Gatesy, S. M. in Functional Morphology in Vertebrate Paleontology (ed. Thomason, J. J.) 219–234 (Cambridge University Press, 1995).
Hutchinson, J. R. The evolution of pelvic osteology and soft tissues on the line to extant birds (Neornithes). Zool. J. Linnean Soc. 131, 123–168 (2001).
Google Scholar
Turner, A. H., Makovicky, P. J. & Norell, M. A. A review of dromaeosaurid systematics and paravian phylogeny. Bull. Am. Museum Nat. Hist. 371, 1–206 (2012).
Google Scholar
Ostrom, J. H. On a new specimen of the Lower Cretaceous theropod dinosaur Deinonychus antirrhopus. Breviora 439, 1–21 (1976).
Bunge, A. Untersuchungen zur Entwickelungsgeschichte des Beckengürtels der Amphibien, Reptilien, und Vögel. PhD thesis, Universität Dorpat (1880).
Johnson, A. On the development of the pelvic girdle and skeleton of the hind limb of the chick. Q. J. Microsc. Sci. 23, 399–411 (1883).
Mehnert, E. Untersuchungen über die entwisklung des os pelvis der vögel. Morphologisches Jahrbuch 13, 259–295 (1887).
Gould, S. J. Ontogeny and Phylogeny (Harvard University Press, 1977).
Mayr, E. Recapitulation reinterpreted: the somatic program. Q. Rev. Biol. 69, 223–232 (1994).
Google Scholar
Abzhanov, A. von Baer’s law for the ages: lost and found principles of developmental evolution. Trends Genet. 29, 712–722 (2013).
Google Scholar
Diogo, R., Smith, C. M. & Ziermann, J. M. Evolutionary developmental pathology and anthropology: a new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine. Dev. Dyn. 244, 1357–1374 (2015).
Google Scholar
Ksepka, D. T. Feathered dinosaurs. Curr. Biol. 30, R1347–R1353 (2020).
Google Scholar
Lowe, C. B., Clarke, J. A., Baker, A. J., Haussler, D. & Edwards, S. V. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol. Biol. Evol. 32, 23–28 (2015).
Bhullar, B.-A. S. et al. How to make a bird skull: major transitions in the evolution of the avian cranium, paedomorphosis, and the beak as a surrogate hand. Integr. Comp. Biol. 56, 389–403 (2016).
Google Scholar
Fabbri, M. et al. The skull roof tracks the brain during the evolution and development of reptiles including birds. Nat. Ecol. Evol. 1, 1543–1550 (2017).
Google Scholar
Bhullar, B.-A. S. et al. A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution 69, 1665–1677 (2015).
Google Scholar
Louchart, A. & Viriot, L. From snout to beak: the loss of teeth in birds. Trends Ecol. Evol. 26, 663–673 (2011).
Google Scholar
O’Connor, P. M. Evolution of archosaurian body plans: skeletal adaptations of an air-sac-based breathing apparatus in birds and other archosaurs. J. Exp. Zool. A 311A, 629–646 (2009).
Google Scholar
Heers, A. M. & Dial, K. P. From extant to extinct: locomotor ontogeny and the evolution of avian flight. Trends Ecol. Evol. 27, 296–305 (2012).
Google Scholar
Mayr, G. Evolution of avian breeding strategies and its relation to the habitat preferences of Mesozoic birds. Evol. Ecol. 31, 131–141 (2017).
Google Scholar
Gatesy, S. M. Caudofemoral musculature and the evolution of theropod locomotion. Paleobiology 16, 170–186 (1990).
Google Scholar
Gatesy, S. M. & Dial, K. P. Locomotor modules and the evolution of avian flight. Evolution 50, 331–340 (1996).
Google Scholar
Hutchinson, J. R. The evolution of locomotion in archosaurs. C. R. Palevol. 5, 519–530 (2006).
Google Scholar
Hutchinson, J. R. & Gatesy, S. M. Adductors, abductors, and the evolution of archosaur locomotion. Paleobiology 26, 734–751 (2000).
Google Scholar
Organ, C. L., Shedlock, A. M., Meade, A., Pagel, M. & Edwards, S. V. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446, 180–184 (2007).
