Endocranial development in non-avian dinosaurs reveals an ontogenetic brain trajectory distinct from extant archosaurs

Domain: earth_science
Published: 2024-08-28
Editorial outcome: minor_revision

Abstract
Modern birds possess highly encephalized brains that evolved from non-avian dinosaurs. Evolutionary shifts in developmental timing, namely juvenilization of adult phenotypes, have been proposed as a driver of head evolution along the dinosaur-bird transition, including brain morphology. Testing this hypothesis requires a sufficient developmental sampling of brain morphology in non-avian dinosaurs. In this study, we harness brain endocasts of a postnatal growth series of the ornithischian dinosaur Psittacosaurus and several other immature and mature non-avian dinosaurs to investigate how evolutionary changes to brain development are implicated in the origin of the avian brain. Using three-dimensional characterization of neuroanatomical shape across archosaurian reptiles, we demonstrate that (i) the brain of non-avian dinosaurs underwent a distinct developmental trajectory compared to alligators and crown birds; (ii) ornithischian and non-avialan theropod dinosaurs shared a similar developmental trajectory, suggesting that their derived trajectory evolved in their common ancestor; and (iii) the evolutionary shift in developmental trajectories is partly consistent with paedomorphosis underlying overall brain shape evolution along the dinosaur-bird transition; however, the heterochronic signal is not uniform across time and neuroanatomical region suggesting a highly mosaic acquisition of the avian brain form.

Introduction
The evolutionary origin of highly encephalized brains in modern birds is not only of interest to avian neuroscience but also has implications for how large brains evolve across vertebrates, including humans. Disentangling how the brain of crown birds (“Aves”) evolved requires study of brain anatomy ancestral to crown birds—that of non-avian dinosaurs. Using skulls and cephalic endocasts (internal molds of the braincase) as proxies for brain shape and size, previous studies have revealed that the evolutionary assembly of the avian brain form proceeded in a mosaic and homoplastic manner from the ancestral dinosaurian pattern1–11. While the tempo and mode of avian brain evolution is well established by recent studies, the mechanism underlying major neuroanatomical transformation along the dinosaur-bird transition remains uncertain3,12. Previous studies have proposed that a mixture of heterochronic processes within the cranium, particularly progenesis (truncation of the ancestral developmental period) and accelerated peramorphosis (evolutionarily driven increases in developmental rates), may underlie major changes to the brain architecture from ancestral archosaurian forms to crown birds3,11–16. However, a good developmental series of neuroanatomical morphologies for non-avian dinosaurs has been lacking to date; and crucial evidence is needed for a reliable inference of evolutionary shifts in brain development along the dinosaur-bird transition.

In this study, we examine an ontogenetic series of endocasts of the ornithischian dinosaur Psittacosaurus lujiatunensis, spanning perinatal to somatically mature individuals (<1-, 7-, 8-, and 10-year-old individuals) that were recently described17,18 (Fig. 1a; Supplementary Fig. 1). This allows for an unprecedented look into how the neuroanatomy of a non-avialan dinosaur species changes with age. We incorporate this developmental dataset into an interspecific dataset of archosaurian endocranial morphology which also includes postnatal ontogenetic series of the domestic chicken (Gallus gallus domesticus) and American alligator (Alligator mississippiensis) as an outgroup3 (Fig. 1a, b). Moreover, we include immature specimens of additional non-avialan dinosaurs17–21 (Lambeosaurus, Corythosaurus, tyrannosaurids, Zanabazar, and an unnamed troodontid; Supplementary Data 1) to further define the overall developmental axis of brain morphology in non-avialan dinosaurs (i.e., excluding Archaeopteryx considered here to be a basal avialan). Using a landmark-based geometric morphometric characterization of endocranial shape (Fig. 1c; Supplementary Table 1), the study aims to investigate how the magnitude and direction of developmental shape changes in brain morphology in non-avian dinosaurs compare to (i) the domestic chicken and the American alligator and (ii) the principal axis of brain shape evolution along the dinosaur-bird transition to evaluate whether heterochronic processes, particularly progenesis, underlie the origins of the highly derived avian brain. In our reporting, endocranial regions are referred to by their underlying soft-tissue features (i.e., “cerebrum” rather than “impression of the cerebrum”).

Here, we show that the endocranial form of non-avian dinosaurs developed and evolved uniquely when compared to crown birds and Alligator mississippiensis. We demonstrate that ornithischians and non-avialan theropod dinosaurs share a common shape-to-size relationship that guides their brain development and evolution. Regional morphometric analyses of endocranial developmental trajectories reveal that non-avian dinosaurs collectively exhibit a mosaic of avian and crocodilian modes of allometric trajectories wherein the cerebrum and optic lobe regions of immature non-avialan dinosaurs resemble those of extant birds whereas the brainstem region follows the trajectory of the crocodilians. Our results thus support a paedomorphic trend occurring along the dinosaur-bird transition that is localized to some but not all regions of the brain.

Results
Endocranial shape morphospaces
To visualize total and regional endocranial shape variation, morphospaces were constructed based on principal components (PC) axes of endocast shape data (Fig. 2). In the morphospace of total endocranial shape, lower PC1 scores are associated with posterolaterally expanded cerebra, ventrally oriented optic lobes, anteroposteriorly compact hindbrains, and higher dorsoventral flexion with respect to both cephalic and pontine flexures as defined by Lautenschlager and Hübner22. Lower PC2 scores correspond to elongated cerebra, dorsoventrally extended optic lobes, anteroposteriorly shortened cerebellum, and greater dorsoventral flexion along the brainstem. As expected, total endocast shape data closely reflect the results found in previous geometric morphometric work where crown birds, alligators, and non-avian dinosaurs individually form clusters along PC1, with Archaeopteryx positioned between crown birds and non-avialan archosaurs along PC1 (Fig. 2a)3. Ornithischian and non-avialan theropod dinosaurs overlap with each other, and mature individuals of both groups strongly overlap with mature endocranial shape of Alligator along PC1 and PC2. With the exception of 7-year-old Psittacosaurus (IVPP V12731), endocasts of immature non-avialan dinosaurs generally exhibit lower PC1 scores closer to the crown bird cluster. The perinatal Psittacosaurus (IVPP V15451) and juvenile troodontid (IGM 100/1126), as well as the small-bodied, purportedly immature tyrannosaurid specimen (CMNH 7541), occupy an intermediary position between crown birds and non-avialan archosaurs along PC1 (Fig. 2a). All other juvenile taxa maintain similar PC2 scores as CMNH 7541 but have higher PC1 scores. Notably, the perinatal Psittacosaurus (IVPP V15451) and juvenile troodontid (IGM 100/1126), overlap in PC2 values as neo- and perinatal Gallus (Fig. 2a).

During development, the immature non-avialan dinosaur endocasts exhibit a posterolaterally expanded cerebrum, more ventrally oriented optic lobes, anteroposteriorly compressed hindbrain, and greater degree of dorsoventral flexion. In the case of IVPP V15451 and IGM 100/1126 (perinate Psittacosaurus and a juvenile troodontid, respectively), the anatomical arrangement of the endocast more closely resembles crown birds than the arrangement found in a somatically immature specimen of the early avialan Archaeopteryx does along PC1. With age, the morphological layout of the non-avialan dinosaur endocast trends towards that of Alligator, where the mature individuals of non-avian dinosaurs and Alligator converge in their ontogenetic trajectories. This is to say that during postnatal development, the cerebrum narrows anteriorly relative to the rest of the endocast, the optic lobes become less bulbous, the hindbrain expands posterolaterally, and the degree of dorsoventral flexion decreases. P. lujiatunensis follows this trend between the perinatal and mature stages (8- and 10-year old) with the 7-year-old showing endocasts that resemble endocranial shape of subadult Alligator (Fig. 2a). The seemingly strange position of 7-year-old Psittacosaurus may be due to the dorsoventrally shallower morphology compared to the three other Psittacosaurus endocasts, which may be due to moderate degree of deformation (Supplementary Fig. 1). Juvenile hadrosaurs, such as the juvenile Lambeosaurus (ROM 758) and Corythosaurus (ROM 759), generally plot more closely with alligators than crown birds, but it is unclear, with current sampling, if perinatal individuals would plot more closely to crown birds as is the case with Psittacosaurus.

