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doi:10.1038/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. WWW.NATURE.COM/NATURE 1

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 WWW.NATURE.COM/NATURE

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. WWW.NATURE.COM/NATURE 3

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 0.400 0.122 123 Brotogeris chrysopteris UTCT 0.163 0.066 123 Bucorvus abyssinicus UTCT 0.263 0.117 143 Chauna chavaria UTCT 0.295 0.102 115 Chordeiles minor UTCT 0.059 0.054 381 Coragyps atratus UTCT 0.121 0.055 300 Eudyptes chrysocome AMNH 0.104 0.104 1100 Fregata magnificens UTCT 0.128 0.059 269 Gavia immer UTCT 0.109 0.051 408 Grus canadensis UTCT 0.166 0.076 246 Haliaeetus leucocephalus UTCT 0.169 0.077 245 Melanerpes aurifron UTCT 0.060 0.052 311 Phaethon rubricada UTCT 0.174 0.051 171 Phalacrocorax penicillatus UTCT 0.115 0.049 399 Phoebastria immutabilis UTCT 0.138 0.063 313 Podilymbus podiceps UTCT 0.056 0.026 379 Ptilinopus melanospilus UTCT 0.121 0.056 290 Struthio camelus SUNY 0.310 0.250 209 Incisivosaurus IVPP V gauthieri 13326 SUNY 0.310 0.187 147 Conchoraptor gracilis 100/3006 OU 0.092 0.092 550 Citipati osmolskae 100/978 UTCT 0.250 0.196 360 Khaan mckennai 100/973 UTCT 0.164 0.076 328 Zanabazar junior 100/1 UTCT 0.450 0.230 195 Unnamed UTCT 0.047 0.043 1710 4 WWW.NATURE.COM/NATURE

RESEARCH troodontid* 100/1126 Tsaagan UTCT 0.475 0.234 124 mangas 100/1015 Archaeopteryx BMNH UTCT 0.023 0.020 996 lithographica 37001 Shuvuuia 100/977 UTCT 0.251 0.101 195 deserti Alioramus UTCT 0.250 0.294 490 altai 100/1844 *see Turner et al. (2012) 15 for phylogenetic position of 100/1126. WWW.NATURE.COM/NATURE 5

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 0.17 6.76 0.055 4.69 0.95 0.53 0.53 Brotogeris chrysopteris 0.02 1.98 0.009 1.53 0.20 0.16 0.06 Bucorvus abyssinicus 1.26 22.04 0.006 16.81 2.84 1.70 0.68 Chauna chavaria 1.20 7.69 0.036 5.18 0.90 1.00 0.58 Chordeiles minor 0.01 0.87 0.006 0.46 0.24 0.11 0.06 Coragyps atratus 0.90 8.68 0.234 5.95 0.99 0.96 0.55 Eudyptes chrysocome 2.33 11.43 0.009 8.05 1.07 1.62 0.68 Fregata magnificens 0.17 9.11 0.015 6.09 0.88 1.62 0.49 Gavia immer 0.30 9.87 0.041 5.50 1.62 1.94 0.77 Grus canadensis 2.18 15.10 0.026 11.08 1.95 0.89 1.15 Haliaeetus leucocephalus 2.06 17.69 0.032 12.24 2.16 2.18 1.07 Melanerpes aurifron 0.01 2.20 0.003 1.57 0.20 0.34 0.08 Phaethon rubricada 0.03 4.02 0.010 2.22 0.73 0.76 0.29 Phalacrocorax penicillatus 0.26 12.28 0.027 8.36 1.40 1.63 0.86 Phoebastria immutabilis 0.43 14.33 0.206 9.45 1.44 2.40 0.85 Podilymbus podiceps 0.05 2.48 0.008 1.63 0.41 0.26 0.17 Ptilinopus melanospilus 0.10 1.11 0.003 0.63 0.27 0.13 0.07 Struthio camelus 59.30 56.31 0.274 36.85 7.61 6.45 5.13 Incisivosaurus IVPP V gauthieri 13326-5.52 0.029 2.38 1.20 1.07 0.83 Conchoraptor gracilis c 100/3006 5.02 9.44 - * 4.27 1.57 2.49 1.07 Citipati osmolskae 100/978 85.96 22.62 0.569 9.52 3.60 5.16 3.78 Khaan mckennai 100/973 12.61 8.83 0.028 3.71 1.31 1.60 2.17 Zanabazar junior 100/1 49.30 ** 25.14 1.080 14.81 4.75 3.16 2.35 6 WWW.NATURE.COM/NATURE