Gegenbaur, C. Gundriss der Vergleichenden Anatomie (Engelmann, 1878).
Huxley, T. H. Further evidence of the affinity between the dinosaurian reptiles and birds. Q. J. Geol. Soc. Lond. 26, 12–31 (1870).
Google Scholar
Carroll, S. B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134, 25–36 (2008).
Google Scholar
Romer, A. S. The development of the thigh musculature of the chick. J. Morphol. Physiol. 43, 347–385 (1927).
Google Scholar
Schroeter, S. & Tosney, K. W. Spatial and temporal patterns of muscle cleavage in the chick thigh and their value as criteria for homology. Am. J. Anat. 191, 325–350 (1991).
Google Scholar
Kardong, K. V. Vertebrates: Comparative Anatomy, Function, Evolution 8th edn (McGraw-Hill Education, 2019).
Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).
Google Scholar
Egawa, S., Saito, D., Abe, G. & Tamura, K. Morphogenetic mechanism of the acquisition of the dinosaur-type acetabulum. R. Soc. Open Sci. 5, 180604 (2018).
Google Scholar
Hutchinson, J. R. The evolution of hindlimb tendons and muscles on the line to crown-group birds. Comp. Biochem. Physiol. A 133, 1051–1086 (2002).
Google Scholar
Giffin, E. B. Postcranial paleoneurology of the Diapsida. J. Zool. 235, 389–410 (1995).
Google Scholar
Carpenter, E. M. Hox genes and spinal cord development. Dev. Neurosci. 24, 24–34 (2002).
Google Scholar
Gaunt, S. J. Evolutionary shifts of vertebrate structures and Hox expression up and down the axial series of segments: a consideration of possible mechanisms. Int. J. Dev. Biol. 44, 109–117 (2000).
Google Scholar
Diogo, R., Ziermann, J., Molnar, J., Siomava, N. & Abdala, V. Muscles of Chordates: Development, Homologies and Evolution (Taylor & Francis, 2018).
Felice, R. N., Randau, M. & Goswami, A. A fly in a tube: macroevolutionary expectations for integrated phenotypes. Evolution 72, 2580–2594 (2018).
Google Scholar
Olson, E. C. & Miller, R. L. Morphological Integration (University of Chicago Press, 1958).
Schlosser, G. in Modularity in Development and Evolution (eds Schlosser, G. & Wagner, G. P.) 519–582 (University of Chicago Press, 2004).
Lee, H. W., Esteve-Altava, B. & Abzhanov, A. Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs. Sci. Rep. 10, 16138 (2020).
Google Scholar
Felice, R. N. et al. Evolutionary integration and modularity in the archosaur cranium. Integr. Comp. Biol. 59, 371–382 (2019).
Google Scholar
Goswami, A., Smaers, J. B., Soligo, C. & Polly, P. D. The macroevolutionary consequences of phenotypic integration: from development to deep time. Philos. Trans. R. Soc. B 369, 20130254 (2014).
Google Scholar
Iijima, M. & Kobayashi, Y. Convergences and trends in the evolution of the archosaur pelvis. Paleobiology 40, 608–624 (2014).
Google Scholar
Adams, D. C. Evaluating modularity in morphometric data: challenges with the RV coefficient and a new test measure. Methods Ecol. Evol. 7, 565–572 (2016).
Google Scholar
Bjarnason, A. & Benson, R. A 3D geometric morphometric dataset quantifying skeletal variation in birds. MorphoMuseuM 7, e125 (2021).
Google Scholar
Giffin, E. B. Endosacral enlrgements in dinosaurs. Mod. Geol. 16, 101–112 (1991).
Giffin, E. B. Paleoneurology: reconstructing the nervous systems of dinosaurs. Paleontol. Soc. Special Pub. 7, 229–242 (1994).
Google Scholar
Ferguson, M. W. J. in Biology of the Reptilia Vol. 14 (eds Gans, C. et al.) 329–492 (John Wiley and Sons, 1985).
Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49–92 (1951).
Google Scholar
Ainsworth, S. J., Stanley, R. L. & Evans, D. J. R. Developmental stages of the Japanese quail. J. Anat. 216, 3–15 (2010).