In general, the morphospace of cerebrum shape (Fig. 2b) generally mirrors the pattern observed in total endocranial shape, where the alligator, non-avian dinosaurs, and crown birds form clusters with partial overlap along the PC1 axis. This axis encompasses the spectrum from the more globular cerebrum in modern birds to more anteroposteriorly elongated profile in mature alligators. The orientation of the PC2 axis corresponds closely to the ontogenetic series of Alligator, which encompasses an anteroposteriorly constricted cerebrum in immature individuals to a more elongated profile in mature alligators. Overall, non-avian dinosaurs group together in the area of morphospace between mature alligators and crown birds. Among non-avian dinosaurs, the cerebrum shape of immature specimens, troodontids, and tyrannosaurids (such as the taxonomically problematic ?Nanotyrannus specimen CMNH 7541) group closest to crown birds (Fig. 2b). Endocranial shape of relatively mature ornithischian dinosaurs, including that of hadrosaurs and Psittacosaurus, overlap with that of mature alligators (Fig. 2b).

In the cerebellum shape morphospace, crown birds and Archaeopteryx form a group that is almost completely separated from alligators along PC2 (Fig. 2c). The PC1 axis is primarily associated with the anteroposterior extent and dorsoventral depth of the cerebellum. The PC2 axis mostly corresponds to the dorsoventral curvature. Non-avialan dinosaurs overlap both crown birds and alligators in cerebellar shape along both PC1 and PC2 axes. Relatively mature specimens of tyrannosaurids, troodontids, and hadrosaurs strongly overlap with relatively mature alligators. Interestingly, all the Psittacosaurus specimens lie among crown birds regardless of ontogenetic stage, although this similarity is likely due to the presence of a prominent dorsal eminence, thought to represent space occupied by non-neuronal soft tissues (e.g., venous sinus, meninges), on the cerebellum (Fig. 1a; Supplementary Fig. 1). Apart from the juvenile hadrosaurs, Lambeosaurus (ROM 758) and Corythosaurus (ROM 759), all juvenile specimens of troodontids, the small-bodied tyrannosaurid specimen CMNH 7541, and other ornithischian dinosaurs, overlap with crown birds in PC2 values.

In optic lobe shape morphospace (Fig. 2d), the distinctions between alligators, non-avian dinosaurs, and crown birds are more apparent, particularly along PC1, which documents the range from the anteroposteriorly constricted and dorsoventrally elongated optic lobes in alligators to the hemispherical optic lobes in modern birds and some non-avian dinosaurs. PC2 encompasses the range from convex to topologically flat optic lobes. Alligators and crown birds overlap along PC2 due to their convex optic lobes. Optic lobes of some non-avian dinosaurs closely resemble those of alligators and crown birds. For example, the subadult Psittacosaurus (PKUP V1054) lies very close to alligators (which could be due to taphonomic deformation as noted above) and away from other congeneric specimens in PC1 values. The perinatal Psittacosaurus (IVPP V15451), the oviraptorid Khaan (IGM 100/973), and Archaeopteryx are adjacent to the area of morphospace occupied by crown birds.

The morphospace for brainstem shape visually separates crown birds and all other taxa sampled in this study along PC2 (Fig. 2e). The PC1 axis largely documents the ontogenetic shape changes in alligators and chickens, from a mediolaterally expanded and dorsoventrally curved brainstem in perinatal specimens to anteroposteriorly elongated and weaker dorsoventral flexion in adults. Along PC2, crown birds and the chicken ontogenetic series cluster together, while non-avian dinosaurs overlap considerably with adult and subadult alligators. More immature alligators were grouped with Archaeopteryx, relatively immature Psittacosaurus specimens (IVPP V15451, PKUP V1053, and PKUP V1054), and the immature troodontid IGM 100/1126 (Fig. 2e).

Allometric trajectories
To compare shape-to-size relationships, we visualized and tested how non-avian dinosaur endocrania differed from allometric trends in crown birds, together with developmental trajectories of Gallus and Alligator. For visualization of allometric trends, PC1 of residuals from the common allometric trend (RSC1) were plotted against scores along the allometric trend line (CAC: common allometric component) for all endocrania sampled (Fig. 3). As in previous work5, total shape variation among the endocrania of crown birds is allometrically divergent from non-avian dinosaurs and Alligator (Fig. 3a). As expected, crown birds occupy a restricted size range along the CAC axis but exhibit a high degree of shape variation along the RSC1 axis. The ontogenetic series of chickens overlaps the interspecific trajectories of the other crown birds used in this study (Fig. 3a). Whereas immature non-avian dinosaurs exhibit endocranial shapes that are distinct from both crown birds and alligators, more mature specimens of ornithischian and non-avian theropod dinosaurs converge towards the endocranial shape of mature Alligator. More immature Alligator specimens deviate further from crown birds along RSC1.

The allometric trajectory of cerebrum shape in crown birds, along with the ontogenetic series of chickens, are separate from the entire ontogenetic series of Alligator (Fig. 3b). With the exception of perinatal Psittacosaurus (IVPP V15451), sampled ornithischian taxa exhibit cerebrum shapes that overlie the relatively mature alligators. Notably, the perinatal Psittacosaurus specimen (IVPP V15451) aligns with crown birds in RSC1 values, whereas the juvenile Lambeosaurus (ROM 758), juvenile Corythosaurus (ROM 159) and more mature ornithischian dinosaurs have RSC1 values that are closer to adult Alligator. Non-avian theropods span the range of endocranial shape of alligators and modern birds, where the oviraptorid Citipati and the tyrannosaurid CMNH 7541 are within the area occupied by some of the crown birds, such as Phalacrocorax (cormorant) and Raphus (dodo). Hadrosaurs have a larger RSC1 score than the other non-avian dinosaur taxa sampled, with subadult Psittacosaurus having the lowest. Alligators span the most along RSC1, with hatchlings having large RSC1 scores that decrease notably as they mature to adulthood (Fig. 3b).

Similar to the cerebrum, allometric trajectories of the alligator and crown bird cerebella are distinct, with non-avian dinosaurs overlapping with these two taxa (Fig. 3c). Psittacosaurus, immature theropods, and non-avian maniraptoran dinosaurs group within or near crown birds, with the juvenile Lambeosaurus (ROM 758) and more mature non-avian dinosaurs more closely resembling adult Alligator (Fig. 3c). Adult and subadult Psittacosaurus plot with crown birds along with Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247) specimens, while the juvenile and subadult hadrosaurs align more closely with Alligator (Fig. 3c). It is worth noting that non-avian dinosaur taxa positioned close to crown birds, including Zanabazar and CMNH 7541, show prominent dorsal eminence in the endocast.

For the optic lobe, crown birds and Archaeopteryx group together along the RSC1 axis (Fig. 3d). Non-avian dinosaurs loosely group together, with the oviraptorosaurs Incisivosaurus and Khaan closely resembling the optic lobe shape of crown birds and Archaeopteryx and the subadult Psittacosaurus (PKUP V1054) positioned with adult Alligator (Fig. 3d). The perinatal Psittacosaurus (IVPP V15451) and immature troodontids Zanabazar and unnamed troodontid (IGM 100/1126) are closer to the RSC1 values of crown birds than other endocasts from non-avian dinosaurs. Based on the plot, it is uncertain whether non-avian dinosaurs align more closely with the allometric trajectories of alligators and/or crown birds.

Allometric trajectories of brainstem shape of crown birds and Gallus ontogeny are mostly distinct from ontogenetic series of Alligator but converge throughout postnatal ontogeny of the brainstem (Fig. 3e). Archaeopteryx and non-avian dinosaurs of all ages align with the ontogenetic series of Alligator. In particular, the perinatal Psittacosaurus (IVPP V15451) and juvenile troodontid IGM 100/1126 follow the trend line of Alligator ontogeny, away from the allometric trajectory governing scaling relationships across crown birds and chicken development. As such, the results suggest that both ornithischian and non-avian theropod dinosaurs resembled an alligator-grade scaling relationship in brainstem shape.

In addition to visual comparison of allometric trajectories, we also statistically tested the differences in allometric trajectories. The non-avian dinosaur with the most complete ontogenetic series of cranial endocasts in our study, P. lujiatunensis, was compared against allometric trends in chickens and alligators and was found to have a distinct allometric trajectory. This result is confirmed by MANOVA on full Procrustes coordinate data against log-transformed centroid size and trajectory analyses for mean angle differences (Supplementary Table 2), when compared to Gallus (MANOVA: R2=0.352; P<0.0001; trajectory analysis: mean distance=0.218, P<0.0001; angle difference=16.8°, P<0.0001) and Alligator (MANOVA: R2=0.210; P<0.0001; trajectory analysis: mean distance=0.152, P<0.0001; angle difference=11.6°, P<0.0001).

