers and Wings of Archeopteryx, and the Question of Her Flight Ability, in Hecht, M. K., Ostrom, J. H., Viohl, G., and Wellnhofer, P., eds., The Beginnings of Birds: Eichstatt, Fruende des Jura- Museums, p. 249-260.}" } @misc{kingsolver1985aerodynamics3, author = "Kingsolver, J. G. and Koehl, M. A. R", title = "Aerodynamics, thermoregulation and the evolution of insect wings", year = "1985", howpublished = "Differential scaling and evolutionary changes: Evolution, v. 39, p. 488-504", note = "talkorigins\_source = {true}; raw\_reference = {Kingsolver, J. G., and Koehl, M. A. R., 1985, Aerodynamics, thermoregulation and the evolution of insect wings: Differential scaling and evolutionary changes: Evolution, v. 39, p. 488-504.}" } @misc{lewin1985how5, author = "Lewin, R", title = "How does half a bird fly?", year = "1985", howpublished = "Science, v. 230, p. 530-531", note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1985, How does half a bird fly?: Science, v. 230, p. 530-531.}" } @misc{norberg1985evolution7, author = "Norberg, U. M", title = "Evolution of vertebrate flight", year = "1985", howpublished = "An areodynamic model for the transition from gliding to active flight: American Naturalist, v. 126, p. 303-327", note = "talkorigins\_source = {true}; raw\_reference = {Norberg, U. M., 1985, Evolution of vertebrate flight: An areodynamic model for the transition from gliding to active flight: American Naturalist, v. 126, p. 303-327.}" } @misc{bock1986the1, author = "Bock, W. J", title = "The arboreal origin of avian flight", year = "1986", howpublished = "Memoirs of the California Academy of Science, v. 8, p. 57-72", note = "talkorigins\_source = {true}; raw\_reference = {Bock, W. J., 1986, The arboreal origin of avian flight: Memoirs of the California Academy of Science, v. 8, p. 57-72.}" } @article{doi105281zenodo16171435, author = "Gauthier, Jacques", title = "Saurischian monophyly and the origin of birds", year = "1986", journal = "Biodiversity Heritage Library (Smithsonian Institution)", abstract = "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.", url = "https://doi.org/10.5281/zenodo.16171435", doi = "10.5281/zenodo.16171435", openalex = "W1758310936" } @misc{ostrom1986the11, author = "Ostrom, J. H", title = "The Cursorial Origin of Avian Flight, in Padian, K., ed., The Origin of Birds and the Evolution of Flight", year = "1986", howpublished = "San Francisco, California Academy of Sciences, p. 75-81", note = "talkorigins\_source = {true}; raw\_reference = {Ostrom, J. H., 1986, The Cursorial Origin of Avian Flight, in Padian, K., ed., The Origin of Birds and the Evolution of Flight: San Francisco, California Academy of Sciences, p. 75-81.}" } @article{doi101017s247526300000091x, author = "Gauthier, Jacques A. and Padian, Kevin", title = "The Origin of Birds and the Evolution of Flight", year = "1989", journal = "Short Courses in Paleontology", abstract = "One of the most salient advances in vertebrate paleontology in recent decades has been the settling of the question of the origin of birds, a problem that has vexed evolutionary biologists since well before Darwin. To be sure, the consensus is not unanimous, and many details of this branch of the phylogenetic tree are yet to be worked out, but we now have a much clearer picture of this problem than we had a decade ago. Less settled, but equally stimulating, has been the controversy over the origin of flight in birds and other flying vertebrates. Was there a gliding stage? Did flight begin from the ground up or from the trees down? Were birds initially arboreal? What selective pressures drove the ancestors of birds to take advantage of the aerial opportunity?", url = "https://doi.org/10.1017/s247526300000091x", doi = "10.1017/s247526300000091x", openalex = "W3158295341" } @book{doi102307jctt1xp3v3r, author = "Sibley, Charles G. and Ahlquist, Jon E.", title = "Phylogeny and Classification of the Birds", year = "1991", booktitle = "Yale University Press eBooks", abstract = "Part 1: a brief history structure and properties of DNA gene structure and function genetic regulation DNA reassociation and thermal stability the sequence organization of the genome the families of repeated DNA homology comparative DNA-DNA studies materials and methods data analysis tempo of evolution demographic factors and rates of DNA evolution a chronological survey of the classification of birds principles and methods of classification classification of birds based on DNA-DNA hybridization melting curves and dendrograms. Part 2: accounts of the groups of birds.", url = "https://doi.org/10.2307/j.ctt1xp3v3r", doi = "10.2307/j.ctt1xp3v3r", openalex = "W1564490336" } @article{doi101126science2555046845, author = "Sereno, Paul C. and Chenggang, Rao", title = "Early Evolution of Avian Flight and Perching: New Evidence from the Lower Cretaceous of China", year = "1992", journal = "Science", abstract = "Fossil bird skeletons discovered in Lower Cretaceous lake deposits in China shed new light on the early evolution of avian flight and perching. The 135 million-year-old sparrow-sized skeletons represent a new avian, Sinornis santensis, n. gen. n. sp., that preserves striking primitive features such as a flexible manus with unguals, a footed pubis, and stomach ribs (gastralia). In contrast to Archaeoperyx, however, Sinornis exhibits advanced features such as a broad sternum, wing-folding mechanism, pygostyle, and large fully reversed hallux. Modern avian flight function and perching capability, therefore, must have evolved in small-bodied birds in inland habitats not long after Archaeopteryx.", url = "https://doi.org/10.1126/science.255.5046.845", doi = "10.1126/science.255.5046.845", openalex = "W2095317708", references = "doi1010160031018275900115, doi101038022457a0, doi101038331433a0, doi101098rstb19910056, doi101111j1469185x1979tb01013x, doi101111j146979981990tb04039x, doi101111j1474919x1973tb02636x, doi101126science20343841021, doi101126science24148721495, gregor1988the" } @article{doi101038378349a0, author = "Chiappe, Luis M.", title = "The first 85 million years of avian evolution", year = "1995", journal = "Nature", url = "https://doi.org/10.1038/378349a0", doi = "10.1038/378349a0", openalex = "W2043805700" } @article{doi1023072937160, author = "Martin, Thomas E.", title = "Avian Life History Evolution in Relation to Nest Sites, Nest Predation, and Food", year = "1995", journal = "Ecological Monographs", abstract = "Food limitation is generally thought to underlie much of the variation in life history traits of birds. I examined variation and covariation of life history traits of 123 North American Passeriformes and Piciformes in relation to nest sites, nest predation, and foraging sites to examine the possible roles of these ecological factors in life history evolution of birds. Annual fecundity was strongly inversely related to adult survival, even when phylogenetic effects were controlled. Only a little of the variation in fecundity and survival was related to foraging sites, whereas these traits varied strongly among nest sites. Interspecific differences in nest predation were correlated with much of the variation in life history traits among nest sites, although energy trade—offs with covarying traits also may account for some variation. For example, increased nest predation is associated with a shortened nestling period and both are associated with more broods per year, but number of broods is inversely correlated with clutch size, possibly due to an energy trade—off. Number of broods was much more strongly correlated with annual fecundity and adult survival among species than was clutch size, suggesting that clutch size may not be the primary fecundity trait on which selection is acting. Ultimately, food limitation may cause trade—offs between annual fecundity and adult survival, but differences among species in fecundity and adult survival may not be explained by differences in food abundance and instead represent differing tactics for partitioning similar levels of food limitation. Variation in fecundity and adult survival is more clearly organized by nest sites and more closely correlated with nest predation; species that use nest sites with greater nest predation have shorter nestling periods and more broods,yielding higher fecundity, which in turn is associated with reduced adult survival. Fecundity also varied with migratory tendencies; short—distance migrants had more broods and greater fecundity than did neotropical migrants and residents using similar nest sites. However, migratory tendencies and habitat use were confounded, making separation of these two effects difficult. Nonetheless, the conventional view that neotropical migrants have fewer broods than residents was not supported when nest site effects were controlled.", url = "https://doi.org/10.2307/2937160", doi = "10.2307/2937160", openalex = "W2055512957", references = "doi101086282461, doi101086282697, doi101086400074, doi101086409052, doi101086410622, doi101093sysbio41118, doi101098rstb19890106, doi101111j1474919x1947tb04155x, doi101111j1474919x1968tb00058x, doi1023071446122, doi1023071935217, doi1023072874, doi10230740168301, doi1023075403, doi102307jctt1xp3v3r" } @article{doi101111j155856461996tb04496x, author = "Gatesy, Stephen M. and Dial, Kenneth P.", title = "LOCOMOTOR MODULES AND THE EVOLUTION OF AVIAN FLIGHT", year = "1996", journal = "Evolution", abstract = {The evolution of avian flight can be interpreted by analyzing the sequence of modifications of the primitive tetrapod locomotor system through time. Herein, we introduce the term "locomotor module" to identify anatomical subregions of the musculoskeletal system that are highly integrated and act as functional units during locomotion. The first tetrapods, which employed lateral undulations of the entire body and appendages, had one large locomotor module. Basal dinosaurs and theropods were bipedal and possessed a smaller locomotor module consisting of the hind limb and tail. Bird flight evolved as the superimposition of a second (aerial) locomotor capability onto the ancestral (terrestrial) theropod body plan. Although the origin of the wing module was the primary innovation, alterations in the terrestrial system were also significant. We propose that the primitive theropod locomotor module was functionally and anatomically subdivided into separate pelvic and caudal locomotor modules. This decoupling freed the tail to attain a new and intimate affiliation with the forelimb during flight, a configuration unique to birds. Thus, the evolution of flight can be viewed as the origin and novel association of locomotor modules. Differential elaboration of these modules in various lineages has produced the diverse locomotor abilities of modern birds.}, url = "https://doi.org/10.1111/j.1558-5646.1996.tb04496.x", doi = "10.1111/j.1558-5646.1996.tb04496.x", openalex = "W2314993465", references = "doi101016b9780122494055500094, doi101016s0016699588800664, doi101017s0094837300009866, doi101017s0094837300025495, doi101038361064a0, doi101038362623a0, doi10108002724634199410011523, doi1023073514548, doi105281zenodo16171435, doi105860choice326223, openalexw1504554173, openalexw2788234611" } @article{doi101038385247a0, author = "Varricchio, David J. and Jackson, Frankie D. and Borkowski, John J. and Horner, John R.", title = "Nest and egg clutches of the dinosaur Troodon formosus and the evolution of avian reproductive traits", year = "1997", journal = "Nature", url = "https://doi.org/10.1038/385247a0", doi = "10.1038/385247a0", openalex = "W2069689847", references = "doi101007bf00344996, doi101017cbo9780511585739020, doi101017cbo9780511975622004, doi101038332256a0, doi101038378774a0, doi101111j1469185x1977tb01346x, doi101139e96046, doi105860choice272722, openalexw1504470482, openalexw657672288" } @article{doi105860choice343307, title = "The origin and evolution of birds", year = "1997", journal = "Choice Reviews Online", abstract = "This text is a comprehensive and illustrated discussion of the origin of and of avian flight. Ornithologist and evolutionary biologist Alan Feduccia, author of Age of Birds, here draws on fossil evidence and studies of the structure and biochemistry of living to present knowledge and data on avian evolution and propose a model of this evolutionary process. Feduccia begins with an overview of bird evolution, giving his opinions about the controversial problem in verte-brate paleontology: whether evolved directly from bipedal, terrestrial dinosaurs (the ground-up theory) or from the precursors of dinosaurs - perhaps small arboreal thecodonts (the trees-down theory). He then provides information about the origin of avian flight and feathers and discusses the most dramatic discoveries in avian paleontolgy of the past few decades - the opposite birds that were the dominant landbirds of the Mesozoic. Feduccia next offers a theory of avian evolution during the Tertiary, arguing that the evolution of follows a pattern similar to that of mammals, with an explosive (rather than gradual) evolution lasting only 5 to 10 million years. In the second half of the book he summarizes the evolution of all the modern orders of birds, discussing such subjects as the evolution of filter-feeding in ducks and flamingos, the evolution of flightlessness, the evolution of of prey and the rise of landbirds. The book also includes reconstructions of ancient fossil that have been prepared by bird artist John O'Neill.", url = "https://doi.org/10.5860/choice.34-3307", doi = "10.5860/choice.34-3307", openalex = "W1555551215" } @article{doi101017s0006323197005100, author = "PADIAN, KEVIN and Chiappe, Luis M.", title = "The origin and early evolution of birds", year = "1998", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "Birds evolved from and are phylogenetically recognized as members of the theropod dinosaurs; their first known member is the Late Jurassic Archaeopteryx, now represented by seven skeletons and a feather, and their closest known non-avian relatives are the dromaeosaurid theropods such as Deinonychus.Bird flight is widely thought to have evolved from the trees down, but Archaeopteryx and its outgroups show no obvious arboreal or tree-climbing characters, and its wing planform and wing loading do not resemble those of gliders.The ancestors of birds were bipedal, terrestrial, agile, cursorial and carnivorous or omnivorous.Apart from a perching foot and some skeletal fusions, a great many characters that are usually considered ' avian ' (e.g. the furcula, the elongated forearm, the laterally flexing wrist and apparently feathers) evolved in non-avian theropods for reasons unrelated to birds or to flight.Soon after Archaeopteryx, avian features such as the pygostyle, fusion of the carpometacarpus, and elongated curved pedal claws with a reversed, fully descended and opposable hallux, indicate improved flying ability and arboreal habits.In the further evolution of birds, characters related to the flight apparatus phylogenetically preceded those related to the rest of the skeleton and skull.Mesozoic birds are more diverse and numerous than thought previously and the most diverse known group of Cretaceous birds, the Enantiornithes, was not even recognized until 1981.The vast majority of Mesozoic bird groups have no Tertiary records: Enantiornithes, Hesperornithiformes, Ichthyornithiformes and several other lineages disappeared by the end of the Cretaceous.By that time, a few Linnean ' Orders ' of extant birds had appeared, but none of these taxa belongs to extant ' families ', and it is not until the Paleocene or (in most cases) the Eocene that the majority of extant bird ' Orders ' are known in the fossil record.There is no evidence for a major or mass extinction of birds at the end of the Cretaceous, nor for a sudden ' bottleneck ' in diversity that fostered the early