Google Scholar
Dingerkus, G. & Uhler, D. Enzyme clearing of Alcian blue stained whole small vertebrates for demonstration of cartilage. Stain Technol. 52, 229–232 (1977).
Google Scholar
Ovchinnikov, D. Alcian blue/Alizarin red staining of cartilage and bone in mouse. Cold Spring Harbor Protoc. 2009, pdb.prot5170 (2009).
Google Scholar
Rigueur, D. & Lyons, K. M. Whole-mount skeletal staining. Methods Mol. Biol. 1130, 113–121 (2014).
Google Scholar
Schultze, O. Ueber herstellung und conservirung durchsichtiger embryonen zum stadium der skeletbildung. Anatomischer Anzeiger 13, 3–5 (1897).
Horobin, R. W. in Educational Guide Special Stains and H&E 2nd edn (eds Kumar, G. L. & Kiernan, J. A.) 159–166 (Carpinteria, 2010).
Carril, J., Tambussi, C. P. & Rasskin-Gutman, D. The network ontogeny of the parrot: altriciality, dynamic skeletal assemblages, and the avian body plan. Evol. Biol. 48, 41–53 (2021).
Google Scholar
Maxwell, E. E. Comparative embryonic development of the skeleton of the domestic turkey (Meleagris gallopavo) and other galliform birds. Zoology 111, 1095–1113 (2008).
Google Scholar
Maxwell, E. E. Ossification sequence of the avian order Anseriformes, with comparison to other precocial birds. J. Morphol. 269, 1095–1113 (2008).
Google Scholar
Maxwell, E. E. & Harrison, L. B. Ossification sequence of the common tern (Sterna hirundo) and its implications for the interrelationships of the Lari (Aves, Charadriiformes). J. Morphol. 269, 1056–1072 (2008).
Google Scholar
Maxwell, E. E. & Larsson, H. C. E. Comparative ossification sequence and skeletal development of the postcranium of palaeognathous birds (Aves: Palaeognathae). Zool. J. Linnean Soc. 157, 169–196 (2009).
Google Scholar
Ikeda, T. et al. Distinct roles of Sox5, Sox6, and Sox9 in different stages of chondrogenic differentiation. J. Bone Mineral Metab. 23, 337–340 (2005).
Google Scholar
Lefebvre, V., Behringer, R. R. & de Crombrugghe, B. L-Sox5, Sox6 and Sox9 control essential steps of the chondrocyte differentiation pathway. Osteoarthritis Cartilage 9, S69–S75 (2001).
Google Scholar
Smits, P. et al. The transcription factors L-Sox5 and Sox6 are essential for cartilage formation. Dev. Cell 1, 277–290 (2001).
Google Scholar
Cancedda, R., Castagnola, P., Cancedda, F. D., Dozin, B. & Quarto, R. Developmental control of chondrogenesis and osteogenesis. Int. J. Dev. Biol. 44, 707–714 (2000).
Google Scholar
Eames, B. F., De La Fuente, L. & Helms, J. A. Molecular ontogeny of the skeleton. Birth Defects Res. C 69, 93–101 (2003).
Google Scholar
Miller, E. J. & Matukas, V. J. Chick cartilage collagen: a new type of α1 chain not present in bone or skin of the species. Proc. Natl Acad. Sci. USA 64, 1264–1268 (1969).
Google Scholar
Zhang, G., Eames, B. F. & Cohn, M. J. Evolution of vertebrate cartilage development. Curr. Topics Dev. Biol. 86, 15–42 (2009).
Google Scholar
Ninomiya, Y., Showalter, A. & Olsen, B. in The Role of Extracellular Matrix in Development (ed. Trelstad, R. L.) 255–275 (Alan R. Liss, 1984).
Botelho, J. F., Smith-Paredes, D., Nuñez-Leon, D., Soto-Acuña, S. & Vargas, A. O. The developmental origin of zygodactyl feet and its possible loss in the evolution of Passeriformes. Proc. R. Soc. B 281, 20140765 (2014).
Google Scholar
Botelho, J. F. et al. Skeletal plasticity in response to embryonic muscular activity underlies the development and evolution of the perching digit of birds. Sci. Rep. 5, 09840 (2015).
