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1 doi: /nature12424 Figure S1. Bivariate plots of log-transformed data of body size. Body size is plotted against a, olfactory bulb volume, b, optic lobe volume, c, cerebellum volume, and d, brain stem volume. Colours indicate crown birds (blue), non-maniraptoran theropods (white), oviraptorosaurs (red), deinonychosaurs (yellow), Archaeopteryx lithographica (green). Reduced major-axis regression line for entire sample (solid), crown group birds (large dashes), and non-avian theropods (small dashes). Regression statistics are given in Table S3. 1

2 RESEARCH SUPPLEMENTARY INFORMATION Figure S2. Bivariate plots of log-transformed data of total endocranial volume. Total endocranial volume is plotted against a, olfactory volume, b, optic lobe volume, and c, brain stem volume. Colours indicate crown birds (blue), oviraptorosaurs (red), deinonychosaurs (yellow), Archaeopteryx lithographica (green). Reduced major-axis regression line for entire sample (solid), crown group birds (large dashes), and non-avian theropods (small dashes). Regression statistics are given in Table S4. 2

3 RESEARCH Figure S3. Endocranial casts of Archaeopteryx (above) and loon, Gavia immer (below). The cerebral indention potentially homologous with the avian wulst is highlighted by a dotted line. Anterior is to the left, and endocasts are scaled to the same size. 3

4 RESEARCH SUPPLEMENTARY INFORMATION Table S1. CT scanning parameters Taxon Specimen # Scanning facility z-spacing (mm) x-, y-spacing (mm) Number of slices through skull Anas platyrhynchus UTCT Brotogeris chrysopteris UTCT Bucorvus abyssinicus UTCT Chauna chavaria UTCT Chordeiles minor UTCT Coragyps atratus UTCT Eudyptes chrysocome AMNH Fregata magnificens UTCT Gavia immer UTCT Grus canadensis UTCT Haliaeetus leucocephalus UTCT Melanerpes aurifron UTCT Phaethon rubricada UTCT Phalacrocorax penicillatus UTCT Phoebastria immutabilis UTCT Podilymbus podiceps UTCT Ptilinopus melanospilus UTCT Struthio camelus SUNY Incisivosaurus IVPP V gauthieri SUNY Conchoraptor gracilis 100/3006 OU Citipati osmolskae 100/978 UTCT Khaan mckennai 100/973 UTCT Zanabazar junior 100/1 UTCT Unnamed UTCT

5 RESEARCH troodontid* 100/1126 Tsaagan UTCT mangas 100/1015 Archaeopteryx BMNH UTCT lithographica Shuvuuia 100/977 UTCT deserti Alioramus UTCT altai 100/1844 *see Turner et al. (2012) 15 for phylogenetic position of 100/

6 RESEARCH SUPPLEMENTARY INFORMATION total endocranium Table S2. Raw Volumetric Data for endocranial regions (cm 3 ). Body mass given in kg. Taxon specimen # body mass olfactory bulbs cerebrum optic lobes cerebellum brain stem Anas platyrhynchus Brotogeris chrysopteris Bucorvus abyssinicus Chauna chavaria Chordeiles minor Coragyps atratus Eudyptes chrysocome Fregata magnificens Gavia immer Grus canadensis Haliaeetus leucocephalus Melanerpes aurifron Phaethon rubricada Phalacrocorax penicillatus Phoebastria immutabilis Podilymbus podiceps Ptilinopus melanospilus Struthio camelus Incisivosaurus IVPP V gauthieri Conchoraptor gracilis c 100/ * Citipati osmolskae 100/ Khaan mckennai 100/ Zanabazar junior 100/ **