Tertiary origination of living bird ' Orders '.", url = "https://doi.org/10.1017/s0006323197005100", doi = "10.1017/s0006323197005100", openalex = "W4237590069", references = "crossref1976allosaurus, doi1010160169534791900818, doi101016s0016699588800664, doi101016s0047248477800158, doi101038292051a0, doi101038331433a0, doi101038362623a0, doi101038381226a0, doi101086407902, doi101098rstb19910056, doi101098rstb19920051, doi101111j109583121976tb00244x, doi101126science2555046845, doi101126science27553031109, doi1023071441916, doi1023072992353, doi102307jctvqc6gzx, doi105860choice343307, doi105860choice353642, openalexw2991310333" } @article{doi101111j1469185x1997tb00024x, author = "Padian, Kevin and Chiappe, Luis M.", title = "The origin and early evolution of birds", year = "1998", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "ABSTRACT Birds evolved from and are phylogenetically recognized as members of the theropod dinosaurs; their first known member is the Late Jurassic Archaeopteryx, now represented by seven skeletons and a feather, and their closest known non‐avian relatives are the dromaeosaurid theropods such as Deinonychus. Bird flight is widely thought to have evolved from the trees down, but Archaeopteryx and its outgroups show no obvious arboreal or tree‐climbing characters, and its wing planform and wing loading do not resemble those of gliders. The ancestors of birds were bipedal, terrestrial, agile, cursorial and carnivorous or omnivorous. Apart from a perching foot and some skeletal fusions, a great many characters that are usually considered ‘avian’ (e.g. the furcula, the elongated forearm, the laterally flexing wrist and apparently feathers) evolved in non‐avian theropods for reasons unrelated to birds or to flight. Soon after Archaeopteryx, avian features such as the pygostyle, fusion of the carpometacarpus, and elongated curved pedal claws with a reversed, fully descended and opposable hallux, indicate improved flying ability and arboreal habits. In the further evolution of birds, characters related to the flight apparatus phylogenetically preceded those related to the rest of the skeleton and skull. Mesozoic birds are more diverse and numerous than thought previously and the most diverse known group of Cretaceous birds, the Enantiornithes, was not even recognized until 1981. The vast majority of Mesozoic bird groups have no Tertiary records: Enantiornithes, Hesperornithiformes, Ichthyornithiformes and several other lineages disappeared by the end of the Cretaceous. By that time, a few Linnean ‘Orders’ of extant birds had appeared, but none of these taxa belongs to extant ‘families’, and it is not until the Paleocene or (in most cases) the Eocene that the majority of extant bird ‘Orders’ are known in the fossil record. There is no evidence for a major or mass extinction of birds at the end of the Cretaceous, nor for a sudden ‘bottleneck’ in diversity that fostered the early Tertiary origination of living bird ‘Orders’.", url = "https://doi.org/10.1111/j.1469-185x.1997.tb00024.x", doi = "10.1111/j.1469-185x.1997.tb00024.x", openalex = "W2127438693", references = "doi101016b978012249408650011x, doi101016s0016699588800664, doi101016s0047248477800158, doi101038292051a0, doi101038331433a0, doi101038362623a0, doi101038378774a0, doi101038387390a0, doi101038nature01420, doi101038nature02706, doi101086407902, doi101098rstb19910056, doi101098rstb19920051, doi101111j109583121976tb00244x, doi101111j155856461996tb04496x, doi101126science1078237, doi101126science2555046845, doi101126science2665186779, doi101146annurevea03050175000415, doi1023071441916, doi1023073514548, doi102307jctt1xp3v3r, doi105281zenodo16171435, doi105860choice300927, doi105860choice343307, doi105860choice353642, houck1990allometric, openalexw1879660213, openalexw2991310333, openalexw3146596760, ostrom2019osteology" } @article{doi105860choice353862, author = "Williams", title = "The rise of birds: 225 million years of evolution", year = "1998", journal = "Choice Reviews Online", abstract = "The field of paleontology is beset by controversy, and few areas are as contentious as the evolution of birds. This important book should stand beside Alan Feduccia's The Origin and Evolution of Birds (CH, Feb'97), found in most undergraduate- and graduate-level libraries. Both books are well produced and written in clear English (Chatterjee uses less technical language). Both review the complex and often confusing history of avian evolution, including a discussion of Archeopteryx and possible dinosaur forebears. The principal difference is that Chatterjee puts his controversial discovery, Protoavis, as the centerpiece of the field while Feduccia is more skeptical although not dismissive. The Rise of Birds includes much other material, however, and is not simply a polemic for Protoavis. There are a thorough analysis of the origin of flight, the importance of the great K-T extinction that ended the age of dinosaurs and ushered in the age of birds and mammals, the evolution of more recent birds, and a chapter on the past and present impact of humans on birds. The figures are clear and well thought out. Good bibliography (smaller than Feduccia's). Upper-division undergraduates through faculty.", url = "https://doi.org/10.5860/choice.35-3862", doi = "10.5860/choice.35-3862", openalex = "W832377592" } @article{doi101126science29054981955, author = "Zhang, Fucheng and Zhou, Zhonghe", title = "A Primitive Enantiornithine Bird and the Origin of Feathers", year = "2000", journal = "Science", abstract = "A fossil enantiornithine bird, Protopteryx fengningensis gen. et sp. nov., was collected from the Early Cretaceous Yixian Formation of Northern China. It provides fossil evidence of a triosseal canal in early birds. The manus and the alular digit are long, as in Archaeopteryx and Confuciusornis, but are relatively short in other enantiornithines. The alula or bastard wing is attached to an unreduced alular digit. The two central tail feathers are scalelike without branching. This type of feather may suggest that modern feathers evolved through the following stages: (i) elongated scale, (ii) central shaft, (iii) barbs, and finally (iv) barbules and barbicel.", url = "https://doi.org/10.1126/science.290.5498.1955", doi = "10.1126/science.290.5498.1955", openalex = "W1973634929", references = "doi10103820670, doi101038292051a0, doi10103831635, doi10103834356, doi101038378349a0, doi101038382442a0, doi10103845769, doi101086407902, doi101111j1469185x1997tb00024x, doi101126science28454232137, openalexw2607033038" } @article{doi10103835086500, author = "Padian, Kevin and de Ricqlès, Armand J. and Horner, John R.", title = "Dinosaurian growth rates and bird origins", year = "2001", journal = "Nature", url = "https://doi.org/10.1038/35086500", doi = "10.1038/35086500", openalex = "W2052940923", references = "chinsamy1998polar, crossref1998encyclopedia, doi101016s0764446900001815, doi101017s0094837300006588, doi101017s0094837300013543, doi101017s0094837300021308, doi10103831635, doi10103835047056, doi10108002724634199310011490, doi101093oso97801951060840010001, doi101111j109636422000tb02201x, doi1016660094837320000260466lhotts20co2, doi1016660094837320010270039coosea20co2, doi1016710272463420000200115lbhoth20co2, doi105860choice353642, houck1990allometric, openalexw1585246501, openalexw2607033038, openalexw563887495, openalexw575222456" } @article{doi101111j109636422001tb01314x, author = "Hutchinson, John R.", title = "The evolution of femoral osteology and soft tissues on the line to extant birds (Neornithes)", year = "2001", journal = "Zoological Journal of the Linnean Society", abstract = "Femoral osteology and soft tissues evolved in a stepwise pattern in archosauromorph reptiles on the line to crown group birds. Crocodylia retains most ancestral archosaurian traits, whereas Dinosauromorpha (including birds) acquired many more derived traits. The complex sequence of changes included major shifts of several thigh muscle insertions. Medial rotation of the proximal femur (e.g. the femoral head) in archosaurs moved the greater trochanter laterally, bringing along the insertion of M. pubo‐ischio‐femoralis externus. Within Dinosauromorpha, the lesser trochanter moved proximally away from the trochanteric shelf. Presumably the lesser trochanter indicates the insertion of M. iliotrochantericus caudalis whereas the trochanteric shelf indicates the insertion of M. iliofemoralis externus. An accessory trochanter at the base of the lesser trochanter marks the insertion of M. pubo‐ischio‐femoralis internus 2 in tetanuran theropods. I propose hypotheses for the homologies of several intermuscular lines and other features on the femoral shaft. On the line to Neornithes, most changes of femoral morphology predated Aves and the origin of flight; few femoral features are unique to birds. Overall, the pattern of morphological evolution is consistent with stepwise functional evolution of the hindlimb within Dinosauromorpha on the line to Neornithes. The clade Ornithurae evolved the last few hindlimb apomorphies that characterize extant birds, in conjunction with more flexed hip and knee joints.", url = "https://doi.org/10.1111/j.1096-3642.2001.tb01314.x", doi = "10.1111/j.1096-3642.2001.tb01314.x", openalex = "W2020878527", references = "coria1995a, doi101007bf02985709, doi101016b9781483231426500124, doi101017cbo9780511608377010, doi101017s0022336000026706, doi101017s0094837300009866, doi101038248168a0, doi101038292051a0, doi101038387390a0, doi10103845769, doi10108002724634199110011386, doi10108002724634199110011426, doi10108002724634199310011511, doi10108002724634199410011523, doi10108002724634199410011538, doi10108002724634199710011027, doi101086283367, doi101093sysbio33183, doi101098rstb19610007, doi101098rstb19650003, doi101098rstb19830079, doi101098rstb19850092, doi101098rstb19920117, doi101098rstb19990489, doi101111j109583121976tb00244x, doi101111j109600311988tb00514x, doi101111j109600311991tb00045x, doi101111j109600311995tb00092x, doi101111j109636422001tb01313x, doi101111j146979981991tb04794x, doi101111j155856461996tb04496x, doi101126science2555046845, doi101126science27853411267, doi101126science27953581915, doi101139e72031, doi101139e93179, doi1015468p4gnhz, doi1016660094837320000260734aaateo20co2, doi1023071292217, doi10230730135049, doi104095101672, doi105281zenodo1038220, doi105281zenodo16120887, doi105281zenodo16171435, doi105281zenodo16492064, doi105479si03629236110i, doi105860choice300927, doi105860choice326223, doi105860choice392183, doi105962p226819, gregor1988the, madsen1976a, openalexw2788234611, openalexw617951419, openalexw638862129, openalexw646636017, rowe1989a, walker1964triassic" } @article{doi101016s1095643302001587, author = "Hutchinson, John R.", title = "The evolution of hindlimb tendons and muscles on the line to crown-group birds", year = "2002", journal = "Comparative Biochemistry and Physiology Part A Molecular \& Integrative Physiology", url = "https://doi.org/10.1016/s1095-6433(02)00158-7", doi = "10.1016/s1095-6433(02)00158-7", openalex = "W1981418482", references = "doi10103820167, doi10103832884, doi1010384151018a, doi1016660094837320000260734aaateo20co2" } @article{doi101002jezb26, author = "Sawyer, Roger H. and Knapp, Loren W.", title = "Avian skin development and the evolutionary origin of feathers", year = "2003", journal = "Journal of Experimental Zoology Part B Molecular and Developmental Evolution", abstract = {The discovery of several dinosaurs with filamentous integumentary appendages of different morphologies has stimulated models for the evolutionary origin of feathers. In order to understand these models, knowledge of the development of the avian integument must be put into an evolutionary context. Thus, we present a review of avian scale and feather development, which summarizes the morphogenetic events involved, as well as the expression of the beta (beta) keratin multigene family that characterizes the epidermal appendages of reptiles and birds. First we review information on the evolution of the ectodermal epidermis and its beta (beta) keratins. Then we examine the morphogenesis of scutate scales and feathers including studies in which the extraembryonic ectoderm of the chorion is used to examine dermal induction. We also present studies on the scaleless (sc) mutant, and, because of the recent discovery of "four-winged" dinosaurs, we review earlier studies of a chicken strain, Silkie, that expresses ptilopody (pti), "feathered feet." We conclude that the ability of the ectodermal epidermis to generate discrete cell populations capable of forming functional structural elements consisting of specific members of the beta keratin multigene family was a plesiomorphic feature of the archosaurian ancestor of crocodilians and birds. Evidence suggests that the discrete epidermal lineages that make up the embryonic feather filament of extant birds are homologous with similar embryonic lineages of the developing scutate scales of birds and the scales of alligators. We believe that the early expression of conserved signaling modules in the embryonic skin of the avian ancestor led to the early morphogenesis of the embryonic feather filament, with its periderm, sheath, and barb ridge lineages forming the first protofeather. Invagination of the epidermis of the protofeather led to formation of the follicle providing for feather renewal and diversification. The observations that scale formation in birds involves an inhibition of feather formation coupled with observations on the feathered feet of the scaleless (High-line) and Silkie strains support the view that the ancestor of modern birds may have had feathered hind limbs similar to those recently discovered in nonavian dromaeosaurids. And finally, our recent observation on the bristles of the wild turkey beard raises the possibility that similar integumentary appendages may have adorned nonavian dinosaurs, and thus all filamentous integumentary appendages may not be homologous to modern feathers.