Google Scholar
Huh, J. W., Laurer, H. L., Raghupathi, R., Helfaer, M. A. & Saatman, K. E. Rapid loss and partial recovery of neurofilament immunostaining following focal brain injury in mice. Exp. Neurol. 175, 198–208 (2002).
Google Scholar
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Google Scholar
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
Google Scholar
Bookstein, F. L. Morphometric Tools for Landmark Data: Geometry and Biology (Cambridge University Press, 1997).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).
Geomorph: software for geometric morphometric analyses (R package version 3.2.1) (2020).
Rohlf, F. J. The TPS series of software. Hystrix 26, 9–12 (2015).
Charrad, M., Ghazzali, N., Boiteau, V. & Niknafs, A. NbClust: an R package for determining the relevant number of clusters in a data set. J. Stat. Softw. 61, 1–36 (2014).
Google Scholar
Buser, T. J., Sidlauskas, B. L. & Summers, A. P. 2D or not 2D? Testing the utility of 2D vs. 3D landmark data in geometric morphometrics of the sculpin subfamily Oligocottinae (Pisces; Cottoidea). Anat. Rec. 301, 806–818 (2018).
Google Scholar
Oksanen, J. et al. vegan: community ecology package (R package version 2.5-7). https://CRAN.R-project.org/package=vegan (2020).
Adams, D. C., Rohlf, F. J. & Slice, D. E. A field comes of age: geometric morphometrics in the 21st century. Hystrix 24, 7–14 (2013).
Theska, T., Sieriebriennikov, B., Wighard, S. S., Werner, M. S. & Sommer, R. J. Geometric morphometrics of microscopic animals as exemplified by model nematodes. Nat. Protoc. 15, 2611–2644 (2020).
Google Scholar
Goodall, C. Procrustes methods in the statistical analysis of shape. J. R. Stat. Soc. B 53, 285–339 (1991).
Google Scholar
Drake, A. G. & Klingenberg, C. P. The pace of morphological change: historical transformation of skull shape in St Bernard dogs. Proc. Biol. Sci. 275, 71–76 (2008).
Google Scholar
Friendly, M. HE plots for repeated measures designs. J. Stat. Softw. 37, 1–40 (2010).
Google Scholar
Agnolin, F. L., Motta, M. J., Brissón Egli, F., Lo Coco, G. & Novas, F. E. Paravian phylogeny and the dinosaur–bird transition: an overview. Front. Earth Sci. 6, 252 (2019).
Google Scholar
Erickson, G. M. et al. Insights into the ecology and evolutionary success of crocodilians revealed through bite-force and tooth-pressure experimentation. PLoS ONE 7, e31781 (2012).
Google Scholar
Ezcurra, M. D. The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms. PeerJ 4, e1778 (2016).
Google Scholar
Nesbitt, S. J. The early evolution of archosaurs: relationships and the origin of major clades. Bull. Am. Museum Nat. Hist. 352, 1–292 (2011).
Google Scholar
Nesbitt, S. J. et al. A mid-Cretaceous tyrannosauroid and the origin of North American end-Cretaceous dinosaur assemblages. Nat. Ecol. Evol. 3, 892–899 (2019).
Google Scholar
Pritchard, A. C. & Sues, H.-D. Postcranial remains of Teraterpeton hrynewichorum (Reptilia: Archosauromorpha) and the mosaic evolution of the saurian postcranial skeleton. J. Syst. Paleontol. 17, 1745–1765 (2019).
Google Scholar
Rauhut, O. W. M., Hübner, T. R. & Lanser, K.-P. A new megalosaurid theropod dinosaur from the late Middle Jurassic (Callovian) of north-western Germany: implications for theropod evolution and faunal turnover in the Jurassic. Palaeontologia Electronica 19, 29A (2016).
Cau, A. The assembly of the avian body plan: a 160-million-year long process. Boll. Soc. Paleontol. Ital. 57, 1–25 (2018).
Cau, A., Brougham, T. & Naish, D. The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird? PeerJ 3, e1032 (2015).
Google Scholar
Perrin, A. Recherches sur les affinités zoologiques de l’Hatteria punctata. Ann. Sci. Nat. 20, 33–102 (1895).