7 RESEARCH unnamed troodontid c Tsaagan mangas Archaeopteryx lithographica c Shuvuuia deserti Alioramus altai Tyrannosaurus rex a 100/ / BMNH / / AMNH UMNH VP Allosaurus fragilis a Acrocanthosaurus OMNH atokensis *Olfactory bulbs for Conchoraptor gracilis are present but too small to measure accurately. **Body size of Zanabazar junior estimated based on Saurornithoides mongoliensis 19, a closely related taxon. Body size scaled using overlapping elements found in both taxa. Body size of Tsaagan mangas estimated based on another specimen, IVPP V , 20. Body size scaled using overlapping elements found in both taxa. Body size of Tyrannosaurus rex estimated based on another specimen, FMNH PR Body size scaled using overlapping elements found in both taxa. a Endocranial volumes taken from Larsson et al. (2000) 5. b Endocranial volume taken from Franzosa and Rowe (2005) 22. c Endocranial volumes for these taxa were calculated by doubling the undistorted halves of the endocasts. 7

8 RESEARCH SUPPLEMENTARY INFORMATION Table S3. Regression statistics for partitions vs. body size region statistic Whole Sample Crown Birds Non-avian Theropods uncorrectecorrectecorrected un- un- corrected corrected corrected slope total y- endocranium intercept r slope olfactory y- bulbs intercept r slope cerebrum y- intercept r slope optic y- lobes intercept r slope cerebellum intercept y r slope brain y- stem intercept r

9 RESEARCH Table S4. Regression statistics for partitions vs. endocranial volume region statistic Whole Sample Crown Birds Non-avian Theropods uncorrectecorrectecorrected un- un- corrected corrected corrected slope olfactory y- bulbs intercept r slope cerebrum y- intercept r slope optic y- lobes intercept r slope cerebellum intercept y r slope brain y- stem intercept r

10 RESEARCH SUPPLEMENTARY INFORMATION Table S5. PCA loadings Axis 1 Axis 2 Axis 3 Axis 4 Axis 5 relative olfactory volume relative cerebral volume relative optic volume relative cerebellar volume relative brain stem volume Abbreviations AMNH, American Museum of Natural History; BMNH, Natural History Museum, London;, Geological Institute, Ulaan Baatar, Mongolia; IVPP, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing; OMNH, Sam Noble Oklahoma Museum of Natural History, Oklahoma City; OU, Ohio University, Athens; SUNY, State University of New York, Stony Brook; UMNH, Natural History Museum of Utah, Salt Lake City; UTCT, University of Texas at Austin, High-resolution X-ray CT Facility 10

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12 RESEARCH SUPPLEMENTARY INFORMATION 12. Midford, P. E., Garland, T.G. Jr., & Maddison, W.P. PDAP:PDTREE: A translation of the PDTREE application of Garland et al. s Phenotypical Diversity Analysis Program. Available at (2010) 13. Felsenstein, J. Phylogenies and the comparative method. American Naturalist 125, 1 15 (1985) 14. Smith, N. D., Makovicky, P. J., Hammer, W. R. & Currie, P. J. Osteology of Crylophosaurus ellioti (Dinosauria: Theropoda) from the Early Jurassic of Antarctica and implications for early theropod evolution. Zoological Journal of the Linnean Society 151, (2007) 15. Turner, A. H., Makovicky, P. J. & Norell, M. A. A review of dromaiosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History 371, (2012) 16. Mayr, G. and Clarke, J. The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters. Cladistics 19, (2003) 17. Livezey, B. C. & Zusi, R. L. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society 149, 1-95 (2007) 18. de Winter, W. & Oxnard, C. E. Evolutionary radiations and convergences in the structural organization of mammalian brains. Nature 409, (2001) 19. Norell, M. A. et al. A review of the Mongolian Cretaceous dinosaur Saurornithoides (Troodontidae: Theropoda). Amer. Mus. Nov. 3654, 1 63 (2009) 20. Xu, X. et al. A new dromaeosaurid (Dinosauria: Theropoda) from the Upper Cretaceous Wulansuhai Formation of Inner Mongolia, China. Zootaxa. 2403, 1 9 (2010) 12

13 RESEARCH 21. Brochu, C. A. Osteology of Tyrannosaurus rex: insights from a nearly complete skeleton and high-resolution computed tomographic analysis of the skull. Soc. Vert. Paleontol. Memoir 7, (2003) 22. Franzosa, J. W., & Rowe, T. Cranial endocast of the Cretaceous theropod dinosaur Acrocanthosaurus atokensis. J. Vert. Paleontol. 25, (2005) 13