}, url = "https://doi.org/10.1002/jez.b.26", doi = "10.1002/jez.b.26", openalex = "W2167646349", references = "doi10103834279, unwin1998feathers" } @article{doi101126science1078237, author = "Dial, Kenneth P.", title = "Wing-Assisted Incline Running and the Evolution of Flight", year = "2003", journal = "Science", abstract = "Flapping wings of galliform birds are routinely used to produce aerodynamic forces oriented toward the substrate to enhance hindlimb traction. Here, I document this behavior in natural and laboratory settings. Adult birds fully capable of aerial flight preferentially employ wing-assisted incline running (WAIR), rather than flying, to reach elevated refuges (such as cliffs, trees, and boulders). From the day of hatching and before attaining sustained aerial flight, developing ground birds use WAIR to enhance their locomotor performance through improved foot traction, ultimately permitting vertical running. WAIR provides insight from behaviors observable in living birds into the possible role of incipient wings in feathered theropod dinosaurs and offers a previously unstudied explanation for the evolution of avian flight.", url = "https://doi.org/10.1126/science.1078237", doi = "10.1126/science.1078237", openalex = "W1985053875", references = "doi10100797814615678751, doi1010160031018288901496, doi10103819967, doi10103831635, doi10103835017641, doi101086284076, doi101093oso97801951060840010001, doi101242jeb1992263, doi105860choice343307, openalexw23418293" } @article{doi101111j001438202004tb00884x, author = "Fain, Matthew G. and Houde, Peter", title = "PARALLEL RADIATIONS IN THE PRIMARY CLADES OF BIRDS", year = "2004", journal = "Evolution", abstract = "Knowledge of avian phylogeny is prerequisite to understanding the circumstances and timing of the diversification of birds and the evolution of morphological, behavioral, and life-history traits. Recent molecular datasets have helped to elucidate the three most basal clades in the tree of living birds, but relationships among neoavian orders (the vast majority of birds) remain frustratingly vexing. Here, we examine intron 7 of the beta-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date. These data suggest that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals. Some members of the putative respective clades have long been recognized as examples of convergent evolution, but it was not appreciated that they might be parts of diverse parallel radiations. In contrast, some traditional orders of birds are suggested by these data to be polyphyletic, with representative families in both radiations.", url = "https://doi.org/10.1111/j.0014-3820.2004.tb00884.x", doi = "10.1111/j.0014-3820.2004.tb00884.x", openalex = "W2096731214", references = "doi101093oso97801951060840010001, doi101111j109600312003tb00387x" } @article{doi101126science1144066, author = "Turner, Alan H. and Pol, Diego and Clarke, Julia A. and Erickson, Gregory M. and Norell, Mark A.", title = "A Basal Dromaeosaurid and Size Evolution Preceding Avian Flight", year = "2007", journal = "Science", abstract = "Fossil evidence for changes in dinosaurs near the lineage leading to birds and the origin of flight has been sparse. A dinosaur from Mongolia represents the basal divergence within Dromaeosauridae. The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred. In contrast to the sustained small body sizes among avialans throughout the Cretaceous Period, the two dinosaurian lineages most closely related to birds, dromaeosaurids and troodontids, underwent four independent events of gigantism, and in some lineages size increased by nearly three orders of magnitude. Thus, change in theropod body size leading to flight's origin was not unidirectional.", url = "https://doi.org/10.1126/science.1144066", doi = "10.1126/science.1144066", openalex = "W2014243367", references = "doi101007s0011400405704, doi10103835047056, doi10103835086500, doi101038415780a, doi101038nature02898, doi101038nature03285, doi101038nature03996, doi101111j14697580200600534x, doi101126science27953581915, doi101126science28454232137, doi10120600030082200635451andtfu20co2" } @article{doi101007s0011400804883, author = "Hutchinson, John R. and Allen, Vivian", title = "The evolutionary continuum of limb function from early theropods to birds", year = "2008", journal = "Die Naturwissenschaften", url = "https://doi.org/10.1007/s00114-008-0488-3", doi = "10.1007/s00114-008-0488-3", openalex = "W2164139482", references = "carpenter2005the, coombs1980swimming, doi101002jmor10406, doi1010079789400904095, doi101016s002192900000155x, doi101016s0966636202000681, doi101038261129a0, doi1010384151018a, doi101073pnas0507106102, doi10108002724634199710010977, doi10108010635150802022231, doi101111j10963642200600245x, doi101111j14697580200600534x, doi101111j14754983200600585x, doi101111j15585646200700206x, doi101126science1078237, doi101126science2251499, doi101126science2740914, doi101126science28454232137, doi101130g23452a1, doi101144gslsp20042280106, doi101152jappl20008951991, doi10117702783649922066655, doi101242jeb001701, doi101242jeb005801, doi1016660094837320000260734aaateo20co2, doi1016660094837320050310676aohmma20co2, doi101666040141, doi105281zenodo16171435, doi105860choice326223, doi105860choice421568, doi105860choice434677" } @article{doi101007s1143400900096, author = "Xu, Xing and Zhao, Qi and Norell, Mark A. and Sullivan, Corwin and Hone, David W. E. and Erickson, Gregory M. and Wang, Xiaolin and Han, Fenglu and Guo, Yu", title = "A new feathered maniraptoran dinosaur fossil that fills a morphological gap in avian origin", year = "2008", journal = "Science Bulletin", url = "https://doi.org/10.1007/s11434-009-0009-6", doi = "10.1007/s11434-009-0009-6", openalex = "W2005521090", references = "doi101139e03011, doi10560219780801881206" } @article{doi10108010635150802022231, author = "Clarke, Julia A. and Middleton, Kevin M.", title = "Mosaicism, Modules, and the Evolution of Birds: Results from a Bayesian Approach to the Study of Morphological Evolution Using Discrete Character Data", year = "2008", journal = "Systematic Biology", abstract = {The study of morphological evolution after the inferred origin of active flight homologous with that in Aves has historically been characterized by an emphasis on anatomically disjunct, mosaic patterns of change. Relatively few prior studies have used discrete morphological character data in a phylogenetic context to quantitatively investigate morphological evolution or mosaic evolution in particular. One such previously employed method, which used summed unambiguously optimized synapomorphies, has been the basis for proposing disassociated and sequential "modernizing" or "fine-tuning" of pectoral and then pelvic locomotor systems after the origin of flight ("pectoral early-pelvic late" hypothesis). We use one of the most inclusive phylogenetic data sets of basal birds to investigate properties of this method and to consider the application of a Bayesian phylogenetic approach. Bayes factor and statistical comparisons of branch length estimates were used to evaluate support for a mosaic pattern of character change and the specific pectoral early-pelvic late hypothesis. Partitions were defined a priori based on anatomical subregion (e.g., pelvic, pectoral) and were based on those hypothesized using the summed synapomorphy approach. We compare 80 models all implementing the M(k) model for morphological data but varying in the number of anatomical subregion partitions, the models for among-partition rate variation and among-character rate variation, as well as the branch length prior. Statistical analysis reveals that partitioning data by anatomical subregion, independently estimating branch lengths for partitioned data, and use of shared or per partition gamma-shaped among-character rate distribution significantly increases estimated model likelihoods. Simulation studies reveal that partitioned models where characters are randomly assigned perform significantly worse than both the observed model and the single-partition equal-rate model, suggesting that only partitioning by anatomical subregion increases model performance. The preference for models with partitions defined a priori by anatomical subregion is consistent with a disjunctive pattern of character change for the data set investigated and may have implications for parameterization of Bayesian analyses of morphological data more generally. Statistical tests of differences in estimated branch lengths from the pectoral and pelvic partitions do not support the specific pectoral early-pelvic late hypothesis proposed from the summed synapomorphy approach; however, results suggest limited support for some pectoral branch lengths being significantly longer only early at/after the origin of flight.}, url = "https://doi.org/10.1080/10635150802022231", doi = "10.1080/10635150802022231", openalex = "W2118740788", references = "doi1010079780387217062, doi101007bf00160154, doi10108001621459199510476572, doi101080106351501753462876, doi10108010635150490264699, doi10108010635150600755396, doi101093bioinformatics178754, doi101093bioinformaticsbtg180, doi101111j14697580200600534x, doi101242jeb001701, doi102992014590582006371pon20co2, doi105860choice353862, doi105860choice392183, openalexw2994240441, openalexw3217097258" } @article{doi101111j14697580200800880x, author = "Zhou, Zhonghe and Clarke, Julia A. and Zhang, Fucheng", title = "Insight into diversity, body size and morphological evolution from the largest Early Cretaceous enantiornithine bird", year = "2008", journal = "Journal of Anatomy", abstract = "Most of Mesozoic bird diversity comprises species that are part of one of two major lineages, namely Ornithurae, including living birds, and Enantiornithes, a major radiation traditionally referred to as 'opposite birds'. Here we report the largest Early Cretaceous enantiornithine bird from north-east China, which provides evidence that basal members of Enantiornithes share more morphologies with ornithurine birds than previously recognized. Morphological evolution in these two groups has been thought to be largely parallel, with derived members of Enantiornithes convergent on the 'advanced' flight capabilities of ornithurine birds. The presence of an array of morphologies previously thought to be derived within ornithurine and enantiornithine birds in a basal enantiornithine species provides evidence of the complex character evolution in these two major lineages. The cranial morphology of the new specimen is among the best preserved for Mesozoic avians. The new species extends the size range known for Early Cretaceous Enantiornithes significantly and provides evidence of forelimb to hind limb proportions distinct from all other known members of the clade. As such, it sheds new light on avian body size evolution and diversity, and allows a re-evaluation of a previously proposed hypothesis of competitive exclusion among Early Cretaceous avian clades.", url = "https://doi.org/10.1111/j.1469-7580.2008.00880.x", doi = "10.1111/j.1469-7580.2008.00880.x", openalex = "W2012419237", references = "doi1010292004gl019790, doi101073pnas0507106102, doi101111j109636422001tb01314x, doi101111j14636409200600234x, doi101111j14697580200600534x, doi101126science1144066, doi101126science29054981955, doi1012060003008220023870001tmappo20co2, doi1012060003009020042860001mptaso20co2, doi1016660022336020030770822mbatho20co2, doi10230730135049, doi105281zenodo16171435, doi105860choice405235, openalexw2607033038" } @article{doi101126science1157704, author = "Hackett, Shannon J. and Kimball, Rebecca T. and Reddy, Sushma and Bowie, Rauri C. K. and Braun, Edward L. and Braun, Michael J. and Chojnowski, Jena L. and Cox, W. Andrew and Han, Kin-Lan and Harshman, John and Huddleston, Christopher J. and Marks, Ben D. and Miglia, Kathleen J. and Moore, William S. and Sheldon, Frederick H. and Steadman, David W. and Witt, Christopher C. and Yuri, Tamaki", title = "A Phylogenomic Study of Birds Reveals Their Evolutionary History", year = "2008", journal = "Science", abstract = "Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.", url = "https://doi.org/10.1126/science.1157704", doi = "10.1126/science.1157704", openalex = "W2107555182", references = "doi101006mpev19980603, doi101038nrg1603, doi101093bioinformaticsbtl446, doi101093sysbio422182, doi101098rsbl20060523, doi101111j109600312003tb00387x, doi101111j10963642200600293x, doi1023072992540, doi102307jctt1xp3v3r, doi105962bhltitle14581, openalexw1569611434" } @article{doi101126science1163245, author = "Varricchio, David J. and Moore, Jason R. and Erickson, Gregory M. and Norell, Mark A. and Jackson, Frankie D. and Borkowski, John J.", title = "Avian Paternal Care Had Dinosaur Origin", year = "2008", journal = "Science", abstract = "The repeated discovery of adult dinosaurs in close association with egg clutches leads to speculation over the type and extent of care exhibited by these extinct animals for their eggs and young. To assess parental care in Cretaceous troodontid and oviraptorid dinosaurs, we examined clutch volume and the bone histology of brooding adults. In comparison to four archosaur care regressions, the relatively large clutch volumes of Troodon, Oviraptor, and Citipati scale most closely with a bird-paternal care model. Clutch-associated adults lack the maternal and reproductively associated histologic features common to extant archosaurs. Large clutch volumes and a suite of reproductive features shared only with birds favor paternal care, possibly within a polygamous mating system. Paternal care in both troodontids and oviraptorids indicates that this care system evolved before the emergence of birds and represents birds' ancestral condition. In extant birds and over most adult sizes, paternal and biparental care correspond to the largest and smallest relative clutch volumes, respectively.", url = "https://doi.org/10.1126/science.1163245", doi = "10.1126/science.1163245", openalex = "W2055090154", references = "doi101073pnas0708903105, doi101098rsbl20070254" } @article{doi101007s1205200901334, author = "Chiappe, Luis M.", title = "Downsized Dinosaurs: The Evolutionary Transition to Modern Birds", year = "2009", journal = "Evolution Education and Outreach", abstract = "Living birds are the most diverse land vertebrates and the heirs of a rich chapter in the evolution of life. The origin of modern birds from animals similar to Tyrannosaurus rex is among the most remarkable examples of an evolutionary transition. A wealth of recently discovered fossils has finally settled the century-old controversy about the origin of birds and it has made the evolutionary saga toward modern birds one of the best documented transitions in the history of life. This paper reviews the evidence in support of the origin of birds from meat-eating dinosaurs, and it highlights the array of fossils that connect these fearsome animals with those that fly all around us.", url = "https://doi.org/10.1007/s12052-009-0133-4", doi = "10.1007/s12052-009-0133-4", openalex = "W2028313861", references = "doi101017s247526300000091x, doi101038nature03150, doi101111j109583121976tb00244x, doi101126science1144066, doi101126science28454232137, doi1016660022336020030770822mbatho20co2, doi105281zenodo16171435, doi105860choice300927, doi105860choice343307, doi105860choice353862, openalexw2607033038" } @article{doi101098rspb20110238, author = "Zelenitsky, Darla K. and Therrien, François and Ridgely, Ryan C. and McGee, Amanda and Witmer, Lawrence M.", title = "Evolution of olfaction in non-avian theropod dinosaurs and birds", year = "2011", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "Little is known about the olfactory capabilities of extinct basal (non-neornithine) birds or the evolutionary changes in olfaction that occurred from non-avian theropods through modern birds. Although modern birds are known to have diverse olfactory capabilities, olfaction is generally considered to have declined during avian evolution as visual and vestibular sensory enhancements occurred in association with flight. To test the hypothesis that olfaction diminished through avian evolution, we assessed relative olfactory bulb size, here used as a neuroanatomical proxy for olfactory capabilities, in 157 species of non-avian theropods, fossil birds and living birds. We show that relative olfactory bulb size increased during non-avian maniraptoriform evolution, remained stable across the non-avian theropod/bird transition, and increased during basal bird and early neornithine evolution. From early neornithines through a major part of neornithine evolution, the relative size of the olfactory bulbs remained stable before decreasing in derived neoavian clades. Our results show that, rather than decreasing, the importance of olfaction actually increased during early bird evolution, representing a previously unrecognized sensory enhancement. The relatively larger olfactory bulbs of earliest neornithines, compared with those of basal birds, may have endowed neornithines with improved olfaction for more effective foraging or navigation skills, which in turn may have been a factor allowing them to survive the end-Cretaceous mass extinction.", url = "https://doi.org/10.1098/rspb.2011.0238", doi = "10.1098/rspb.2011.0238", openalex = "W2144479326", references = "doi101002ar20983, doi101016s0065345413600017, doi101038nature02706, doi101073pnas1006970107, doi101086284325, doi101093sysbio423265, doi101098rspb20090885, doi101111j155856461951tb02756x, doi101126science1157704, doi101126science2865440711, doi101136bjo592111c, doi1012019781420064452, doi1012060003009020042860001mptaso20co2, doi101242jeb002246, doi101371journalpone0007390, doi1023072407154, doi105860choice421568, larsson2000forebrain, openalexw2611511275, russell1969a" } @article{doi101371journalpone0028964, author = "Fowler, Denver W. and Freedman, Elizabeth A. and Scannella, John B. and Kambic, Robert E.", title = "The Predatory Ecology of Deinonychus and the Origin of Flapping in Birds", year = "2011", journal = "PLoS ONE", abstract = {Most non-avian theropod dinosaurs are characterized by fearsome serrated teeth and sharp recurved claws. Interpretation of theropod predatory ecology is typically based on functional morphological analysis of these and other physical features. The notorious hypertrophied 'killing claw' on pedal digit (D) II of the maniraptoran theropod Deinonychus (Paraves: Dromaeosauridae) is hypothesized to have been a predatory adaptation for slashing or climbing, leading to the suggestion that Deinonychus and other dromaeosaurids were cursorial predators specialized for actively attacking and killing prey several times larger than themselves. However, this hypothesis is problematic as extant animals that possess similarly hypertrophied claws do not use them to slash or climb up prey. Here we offer an alternative interpretation: that the hypertrophied D-II claw of dromaeosaurids was functionally analogous to the enlarged talon also found on D-II of extant Accipitridae (hawks and eagles; one family of the birds commonly known as "raptors"). Here, the talon is used to maintain grip on prey of subequal body size to the predator, while the victim is pinned down by the body weight of the raptor and dismembered by the beak. The foot of Deinonychus exhibits morphology consistent with a grasping function, supportive of the prey immobilisation behavior model. Opposite morphological trends within Deinonychosauria (Dromaeosauridae + Troodontidae) are indicative of ecological separation. Placed in context of avian evolution, the grasping foot of Deinonychus and other terrestrial predatory paravians is hypothesized to have been an exaptation for the grasping foot of arboreal perching birds. Here we also describe "stability flapping", a novel behaviour executed for positioning and stability during the initial stages of prey immobilisation, which may have been pivotal to the evolution of the flapping stroke. These findings overhaul our perception of predatory dinosaurs and highlight the role of exaptation in the evolution of novel structures and behaviours.}, url = "https://doi.org/10.1371/journal.pone.0028964", doi = "10.1371/journal.pone.0028964", openalex = "W2059526119", references = "carpenter2005the, crossref1976allosaurus, doi101002ar20986, doi101007s0011400804883, doi101017cbo9780511608377011, doi10103831635, doi10103835047056, doi10103845769, doi10108002724634198710011651, doi10108010618600199610474713, doi101126science1144066, doi101126science27953581915, doi101666040141, doi1023071390807, doi102307jctvqc6gzx, russell1969a, wilson1985stenonychosaurus" } @article{doi101038nature12059, author = "Allen, Vivian and Bates, Karl T. and Li, Zhiheng and Hutchinson, John R.", title = "Linking the evolution of body shape and locomotor biomechanics in bird-line archosaurs", year = "2013", journal = "Nature", url = "https://doi.org/10.1038/nature12059", doi = "10.1038/nature12059", openalex = "W2095233827", references = "doi101002jmor1052090107, doi101007s0011400804883, doi1016660094837320000260734aaateo20co2" } @article{doi101038nature12424, author = "Balanoff, Amy M. and Bever, Gabe S. and Rowe, Timothy B. and Norell, Mark A.", title = "Evolutionary origins of the avian brain", year = "2013", journal = "Nature", url = "https://doi.org/10.1038/nature12424", doi = "10.1038/nature12424", openalex = "W2087236312", references = "christiansen2004mass, doi1010020471733849, doi101002ar20983, doi1010079783642182624, doi101016016622369593932n, doi101038nature01342, doi101038nature02706, doi101038nature11146, doi101111j109600311988tb00514x, doi101126science1203117, doi1012067481, doi1023072407154, doi105860choice340925, larsson2000forebrain, openalexw2983381470" } @misc{heers2013evolution, author = "Heers, Ashley M", title = "Evolution of Avian Flight", year = "2013", booktitle = "Encyclopedia of Life Sciences", abstract = "The origin of birds and of bird flight has drawn scientific interest since the inception of evolutionary thinking. Though early investigations were hampered by a paucity of fossils, new discoveries have filled in many gaps and provided unprecedented detail into morphological changes that attended the evolutionary appearance of birds and bird flight. Birds are now widely regarded as the descendents of theropod dinosaurs. In contrast, form–function relationships and behaviours that might have facilitated the evolutionary acquisition of flight remain widely debated. Given the versatility of extant birds, we should not expect to find only one solution to this problem. Nevertheless, much debate seems to stem not from looking for multiple plausible functions and behaviours, but rather from traditional ‘ground up’ versus ‘trees down’ assumptions and a general lack of experimental and ecological support for inferred form–function relationships. Many researchers have therefore called for more rigorous hypothesis testing, and a plethora of new techniques and perspectives are up to the challenge. Key Concepts: Birds are the descendents of bipedal theropod dinosaurs. Evolutionary assembly of the avian body plan occurred gradually, with bird‐like wings evolving before bird‐like skeletons, in conjunction with a reduction in body size and then a cranial shift in centre of mass. These changes took place via a series of transitional anatomical stages that were presumably associated with transitional functions and behaviours before becoming co‐opted for flapping flight. Many origin‐of‐flight hypotheses have been proposed, and it is challenging to discriminate among them. Much debate seems to stem from traditional ‘ground up’ versus ‘trees down’ assumptions and a general lack of experimental and ecological support for inferred form–function relationships. A growing number of researchers have therefore suggested that hypotheses must be consistent not only with the fossil record, but also with experimental support for form–function relationships and behaviours inferred by origin‐of‐flight scenarios. New techniques and perspectives are meeting this challenge and providing more rigorous insight into the origin of flight in birds. For example, recent work on developing birds with dinosaur‐like anatomies clearly demonstrates that behaviours involving the cooperative use of wings and legs (e.g. wing‐assisted incline running and steaming) act as a developmental (or evolutionary) bridge between leg‐based terrestrial locomotion and wing‐based aerial locomotion, by allowing developing birds (or evolving dinosaurs) to supplement their wings with their legs until the wings can fully support body weight during flight.", url = "https://doi.org/10.1002/9780470015902.a0024965", doi = "10.1002/9780470015902.a0024965", openalex = "W2149563064", references = "doi10103831635, doi10103834356, doi101038374227a0, doi101038nature11631, doi101126science860134, doi10560219780801882210, doi105860choice326223, doi105962bhltitle50860, doi105962bhltitle82303" } @article{doi101016jcub201408034, author = "Brusatte, Stephen L. and Lloyd, Graeme T. and Wang, Steve C. and Norell, Mark A.", title = "Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition", year = "2014", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2014.08.034", doi = "10.1016/j.cub.2014.08.034", openalex = "W2000971221", references = "crossref1976allosaurus, doi10100703064746897, doi101007s001140090614x, doi101016jcretres201103005, doi101016jearscirev201004001, doi101016jjafrearsci201205005, doi101017s0006323197005100, doi101017s009483730001263x, doi10103832884, doi10103835086558, doi101038378774a0, doi101038nature02855, doi101038nature03996, doi101038nature04511, doi101038nature07447, doi101038nature10288, doi101038nature10906, doi101038nature12168, doi101038ncomms1815, doi101073pnas1006970107, doi101080027246342010520779, doi101093aesa383396, doi101111evo12150, doi101111j10960031200700161x, doi101111j10960031200800217x, doi101111j10963642200900571x, doi101111j14209101201002039x, doi101111j1469185x1997tb00024x, doi101111j14697580200600534x, doi101111j15585646201001025x, doi101111j2041210x201100169x, doi101111j2041210x201200223x, doi101126science1144066, doi101126science1161833, doi101126science1193304, doi101126science1252243, doi101144sp31516, doi10120600030082200635451andtfu20co2, doi1012067481, doi101371journalpbio1001853, doi101371journalpone0031838, doi1022179revmacn14372, doi1022179revmacn8325, doi105281zenodo16171435, doi105281zenodo16651680, openalexw2183707334" } @article{doi1011112041210x12226, author = "Campione, Nicolás E. and Evans, David C. and Brown, Caleb M. and Carrano, Matthew T.", title = "Body mass estimation in non‐avian bipeds using a theoretical conversion to quadruped stylopodial proportions", year = "2014", journal = "Methods in Ecology and Evolution", abstract = "Summary Body mass is strongly related to both physiological and ecological properties of living organisms. As a result, generating robust, broadly applicable models for estimating body mass in the fossil record provides the opportunity to reconstruct palaeobiology and investigate evolutionary ecology on a large temporal scale. A recent study provided strong evidence that the minimum circumference of stylopodial elements (humerus and femur) is conservatively associated with body mass in living quadrupeds. Unfortunately, this model is not directly applicable to extinct bipeds, such as non‐avian dinosaurs. This study presents a new equation that mathematically corrects the quadruped equation for use in bipeds. It is derived from the systemic difference in the circumference‐to‐area scaling relationship of two circles (hypothetical quadruped) and one circle (hypothetical biped), which represent the cross‐section of the main weight‐bearing limb bones. When applied to a newly constructed data set of femoral circumferences and body masses in living birds, the new equation reveals errors that are significantly lower than other published equations, but significantly higher than the error inherent in the avian data set. Such errors, however, are expected given the unique overall femoral circumference–body mass scaling relationship found in birds. Body mass estimates for a sample of bipedal dinosaurs using the new model are consistent with recent estimates based on volumetric life reconstructions, but, in contrast, this equation is simpler to use, with the concomitant potential to provide a wider set of body mass estimates for extinct bipeds. Although it is evident that no one estimation model is flawless, the combined use of the corrected quadrupedal equations and the previously published quadrupedal equation offer a consistent approach with which to estimate body masses in both quadrupeds and bipeds. These models have implications for conducting large‐scale macroevolutionary analyses of body size throughout the evolutionary history of terrestrial vertebrates, and, in particular, across major changes in body plan, such as the evolution of bipedality in archosaurs and quadrupedality in dinosaurs.", url = "https://doi.org/10.1111/2041-210x.12226", doi = "10.1111/2041-210x.12226", openalex = "W2003789729", references = "christiansen2004mass, doi101002jmor10470, doi101002sici10968644199602992345aidajpa930co2x, doi101016jpalaeo201206027, doi101016s0022519384800314, doi101086285558, doi101111evo12150, doi101111j109636421985tb00871x, doi101111j109636422001tb01314x, doi101111j1469185x201100190x, doi101111j146979981985tb04915x, doi101111j2041210x201100153x, doi101126science1061967, doi101126science17940791201, doi101152jappl1975394619, doi101186174170071060, doi101371journalpbio1001853, doi101371journalpone0051925, doi101371journalpone0081917, doi101371journalpone0082000" } @article{doi101126science1251385, author = "Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M. and Lee, Chul and Storz, Jay F. and Antunes, Agostinho and Greenwold, Matthew J. and Meredith, Robert W. and Ödeen, Anders and Cui, Jie and Zhou, Qi and Xu, Luohao and Pan, Hailin and Wang, Zongji and Jin, Lijun and Zhang, Pei and Hu, Haofu and Yang, Wei and Hu, Jiang and Xiao, Jin and Yang, Zhikai and Liu, Yang and Xie, Qiaolin and Yu, Hao and Lian, Jinmin and Wen, Ping and Zhang, Fang and Li, Hui and Zeng, Yongli and Xiong, Zijun and Liu, Shiping and Zhou, Long and Huang, Zhiyong and An, Na and Wang, Jie and Zheng, Qiumei and Xiong, Yingqi and Wang, Guangbiao and Wang, Bo and Wang, Jingjing and Fan, Yu and da Fonseca, Rute R. and Alfaro‐Núñez, Alonzo and Schubert, Mikkel and Orlando, Ludovic and Mourier, Tobias and Howard, Jason T. and Ganapathy, Ganeshkumar and Pfenning, Andreas R. and Whitney, Osceola and Rivas, Miriam and Hara, Erina and Smith, Julia and Farré, Marta and Narayan, Jitendra and Slavov, Gancho and Romanov, Michael N and Borges, Rui and Machado, João Paulo and Khan, Imran and Springer, Mark S. and Gatesy, John and Hoffmann, Federico G. and Opazo, Juan C. and Håstad, Olle and Sawyer, Roger H. and Kim, Heebal and Kim, Kyu-Won and Kim, Hyeon Jeong and Cho, Seoae and Li, Ning and Huang, Yinhua and Bruford, Michael W. and Zhan, Xiangjiang and Dixon, Andrew and Bertelsen, Mads F. and Derryberry, Elizabeth P. and Warren, Wesley C. and Wilson, Richard K. and Li, Shengbin and Ray, David A. and Green, Richard E. and O’Brien, Stephen J. and Griffin, Darren and Johnson, Warren E. and Haussler, David and Ryder, Oliver A. and Willerslev, Eske and Graves, Gary R. and Alström, Per and Fjeldså, Jon and Mindell, David P. and Edwards, Scott V. and Braun, Edward L. and Rahbek, Carsten and Burt, David W. and Houde, Peter and Zhang, Yong", title = "Comparative genomics reveals insights into avian genome evolution and adaptation", year = "2014", journal = "Science", abstract = "Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.", url = "https://doi.org/10.1126/science.1251385", doi = "10.1126/science.1251385", openalex = "W2167406239", references = "doi101016b9780121005436500271, doi101016jtig201002002, doi101016jtree201109004, doi101038nature05621, doi101038nature05634, doi101038nature10842, doi101038nature11631, doi101093bioinformaticsbts199, doi101093molbevmsp259, doi101111j10963642200600293x, doi101111j2041210x201100169x, doi101126science1211028, doi101126science1228282, doi101126science1254390, doi105860choice405235, openalexw1635425035" } @article{doi101126science1252243, author = "Lee, Michael S. Y. and Cau, Andrea and Naish, Darren and Dyke, Gareth J.", title = "Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds", year = "2014", journal = "Science", abstract = "Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.", url = "https://doi.org/10.1126/science.1252243", doi = "10.1126/science.1252243", openalex = "W2068703220", references = "christiansen2004mass, doi101016jearscirev201004001, doi101038nature10906, doi101038nature11146, doi101038nature12168, doi101073pnas1203238109, doi10108001621459199510476572, doi101080106351501753462876, doi101080147720192010484650, doi101080147720192011630927, doi101093bioinformaticsbtm388, doi101093molbevmss075, doi101093oxfordjournalsmolbeva003872, doi101093sysbiosys029, doi101098rspb20122526, doi101111evo12150, doi101111j10963642200900591x, doi101111j1469185x200900094x, doi101126science1193304, doi101126science1225376, doi101126science1228753, doi101371journalpbio0040088, doi101371journalpbio1001853, doi1022179revmacn14372, doi102307409735, doi105281zenodo16171435, nesbitt2013the, openalexw2611511275, rauhut2003a" } @article{doi101126science1253293, author = "Xu, Xing and Zhou, Zhonghe and Dudley, Robert and Mackem, Susan and Chuong, Cheng‐Ming and Erickson, Gregory M. and Varricchio, David J.", title = "An