Methods
Specimens
We amassed 85 previously published endocranial reconstructions that span 52 species of non-avian and avian dinosaurs in addition to American alligators (Supplementary Data 1). The data include interspecific sampling of 36 crown birds, a juvenile Archaeopteryx33, and 19 non-avian dinosaurs1,3,17–20,34, plus ontogenetic series of the domestic chicken (Gallus gallus; n=14), the American alligator (Alligator mississippiensis; n=14), and the ornithischian Psittacosaurus lujiatunensis3,17,35 (n=4; Supplementary Fig. 1). Among non-avian dinosaurs, several isolated immature specimens of both ornithischian and non-avian theropod dinosaurs, including Lambeosaurus (ROM 758) and troodontids Zanabazar and an unnamed specimen IGM 100/1126 were sampled for both ontogenetic and phylogenetic diversity19–21,36–39. The taxonomically ambiguous tyrannosaurid specimen, CMNH 7541, has been considered a relatively immature specimen within Tyrannosauridae40–45. The major results and conclusions of this study are not dependent on the taxonomic assignment of this specimen, but rather the ontogenetic stage of CMNH 7541. Considering that no specimen attributable to a tyrannosaurid similar to, and including, CMNH 7541 has preserved an external fundamental system that indicates the cessation of rapid growth and the onset of skeletal maturity32,40, we treat CMNH 7541 as an immature individual. The specimen and data acquisition protocols for Alligator and Gallus specimens were approved by Institutional Animal Care and Use Committee at respective institutions (Stony Brook IACUC Protocol #236370-1; Oklahoma State University Center for Health Sciences IACUC Protocol #2015-1; American Museum of Natural History 2014). Please refer to the references listed in Supplementary Data 1 for additional details about those specimens.

Imaging and endocranial reconstructions
Endocranial reconstructions were generated from computed tomography (CT) imaging of cranial specimens. Considering the incomplete nature of the PKUP 1053 and PKUP 1054 endocasts from previous study18, they were reconstructed again for this study. We found that the original specimens and reconstructed models were of sufficient quality for morphometric analysis. These reconstructions were paired with two other Psittacosaurus specimens, IVPP V15451, and IVPP V12617, to reconstruct an ontogenetic series for the species P. lujiatunensis. The endocast of the tyrannosaurid Alioramus altai (IGM 100/1844) was retrodeformed using a local symmetrization algorithm46 implemented in the “Morpho” R package47 due to its sheared appearance. Because the combined data comprise multiple sources, the scanner, scanning parameters, and segmentation protocol naturally differ across datasets (Supplementary Data 1). Nevertheless, we considered variation in resulting shape data due to differences in these practices to be negligible compared to the large interspecific variation observed across archosaurs48. However, to adopt some standardization across endocranial reconstructions, we used the “QuickSmooth” function in Geomagic Wrap v2021 (3D Systems, Rock Hill, SC, USA) to remove cranial nerve and vascular projections from the main body of all the endocasts at the base.

Morphometric data
We adopted the same high-density 3D landmark scheme from previous studies to characterize the overall shape of endocasts and their major regions, including the cerebrum, optic lobe, cerebellum, and brainstem3,34,35 (Fig. 1c; Supplementary Table 1). The ‘patch’ tool in Landmark Editor v3.649 was used to place discrete landmarks that are anatomically defined, curve semi-landmarks that delimit regions, and surface semi-landmarks that capture the surface morphology within regions on both left and right sides of the endocast. We did not collect coordinate data from the olfactory tract and bulbs due to their incomplete preservation in the fossils, as well as their diminutive size in most crown birds. We acknowledge that endocasts are generally accurate representations of actual brain morphology among archosaurs35,50, but their correspondence is relatively low in the hindbrain due to greater presence of tissues surrounding the brain. This correspondence is lower in crocodilians27 and presumably in non-avian dinosaurs, especially the presence of dorsal eminence in some endocasts19,20,51.

The coordinate data were subjected to generalized Procrustes alignment52,53 minimizing total bending energy, allowing semi-landmarks to slide on the mesh surface54,55 using the “slider3d” and “gpagen” functions in the “Morpho”56 and “geomorph”57 R packages. After alignment, (semi-)landmarks on the right side were removed to remove redundant shape information while minimizing artifacts caused by alignment of one-sided coordinate data of bilaterally symmetric structures58,59. We extracted centroid size from the pre-aligned coordinate data, in addition to the shape data to be analyzed comprising 14 discrete landmarks, 49 curve semi-landmarks, and 56 surface semi-landmarks (Supplementary Data 2, 3). For region-specific analyses, the size and shape of each region were extracted by calculating centroid size and performing localized alignment on a subset of landmarks that characterize each region.

Time-calibrated phylogeny
To perform phylogenetic comparative analysis, we constructed a time-calibrated phylogeny that includes all the sampled species. Because the crown group sampling is equivalent to a previous study3, fossil taxa were grafted to the existing tree file (additional details on the base tree construction3). These additional taxa included Corythosaurus, Hypacrosaurus, Psittacosaurus, Gorgosaurus, and Tyrannosaurus, which were incorporated into the existing phylogeny based on the mid-point of range of first occurrence age recorded on the Paleobiology Database (paleobiodb.org). When the maximum age of a species was identical to that of its clade, the age of the internal node was set to equally bisect the parent and descendent branches (“Equal Branching Method”)60.