Osawa, G. Beitrage zur Anatomie der Hatteria punctata. Arch. Mikrosk. Anat. 51, 48–691 (1898).
Gregory, W. K. & Camp, C. L. Studies in comparative myology and osteology III. Bull. Am. Museum Nat. Hist. 38, 447–563 (1918).
Byerly, T. The myology of Sphenodon puncatum. Univ. Iowa Stud. Nat. Hist. 11, 3–51 (1925).
Walker, A. D. in Problems in Vertebrate Evolution (eds Andrews, S. M. et al.) 319–358 (Linnean Society, 1977).
Rowe, T. B. Homology and evolution of the deep dorsal thigh musculature in birds and other reptilia. J. Morphol. 189, 327–346 (1986).
Google Scholar
Dilkes, D. W. Appendicular myology of the hadrosaurian dinosaur Maiasaura peeblesorum from the Late Cretaceous (Campanian) of Montana. Trans. R. Soc. Edin. 90, 87–125 (1999).
Google Scholar
Carrano, M. T. & Hutchinson, J. R. Pelvic and hindlimb musculature of Tyrannosaurus rex (Dinosauria: Theropoda). J. Morphol. 253, 207–228 (2002).
Google Scholar
Allen, V. et al. Comparative architectural properties of limb muscles in Crocodylidae and Alligatoridae and their relevance to divergent use of asymmetrical gaits in extant Crocodylia. J. Anat. 225, 569–582 (2014).
Google Scholar
Klinkhamer, A. J., Wilhite, D. R., White, M. A. & Wroe, S. Digital dissection and three-dimensional interactive models of limb musculature in the Australian estuarine crocodile (Crocodylus porosus). PLoS ONE 12, e0175079 (2017).
Google Scholar
George, J. C. & Berger, A. J. Avian Myology (Academic Press, 1966).
Vanden Berge, J. C. & Zweers, G. A. in Handbook of Avian Anatomy: Nomina Anatomica Avium (eds Baumel, J. J. et al.) 189–250 (Publications of the Nuttall Ornithological Club 23, 1993).
Wellnhofer, P. Archaeopteryx: The Icon of Evolution (Verlag Dr. Friedrich Pfeil, 2009).
Padian, K. & Chiappe, L. M. The origin of birds and their flight. Sci. Am. 278, 38–47 (1998).
Google Scholar
Xu, X., You, H., Du, K. & Han, F. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475, 465–470 (2011).
Google Scholar
Demuth, O. E., Rayfield, E. J. & Hutchinson, J. R. 3D hindlimb joint mobility of the stem-archosaur Euparkeria capensis with implications for postural evolution within Archosauria. Sci. Rep. 10, 15357 (2020).
Google Scholar
Gilmore, C. W. Osteology of the carnivorous Dinosauria in the United States National Museum, with special reference to the genera Antrodemus (Allosaurus) and Ceratosaurus. Bull. US Natl Museum 110, 1–159 (1920).
Barsbold, R., Osmólska, H., Watabe, M., Currie, P. J. & Tsogtbaatar, K. A new oviraptorosaur (Dinosauria, Theropoda) from Mongolia: the first dinosaur with a pygostyle. Acta Palaeontol. Polonica 45, 97–106 (2000).
Sullivan, R. M., Jasinski, S. E. & Van Tomme, M. P. A. A new caenagnathid Ojoraptorsaurus boerei, n. gen., n. sp. (Dinosauria, Oviraptorosauria), from the Upper Ojo Alamo Formation (Naashoibito Member), San Juan Basin, New Mexico. New Mexico Museum Nat. Hist. Sci. Bull. 53, 418–428 (2011).
Kardon, G. Muscle and tendon morphogenesis in the avian hind limb. Development 125, 4019–4032 (1998).
Google Scholar
Alberch, P., Gould, S. J., Oster, G. F. & Wake, D. B. Size and shape in ontogeny and phylogeny. Paleobiology 5, 296–317 (1979).
Google Scholar
Romer, A. S. The development of tetrapod limb musculature—the thigh of Lacerta. J. Morphol. 71, 251–298 (1942).