integrative approach to understanding bird origins", year = "2014", journal = "Science", abstract = "Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model.", url = "https://doi.org/10.1126/science.1253293", doi = "10.1126/science.1253293", openalex = "W2033992760", references = "doi101002sici1097010x199912152854291aidjez130co29, doi10100797814615698316, doi101016jcub201209052, doi10103831635, doi10103834356, doi10103835086500, doi10103835086558, doi101038368196a0, doi101038378774a0, doi101038385247a0, doi101038387390a0, doi101038415780a, doi101038nature00930, doi101038nature01342, doi101038nature02898, doi101038nature03996, doi101038nature04511, doi101038nature05621, doi101038nature07447, doi101038nature07856, doi101038nature08322, doi101038nature08740, doi101038nature11146, doi101038nature12168, doi101038nature12424, doi101038nature12973, doi101038nature13467, doi101073pnas1203238109, doi10108002724634199910011125, doi101098rsbl20070254, doi101111j10963642200600245x, doi101111j1469185x201100190x, doi101111j155856461996tb04496x, doi101126science1078237, doi101126science1144066, doi101126science1180219, doi101126science1213780, doi101126science1225376, doi101126science1228753, doi101126science1252243, doi101126science1253143, doi101126science28454232137, doi101139e03011, doi1012067481, doi101371journalpone0003303, doi101371journalpone0007390, doi101371journalpone0036790, doi101371journalpone0081917, doi1015468gbdyof, doi105281zenodo16171435, doi105860choice421568, ostrom2019osteology" } @article{doi101371journalpbio1001853, author = "Benson, Roger and Campione, Nicolás E. and Carrano, Matthew T. and Mannion, Philip D. and Sullivan, Corwin and Upchurch, Paul and Evans, David C.", title = "Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage", year = "2014", journal = "PLoS Biology", abstract = "Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614-622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.", url = "https://doi.org/10.1371/journal.pbio.1001853", doi = "10.1371/journal.pbio.1001853", openalex = "W2155522161", references = "doi101007b97636, doi101017s009483730001263x, doi101017s009483730001280x, doi10103835086500, doi10103844766, doi101038nature11631, doi10108010635150490445706, doi101086284325, doi101093bioinformaticsbtm538, doi101093oso97801985052350010001, doi101093oso97801985404720010001, doi101098rspb20122526, doi101111j001438202003tb00285x, doi101111j1469185x201000137x, doi101111j15585646201201723x, doi101126science1144066, doi101126science1161833, doi101146annurevecolsys39110707173447, doi101159000452856, doi101186174170071060, doi101198tech2003s146, doi101371journalpbio1001853, doi101371journalpone0007390, doi101371journalpone0044318, doi10166612041, martinsander2006bone, openalexw2145250129" } @article{doi101016jcub201508003, author = "Brusatte, Stephen L. and O’Connor, Jingmai K. and Jarvis, Erich D.", title = "The Origin and Diversification of Birds", year = "2015", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2015.08.003", doi = "10.1016/j.cub.2015.08.003", openalex = "W1883905760", references = "alvarez1980extraterrestrial, bakker1972anatomical, doi101016jcub201209052, doi101016jcub201408034, doi101016jearscirev201004001, doi101017s0006323197005100, doi10103831635, doi10103834356, doi10103835086500, doi10103835086558, doi101038385247a0, doi101038nature01342, doi101038nature01420, doi101038nature03150, doi101038nature07856, doi101038nature08322, doi101038nature11631, doi101038nature12168, doi101038nature12424, doi101038nature12973, doi101038nature13467, doi101038nature14423, doi101038ncomms7987, doi101073pnas1110395108, doi101093auk12041206, doi101093nsrnwu055, doi101111brv12128, doi101111evo12150, doi101111j10963642200600293x, doi101111j1469185x1997tb00024x, doi101111j1469185x201100190x, doi101111j14697580200600534x, doi101126science1144066, doi101126science1177265, doi101126science1180219, doi101126science1228753, doi101126science1251385, doi101126science1252243, doi101126science1253143, doi101126science1253293, doi101126science1253451, doi101126science20844481095, doi101126science29054981955, doi101144gsjgs15420265, doi1012063521, doi1012067481, doi101371journalpbio1001853, doi101371journalpone0003303, doi101371journalpone0007390, doi105281zenodo16171435, larsson2000forebrain, openalexw3146596760, ostrom2019osteology" } @article{doi101038nature15697, author = "Prum, Richard O. and Berv, Jacob S. and Dornburg, Alex and Field, Daniel J. and Townsend, Jeffrey P. and Lemmon, Emily Moriarty and Lemmon, Alan R.", title = "A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing", year = "2015", journal = "Nature", url = "https://doi.org/10.1038/nature15697", doi = "10.1038/nature15697", openalex = "W1887892324", references = "doi101038nature11631, doi101073pnas0401892101, doi101073pnas1110395108, doi101093bioinformaticsbtq706, doi101093bioinformaticsbtu033, doi101093molbevmsl150, doi101093molbevmss020, doi101093molbevmss075, doi101093molbevmst010, doi101093sysbiosyr107, doi101098rspb20120683, doi101126science1157704, doi101126science1253451, doi101126science1257570, doi1012060003009020042860001mptaso20co2, doi101371journalpbio0040088" } @article{doi101098rspb20142864, author = "Feo, Teresa J. and Field, Daniel J. and Prum, Richard O.", title = "Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight", year = "2015", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "The geometry of feather barbs (barb length and barb angle) determines feather vane asymmetry and vane rigidity, which are both critical to a feather's aerodynamic performance. Here, we describe the relationship between barb geometry and aerodynamic function across the evolutionary history of asymmetrical flight feathers, from Mesozoic taxa outside of modern avian diversity (Microraptor, Archaeopteryx, Sapeornis, Confuciusornis and the enantiornithine Eopengornis) to an extensive sample of modern birds. Contrary to previous assumptions, we find that barb angle is not related to vane-width asymmetry; instead barb angle varies with vane function, whereas barb length variation determines vane asymmetry. We demonstrate that barb geometry significantly differs among functionally distinct portions of flight feather vanes, and that cutting-edge leading vanes occupy a distinct region of morphospace characterized by small barb angles. This cutting-edge vane morphology is ubiquitous across a phylogenetically and functionally diverse sample of modern birds and Mesozoic stem birds, revealing a fundamental aerodynamic adaptation that has persisted from the Late Jurassic. However, in Mesozoic taxa stemward of Ornithurae and Enantiornithes, trailing vane barb geometry is distinctly different from that of modern birds. In both modern birds and enantiornithines, trailing vanes have larger barb angles than in comparatively stemward taxa like Archaeopteryx, which exhibit small trailing vane barb angles. This discovery reveals a previously unrecognized evolutionary transition in flight feather morphology, which has important implications for the flight capacity of early feathered theropods such as Archaeopteryx and Microraptor. Our findings suggest that the fully modern avian flight feather, and possibly a modern capacity for powered flight, evolved crownward of Confuciusornis, long after the origin of asymmetrical flight feathers, and much later than previously recognized.", url = "https://doi.org/10.1098/rspb.2014.2864", doi = "10.1098/rspb.2014.2864", openalex = "W1986640165", references = "doi101038nature13467, doi101371journalpone0082000, doi101666040141" } @article{doi101126sciadv1501005, author = "Claramunt, Santiago and Cracraft, Joël", title = "A new time tree reveals Earth history’s imprint on the evolution of modern birds", year = "2015", journal = "Science Advances", abstract = "Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.", url = "https://doi.org/10.1126/sciadv.1501005", doi = "10.1126/sciadv.1501005", openalex = "W2256663809", references = "doi101038nature03150, doi101038nature15697, doi101073pnas1110395108, doi101098rspb20001368, doi101111j10958312201101657x, doi101111j10963642200600293x, doi101146annurevearth031208100055, doi101146annurevearth050212124217, doi101371journalpone0052455, doi1021425f55419694" } @article{doi101073pnas1613813113, author = "Griffin, Christopher T and Nesbitt, Sterling J", title = "Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds.", year = "2016", journal = "Proceedings of the National Academy of Sciences of the United States of America", abstract = "Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.", url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC5187714/", doi = "10.1073/pnas.1613813113", openalex = "W2560017686", pmcid = "PMC5187714", pmid = "27930315", references = "carr1999craniofacial, doi101002sici109746871996082292121aidjmor130co24, doi101007s1205200901334, doi101016jcub201408034, doi101016jearscirev201004001, doi101016s0012825203000825, doi10103835086500, doi10103835086558, doi101038nature02699, doi101073pnas1505252112, doi10108002724634199610011283, doi101111bij12746, doi105860choice392183" } @article{doi101093icbicw069, author = "Bhullar, Bhart‐Anjan S. and Hanson, Michael and Fabbri, Matteo and Pritchard, Adam C. and Bever, Gabe S. and Hoffman, Eva A.", title = "How to Make a Bird Skull: Major Transitions in the Evolution of the Avian Cranium, Paedomorphosis, and the Beak as a Surrogate Hand", year = "2016", journal = "Integrative and Comparative Biology", abstract = "The avian skull is distinctive in its construction and in its function. Much of bird anatomical variety is expressed in the beak; but the beak itself, largely formed of the premaxillary bone, is set upon a shortened face and a bulbous, enlarged braincase. Here, we use original anatomical observations and reconstructions to describe the overall form of the avian skull in a larger context and to provide a general account of the evolutionary transformation from the early dinosaur skull-the skull of an archosaurian macropredator-to that of modern birds. Facial shortening, the enlargement of the braincase around an enlarged brain (with consequential reduction of circumorbital elements and the adductor chamber), and general thinning and looser articulation of bones are trends. Many of these owe to juvenilization or paedomorphosis, something that is abundantly evident from comparison of a juvenile early theropod (Coelophysis) to early avialans like Archaeopteryx Near the avian crown, the premaxilla becomes dramatically enlarged and integrated into the characteristic mobile kinetic system of birds. We posit that this addition of a large element onto the skull may be biomechanically feasible only because of the paedomorphic shortening of the face; and kinesis of the beak only because of the paedomorphic thinning of the bones and loosening of articulations, as played out in reverse during the maturation of Coelophysis Finally, the beak itself becomes elaborated as the hands are integrated into the wing. There are structural, kinematic, and neurological similarities between avian pecking and primate grasping. The ability to precision-select high-quality food against a complex but depauperate background may have permitted crown birds to survive the end-Cretaceous cataclysm by feeding on insects, seeds, and other detritus after the collapse of higher trophic levels in the food web.", url = "https://doi.org/10.1093/icb/icw069", doi = "10.1093/icb/icw069", openalex = "W2464686792", references = "doi101016jcub201508003, doi101017s0094837300006588, doi101038379249a0, doi101038nature15697, doi101038nature19417, doi101038ncomms7987, doi101038nrn1606, doi101080027246342012719176, doi101080147720192010526639, doi101098rspb20110238, doi101111evo12684, doi101111j109600311988tb00514x, doi101126science1098095, doi101139e05044, doi1012063521, doi105281zenodo16171435, houck1990allometric, openalexw2506868775" } @article{doi101111brv12280, author = "Lovegrove, Barry G.", title = "A phenology of the evolution of endothermy in birds and mammals", year = "2016", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "Recent palaeontological data and novel physiological hypotheses now allow a timescaled reconstruction of the evolution of endothermy in birds and mammals. A three-phase iterative model describing how endothermy evolved from Permian ectothermic ancestors is presented. In Phase One I propose that the elevation of endothermy - increased metabolism and body temperature (T b) - complemented large-body-size homeothermy during the Permian and Triassic in response to the fitness benefits of enhanced embryo development (parental care) and the activity demands of conquering dry land. I propose that Phase Two commenced in the Late Triassic and Jurassic and was marked by extreme body-size miniaturization, the evolution of enhanced body insulation (fur and feathers), increased brain size, thermoregulatory control, and increased ecomorphological diversity. I suggest that Phase Three occurred during the Cretaceous and Cenozoic and involved endothermic pulses associated with the evolution of muscle-powered flapping flight in birds, terrestrial cursoriality in mammals, and climate adaptation in response to Late Cenozoic cooling in both birds and mammals. Although the triphasic model argues for an iterative evolution of endothermy in pulses throughout the Mesozoic and Cenozoic, it is also argued that endothermy was potentially abandoned at any time that a bird or mammal did not rely upon its thermal benefits for parental care or breeding success. The abandonment would have taken the form of either hibernation or daily torpor as observed in extant endotherms. Thus torpor and hibernation are argued to be as ancient as the origins of endothermy itself, a plesiomorphic characteristic observed today in many small birds and mammals.", url = "https://doi.org/10.1111/brv.12280", doi = "10.1111/brv.12280", openalex = "W2346237294", references = "doi101002ara20206, doi101016jcub201408034, doi101016jcub201508003, doi101038nature11146, doi101038nature12424, doi101038nature12973, doi101038nature13467, doi101038nature13718, doi101073pnas1203238109, doi101073pnas1519387112, doi101086422766, doi101086425185, doi101098rspb20110238, doi101098rspb20130508, doi101111brv12157, doi101111j1469185x201100190x, doi101126science1180219, doi101126science1200043, doi101126science1206196, doi101126science1213780, doi101126science1228753, doi101126science1253143, doi101126science1253293, doi101371journalpone0068714, doi1016660094837320030290605etatoo20co2, doi1016710272463420050250865hitrif20co2" } @article{doi101111nyas13295, author = "Kapusta, Aurélie and Suh, Alexander", title = "Evolution of bird genomes—a transposon's‐eye view", year = "2016", journal = "Annals of the New York Academy of Sciences", abstract = {Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.