Analysis
All statistical analyses for this project were performed in R v4.2.161. Patterns of endocast shape variation were visualized as morphospaces for the cerebrum, cerebellum, optic lobe, and brainstem regions of the endocasts and were constructed using scores from PCA made from shape data. The functions physignal, procD.lm, and procD.pgls of the geomorph package were used to assess the level of phylogenetic signal, allometry, and evolutionary allometry, with 1000 pseudoreplications. The multivariate statistical tests outlined above were chosen due to their robusticity against type I errors and loss of power that often accompanies differences in specimen and landmark sampling62–64. Allometric trends were visualized by plotting the PC1 of residuals from the overall shape-to-size relationship against scores along this allometric relationship65. We used Morpho package’s “CAC” function to extract CAC scores and residuals from shape data. Statistical differences between endocranial shapes and allometric trajectories between clades were tested with the procD.lm function, where differences in clades were tested on data accounting for log-transformed centroid size. In addition, we used the “trajectory.analysis” function in the “RRPP” R package66 to test for differences between vectors of evolutionary and developmental shape change in total shape space.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "King et al. present a new study addressing the question of how the evolution of ontogenetic trajectories across the dinosaur-bird transition affected the origin of the modern avian brain. The authors conclude that crocodilians, non-avian dinosaurs, and modern birds show different trajectories. Although previous studies already tackled the question, the main novelty of the study relies on the inclusion of ontogenetic series of non-avian dinosaurs, which were previously neglected. Overall, I enjoyed the manuscript and I suggest publication of the study. I have a few major comments that should be addressed by the authors:\n- The authors focus on heterochronic events that affected the head and the nervous system. However, what about the trend in miniaturization that is affecting the origin of birds? As stated in previous studies, multiple events of ontogenetic truncation affected the evolution of the head in the dinosaur-bird transition, but the miniaturization process leading to modern birds does not follow heterochronic trends per se. I would ask the authors to discuss this in the manuscript, considering that analyses regarding allometry per se are already present in the study.\n- I agree with the general conclusions, but I don’t understand why the authors continue emphasizing that different ontogenetic trajectories among non-avian dinosaurs are surprising: the phenotype of their nervous system among non-avian dinosaurs differs from modern crocodiles and birds as a result of mosaic evolution. If we assume that an adult phenotype is the result of a specific developmental trajectory, as it is generally the case among amniotes, then this shouldn’t be surprising. I would adjust the text accordingly.\n- I would ask the authors to image all ontogenetic stages of the ontogenetic series included in the study in figure 1. At the moment, only few endocasts are represented. I think this is insufficient for the scope of the study.\n- I noticed that in most plots, some data points are labelled with catalogue numbers. Please, change this with the name of the taxon and ontogenetic stage: it would be very difficult for a general reader to follow the plots without having a clear expertise in this field.\n- Some of the ontogenetic stages are well characterized in terms of age, but others are not. How did the authors homologize ontogenetic stages between modern and extinct species? This is fundamental to clarify considering that heterochrony requires such knowledge between compared species to infer heterochronic trends. A section in the methods is necessary. Moreover, I would add a paragraph regarding such limitations in the discussion.\n- In the last part of the discussion, the authors argue that their results do not support a single heterochronic event leading to modern birds. I agree, but the original studies infer multiple heterochronic events, not just one. I would suggest the authors to revise this part of the discussion.\n- Finally, there are fundamental references that are missing to justify some of the assumptions/statements in the intro and discussion that should be cited in the main text\nHeterochrony of the head:\n- Plateau, O., & Foth, C. (2020). Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution. Communications Biology, 3(1), 195.\n- Lee, H. W., Esteve-Altava, B., & Abzhanov, A. (2020). Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs. Scientific Reports, 10(1), 16138.\n- Navalón, G., Nebreda, S. M., Bright, J. A., Fabbri, M., Benson, R. B., Bhullar, B. A., ... & Rayfield, E. J. (2021). Craniofacial development illuminates the evolution of nightbirds (Strisores). Proceedings of the Royal Society B, 288(1948), 20210181.\nHeterochrony and mosaic evolution of the nervous system:\n- Kundrát, M., Xu, X., Hančová, M., Gajdoš, A., Guo, Y., & Chen, D. (2018). Evolutionary disparity in the endoneurocranial configuration between small and gigantic tyrannosauroids. Historical Biology.\n- Chiappe, L. M., Navalón, G., Martinelli, A. G., Nava, W., & Field, D. J. (2022). Fossil basicranium clarifies the origin of the avian central nervous system and inner ear. Proceedings of the Royal Society B, 289(1983), 20221398.\n- Fabbri, M., Mongiardino Koch, N., Pritchard, A. C., Hanson, M., Hoffman, E., Bever, G. S., ... & Bhullar, B. A. S. (2017). The skull roof tracks the brain during the evolution and development of reptiles including birds. Nature ecology & evolution, 1(10), 1543-1550.\n- Alonso, P. D., Milner, A. C., Ketcham, R. A., Cookson, M. J., & Rowe, T. B. (2004). The avian nature of the brain and inner ear of Archaeopteryx. Nature, 430(7000), 666-669.\n- Kundrát, M. (2007). Avian-like attributes of a virtual brain model of the oviraptorid theropod Conchoraptor gracilis. Naturwissenschaften, 94(6), 499-504.\n- Larsson, H. C., Sereno, P. C., & Wilson, J. A. (2000). Forebrain enlargement among nonavian theropod dinosaurs. Journal of vertebrate Paleontology, 20(3), 615-618.\n- Torres, C. R., Norell, M. A., & Clarke, J. A. (2021). Bird neurocranial and body mass evolution across the end-Cretaceous mass extinction: The avian brain shape left other dinosaurs behind. Science Advances, 7(31), eabg7099.\nModern crocodiles as examples of the plesiomorphic condition of archosaurs\n- Fabbri, M., & Bhullar, B. A. S. (2022). The endocast of Euparkeria sheds light on the ancestral archosaur nervous system. Palaeontology, 65(6), e12630.\n- Brown, E. E., Butler, R. J., Ezcurra, M. D., Bhullar, B. A. S., & Lautenschlager, S. (2020). Endocranial anatomy and life habits of the Early Triassic archosauriform Proterosuchus fergusi. Palaeontology, 63(2), 255-282.\n- Lessner, E. J., & Stocker, M. R. (2017). Archosauriform endocranial morphology and osteological evidence for semiaquatic sensory adaptations in phytosaurs. Journal of Anatomy, 231(5), 655-664.", "reviewer_2": "The manuscript \"Endocranial development in non-avian dinosaurs reveals an ontogenetic brain trajectory distinct from extant archosaurs\" by King and colleagues uses geometric morphometric shape analyses to compare endocranial shape of non-avian dinosaurs with that of birds and crocodylians in light of ontogenetic variation. The manuscript is well written, the methods and sampling are adequate and the results are interesting, showing an intermediate brain ontogenesis in non-avian dinosaurs, when compared with the extant phylogenetic bracket. The interpretations of the results sound fine to me. However, I some comments (listed in the PDF attached) that should be addressed. In sum, I support the publication of the manuscript in Nature Communication after a minor revision.", "reviewer_3": "Dear Dr. King and colleagues,\nI enjoyed reading your manuscript and found the topic really interesting. I have no doubt that this manuscript will form the starting point of a long and interesting research. Please find listed few comments that I'd like you to address.\nSincerely\nIntroduction\n1. Line 54: “A reliable inference of evolutionary shifts in development requires sampling of adequate developmental series for non-avian dinosaurs.” Could you please explain what do you mean by “adequate”? Previous studies working on origins of the avian brain are using non-avian theropod dinosaurs that are phylogenetically close to the origins of birds (e.g., Balanoff et al. 2013, 2016; Ksepka et al. 2020; Watanabe et al. 2021). Here, you are mainly using an ontogenetic series of endocasts of the ornithischian dinosaur Psittacosaurus. Could you please consider adding few sentences in the introduction that would help to understand how this species is adequate on this topic?\n2. Line 61: “Moreover, we include immature specimens of additional non-avialan dinosaurs to further define the overall developmental axis of brain morphology in non-avialan dinosaurs” Could you please add the names of the additional non-avialan dinosaurs here? In addition, references 7 and 8 cited at the end of this sentence correspond to studies on Psittacosaurus, is that okay?\nMaterial and Methods\n1. I found “difficult” to distinguish in Table 1 which specimens are birds and which ones are non-avian dinosaurs. Could you please consider adding a column “clade” that would help to identify the specimens for a non-specialist like me?\n2. Archaeopteryx is indicated as juvenile in Table 1, is that correct? I am asking because I did not find any mention of that in the text.\n3. Lines 323-325: “The taxonomically ambiguous tyrannosaurid specimen, CMNH 7541, is considered a juvenile form of Tyrannosaurus rex or of a distinct taxon Nanotyrannus in this study”. This sentence is a little bit confusing. In your results, CMNH 7541 is clearly indicated as a juvenile specimen, so why this is not clearly stated in the Mat & Meth?