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Supplementary Materials a PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 Standard Deviation 2.145 1.304 0.923 0.614 0.507 0.400 0.217 0.061

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Supplementary Materials a PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 Standard Deviation 2.145 1.304 0.923 0.614 0.507 0.400 0.217 0.061 1 Supplementary Materials A PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 Standard 2.145 1.304 0.923 0.614 0.507 0.400 0.217 0.061 deviation Proportion 0.575 0.213 0.106 0.047 0.032 0.020 0.006 0.000 of Variance Cumulative 0.575 0.788 0.894 0.941 0.974 0.994 1.000 1.000 Proportion B PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 Standard 1.883 1.318 1.091 1.003 0.556 0.404 0.217 0.035 deviation Proportion 0.443 0.217 0.149 0.126 0.039 0.020 0.006 0.000 of Variance Cumulative 0.443 0.660 0.809 0.935 0.974 0.994 1.000 1.000 Proportion C PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 Standard 1.814 1.399 1.115 0.938 0.605 0.460 0.229 0.030 deviation Proportion 0.414 0.242 0.155 0.110 0.046 0.026 0.007 0.000 of Variance Cumulative 0.414 0.656 0.811 0.921 0.967 0.993 1.000 1.000 Proportion Table S1: Variance distribution across principal components for all taxa (A), when modern birds were excluded (B), and when adult birds were excluded (C). 2 Taxa Name First Last occurrence occurrence Riojasuchus 228 208.5 tenuisceps Aetosaurus 228 208.5 ferratus Desmatosuchus 237 208.5 haplocerus Sphenosuchus 201.3 190.8 acutus Dibothrosuchus 199.3 190.8 elaphros Dakosaurus 152.1 139.8 andiniensis Alligator 66 0 mississippiensis Crocodylus 0.126 0 moreletii Psittacosaurus 125.45 122.46 lujiatunensis Eoraptor 237 228 lunensis Plateosaurus 228 208.5 engelhardti Coelophysis 228 201.3 bauri Dilophosaurus 199.3 182.7 wetherilli Compsognathus 157.3 145 longipes Citipati 83.6 72.1 osmolskae Velociraptor 100.5 66 mongoliensis Archaeopteryx 152.1 125.45 Ichthyornis 89.8 70.6 dispar Nothura 6.8 0.012 Gallus gallus 0.126 0 Geospiza fortis 0.0117 0 3 Table S2: First and last occurrence dates (million years ago) obtained from Paleobiology Database and used to calibrate phylogenetic tree. Species-level occurrence dates were obtained except for Nothura and Archaeopteryx. For Nothura and Archaeopteryx, genus-level occurrence dates were used. Because Nothura was an extant species, a value of 0 was used for its last occurrence in the analysis. 4 Internal nodes Date (Million years ago) Ornithodira-Crurotarsi- 250.4 Avemetatarsalia Galloanserae- 86.5 Neoaves/Neognathae Palaeognathae- 86.5 Neognathae/Neornithes Table S3: Internal nodes used to calibrate the phylogenetic tree and were based on fossil dates from Benton and Donoghue (2007). Module p value Bones grouped in each module 1 2e-04 R.Postorbital, R.Quadratojugal, R.Squamosal, R.Parietal, R.Opisthotic, L.Opisthotic, R.Postfrontal, R.Quadrate, Supraoccipital, Basioccipital 2 9e-05 R.Premaxilla, L.Premaxilla, R.Vomer, L.Vomer, R.Pterygoid, L.Pterygoid, R.Ectopterygoid, L.Ectopterygoid, R.Palatine, L.Palatine, Basisphenoid 3 0.00249 L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Postorbital, L.Jugal, L.Quadratojugal, L.Squamosal, L.Quadrate 4 0.09653 R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal 5 0.08986 