}, url = "https://doi.org/10.1111/nyas.13295", doi = "10.1111/nyas.13295", openalex = "W2564972022", references = "doi101038ncomms12087, doi101126science1253293" } @article{doi101642auk152161, author = "Varricchio, David J. and Jackson, Frankie D.", title = "Reproduction in Mesozoic birds and evolution of the modern avian reproductive mode", year = "2016", journal = "The Auk", abstract = "The reproductive biology of living birds differs dramatically from that of other extant vertebrates. Although some attributes of modern avian reproduction had their origin within theropod dinosaurs like oviraptors and troodontids, even the most derived non-avian theropods lack key features of modern birds. We review the current knowledge of reproduction in Mesozoic birds and 3 lines of evidence that contribute to our understanding of the evolution of the modern avian reproductive mode: (1) efforts to define the ancestral reproductive condition on the basis of extant birds, (2) the fossil record of non-avian theropod dinosaurs, and (3) the fossil record of reproduction in primitive Mesozoic birds (e.g., Enantiornithes).", url = "https://doi.org/10.1642/auk-15-216.1", doi = "10.1642/auk-15-216.1", openalex = "W2501766686", references = "doi101007bf00344996, doi101007s0011401209171, doi101016jcub201508003, doi101038nature01342, doi101038srep18952, doi10108002724634199910011125, doi101093icb202373, doi101093icb253807, doi101098rspb20053458, doi101111j109583121976tb00244x, doi101126science28454232137, doi1012067481, doi101371journalpone0082000, doi105962bhltitle50337, openalexw2131558500, openalexw2607033038" } @article{doi101038nature21074, author = "Cooney, Christopher R. and Bright, Jen A. and Capp, Elliot J. R. and Chira, Angela M. and Hughes, Emma C. and Moody, Christopher J. and Nouri, L. O. and Varley, Zoë K. and Thomas, Gavin H.", title = "Mega-evolutionary dynamics of the adaptive radiation of birds", year = "2017", journal = "Nature", url = "https://doi.org/10.1038/nature21074", doi = "10.1038/nature21074", openalex = "W2585565608", references = "doi10100703064746897, doi101016c20100662092, doi101016jcub201508003, doi101038nature10516, doi101038nature11631, doi101038nature15697, doi101073pnas1302642110, doi101093molbevmss075, doi1011112041210x12035, doi101111j2041210x201100169x, doi101126science1157704, doi101126science1160662, doi1018637jssv033i02, doi105860choice485062" } @article{doi101073pnas1716437115, author = "Felice, Ryan N. and Goswami, Anjali", title = "Developmental origins of mosaic evolution in the avian cranium", year = "2017", journal = "Proceedings of the National Academy of Sciences", abstract = "Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families. We find that the avian cranium is highly modular, consisting of seven independently evolving anatomical regions. The face and cranial vault evolve faster than other regions, showing several bursts of rapid evolution. Other modules evolve more slowly following an early burst. Both the evolutionary rate and disparity of skull modules are associated with their developmental origin, with regions derived from the anterior mandibular-stream cranial neural crest or from multiple embryonic cell populations evolving most quickly and into a greater variety of forms. Strong integration of traits is also associated with low evolutionary rate and low disparity. Individual clades are characterized by disparate evolutionary rates among cranial regions. For example, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close relatives, Falconiformes, exhibit rapid evolution in only the rostrum. Our dense sampling of cranial shape variation demonstrates that the bird skull has evolved in a mosaic fashion reflecting the developmental origins of cranial regions, with a semi-independent tempo and mode of evolution across phenotypic modules facilitating this hyperdiverse evolutionary radiation.", url = "https://doi.org/10.1073/pnas.1716437115", doi = "10.1073/pnas.1716437115", openalex = "W2777898995", references = "doi101038nature21074, doi10108010635150802022231, doi101111evo12684, doi101111j155856461996tb04496x" } @article{doi101038s41467018032968, author = "Voeten, Dennis F. A. E. and Cubo, Jorge and de Margerie, Emmanuel and Röper, Martin and Beyrand, Vincent and Bureš, Stanislav and Tafforeau, Paul and Sanchez, Sophie", title = "Wing bone geometry reveals active flight in Archaeopteryx", year = "2018", journal = "Nature Communications", abstract = "Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomotory context. Here, we compare new data from three Archaeopteryx specimens obtained through phase-contrast synchrotron microtomography to a representative sample of archosaurs employing a diverse array of locomotory strategies. Our analyses reveal that the architecture of Archaeopteryx's wing bones consistently exhibits a combination of cross-sectional geometric properties uniquely shared with volant birds, particularly those occasionally utilising short-distance flapping. We therefore interpret that Archaeopteryx actively employed wing flapping to take to the air through a more anterodorsally posteroventrally oriented flight stroke than used by modern birds. This unexpected outcome implies that avian powered flight must have originated before the latest Jurassic.", url = "https://doi.org/10.1038/s41467-018-03296-8", doi = "10.1038/s41467-018-03296-8", openalex = "W2791698505", references = "doi101371journalpone0033539" } @article{doi101111evo13580, author = "Matysioková, Beata and Remeš, Vladimír", title = "Evolution of parental activity at the nest is shaped by the risk of nest predation and ambient temperature across bird species", year = "2018", journal = "Evolution", abstract = "Incubation is an important component of parental care in birds, and species differ widely in their incubation rhythm. In this comparative study, we focused on factors responsible for those differences. As hypothesized by A. Skutch, increased parental activity at the nest increases the probability of nest depredation. High risk of nest predation should therefore lead to the evolution of lower frequency of parental activity at the nest. We thus expected to find a negative relationship between frequency of nest visits and the risk of nest depredation. Using a large dataset of 256 species of passerines breeding worldwide, we found that the frequency of nest visits decreased as the risk of nest depredation increased and that this effect was strongest in tropical species. Further, foraging bouts were longer in species experiencing warmer ambient temperatures during incubation and those with domed nests. Incubation bouts were longer and frequency of nest visits was lower in species with higher body mass. Our results support the view that natural selection favors lower frequency of nests visits in species under higher risk of nest predation and demonstrate the importance of other factors (temperature, geographic space, nest type, and body mass) in shaping the evolution of incubation rhythm.", url = "https://doi.org/10.1111/evo.13580", doi = "10.1111/evo.13580", openalex = "W2890775365", references = "doi101093acprofoso97801987186660030014" } @article{doi101016jcub201910050, author = "Button, David J. and Zanno, Lindsay E.", title = "Repeated Evolution of Divergent Modes of Herbivory in Non-avian Dinosaurs", year = "2019", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2019.10.050", doi = "10.1016/j.cub.2019.10.050", openalex = "W2993362957", references = "doi101002ar23306, doi101002ar23988, doi10100797836426953391, doi101007s0011401411439, doi101007s0042701605392, doi101016jcub201609040, doi101016jcub201610043, doi101016jpalaeo201803006, doi101038nature24679, doi101038ncomms3827, doi101038srep19165, doi101038srep44942, doi101073pnas1310711110, doi101073pnas1319091111, doi10108002724631003763516, doi101080147720192010488045, doi1010801477201920151059985, doi101086414425, doi101093bioinformatics176520, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtm069, doi101098rsos161086, doi101098rspb20110410, doi101098rspb20122526, doi101098rspb20171219, doi101111j2041210x201100169x, doi101371journalpone0078573, doi101371journalpone0079420, doi101371journalpone0092022, doi101371journalpone0098605, doi101371journalpone0112055, doi1017161paleo180818764, doi102307jctvjsf433, doi105281zenodo13315375, doi105860choice396411, doi107717peerj1032, doi107717peerj1523, openalexw2282537990" } @article{doi101016jcub202003060, author = "Ksepka, Daniel T. and Balanoff, Amy M. and Smith, Neil and Bever, Gabriel S. and Bhullar, Bhart‐Anjan S. and Bourdon, Estelle and Braun, Edward L. and Burleigh, J. Gordon and Clarke, Julia A. and Colbert, Matthew W. and Corfield, Jeremy R. and Degrange, Federico J. and Pietri, Vanesa L. De and Early, Catherine and Field, Daniel J. and Gignac, Paul M. and Gold, Maria Eugenia Leone and Kimball, Rebecca T. and Kawabe, Soichiro and Lefebvre, Louis and Marugán‐Lobón, Jesús and Mongle, Carrie S. and Morhardt, Ashley C. and Norell, Mark A. and Ridgely, Ryan C. and Rothman, Ryan S. and Scofield, R. Paul and Tambussi, Claudia P. and Torres, Christopher R. and van Tuinen, Marcel and Walsh, Stig A. and Watanabe, Akinobu and Witmer, Lawrence M. and Wright, Alexandra K. and Zanno, Lindsay E. and Jarvis, Erich D. and Smaers, Jeroen B.", title = "Tempo and Pattern of Avian Brain Size Evolution", year = "2020", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2020.03.060", doi = "10.1016/j.cub.2020.03.060", openalex = "W3017778753", references = "doi101016jcub201804062, doi101038nature12424, doi1012067481, doi101371journalpone0082000" } @article{doi101093molbevmsaa191, author = "Kuhl, Heiner and Frankl‐Vilches, Carolina and Bakker, Antje and Mayr, Gérald and Nikolaus, Gerhard and Boerno, Stefan and Klages, Sven and Timmermann, Bernd and Gahr, Manfred", title = "An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life", year = "2020", journal = "Molecular Biology and Evolution", abstract = "Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90\% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3'-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3'-UTR sequences resulted in a well-resolved and stable tree topology. The 3'-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3'-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life.", url = "https://doi.org/10.1093/molbev/msaa191", doi = "10.1093/molbev/msaa191", openalex = "W3048434366", references = "doi101073pnas1813206116" } @article{doi101111evo14365, author = "Ducatez, Simon and Field, Daniel J.", title = "Disentangling the avian altricial‐precocial spectrum: Quantitative assessment of developmental mode, phylogenetic signal, and dimensionality", year = "2021", journal = "Evolution", abstract = "The altricial-precocial spectrum describes patterns of variation in avian developmental mode that greatly influence avian life histories. Appraising a given species' position on this spectrum is therefore fundamental to understanding patterns of avian life history evolution. However, evaluating avian developmental mode remains a relatively subjective task reliant on untested assumptions, including the notion that developmental strategies are distributed along a single dimension of statistical variation. Here, we present a quantitative multivariate framework that objectively discriminates among meaningfully different modes of avian development. We gathered information on seven hatchling and post-hatching traits for up to 4000 extant bird species, and find that most traits related to developmental mode show high phylogenetic signal and little intraclade variation, allowing unknown values to be reliably interpolated. Principal component analyses (PCAs) of these traits illustrate that most variation in hatchling state can be quantified along one dimension of trait space. However, our PCAs also reveal an important second dimension explaining variation in post-hatching behavior, enabling factors related to hatchling state and post-hatching behavior to be disentangled. In order to facilitate future macroevolutionary studies of variation in avian developmental strategies, as well as explorations of covariation between developmental mode and other aspects of avian biology, we present PC scores for 9993 extant avian species.", url = "https://doi.org/10.1111/evo.14365", doi = "10.1111/evo.14365", openalex = "W3201713273", references = "doi101093acprofoso97801987186660030014" } @article{doi101186s12915021011051, author = "Lowi‐Merri, Talia M. and Benson, Roger and Claramunt, Santiago and Evans, David C.", title = "The relationship between sternum variation and mode of locomotion in birds", year = "2021", journal = "BMC Biology", abstract = "BACKGROUND: The origin of powered avian flight was a locomotor innovation that expanded the ecological potential of maniraptoran dinosaurs, leading to remarkable variation in modern birds (Neornithes). The avian sternum is the anchor for the major flight muscles and, despite varying widely in morphology, has not been extensively studied from evolutionary or functional perspectives. We quantify sternal variation across a broad phylogenetic scope of birds using 3D geometric morphometrics methods. Using this comprehensive dataset, we apply phylogenetically informed regression approaches to test hypotheses of sternum size allometry and the correlation of sternal shape with both size and locomotory capabilities, including flightlessness and the highly varying flight and swimming styles of Neornithes. RESULTS: We find evidence for isometry of sternal size relative to body mass and document significant allometry of sternal shape alongside important correlations with locomotory capability, reflecting the effects of both body shape and musculoskeletal variation. Among these, we show that a large sternum with a deep or cranially projected sternal keel is necessary for powered flight in modern birds, that deeper sternal keels are correlated with slower but stronger flight, robust caudal sternal borders are associated with faster flapping styles, and that narrower sterna are associated with running abilities. Correlations between shape and locomotion are significant but show weak explanatory power, indicating that although sternal shape is broadly associated with locomotory ecology, other unexplored factors are also important. CONCLUSIONS: These results display the ecological importance of the avian sternum for flight and locomotion by providing a novel understanding of sternum form and function in Neornithes. Our study lays the groundwork for estimating the locomotory abilities of paravian dinosaurs, the ancestors to Neornithes, by highlighting the importance of this critical element for avian flight, and will be useful for future work on the origin of flight along the dinosaur-bird lineage.", url = "https://doi.org/10.1186/s12915-021-01105-1", doi = "10.1186/s12915-021-01105-1", openalex = "W3186553905", references = "doi101016jcub202006105, doi103389feart201800252, doi107717peerj2159" } @article{doi101111ele13898, author = "Tobias, Joseph A. and Sheard, Catherine and Pigot, Alex L. and Devenish, Adam J. M. and Yang, Jingyi and Sayol, Ferran and Neate‐Clegg, Montague H. C. and Alioravainen, Nico and Weeks, Thomas and Barber, Robert A. and Walkden, Patrick A. and MacGregor, Hannah E. A. and Jones, Samuel E. I. and Vincent, Claire and Phillips, Anna G. and Marples, Nicola M. and Montaño‐Centellas, Flavia and Leandro‐Silva, Victor and Claramunt, Santiago and Darski, Bianca and Freeman, Benjamin G. and Bregman, Tom P. and Cooney, Christopher R. and Hughes, Emma C. and Capp, Elliot J. R. and Varley, Zoë K. and Friedman, Nicholas R. and Korntheuer, Heiko and Corrales‐Vargas, Andrea and Trisos, Christopher H. and Weeks, Brian C. and Hanz, Dagmar M. and Töpfer, Till and Bravo, Gustavo A. and Remeš, Vladimír and Nowak, Larissa and Carneiro, Lincoln Silva and R., Amilkar J. Moncada and Matysioková, Beata and Baldassarre, Daniel T. and Martínez‐Salinas, Alejandra and Wolfe, Jared D. and Chapman, Philip M. and Daly, Benjamin G. and Sorensen, Marjorie C. and Neu, Alexander and Ford, Michael A. and Mayhew, Rebekah J. and Silveira, Luís Fábio and Kelly, David and Annorbah, Nathaniel N. D. and Pollock, Henry S. and Grabowska-Zhang, Ada and McEntee, Jay P. and Gonzalez, Juan Carlos T. and Meneses, Camila G. and Muñoz, Marcia C. and Powell, Luke L. and Jamie, Gabriel A. and Matthews, Thomas J. and Johnson, Oscar W. and Brito, Guilherme Renzo Rocha and Zyskowski, Kristof and Crates, Ross and Harvey, Michael and Zevallos, Maura Jurado and Hosner, Peter A. and Bradfer‐Lawrence, Tom and Maley, James M. and Stiles, F. Gary and Lima, Hevana S. and Provost, Kaiya L. and Chibesa, Moses and Mashao, Mmatjie and Howard, Jeffrey T. and Mlamba, Edson and Chua, Marcus A.H. and Li, Bicheng and Gómez, María Isabel and García, Natalia C. and Päckert, Martin and Fuchs, Jérôme and Ali, Jarome R. and