\n4. Lines 325-326: “The results and conclusions of the study are not dependent on the taxonomic assignment of this specimen.” This argument does not constitute a justification with regard to the objective of the paper. The tyrannosaurid specimen CMNH 7541 is considered as juvenile here and both the interpretation and discussion are “impacted” by this choice.\n5. Lines 327-328: “The endocast of the tyrannosaur Alioramus altai (IGM 100/1844) was retrodeformed using a local symmetrization algorithm implemented in the “Morpho” R package due to its sheared appearance.” This sentence, in my opinion, should be placed in the following section “Imaging and Endocranial Reconstructions”.\nIn addition, please state clearly the specimen names for which you have reconstructed the endocasts and consider providing both information and pictures about the new endocasts generated in this study. For instance, the endocast of the Psittacosaurus specimen PKUP V1053 is very incomplete in Zhou et al (2007), is the reconstruction generated here more complete? The “degree of completeness” for each endocast needs to be given as it can have a strong impact on the rest of the study.\n6. In Figure 1c, please indicate the corresponding landmark numbers to help in the identification of the red points.\nIn the caption of Figure 1, please remove the space between lines 535 and 536. In addition, although it is provided in other figures, please consider stating the color code in the caption of Figure 1.\n7. I do not understand the definition of the 13th landmark provided in Table S1. Why “6 (reused)”? In addition, please consider adding information about the extent to which landmarks can be placed accurately on the endocasts.\n8. Line 353: “We acknowledge that endocasts are generally accurate representations of actual brain morphology”. Yes, in birds but it depends on brain regions in other archosaurs. Please rephrase the sentence as it sounds like a statement for all archosaurs whereas you indicate that variability may exist within the clade in the following sentences.\nResults\n1. Lines 85-88: “Notably, the perinatal Psittacosaurus (IVPP V15451) and juvenile troodontid (IGM 100/1126), as well as the juvenile tyrannosaurid (CMNH 7541), also occupy an intermediary position between crown birds and non-avialan archosaurs along PC1 (Fig. 2a).” What about the other immature non-avian dinosaurs? Could you please indicate their location on Fig. 2a? And why such a difference in the distribution of the two troodontids specimens?\n2. Lines 91-93: “In the case of IVPP V15451 and IGM 100/112691 (Psittacosaurus and a troodontid, respectively), the anatomical arrangement of the brain more closely resembles crown birds than the early avialan Archaeopteryx.” I am a little bit confused, maybe I don’t understand the sentence correctly. For me, endocasts of Psittacosaurus and the troodontid specimen share more similarities with Archaeopteryx than with crown birds. Could you please clarify your statement?\n3. Lines 93-94: “With age, the morphological layout of the non-avialan dinosaur endocast trends towards that of crocodilians but maintains an anatomical arrangement that is distinct from both alligators and crown avians.” I agree, endocasts in mature non-avialan dinosaurs are distinct from crown birds, but are they really different from adult alligators? I am not sure. Especially, because the features you are giving in the next sentences (lines 96-98) look like features observed in the endocast of mature alligators. Any statistical test that could support your statement?\n4. Lines 99-100: “These neuroanatomical changes collectively result in an endocast that is anatomically distinct and is arranged all along the same plane.” I don’t understand this sentence. Anatomically distinct from what?\n5. Lines 100-102: “Notably, P. lujiatunensis follows this trend between the perinatal (sub-yearling) and subadult (7 and 8-years-old) stages but reverts towards a more juvenile-like form between the inferred ages of 8 and 10 years old.” The other sub-adult specimen does not show such a trend. Could you clarify/interpret such a difference?\n6. Lines 103-104: “Among the morphospace partitions of the brain, juvenile non-avialan dinosaurs reliably overlapped the crown birds or lay near the avian morphospace in a manner similar to oviraptors and troodontids.” I disagree, the results considering the brainstem morphology (Fig. 2e) is not showing such a distribution (see perinate Psittacosaurus and juvenile T-rex). Please rephrase your statement in order to indicate that variability may exist.\n7. Lines 105-107: “The exception to this is the juvenile Lambeosaurus (ROM 758), as the total endocranial form and cerebrum and brainstem partitions of the closely related juvenile Corythosaurus (ROM 759) plotted more closely to crown birds” I am not sure of the meaning of this sentence. Based on the results in Fig. 2 (please clearly indicate the juvenile Corythosaurus (ROM 759) on the different figures), I rather see the opposite and the juvenile Corythosaurus plots more closely to alligators (you are saying that in the following sentence). Please clarify.\n8. Lines 124-125: “In the cerebellar morphospace, crown birds and Archaeopteryx form a group that is separated from alligators along PC2 (Fig. 2c)” Yes and no, we can see a small overlap.\n9. Line 133: “Apart from the hadrosaur Lambeosaurus (ROM 758),…….” And also the Corythosaurus specimen, right?\n10. Lines 135-137: “During postnatal ontogeny, the endocranial shapes of ornithischian and non-avialan dinosaurs (except Psittacosaurus) begin in the area of morphospace occupied by crown birds and subsequently converge to mature alligators.” You just said in the previous sentence that the position of the juvenile hadrosaur Lambeosaurus (and maybe the juvenile Corythosaurus) overlaps the alligator distribution. Why such a sentence here? Also you are talking here about the cerebellum shape, not the whole endocranial shape, please be more precise.\n11. Line 174: “Notably, the immature specimens of ornithischian dinosaurs align with crown birds in RSC1 values” Even the juvenile specimens of Lambeosaurus and Corythosaurus?\n12. Lines 183-185: “Immature ornithischian and non-avialan dinosaurs group within or near crown birds, with juvenile Lambeosaurus (ROM 758) and relatively mature non-avialan dinosaurs more closely resembling adult Alligator (Fig. 3c).” The end of the sentence contradicts the beginning. You are stating that immature ornithischian dinosaurs are within or near crown birds whereas it is only the Psittacosaurus specimens among the ornithischians, juvenile Lambeosaurus and Corythosaurus are within alligators.\n13. Lines 186-188: “Interestingly, adult and subadult psittacosaurs plot with crown birds along with Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247) specimens, while the juvenile hadrosaur Lambeosaurus (ROM 758) aligns more closely with Alligator.” Please indicate Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247) on Fig. 3. The juvenile Corythosaurus also aligns with alligators right?\n14. Lines 189-190: “For the optic lobe, allometric trends group according to taxon, with crown birds and Archaeopteryx grouping together along the RSC1 axis” Not sure we can say that. Two mature theropod dinosaurs are grouping with crown birds, and one Psittacosaurus specimen plots within alligators.\n15. Lines 193-194: “The perinatal Psittacosaurus (IVPP V15451) and immature troodontids Zanabazar and unnamed troodontid (IGM 100/1126) are similar in RSC1 value to crown birds” They seems to have closer RSC1 values with crown birds but not really similar\nDiscussion\n1. Lines 226-228: “Indeed, they begin somewhat avian-like among perinatal and juvenile individuals and broadly converge to more alligator-grade endocranial morphology. Because this allometric trajectory occurs in both coelurosaurian and ornithischian non-avian dinosaurs,….” Both sentences are a little bit oversimplified, you are not considering the variability you found in your results (the other ornithischian dinosaurs for example do not show such a pattern right?).\n2. Lines 235-236: “In cerebrum, cerebellum, and optic lobe shapes, non-avialan dinosaurs resemble more those of crown birds than alligators”. You basically said in your results that “Based on the plot, it is uncertain whether [optic-lobes in] non-avialan dinosaurs align with the allometric trajectories of alligators and/or crown birds.” (lines 195-196). Again, this statement seems a little bit oversimplified to me and why are not considering other ornithischian dinosaurs?\n3. Lines 239-240: “these outcomes imply that non-avialan dinosaurs underwent distinct brain development compared to crocodilians” At least in Psittacosaurus, not sure that such a rule can be established here from the other ornithischian dinosaurs.\n4. Line 247: “Besides the optic lobe shape being closer to crown birds” I agree closer with birds than with alligators, but also distinct from birds\n5. Lines 248-249: “the brainstem shape of ornithischian dinosaurs visually aligns with the allometric trajectory of alligators (Fig. 3d), whereas that of non-avialan dinosaurs, particularly immature specimens, aligns more closely with crown birds (Fig. 3e).” I think a word is missing here, I mean ornithischian dinosaurs are non-avialan dinosaurs, no? Also you are saying in your results about the brainstem: “As such, the results suggest that both ornithischian and non-avialan dinosaurs resembled an alligator-grade scaling relationship in brainstem shape” (lines 202-204). I am a little bit confused here\n6. Line 257, please remove the dash before “Specifically”\n7. Lines 276-278: “Our results suggest that paedomorphosis plays a role in the total endocranial form and evolution of the avian brain where the form of the bird brain more resembles that of juvenile non-avialan dinosaurs.” Not all non-avialan dinosaurs, only Psittacosaurus.", "reviewer_3_round_2": "Dear authors,\nThank you for sending the revision of your manuscript. All my comments have been taken into account and I have only one concern that should be addressed. In the introduction (line 54), if I am correct, \"However, a good developmental series of neuroanatomical morphologies for non-avian dinosaurs HAS been lacking to date; AND crucial evidence IS needed for a reliable inference of .....