L.Frontal, L.Parietal, L.Postfrontal, L.Prootic, L.Laterosphenoid 6 0.31868 R.Frontal, R.Prootic, R.Laterosphenoid Riojasuchus Module p value Bones grouped in each module 1 3e-05 R.Opisthotic, L.Opisthotic, R.Pterygoid, L.Pterygoid, R.Ectopterygoid, L.Ectopterygoid, R.Exoccipital, L.Exoccipital, Supraorbital, Basioccipital, Basisphenoid 2 0.00289 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Frontal, L.Vomer, L.Palatine 3 0.00289 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Frontal, R.Vomer, R.Palatine 4 0.01064 R.Postorbital, R.Jugal, R.Quadratojugal, R.Squamosal, R.Parietal, R.Postfrontal, R.Quadrate Aetosaurus 5 5 0.01064 L.Postorbital, L.Jugal, L.Quadratojugal, L.Squamosal, L.Parietal, L.Postfrontal, L.Quadrate Module p value Bones grouped in each module 1 0.00121 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Vomer, R.Pterygoid, R.Ectopterygoid, R.Palatine 2 0.00121 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal, L.Vomer, L.Pterygoid, L.Ectopterygoid, L.Palatine 3 0.01395 R.Postorbital, R.Quadratojugal, R.Squamosal, R.Frontal, R.Parietal, R.Postfrontal, R.Quadrate, R.Presphenoid 4 0.01395 L.Postorbital, L.Quadratojugal, L.Squamosal, L.Frontal, L.Parietal, L.Postfrontal, L.Quadrate, L.Presphenoid 5 0.98481 Basioccipital, Basisphenoid Desmatosuchus Module p value Bones grouped in each module 1 0 R.Postorbital, L.Postorbital, R.Quadratojugal, L.Quadratojugal, R.Squamosal, L.Squamosal, R.Frontal, L.Frontal, R.Paroccipital, L.Paroccipital, R.Quadrate, L.Quadrate, R.Prootic, L.Prootic, R.Laterosphenoid, L.Laterosphenoid, R.Basipterygoid, L.Basipterygoid, R.Epiotic, L.Epiotic, Supraoccipital, Basioccipital, Basisphenoid, Parietal 2 0.00698 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal 3 0.00698 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal 4 0.19508 L.Vomer, L.Pterygoid, L.Ectopterygoid, L.Palatine, L.Epipterygoid 5 0.19508 R.Vomer, R.Pterygoid, R.Ectopterygoid, R.Palatine, R.Epipterygoid Sphenosuchus Module p value Bones grouped in each module 1 0 R.Postorbital, L.Postorbital, R.Squamosal, L.Squamosal, R.Frontal, L.Frontal, R.Paroccipital, L.Paroccipital, R.Quadrate, L.Quadrate, R.Prootic, L.Prootic, R.Laterosphenoid, L.Laterosphenoid, Supraoccipital, Basioccipital, Basisphenoid, Parietal 2 0.00176 R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Quadratojugal, R.Vomer, R.Pterygoid, R.Ectopterygoid, R.Palatine 3 0.00176 L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal, L.Quadratojugal, L.Vomer, L.Pterygoid, L.Ectopterygoid, L.Palatine 4 1 R.Premaxilla, L.Premaxilla Dibothrosuchus Module p value Bones grouped in each module D ak os au ru s 6 1 0.00016 R.Postorbital, L.Postorbital, R.Squamosal, L.Squamosal, R.Quadrate, L.Quadrate, R.Exoccipital, L.Exoccipital, Supraorbital, Basioccipital, Frontoparietal 2 0.02225 L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal, L.Quadratojugal, Premaxilla 3 0.03363 R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Quadratojugal 4 0.03159 R.Palatine, L.Palatine, Basisphenoid, Pterygoid Module p value Bones grouped in each module 1 0 R.Postorbital, L.Postorbital, R.Quadratojugal, L.Quadratojugal, R.Squamosal, L.Squamosal, Frontal, Parietal, Supraocciptal, R.Otoccipital, L.Otoccipital, R.Prootic, L.Prootic, Basioccipital, Basisphenoid, R.Laterosphenoid, L.Laterosphenoid, Pterygoid, R.Quadrate, L.Quadrate 