Derryberry, Elizabeth P. and Carlson, Monica L. and Urriza, Rolly C. and Brzeski, Kristin E. and Prawiradilaga, Dewi M. and Rayner, Matt J. and Miller, Eliot T. and Bowie, Rauri C. K. and Lafontaine, René‐Marie and Scofield, R. Paul and Lou, Yingqiang and Somarathna, Lankani and Lepage, Denis and Illif, Marshall and Neuschulz, Eike Lena and Templin, Mathias and Dehling, D. Matthias", title = "AVONET: morphological, ecological and geographical data for all birds", year = "2022", journal = "Ecology Letters", abstract = "Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.", url = "https://doi.org/10.1111/ele.13898", doi = "10.1111/ele.13898", openalex = "W4213419599", references = "doi101038nature11631, doi101038nature21074, doi101038s4155901704025, doi101111j13652664201102048x, doi101111j14610248201001509x, doi1018900814941, openalexw1904943263" } @article{doi107717peerj13919, author = "Benito, Juan and Chen, Albert and Wilson, Laura E. and Bhullar, Bhart‐Anjan S. and Burnham, David A. and Field, Daniel J.", title = "Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds", year = "2022", journal = "PeerJ", abstract = "Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur-bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19 th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.", url = "https://doi.org/10.7717/peerj.13919", doi = "10.7717/peerj.13919", openalex = "W4312112859", references = "doi101016jcretres200806007, doi101016jcub202006105, doi101016jpalaeo201803006, doi101038s4146701909259x, doi101073pnas1613813113, doi101111brv12666, doi101139cjes20170031, doi101139cjes20200145, doi1012060003009044011, doi101371journalpone0032623, doi10166613052, doi103389fevo2022828006, doi107717peerj1032, doi107717peerj7247, doi107717peerj9192" } @article{doi101038s41586024073231, author = "Stiller, Josefin and Feng, Shaohong and Chowdhury, Al-Aabid and Rivas-González, Iker and Duchêne, David A. and Fang, Qi and Deng, Yuan and Kozlov, Alexey M. and Stamatakis, Alexandros and Claramunt, Santiago and Nguyen, Jacqueline M. T. and Ho, Simon Y. W. and Faircloth, Brant C. and Haag, Julia and Houde, Peter and Cracraft, Joël and Balaban, Metin and Mai, Uyen and Chen, Guangji and Gao, Rongsheng and Zhou, Chengran and Xie, YuLong and Huang, Zijian and Cao, Zhen and Yan, Zhi and Ogilvie, Huw A. and Nakhleh, Luay and Lindow, Bent Erik Kramer and Morel, Benoît and Fjeldså, Jon and Hosner, Peter A. and da Fonseca, Rute R. and Petersen, Bent and Tobias, Joseph A. and Székely, Tamás and Kennedy, Jonathan D. and Reeve, Andrew Hart and Liker, András and Stervander, Martin and Antunes, Agostinho and Tietze, Dieter Thomas and Bertelsen, Mads F. and Lei, Fumin and Rahbek, Carsten and Graves, Gary R. and Schierup, Mikkel Heide and Warnow, Tandy and Braun, Edward L. and Gilbert, M. Thomas P. and Jarvis, Erich D. and Mirarab, Siavash and Zhang, Guojie", title = "Complexity of avian evolution revealed by family-level genomes", year = "2024", journal = "Nature", abstract = "(218 taxonomic families, 92\% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.", url = "https://doi.org/10.1038/s41586-024-07323-1", doi = "10.1038/s41586-024-07323-1", openalex = "W4393371874", references = "doi101038nature21074, doi101073pnas1813206116, doi101139z01204" } @article{doi101038s41586024081144, author = "Chiappe, Luis M. and Navalón, Guillermo and Martinelli, Agustín G. and de Souza Carvalho, Ismar and Santucci, Rodrigo and Wu, Yun-Hsin and Field, Daniel J.", title = "Cretaceous bird from Brazil informs the evolution of the avian skull and brain", year = "2024", journal = "Nature", abstract = ". Navaornis provides long-sought insight into the detailed cranial and endocranial morphology of stem birds phylogenetically crownward of Archaeopteryx, clarifying the pattern and timing by which the distinctive neuroanatomy of living birds was assembled.", url = "https://doi.org/10.1038/s41586-024-08114-4", doi = "10.1038/s41586-024-08114-4", openalex = "W4404305447", references = "doi101007s0011401411439, doi101080027246342012719176, doi101098rsos220519, doi101111cla12524, doi10159023174889201500020001" } @article{doi101073pnas2306639121, author = "Kiat, Yosef and O’Connor, Jingmai K.", title = "Functional constraints on the number and shape of flight feathers", year = "2024", journal = "Proceedings of the National Academy of Sciences", abstract = "have remex morphologies consistent with extant volant birds, that of anchiornithines deviate significantly providing strong evidence this clade was not volant. The results of these analyses support a single origin of dinosaurian flight and indicate the early stages of feathered wing evolution are not sampled by the currently available fossil record.", url = "https://doi.org/10.1073/pnas.2306639121", doi = "10.1073/pnas.2306639121", openalex = "W4391757139", references = "doi101016jcub202006105, doi107717peerj4558, doi107717peerj7247" } @article{doi1010802222175120242398641, author = "Shen, Jinyan and Zhang, Hong and Sun, Xiaohong and Zhang, Yaping and Wang, Meng-Jia and Guan, Mengdi and Liu, Lili and Li, Wenxi and Xu, Hongke and Xie, Yujiao and Ren, Anran and Cao, Fengyan and Liu, Wenqiang and Deng, G. and Guo, Jing and Li, Xuyong", title = "Evolution and biological characteristics of H11 avian influenza viruses isolated from migratory birds and pigeons", year = "2024", journal = "Emerging Microbes \& Infections", abstract = "ABSTRACT The emergence of novel avian influenza reassortants in wild birds in recent years is a public health concern. However, the viruses that circulate in migratory birds are not fully understood. In this study, we summarized and categorized global H11 avian influenza viruses and reported that waterfowl and shorebirds are the major reservoirs of the identified H11 viruses. The surveillance data of the 35,749 faecal samples collected from wild bird habitats in eastern China over the past seven years revealed a low prevalence of H11 viruses in birds, with a positive rate of 0.067\% (24 isolates). The phylogenetic analysis of the twenty viruses indicated that H11 viruses have undergone complex reassortment with viruses circulating in waterfowl and shorebirds. These tested viruses do not acquire mammalian adaptive mutations in their genomes and preferentially bind to avian-type receptors. Experimental infection studies demonstrated that the two tested H11N9 viruses of wild bird origin replicated and transmitted more efficiently in ducks than in chickens, whereas the pigeon H11N2 virus isolated from a live poultry market was more adapted to replicate in chickens than in ducks. In addition, some H11 isolates replicated efficiently in mice and caused body weight loss but were not lethal. Our study revealed the role of waterfowl and shorebirds in the ecology and evolution of H11 viruses and the potential risk of introducing circulating H11 viruses into ducks or chickens, further emphasizing the importance of avian influenza surveillance at the interface of migratory birds and poultry.", url = "https://doi.org/10.1080/22221751.2024.2398641", doi = "10.1080/22221751.2024.2398641", is_oa = "true", number = "1", semanticscholar_citation_count = "9", semanticscholar_id = "6bd2542aae9b9e64692d4af9175e049c6fa3ac6f", volume = "13" } @article{doi101128mbio0254224, author = "Mostafa, Ahmed and Naguib, M. and Nogales, A. and Barre, Ramya S. and Stewart, James P. and García-Sastre, Adolfo and Martínez-Sobrido, Luis", title = "Avian influenza A (H5N1) virus in dairy cattle: origin, evolution, and cross-species transmission", year = "2024", journal = "mBio", abstract = "ABSTRACT Since the emergence of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.3.4.4b as a novel reassortant virus from subtype H5N8, the virus has led to a massive number of outbreaks worldwide in wild and domestic birds. Compared to the parental HPAIV H5N8 clade 2.3.4.4b, the novel reassortant HPAIV H5N1 displayed an increased ability to escape species barriers and infect multiple mammalian species, including humans. The virus host range has been recently expanded to include ruminants, particularly dairy cattle in the United States, where cattle-to-cattle transmission was reported. As with the avian 2.3.4.4.b H5N1 viruses, the cattle-infecting virus was found to transmit from cattle to other contact animals including cats, raccoons, rodents, opossums, and poultry. Although replication of the virus in cows appears to be mainly confined to the mammary tissue, with high levels of viral loads detected in milk, infected cats and poultry showed severe respiratory disease, neurologic signs, and eventually died. Furthermore, several human infections with HPAIV H5N1 have also been reported in dairy farm workers and were attributed to exposures to infected dairy cattle. This is believed to represent the first mammalian-to-human transmission report of the HPAIV H5N1. Fortunately, infection in humans and cows, as opposed to other animals, appears to be mild in most cases. Nevertheless, the H5N1 bovine outbreak represents the largest outbreak of the H5N1 in a domestic mammal close to humans, increasing the risk that this already mammalian adapted H5N1 further adapts to human-to-human transmission and starts a pandemic. Herein, we discuss the epidemiology, evolution, pathogenesis, and potential impact of the recently identified HPAIV H5N1 clade 2.3.4.4b in dairy cattle in the United States. Eventually, interdisciplinary cooperation under a One Health framework is required to be able to control this ongoing HPAIV H5N1 outbreak to stop it before further expansion of its host range and geographical distribution.", url = "https://www.semanticscholar.org/paper/e7ff7f483063038e9c5b4035221f838bf3df1b42", doi = "10.1128/mbio.02542-24", is_oa = "true", number = "12", semanticscholar_citation_count = "93", semanticscholar_id = "e7ff7f483063038e9c5b4035221f838bf3df1b42", volume = "15" } @article{doi103201eid3002231274, author = "Seo, Yeram and Cho, A. Y. and Si, Young-Jae and Lee, Song-I and Kim, Dong-ju and Jeong, Hyesung and Kwon, J. and Song, Chang-Seon and Lee, Dong-Hun", title = "Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea, 2022–2023", year = "2024", journal = "Emerging Infectious Diseases", abstract = "During October 2022–March 2023, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus caused outbreaks in South Korea, including 174 cases in wild birds. To understand the origin and role of wild birds in the evolution and spread of HPAI viruses, we sequenced 113 HPAI isolates from wild birds and performed phylogenetic analysis. We identified 16 different genotypes, indicating extensive genetic reassortment with viruses in wild birds. Phylodynamic analysis showed that the viruses were most likely introduced to the southern Gyeonggi-do/northern Chungcheongnam-do area through whooper swans (Cygnus cygnus) and spread southward. Cross-species transmission occurred between various wild bird species, including waterfowl and raptors, resulting in the persistence of HPAI in wild bird populations and further geographic spread as these birds migrated throughout South Korea. Enhanced genomic surveillance was an integral part of the HPAI outbreak response, aiding in timely understanding of the origin, evolution, and spread of the virus.", url = "https://doi.org/10.3201/eid3002.231274", doi = "10.3201/eid3002.231274", is_oa = "true", number = "2", semanticscholar_citation_count = "25", semanticscholar_id = "08699a44f5deb400b77d2d76fc0e0239ecbed07a", volume = "30" } @article{doi101016jcub202510086, author = "Bronzati, Mario and Watanabe, Akinobu and Benson, Roger B J and Müller, Rodrigo T and Witmer, Lawrence M and Ezcurra, Martín D and Montefeltro, Felipe C and Belén von Baczko, M and Bhullar, Bhart-Anjan S and Desojo, Julia B and Knoll, Fabien and Langer, Max C and Lautenschlager, Stephan and Stocker, Michelle R and Turner, Alan H and Werneburg, Ingmar and Nesbitt, Sterling J and Fabbri, Matteo", title = "Neuroanatomical convergence between pterosaurs and non-avian paravians in the evolution of flight.", year = "2025", journal = "Current biology: CB", abstract = "The oldest known pterosaurs lived approximately 220 million years ago1 and were already animals capable of powered flight,2 an ability that later evolved independently among paravian dinosaurs, the group that includes living birds and their closest non-avian relatives.3 Flight is a complex locomotory mode that requires physiological adaptations4 and a dramatic transformation of the body plan, including changes in body proportions, specialized integument, and acquisition of novel neurosensory capabilities.5 Although pterosaurs and birds developed distinct skeletal and integumentary adaptations for flight, they are hypothesized to share neuroanatomical traits linked to aerial locomotion.6,7,8,9 Here, we use geometric morphometrics and phylogenetically informed analyses to assess the origin and evolution of brain shape and size in pterosaurs, tracing the transformation from their non-volant closest relatives (lagerpetids), and compare their trajectory with that in the dinosaur-bird transition. Pterosaurs have globular brains with moderately enlarged hemispheres, more closely resembling non-avian paravians such as troodontids and Archaeopteryx lithographica than living birds. Whereas birds inherited their basic brain structure from their dinosaurian ancestors,10,11,12,13,14,15,16,17 pterosaurs share only the ventrolateralization of the optic lobe with their closest non-volant relatives, the lagerpetids. This suggests that, in contrast to the bird-line archosaurs, where exaptation may have played a central role in the stepwise assembly of the avian brain configuration, brain evolution in pterosaurs seems to have unfolded rapidly at the origin of flight.", url = "https://pubmed.ncbi.nlm.nih.gov/41308650/", doi = "10.1016/j.cub.2025.10.086", openalex = "W4416702051", pmid = "41308650", references = "doi101007bf02291478, doi101016jcub201609040, doi101038nature02048, doi101038nature02706, doi101093bioinformaticsbty633, doi101098rstb19890106, doi1011112041210x12035, doi101111j2041210x201100169x, doi101111j2041210x201200223x, doi1023072992207" } @article{doi101038s41559025027954, author = "Lowi-Merri, Talia M and Benson, Roger and Hu, Han and O'Connor, Jingmai and Claramunt, Santiago and Evans, David C", title = "Enlargement of sternum traits facilitated the evolution of powered flight in birds.", year = "2025", journal = "Nature ecology \& evolution", abstract = "An enlarged sternum with a prominent keel is a central feature of the flight apparatus of modern birds. However, sterna of near-bird dinosaurs (Pennaraptora) and early avialans are either substantially different from those of living birds or absent altogether, raising questions about how specialized sternal structures evolved in birds and how they are related to function. This remains poorly understood because of the fragmentary nature of the fossil record, and the challenges in inferring form and function from crushed fossils. We use ancestral character estimations to trace sternal trait acquisition through the bird stem group, and multivariate phylogenetic regressions to analyse relationships between sternum morphology, body mass and flight capabilities. We find that sternum evolution was episodic: basal members of Pennaraptora had proportionally small sterna, which became larger and more craniocaudally elongated in Avialae. This enlargement precedes the appearance of a midline ridge, a possible precursor of the sternal keel, in Pygostylia. Sternum size increased again in crownward Ornithuromorpha, alongside a fully formed sternal keel and enlarged caudal projections, both critical areas of flight muscle attachment. Sternal experimentation in relation to flight characteristics occurs several times throughout Pennaraptora, including within Paraves and Enantiornithes, indicating that powered