\". Other than that, everything is good for me.\nBest regards,\nR.A"}, "author_response": "REVIEWER COMMENTS\nReviewer #1 (Remarks to the Author):\nKing et al. present a new study addressing the question of how the evolution of ontogenetic trajectories across the dinosaur-bird transition affected the origin of the modern avian brain.\nThe authors conclude that crocodilians, non-avian dinosaurs, and modern birds show\ndifferent trajectories. Although previous studies already tackled the question, the main\nnovelty of the study relies on the inclusion of ontogenetic series of non-avian dinosaurs,\nwhich were previously neglected. Overall, I enjoyed the manuscript and I suggest publication\nof the study. I have a few major comments that should be addressed by the authors:\n- The authors focus on heterochronic events that affected the head and the nervous system.\nHowever, what about the trend in miniaturization that is affecting the origin of birds? As\nstated in previous studies, multiple events of ontogenetic truncation affected the evolution of\nthe head in the dinosaur-bird transition, but the miniaturization process leading to modern\nbirds does not follow heterochronic trends per se. I would ask the authors to discuss this in\nthe manuscript, considering that analyses regarding allometry per se are already present in\nthe study.\nWe have incorporated a section comparing the heterochronic signal we observe in brain\nevolution to the trend in miniaturization occurring along the bird-line dinosaurian lineage:\n“Our results suggest that paedomorphosis plays a role in the total endocranial form and\nevolution of the avian brain where the form of the bird brain more resembles that of juvenile\nnon-avialan dinosaurs. The shift from a non-avialan dinosaur endocranial form to that of an\navian form is best explained through paedomorphosis rather than just miniaturization.\nMiniaturization of the body including the brain – was a stepwise process that reduced the\nbody mass along stem birds and with further reductions in body sizes occurring in avialans\nand pygostylian birds28,29. And while the reduction of the brain size may follow a sustained\nminiaturization and has been shown to occur in faster rates among bird-line theropods than\nother non-avialan dinosaur lineages30, miniaturization does not explain the expression of\njuvenile non-avialan dinosaur traits along the bird brain (see also Torres et al. 2021).” [new\nLn 282-291].\n- I agree with the general conclusions, but I don’t understand why the authors continue\nemphasizing that different ontogenetic trajectories among non-avian dinosaurs are\nsurprising: the phenotype of their nervous system among non-avian dinosaurs differs from\nmodern crocodiles and birds as a result of mosaic evolution. If we assume that an adult\nphenotype is the result of a specific developmental trajectory, as it is generally the case\namong amniotes, then this shouldn’t be surprising. I would adjust the text accordingly.\nWe agree with the reviewer’s comment that if the adult phenotype is different, then the\nallometric trajectories would be different given that the earliest stages of brain development\nresemble one another across vertebrates. However, how they differ throughout ontogenetic\nseries could be insightful, given that several non-avian dinosaurs exhibit endocranial shapes\nthat closely resemble adult alligators. For example, we could anticipate that the ontogenetic\ntrajectories of some non-avian dinosaurs could converge to Alligator trajectories. In addition,\nwe argue that our results showing shared ontogenetic shape trajectories between\nornithischian and theropod taxa is surprising, given disparate neuroanatomical shape\nobserved and reported across non-avian dinosaurs. Nevertheless, we have modified and\nclarified the statements that allude to the “surprising” factor of our results based on the\nreviewer’s comment.\n- I would ask the authors to image all ontogenetic stages of the ontogenetic series included\nin the study in figure 1. At the moment, only few endocasts are represented. I think this is\ninsufficient for the scope of the study.\nWe have included endocast images of intermediate ontogenetic stages to Fig. 1. We\ndecided to not include all specimens for two reasons: (1) we believe adding the intermediate\nontogenetic stages provide information about the overall ontogenetic trends; and (2) the\nfigure would become very crowded as a main text figure.\n- I noticed that in most plots, some data points are labelled with catalogue numbers. Please,\nchange this with the name of the taxon and ontogenetic stage: it would be very difficult for a\ngeneral reader to follow the plots without having a clear expertise in this field.\nOur logic was to include specimen number when there are multiple specimens we sampled\nfor a given genus/species and when the taxonomic affinity is ambiguous: (CMNH 7541,\njuvenile tyrannosaur that has been interpreted as Tyrannosaurus rex or a separate taxon–\nNanotyrannus) or undescribed taxa (IGM 100/1126, a troodontid) as their collections\nnumber. We have followed the reviewer’s suggestion and have included in the caption to\nrefer to Table 1 for specimen number.\n- Some of the ontogenetic stages are well characterized in terms of age, but others are not.\nHow did the authors homologize ontogenetic stages between modern and extinct species?\nThis is fundamental to clarify considering that heterochrony requires such knowledge\nbetween compared species to infer heterochronic trends. A section in the methods is\nnecessary. Moreover, I would add a paragraph regarding such limitations in the discussion.\nWe acknowledge that this point is important to explain in the text. Because the\ndevelopmental staging of non-avian dinosaurs is admittedly course, we have not attempted\nto homologize the growth stages, but based our categorization into ‘juvenile’ and ‘mature’\nbased on previous literature to infer overall patterns of ontogenetic changes. This being said,\nwe believe that our results and conclusions are robust to the coarseness of the\ndevelopmental staging across clades. We have included additional text in both Methods and\nDiscussion section that touches on these points.\n- In the last part of the discussion, the authors argue that their results do not support a single\nheterochronic event leading to modern birds. I agree, but the original studies infer multiple\nheterochronic events, not just one. I would suggest the authors to revise this part of the\ndiscussion.\nWe have clarified that the idea that mixed heterochronic signals characterize the craniofacial\nand brain evolution have been proposed before (Ln 305-306).\n- Finally, there are fundamental references that are missing to justify some of the\nassumptions/statements in the intro and discussion that should be cited in the main text\nHeterochrony of the head:\n- Plateau, O., & Foth, C. (2020). Birds have peramorphic skulls, too: anatomical network\nanalyses reveal oppositional heterochronies in avian skull evolution. Communications\nBiology, 3(1), 195.\n- Lee, H. W., Esteve-Altava, B., & Abzhanov, A. (2020). Evolutionary and ontogenetic\nchanges of the anatomical organization and modularity in the skull of archosaurs. Scientific\nReports, 10(1), 16138.\n- Navalón, G., Nebreda, S. M., Bright, J. A., Fabbri, M., Benson, R. B., Bhullar, B. A., ... &\nRayfield, E. J. (2021). Craniofacial development illuminates the evolution of nightbirds\n(Strisores). Proceedings of the Royal Society B, 288(1948), 20210181.\nPrevious studies have proposed that a mixture of heterochronic processes within the\ncranium, particularly progenesis (truncation of the ancestral developmental period) and\naccelerated peramorphosis (evolutionarily driven increases in developmental rates), may\nunderlie major changes to the brain architecture from ancestral archosaurian forms to crown\nbirds3,11–16 (Ln 49-53)\nHeterochrony and mosaic evolution of the nervous system:\n- Kundrát, M., Xu, X., Hančová, M., Gajdoš, A., Guo, Y., & Chen, D. (2018). Evolutionary\ndisparity in the endoneurocranial configuration between small and gigantic tyrannosauroids.\nHistorical Biology.\nUsing skulls and cephalic endocasts (internal molds of the braincase) as proxies for brain\nshape and size, previous studies have revealed that the evolutionary assembly of the avian\nbrain form proceeded in a mosaic and homoplastic manner from the ancestral dinosaurian\npattern1–11 (Ln 44-47)\nThis then identifies three ontogenetic trajectories for endocast shape in archosaurs, the\ncrocodilian style in which the brain remains elongate throughout life, the avian style which is\na paedomorphic modification in which the brain shortens through life, and the dinosaurian\nstyle which exhibits a mosaic of avian and crocodilian neuroanatomical features – as has\nbeen qualitatively noted interspecifically within clades5. (Ln 236-241)\n- Chiappe, L. M., Navalón, G., Martinelli, A. G., Nava, W., & Field, D. J. (2022). Fossil\nbasicranium clarifies the origin of the avian central nervous system and inner ear.\nProceedings of the Royal Society B, 289(1983), 20221398.\n- Fabbri, M., Mongiardino Koch, N., Pritchard, A. C., Hanson, M., Hoffman, E., Bever, G. S.,\n... & Bhullar, B. A. S. (2017). The skull roof tracks the brain during the evolution and\ndevelopment of reptiles including birds. Nature ecology & evolution, 1(10), 1543-1550.\n- Alonso, P. D., Milner, A. C., Ketcham, R. A., Cookson, M. J., & Rowe, T. B. (2004). The\navian nature of the brain and inner ear of Archaeopteryx. Nature, 430(7000), 666-669.