RESEARCH unnamed troodontid c Tsaagan mangas Archaeopteryx lithographica c Shuvuuia deserti Alioramus altai Tyrannosaurus rex a 100/1126 0.92 3.11 0.021 1.38 0.87 0.50 0.33 100/1015 15.95 3.07 0.042 1.61 0.70 0.31 0.40 BMNH 37001 0.50 1.44 0.077 0.60 0.36 0.24 0.17 100/977 0.25 0.83 0.050 0.41 0.16 0.09 0.12 100/1184 359.0 73.23 6.180 18.70 - - - AMNH 5029 5840.0 343.0-111.80 - - - UMNH VP 7435-169.0-46.7 - - - Allosaurus fragilis a Acrocanthosaurus 10146 3770.0 191.0 - - - - - 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 16923 15, 20. Body size scaled using overlapping elements found in both taxa. Body size of Tyrannosaurus rex estimated based on another specimen, FMNH PR2081 21. 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. WWW.NATURE.COM/NATURE 7

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 0.43 0.77 0.50 0.86 0.62 0.72 total y- endocranium 0.84-0.44 1.10-0.60 0.20-0.39 intercept r 2 0.66 0.50 0.77 0.31 0.89 0.74 slope 0.66 1.32 0.63 1.33 0.96 1.43 olfactory y- bulbs intercept -1.41-1.40-1.34-1.89-1.89-0.63 r 2 0.62 0.25 0.43 0.13 0.73 0.80 slope 0.42 0.85 0.52 0.94 0.59 0.81 cerebrum y- intercept 0.60-0.54 0.93-0.72-1.00-0.49 r 2 0.46 0.50 0.87 0.30 0.92 0.77 slope 0.41 0.68 0.44 0.71 0.67 0.66 optic y- lobes intercept 0.02-0.39 0.19-0.43-0.55-0.46 r 2 0.50 0.41 0.89 0.23 0.58 0.63 slope 0.48 0.84 0.51 0.91 0.84 0.78 cerebellum intercept y- -0.032-0.59 0.18-0.69-0.77-0.61 r 2 0.38 0.43 0.66 0.32 0.55 0.56 slope 0.49 0.68 0.54 0.70 0.74 0.67 brain y- stem intercept -0.25-0.31-0.09-0.33-0.76-0.37 r 2 0.66 0.51 0.82 0.32 0.71 0.75 8 WWW.NATURE.COM/NATURE

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 1.56 1.84 1.50 1.62 1.44 2.15 olfactory y- bulbs intercept -2.66-0.78-2.81-1.10-2.19-0.09 r 2 0.45 0.27 0.42 0.20 0.65 0.86 slope 0.96 1.09 1.04 1.07 0.91 1.14 cerebrum y- intercept -0.21-0.03-0.21-0.01-0.28-0.05 r 2 0.96 0.98 0.99 0.98 0.99 0.99 slope 0.91 0.92 0.89 0.96 0.95 0.85 optic y- lobes intercept -0.75 0.06-0.79-0.13-0.68 0.04 r 2 0.91 0.87 0.92 0.84 0.97 0.97 slope 1.08 1.01 1.02 1.01 1.20 0.99 cerebellum intercept y- -0.94 0.02-0.94 0.02-0.94 0.02 r 2 0.91 0.84 0.91 0.79 0.96 0.97 slope 1.09 0.91 1.08 0.89 1.06 0.92 brain y- stem intercept -1.17 0.04-1.28 0.05-0.92 0.02 r 2 0.84 0.85 0.93 0.83 0.94 0.87 WWW.NATURE.COM/NATURE 9

RESEARCH SUPPLEMENTARY INFORMATION Table S5. PCA loadings Axis 1 Axis 2 Axis 3 Axis 4 Axis 5 relative olfactory 0.46 0.67-0.10 0.94 0.30 volume relative cerebral -0.87 0.04 0.02-0.11 0.47 volume relative optic volume 0.32 0.74 0.31-0.18 0.47 relative cerebellar 0.24-0.64 0.57-0.05 0.46 volume relative brain stem volume 0.28-0.18-0.75-0.25 0.51 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 WWW.NATURE.COM/NATURE

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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, 1 138 (2003) 22. Franzosa, J. W., & Rowe, T. Cranial endocast of the Cretaceous theropod dinosaur Acrocanthosaurus atokensis. J. Vert. Paleontol. 25, 859 864 (2005) WWW.NATURE.COM/NATURE 13