flight may have evolved several times before proliferating in crown-group birds.", url = "https://pmc.ncbi.nlm.nih.gov/articles/5548695/", doi = "10.1038/s41559-025-02795-4", openalex = "W4412640183", pmcid = "5548695", pmid = "40707813", references = "doi101038nature11631, doi101038nature15697, doi101038nmeth2089, doi10108003610927808827599, doi101080106351501753462876, doi101086284325, doi101098rstb19890106, doi101109tac19741100705, doi101111j2041210x201100169x, doi10118614712105788" } @article{doi101038s41559025028171, title = "Bird sternum evolution facilitated the origins of powered flight", year = "2025", journal = "Nature Ecology \& Evolution", url = "https://www.semanticscholar.org/paper/183da9f6dc3a6510df3b1249649fdcf0971cc9b6", doi = "10.1038/s41559-025-02817-1", is_oa = "true", number = "9", pages = "1560-1561", semanticscholar_id = "183da9f6dc3a6510df3b1249649fdcf0971cc9b6", volume = "9" } @article{doi101038s41586025089124, author = "O’Connor, Jingmai K. and Clark, Alexander D. and Kuo, Pei‐Chen and Kiat, Yosef and Fabbri, Matteo and Shinya, Akiko and Beek, Constance Van and Lu, Jing and Wang, Min and Hu, Han", title = "Chicago Archaeopteryx informs on the early evolution of the avian bauplan", year = "2025", journal = "Nature", url = "https://doi.org/10.1038/s41586-025-08912-4", doi = "10.1038/s41586-025-08912-4", openalex = "W4410362148", references = "doi101007s0011401411439" } @article{doi101073pnas2411138122, author = "Wilken, A. T. and Sellers, K. and Cost, Ian N and Davis, Julian and Middleton, K. M. and Witmer, L. and Holliday, C.", title = "Avian cranial kinesis is the result of increased encephalization during the origin of birds", year = "2025", journal = "Proceedings of the National Academy of Sciences of the United States of America", abstract = "Significance Biomechanical innovations are the underpinning of many great transitions in vertebrate evolution. The origin of birds is marked by radical transformations of the braincase, palate, and snout into a kinetic feeding system. New fossil discoveries hint that palate mechanics have played a crucial role in the diversification and success of birds, yet to date, there is no rigorous biomechanical framework for interpreting palate function in birds and other theropod dinosaurs. Here, we use three dimensional (3D) muscle modeling and linkage analysis to elucidate the origins of powered cranial kinesis in avian dinosaurs. Powered cranial kinesis did not evolve until neognaths. This study highlights the importance of integrating biomechanical modeling and phylogenetic methods for understanding key innovations in the origins of major clades.", url = "https://www.semanticscholar.org/paper/0dba1d1361894d176f61559cc2fad072475e34a6", doi = "10.1073/pnas.2411138122", is_oa = "true", number = "13", semanticscholar_citation_count = "7", semanticscholar_id = "0dba1d1361894d176f61559cc2fad072475e34a6", volume = "122" } @article{doi1010802222175120252465308, author = "Wu, Jiaying and Zhang, Xiaoqing and Zhao, Yubo and Zhang, Shunyuan and Wang, Yanhai and Yang, Wenxue and Liu, Haizhou and Feng, Jiangpeng and Tan, Wenzhuo and Wang, Ke and Shi, Qianqian and Wei, Qichao and Sun, Jianqing and Zhang, Yuan and Chen, Jianjun", title = "North American-origin influenza A (H10) viruses in Eurasian wild birds (2022–2024): implications for the emergence of human H10N5 virus", year = "2025", journal = "Emerging Microbes \& Infections", abstract = "ABSTRACT During our surveillance of avian influenza viruses (AIVs) in wild birds across China, H10Nx viruses were isolated from diverse migratory flyways between 2022 and 2024. We identified one wild-bird H10N5 strain that shared a common ancestor with the human H10N5 virus in multiple gene segments. Phylogenetic and molecular dating revealed the origin and evolution of H10N5, highlighting the need for continued monitoring.", url = "https://doi.org/10.1080/22221751.2025.2465308", doi = "10.1080/22221751.2025.2465308", is_oa = "true", number = "1", semanticscholar_citation_count = "2", semanticscholar_id = "b22187d706f8048cab83fe2829808937fdd84e9a", volume = "14" } @article{doi101093zoolinneanzlaf149, author = "Duan, Menghan and Li, Li and Wang, Shiying and Stidham, Thomas A. and Wang, Renfei and Dong, Xinwei and Hu, Dongyu", title = "Morphology of the forelimb of Confuciusornis and its implications for early flight evolution", year = "2025", journal = "Zoological Journal of the Linnean Society", abstract = "Abstract The morphological transformation of a highly mobile, grasping forelimb into a flapping wing is a key transition in the evolution of bird flight. This evolutionary transformation is characterized by more canalized (restricted) elbow and wrist mobility and a diminished prehensile (grasping) ability of the digits, requiring a suite of osteological modifications. Here, we employ micro-computed tomographic (μCT) imaging to reconstruct the forelimbs of Confuciusornis based on a new specimen from the Lower Cretaceous Jehol Group in western Liaoning, China. Our rendering is the first three-dimensional reconstruction of the forelimb for this key Early Cretaceous bird, revealing critical osteological details that advance our understanding of early flight evolution. The reconstruction reveals previously unrecognized features including canalized structures in the elbow and wrist joints, a relatively smaller triangular pisiform, a hook-like projection on the alular metacarpal, and distinctive digital morphology. We provide detailed morphological descriptions of the elbow, wrist, and metacarpophalangeal and interphalangeal joints, which are essential for evaluating flight capabilities, forelimb folding mechanics, and manual grasping ability. Furthermore, our data support the presence of a cushion-like bone at the distal end of the alular metacarpal of Confuciusornis and demonstrate fusion of this cushion-like bone with the cranial condyle.", url = "https://doi.org/10.1093/zoolinnean/zlaf149", doi = "10.1093/zoolinnean/zlaf149", openalex = "W4416294577", references = "doi101016jxinn2025101086, doi10103835047056, doi10103845769, doi101038nature00930, doi101038nature08322, doi101038s41586025092323, doi101038s42003022043166, doi101111j10963642200600245x, doi101111j14697580200800880x, doi101126science1078237, doi101139e03011, doi1012060003009020042860001mptaso20co2, sereno1997the" } @article{doi101098rspb20251647, author = "Orkney, Andrew and Rothier, Priscila S and Hedrick, Brandon P", title = "Great expectations: altricial developmental strategies are associated with more flexible evolution of limb skeleton proportions in birds.", year = "2025", journal = "Proceedings. Biological sciences", abstract = "Birds have repeatedly evolved diverse developmental strategies, including multiple origins of sophisticated parental care, making them a model system to explore the consequences of developmental strategy upon phenotypic evolution. Here, we assess evolutionary covariance between limb proportions and ecological diversity of different bird lineages with altricial (high parental care) or precocial (lower parental care) developmental strategies. In addition, we model overall rates of evolutionary divergence between wing and leg skeletal proportions, allowing us to investigate the influence of developmental strategy upon adaptive traits. We show that while wing and leg proportions evolve independently of one another in altricial lineages, conforming to a modular pattern of evolution attested in birds more generally, there are strong correlations between wing and leg trait evolution in precocial lineages. Unlike precocial groups, divergent wing and leg evolution in altricial lineages is associated with access to novel flight-style combinations and is strongly associated with body mass. This suggests an adaptive association with mechanisms of growth and development. Inspection of internal wing proportions within major clades demonstrates that lineages with more altricial developmental strategies explore a wider range of mechanically relevant wing proportions, such as Brachial Index.", url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12503937/", doi = "10.1098/rspb.2025.1647", openalex = "W4414903818", pmcid = "PMC12503937", pmid = "41057007", references = "doi101007s1169200990765, doi101016jcageo200611017, doi101016jcub201910009, doi101038nature01342, doi101080106351500750049806, doi101086303327, doi101093oso97801951060840010001, doi1011112041210x12420, doi101111j2041210x201100169x, doi1023072529140" } @article{doi10110120250404647043, author = "Marek, Ryan D. and Felice, R.", title = "Correlated evolution of the neck, head and forelimb across the theropod-bird transition", year = "2025", journal = "bioRxiv", abstract = "Powered flight has required birds to undergo numerous dramatic and coordinated evolutionary responses across the entire body, yet studies are limited to a small number of traits and often exclude a critical component of the vertebrate skeleton – the vertebrae. The neck is a critical region of the avian spine as it operates in tandem with the head as a surrogate forelimb across a diverse array of behaviours. However, the drivers of cervical vertebral evolution remain poorly understood. Here, we model shifts in adaptive optima and evolutionary rates of the neck, forelimb and head of extinct dinosaurs and extant birds to test if these modules co-evolved. We observe a co-occurrence of adaptive optima shifts for neck and forelimb proportion at the base of Avialae – to vertebrae adapted for stability and a forelimb better adapted for flight. These patterns are due to shifts in neck and forelimb allometry and suggest that heterochrony is an important factor in avian neck and forelimb evolution. Further, we find lower rates of both neck and forelimb evolution in birds compared to their non-avian theropod ancestors. The coordinated evolutionary response of the neck and forelimb is a derived feature of Avialae that initially evolved to stabilise in-flight vision. This axio-appendicular co-evolution has contributed to avian macroevolutionary dynamics by facilitating the evolution of a novel locomotory mode without sacrificing the grasping capability needed to directly interact with a huge diversity of environments.", url = "https://www.semanticscholar.org/paper/0469bdab98282bba8d963cd2c4532dcb93f64b1c", doi = "10.1101/2025.04.04.647043", is_oa = "true", semanticscholar_id = "0469bdab98282bba8d963cd2c4532dcb93f64b1c" } @article{doi101186s1286202502454z, author = "Lo Coco, Gastón E and Motta, Matías J and Agnolín, Federico L and Novas, Fernando E", title = "Reconstruction of pectoral musculature in non-avialan paravians and basal birds: implications in the acquisition of flapping flight.", year = "2025", journal = "BMC ecology and evolution", abstract = "Several studies analyzed the origin of flapping birds, but only a few of them explored the scapular girdle myology in early birds and non-avian paravians. We analyze the pectoral girdle morphology in different groups of non-ornithothoracine paravians with the aim to hypothesize the anchorage sites of selected pectoral muscles and determine their main functions in forelimb movements. Notably, the pectoral girdle remained morphologically stable among non-ornithothoracine paravians since certain aspects of the coracoid and scapula are similar in non-flying taxa, such as the cursorial Buitreraptor, as well as those with the ability to fly, such as the four-winged Microraptor, the long-tailed Archaeopteryx and the pygostylians Confuciusornis and Sapeornis. The distinctions among these taxa are slightly discernible in bone morphology, but they are obvious in the forelimbs feather coverage. In this sense, main pectoral muscles (i.e., mm. supracoracoideus, pectoralis and deltoideus scapularis/major) had similar origin and insertion places, and their inferred functions were similar across a wide array of body shapes of early paravians. The most significant muscular changes occurred in the common ancestor of Pygostylia, and consisted in the displacement of the origin of the mm. biceps brachii and coracobrachialis p. cranialis, accompanying the greater development of the acrocoracoid process and the loss of the subglenoid fossa. These modifications allowed more muscles to participate in humeral protraction and in the maintenance of wing extension. Subsequently, in the Ornithothoraces node, coracoid transformations contributed to the medial reorientation of the supracoracoidal canal thus allowing the m. supracoracoideus to fulfill a wing elevation function. Our study suggests that in non-ornithothoracine paravians, the main movements of the forelimb (either fliers or not) were predominantly craniodorsal to caudoventral. The humeral movements were performed in a similar manner, in which the main elevators were the mm. deltoideus and latissimus dorsi group, while the mm. supracoracoideus and pectoralis would have acted as protractor and depressor, respectively. Therefore, the ability to maintain a continuous flapping flight present in extant volant birds may have been acquired at the Ornithothoraces node, while Archaeopterygidae, Confuciusornithidae and Omnivoropterygidae may have had functional flight, short in duration and space displacement.", url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12548140/", doi = "10.1186/s12862-025-02454-z", openalex = "W4415467005", pmcid = "PMC12548140", pmid = "41131457", references = "doi101002ara10097, doi101016jcub201508003, doi101038nature02855, doi101038nature08322, doi101038nature12059, doi101038nature24679, doi101038s41559025027954, doi101086407902, doi101126science1078237, doi101126science1253293, doi1012067481" } @article{doi101016jxinn2025101086, author = "O'Connor, Jingmai K and Clark, Alexander D and Kuo, Pei-Chen and Wang, Min and Shinya, Akiko and Van Beek, Constance and Chang, Huali", title = "Avian features of Archaeopteryx feeding apparatus reflect elevated demands of flight.", year = "2026", journal = "Innovation (Cambridge (Mass.))", abstract = "Powered flight, as the most physically demanding form of vertebrate locomotion, involves elevated energetic demands. The appearance of dinosaurian flight should therefore be associated with novel features related to increased feeding or digestive efficiency. Neornithines have several unique rostral features that facilitate complex oral tasks, increasing feeding efficiency; these include a mechanoreceptive bill-tip organ, highly mobile tongue, and oral papillae. Here, we provide the first evidence for the presence of these features in Archaeopteryx, the oldest known avian dinosaur. Large neurovascular openings at the tip of both the upper and lower jaw indicate the neurovasculature contained within the sensitive rostrum of non-avian theropods exited the tip of the snout. This suggests the presence of a mechanoreceptive soft tissue structure that was apparently widespread in early-diverging toothed birds, adding to the recognized structural diversity of the avian bill-tip organ. The co-occurrence of soft tissue oral papillae and an ossified basihyal indicative of increased tongue mobility is consistent with the interdependence of these structures in extant birds. The appearance of these three features close to the origin of feather-driven flight suggests that they evolved through pressures imposed by the increased caloric demands associated with the transition from terrestrial predator to volant bird.", url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12881756/", doi = "10.1016/j.xinn.2025.101086", openalex = "W4413738998", pmcid = "PMC12881756", pmid = "41658498", references = "doi101016jcub202006105, doi101038nature12424, doi101038nature13467, doi101038nature15697, doi101038nature24679, doi101073pnas1813206116, doi101111j2041210x201200223x, doi101126science1258750, doi101371journalpbio1001853, doi107717peerj16505" }