\n- Kundrát, M. (2007). Avian-like attributes of a virtual brain model of the oviraptorid theropod\nConchoraptor gracilis. Naturwissenschaften, 94(6), 499-504.\n- Larsson, H. C., Sereno, P. C., & Wilson, J. A. (2000). Forebrain enlargement among\nUsing skulls and cephalic endocasts (internal molds of the braincase) as proxies for brain\nshape and size, previous studies have revealed that the evolutionary assembly of the avian\nbrain form proceeded in a mosaic and homoplastic manner from the ancestral dinosaurian\npattern1–11 (Ln 44-47)\n- Torres, C. R., Norell, M. A., & Clarke, J. A. (2021). Bird neurocranial and body mass\nevolution across the end-Cretaceous mass extinction: The avian brain shape left other\ndinosaurs behind. Science Advances, 7(31), eabg7099.\nUsing skulls and cephalic endocasts (internal molds of the braincase) as proxies for brain\nshape and size, previous studies have revealed that the evolutionary assembly of the avian\nbrain form proceeded in a mosaic and homoplastic manner from the ancestral dinosaurian\npattern1–11 (Ln 44-47)\nPrevious studies have proposed that a mixture of heterochronic processes within the\ncranium, particularly progenesis (truncation of the ancestral developmental period) and\naccelerated peramorphosis (evolutionarily driven increases in developmental rates), may\nunderlie major changes to the brain architecture from ancestral archosaurian forms to crown\nbirds3,11–16 (Ln 49-53)\nModern crocodiles as examples of the plesiomorphic condition of archosaurs\n- Fabbri, M., & Bhullar, B. A. S. (2022). The endocast of Euparkeria sheds light on the\nancestral archosaur nervous system. Palaeontology, 65(6), e12630.\n- Brown, E. E., Butler, R. J., Ezcurra, M. D., Bhullar, B. A. S., & Lautenschlager, S. (2020).\nEndocranial anatomy and life habits of the Early Triassic archosauriform Proterosuchus\nfergusi. Palaeontology, 63(2), 255-282.\n- Lessner, E. J., & Stocker, M. R. (2017). Archosauriform endocranial morphology and\nosteological evidence for semiaquatic sensory adaptations in phytosaurs. Journal of\nAnatomy, 231(5), 655-664.\nIf true, this would further support the notion that the crocodilian-like ontogenetic sequence is\nthe plesiomorphic mode among early archosaurs23–25 (Ln 224-225)\nReviewer #2 (Remarks to the Author):\nThe manuscript \"Endocranial development in non-avian dinosaurs reveals an ontogenetic\nbrain trajectory distinct from extant archosaurs\" by King and colleagues uses geometric\nmorphometric shape analyses to compare endocranial shape of non-avian dinosaurs with\nthat of birds and crocodylians in light of ontogenetic variation. The manuscript is well written,\nthe methods and sampling are adequate and the results are interesting, showing an\nintermediate brain ontogenesis in non-avian dinosaurs, when compared with the extant\nphylogenetic bracket. The interpretations of the results sound fine to me. However, I some\ncomments (listed in the PDF attached) that should be addressed. In sum, I support the\npublication of the manuscript in Nature Communication after a minor revision:\nLine 44: Technically, pterosaurs also belong to the stem birds. So maybe it is better to use\nnon-avian avemetatarsalians.\nAvemetatarsalia includes all archosaurs that are more closely related to birds than\ncrocodilians. Pterosaurs, by definition, would also be included in the group “non-avian\nAvemetatarsalia.” However, to avoid any phylogenetic confusion, we have changed “stem\nbirds” to “non-avian dinosaurs and early avialans)\nLine 53: Ref 5, Bhullar et al. 2012 did not sample brain morphologies, but cranial shape.\nBhullar et al. 2012 did not sample endocasts and brain morphologies, but rather discussed\nthe implications of the study for archosaur brain evolution. However, we recognize that the\npreceding sentence describes previous studies that have employed endocasts, so citation\nand reference removed.\nLine 68-69: Given that in most non-avian reptiles the brain fills only about half of the volume\nof the endocranium (Ferreira, et al. (2023). Contrasting Brains and Bones: Neuroanatomical\nEvolution of Turtles (Testudinata). In: Dozo et al. (eds) Paleoneurology of Amniotes .\nSpringer, Cham. https://doi.org/10.1007/978-3-031-13983-3_4) may explain the relationships\nbetween endocast and brain shape as you did in the material and method section.\nThe Watanabe et al. 2019 reference cited in the manuscript has demonstrated the close\nshape correspondence in Alligator mississippiensis and Gallus gallus throughout postnatal\nontogenetic series. In accordance with one of the conclusions of the Watanabe et al. 2019,\nwe consider that the difference in brain and endocranial shapes are negligible relative to the\nneuroanatomical variation across species sampled in this study.\nLine 85: Maybe better to use \"crown bird\"\nFollowing Gauthier, the use of the term Avialae (all taxa closer to Passer than to Troodon\nand Dromaeosaurus), implies the use of the term Aves for the crown.\nThus, referring to the term neornithine for the crown is confusing, as this concept defines\nAves similar to Avialae.\nNeornithes is accepted term for crown birds. However, we have changed “neornithine” to\n“crown”.\nLine 93: Please, clarify you mean an adult Archaeopteryx, because given the close\nrelationship to troodontids, it is likely that Archaeopteryx followed the same developmental\npath.\nThe Archaeopteryx specimen we used in our study was actually immature according to\nErickson et al. 2009. Age aside, we have changed our phrase to say “…anatomical\narrangement of the endocast more closely resembles crown birds than the arrangement\nfound in a juvenile specimen of the early avialan Archaeoptery ”. (Ln 100-102)\nLine 100-102: Please, emphazise more clearly that the ontogenetic trajctory of\nPsittacosaurus differs from alligator and chicken, which ontogenetic trajectories are more or\nless straight following the same shape trend.\nWe believe we make this clear with the statement: “With age, the morphological layout of the\nnon-avialan dinosaur endocast trends towards that of Alligator, where the mature individuals\nof non-avialan dinosaurs and Alligator converge in their ontogenetic trajectories” (Ln 102-\n104). We also emphasize this point in the discussion and conclusion sections, so we\nrespectfully did not make any significant changes based on this specific comment.\nLine 102: Highlighted “…between the inferred ages of 8 and 10 years old”\nWe are unsure what this particular comment means in the PDF.\nLine 105-106: These species are not labled in Fig 2a, making it diffcult to judge this\nstatement.\nThank you for pointing this out. We have added these taxa to Fig. 2a.\nLine 236: brain stem?\nWe have now added “However, this trend is reversed along the brainstem where non-avialan\ndinosaurs and alligators group together and apart from crown birds (Fig. 2e)” to explain the\ntrend that is occurring along the brainstem in addition to the cerebrum, cerebellum, and optic\nlobe partitions. (Ln 244-246)\nLine 257: Highlighted Text\nWayward dash has been removed.\nLine 267: DELETE\nDeleted.\nLine 353: Maybe it is better to refer only to archosurs for this statement. Comparing\nendocast and brain shape in turtles (see Ferreira et al. 2023) the differences are more\ndistinct.\nChanged this statement to say “We acknowledge that endocasts are generally accurate\nrepresentations of actual brain morphology among archosaurs…”. (Ln 376-378)\nLine 391-392: Please also add the MANOVA you mentioned in the result section\nWe had included statistical results (trajectory analysis) as Table S2, even in the original\nsubmission. We have added an explicit statement saying this (new Ln 213-215).\nLine 535-536: Change\"th is\" to \"this\"\nChanged.\nCould you add the most impartant clade names to the phylogeny. The color code does not\nexplain anything. Furthermore, could you highlight which terminal taxa is represented by\njuveniles only, adults only and ontogenetic series?\nWe have modified the figure to include clade names with corresponding colors. The color\nscheme matches how the data points are colored in Fig. 2 and 3. We have also indicated\nwhich specimens are represented by ‘immature’ specimens with asterisks next to their\ntaxonomic names.\nLine 541-542: Please, label the hadrosaur taxa in plot a.\nCorrected accordingly.\nLine 545-546: Please, label the hadrosaur taxa in plot a.\nCorrected accordingly.\nAdd the ontogenetic trajectories to the plot b to e.\nWe have added semi-transparent lines to indicate ontogenetic trajectories.\nTable 1: This table could be also put into the supplements\nWe understand where the reviewer is coming from, and we have debated the pros and cons\nof moving the table to the supplements. Upon further consideration, we have decided to\nkeep the table in the main manuscript to cut down on the number of supplementary materials\nattached to a single manuscript. Perhaps more importantly, having the table in the main\nmanuscript allows for readers to readily view crucial specimen data at a glance rather than\naccessing supplementary files.\nReviewer #3 (Remarks to the Author):\nDear Dr. King and colleagues,\nI enjoyed reading your manuscript and found the topic really interesting. I have no doubt that\nthis manuscript will form the starting point of a long and interesting research. Please find\nlisted few comments that I'd like you to address.\nSincerely\nIntroduction\n1. Line 54: “A reliable inference of evolutionary shifts in development requires sampling of\nadequate developmental series for non-avian dinosaurs.” Could you please explain what do\nyou mean by “adequate”? Previous studies working on origins of the avian brain are using\nnon-avian theropod dinosaurs that are phylogenetically close to the origins of birds (e.g.,\nBalanoff et al. 2013, 2016; Ksepka et al. 2020; Watanabe et al. 2021). Here, you are mainly\nusing an ontogenetic series of endocasts of the ornithischian dinosaur Psittacosaurus. Could\nyou please consider adding few sentences in the introduction that would help to understand\nhow this species is adequate on this topic?