2 0.00893 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal, L.Ectopterygoid Alligator 3 0.00893 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Ectopterygoid 4 0.90879 R.Vomer, L.Vomer, Palatine Adult Module p value Bones grouped in each module 1 0 R.Postorbital, L.Postorbital, R.Quadratojugal, L.Quadratojugal, R.Squamosal, L.Squamosal, Parietal, Supraocciptal, R.Otoccipital, L.Otoccipital, R.Prootic, L.Prootic, Basioccipital, Basisphenoid, R.Laterosphenoid, L.Laterosphenoid, Pterygoid, R.Quadrate, L.Quadrate 2 0.0163 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Jugal, Frontal, L.Ectopterygoid Alligator 3 0.00893 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Ectopterygoid 4 0.90879 R.Vomer, L.Vomer, Palatine Juvenile Module p value Bones grouped in each module 1 0 R.Squamosal, L.Squamosal, Parietal, Supraocciptal, R.Otoccipital, L.Otoccipital, R.Prootic, L.Prootic, Basioccipital, Basisphenoid, R.Laterosphenoid, L.Laterosphenoid, Pterygoid, R.Quadrate, L.Quadrate 2 2e-05 R.Premaxilla, L.Premaxilla, R.Maxilla, L.Maxilla, R.Nasal, L.Nasal, R.Lacrimal, L.Lacrimal, R.Prefrontal, L.Prefrontal, Frontal, R.Vomer, L.Vomer, Palatine 3 0.56195 R.Postorbital, R.Jugal, R.Quadratojugal, R.Ectopterygoid 4 0.56195 L.Postorbital, L.Jugal, L.Quadratojugal, L.Ectopterygoid Crocodylus Module p value Bones grouped in each module Ps itt ac os au ru s 7 1 3e-05 R.Maxilla, L.Maxilla, R.Lacrimal, L.Lacrimal, R.Jugal, L.Jugal, R.Ectopterygoid, L.Ectopterygoid, R.Pterygoid, L.Pterygoid, Vomer, Palatine, Parasphenoid 2 0.00299 L.Quadratojugal, L.Squamosal, L.Frontal, L.Supraoccipital, L.Postorbital, L.Quadrate, L.Paroccipital.process, L.Laterosphenoid, L.Prootic, Parietal 3 0.00369 R.Premaxilla, L.Premaxilla, R.Nasal, L.Nasal, R.Prefrontal, L.Prefrontal, Rostral 4 0.05599 R.Quadratojugal, R.Squamosal, R.Supraoccipital, R.Quadrate, R.Paroccipital.process, R.Prootic 5 0.99079 R.Frontal, R.Postorbital, R.Laterosphenoid 6 0.65845 Basioccipital, Basisphenoid Module p value Bones grouped in each module 1 0.00101 L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Postorbital, L.Jugal, L.Frontal, L.Palatine, L.Laterosphenoid 2 0.00101 R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Postorbital, R.Jugal, R.Frontal, R.Palatine, R.Laterosphenoid 3 0.04284 L.Quadratojugal, L.Squamosal, L.Paroccipital.process, L.Quadrate, Basioccipital 4 0.18217 R.Ectopterygoid, L.Ectopterygoid, R.Pterygoid, L.Pterygoid, Basisphenoid 5 0.04318 R.Quadratojugal, R.Squamosal, R.Paroccipital.process, R.Quadrate 6 0.82711 R.Parietal, L.Parietal, Supraoccipital 7 0.09382 R.Premaxilla, L.Premaxilla, Vomer Eoraptor Module p value Bones grouped in each module 1 0.00418 R.Postorbital, R.Squamosal, R.Opisthotic, R.Ectopterygoid, R.Quadrate, R.Pterygoid, Basioccipital, Basisphenoid 2 0.00474 R.Premaxilla, R.Maxilla, R.Nasal, R.Lacrimal, R.Prefrontal, R.Jugal, R.Quadratojugal, R.Frontal 3 0.2651 L.Postorbital, L.Jugal, L.Quadratojugal, L.Ectopterygoid, L.Quadrate, L.Pterygoid 4 0.01719 L.Premaxilla, L.Maxilla, L.Nasal, L.Lacrimal, L.Prefrontal, L.Frontal 5 0.02063 L.Squamosal, R.Parietal, L.Parietal, L.Opisthotic, Supraoccipital 6 0.04318 R.Vomer, L.Vomer, R.Palatine, L.Palatine Plateosaurus Module p value Bones grouped in each module 1 3e-05 L.Lacrimal,
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