\nAdded “Endocranial series from P. lujiatunensis allows for an unprecedented look into how\nthe neuroanatomy of a non-avialan dinosaur species changes with age. We incorporate this\nnew developmental dataset into an interspecific dataset of archosaurian endocranial\nmorphology which also includes postnatal ontogenetic series of the domestic chicken (Gallus\ngallus domesticus), and American alligator (Alligator mississippiensis) as an outgroup3 (Fig.\n1a, b). Moreover, we include immature specimens of additional non-avialan dinosaurs17–21\n(Lambeosaurus, Corythosaurus, tyrannosaurids, Zanabazar, and another troodontid; Table\n1) to further define the overall developmental axis of brain morphology in non-avialan\ndinosaurs (i.e., excluding Archaeopteryx considered here to be a basal avialan)”. (Ln 58-66)\n2. Line 61: “Moreover, we include immature specimens of additional non-avialan dinosaurs\nto further define the overall developmental axis of brain morphology in non-avialan\ndinosaurs” Could you please add the names of the additional non-avialan dinosaurs here? In\naddition, references 7 and 8 cited at the end of this sentence correspond to studies on\nPsittacosaurus, is that okay?\nThe non-avialan dinosaurs that contain ontogenetic data have been added in this sentence.\nAnd yes, references 17 and 18 refer to Psittacosaurus, but 19 through 21 indicate where the\nextra ontogenetic dinosaur data came from.\nMaterial and Methods\n1. I found “difficult” to distinguish in Table 1 which specimens are birds and which ones are\nnon-avian dinosaurs. Could you please consider adding a column “clade” that would help to\nidentify the specimens for a non-specialist like me?\nWe have now added a column that identifies each specimen to a higher classification that is\nmost frequently used in manuscripts for easier recognition by readers.\n2. Archaeopteryx is indicated as juvenile in Table 1, is that correct? I am asking because I\ndid not find any mention of that in the text.\nYes, this Archaeopteryx specimen (WDC CSG 100) has been shown to be juvenile based on\nErickson et al. 2009.\n3. Lines 323-325: “The taxonomically ambiguous tyrannosaurid specimen, CMNH 7541, is\nconsidered a juvenile form of Tyrannosaurus rex or of a distinct taxon Nanotyrannus in this\nstudy”. This sentence is a little bit confusing. In your results, CMNH 7541 is clearly indicated\nas a juvenile specimen, so why this is not clearly stated in the Mat & Meth?\nThis statement has been rearranged to say “The taxonomically ambiguous tyrannosaurid\nspecimen, CMNH 7541, has been considered a relatively immature specimen within\nTyrannosauridae39–43. (Ln 340-342)\n4. Lines 325-326: “The results and conclusions of the study are not dependent on the\ntaxonomic assignment of this specimen.” This argument does not constitute a justification\nwith regard to the objective of the paper. The tyrannosaurid specimen CMNH 7541 is\nconsidered as juvenile here and both the interpretation and discussion are “impacted” by this\nchoice.\nWe have now added the following statement to clarify our meaning of the importance of\nphylogeny and ontogeny in regards to CMNH 7541: “The major results and conclusions of\nthis study are not dependent on the taxonomic assignment of this specimen, but rather the\nontogenetic stage of CMNH 7541. Considering that no organism attributable to a\ntyrannosaur similar to, and including, CMNH 7541 has preserved an external fundamental\nsystem that indicates the cessation of rapid growth and the onset of skeletal maturity39,45, we\ntreat CMNH 7541 as an immature individual” (Ln 342-346)\n5. Lines 327-328: “The endocast of the tyrannosaur Alioramus altai (IGM 100/1844) was\nretrodeformed using a local symmetrization algorithm implemented in the “Morpho” R\npackage due to its sheared appearance.” This sentence, in my opinion, should be placed in\nthe following section “Imaging and Endocranial Reconstructions”.\nWe agree. The suggested statement has been moved to the following section.\nIn addition, please state clearly the specimen names for which you have reconstructed the\nendocasts and consider providing both information and pictures about the new endocasts\ngenerated in this study. For instance, the endocast of the Psittacosaurus specimen PKUP\nV1053 is very incomplete in Zhou et al (2007), is the reconstruction generated here more\ncomplete? The “degree of completeness” for each endocast needs to be given as it can\nhave a strong impact on the rest of the study.\nIVPP V 15451 and IVPP V12731 were reconstructed. The reviewer is correct that the\nmodels used for Zhou et al (2017) were incomplete. Both PKUP specimens were\nreconstructed again as part of a separate project where much of the areas that were missing\nin the Zhou et al (2017) study – the pituitary fossa and area around the anterior olfactory\napparatus, in particular – were able to be reconstructed in better detail. However,\nconsidering that both the published and reconstructed versions of the PKUP specimens\npreserved the morphology necessary to perform our statistical tests, the degree of\ncompleteness in both versions of models is sufficient. To reflect this, we have added\n“Considering the incomplete nature of the PKUP 1053 and PKUP 1054 endocasts18, they\nwere reconstructed again for this study. We found that the original specimens and\nreconstructed models were of sufficient quality for morphometric analysis. These\nreconstructions were paired with two other Psittacosaurus specimens, IVPP V15451 and\nIVPP V12617, to reconstruct an ontogenetic series for the species P. lujiatunensis.” (Ln 355-\n359)\n6. In Figure 1c, please indicate the corresponding landmark numbers to help in the\nidentification of the red points.\nWe have added numbers for discrete landmarks corresponding to the numbering we list in\nTable S1.\nIn the caption of Figure 1, please remove the space between lines 535 and 536. In addition,\nalthough it is provided in other figures, please consider stating the color code in the caption\nof Figure 1.\nThe errant space has been deleted and branch color scheme has been explained in the\ncaption.\n7. I do not understand the definition of the 13th landmark provided in Table S1. Why “6\n(reused)”? In addition, please consider adding information about the extent to which\nlandmarks can be placed accurately on the endocasts.\nWe have added an explanation for how Landmark 6 is treated in the table caption for Table\nS1.\n8. Line 353: “We acknowledge that endocasts are generally accurate representations of\nactual brain morphology”. Yes, in birds but it depends on brain regions in other archosaurs.\nPlease rephrase the sentence as it sounds like a statement for all archosaurs whereas you\nindicate that variability may exist within the clade in the following sentences.\nSentence updated to “We acknowledge that endocasts are generally accurate\nrepresentations of actual brain morphology among archosaurs18,33...” to indicate that we are\nspecifically talking about archosaurs (Ln 376-378)\nResults\n1. Lines 85-88: “Notably, the perinatal Psittacosaurus (IVPP V15451) and juvenile troodontid\n(IGM 100/1126), as well as the juvenile tyrannosaurid (CMNH 7541), also occupy an\nintermediary position between crown birds and non-avialan archosaurs along PC1 (Fig. 2a).”\nWhat about the other immature non-avian dinosaurs? Could you please indicate their\nlocation on Fig. 2a? And why such a difference in the distribution of the two troodontids\nspecimens?\nWe have now added “All other juvenile taxa maintain similarly high PC2 scores as CMNH\n7541 but have higher PC1 scores. Notably, the perinatal Psittacosaurus (IVPP V15451) and\njuvenile troodontid (IGM 100/1126), overlap in PC2 values as neo- and perinatal Gallus (Fig.\n2a).” to explain the pattern exhibited by the remaining juvenile taxa used in this study. The\ndifference between the two troodontid specimens are likely driven by the increased overall\nflexion and extent of the dorsal eminence, which is prominent in Zanabazar compared to the\nunnamed troodontid. The hadrosaurs in our sample exhibit similar differences when you\ncompare the juvenile Corythosaurus and Lambeosaurus specimens in Figure 2a. It is\npossible that ontogenetic differences plays a part in the differences, although it is unclear at\nthis moment why non-avialan dinosaur taxa show varying degrees of dorsal eminence. This\nsection has also been moved up to the preceding paragraph (Ln 94-96).\n2. Lines 91-93: “In the case of IVPP V15451 and IGM 100/112691 (Psittacosaurus and a\ntroodontid, respectively), the anatomical arrangement of the brain more closely resembles\ncrown birds than the early avialan Archaeopteryx.” I am a little bit confused, maybe I don’t\nunderstand the sentence correctly. For me, endocasts of Psittacosaurus and the troodontid\nspecimen share more similarities with Archaeopteryx than with crown birds. Could you\nplease clarify your statement?\nCertainly. You are correct in that the two dinosaur endocrania share a lot in common with\nArchaeopteryx; however, our statement is meant to note that both the troodontid and\nperinate Psittacosaurus lie more closely to crown birds than the Archaeopteryx specimen\ndoes along PC1. This phrase has been reworded to say “...the anatomical arrangement of\nthe endocast more closely resembles crown birds than the arrangement found in a juvenile\nspecimen of the early avialan Archaeopteryx does along PC1” for greater clarity (Ln 100-\n102)\n3. Lines 93-94: “With age, the morphological layout of the non-avialan dinosaur endocast\ntrends towards that of crocodilians but maintains an anatomical arrangement that is distinct\nfrom both alligators and crown avians.” I agree, endocasts in mature non-avialan dinosaurs\nare distinct from crown birds, but are they really different from adult alligators? I am not sure.\nEspecially, because the features you are giving in the next sentences (lines 96-98) look like\nfeatures observed in the endocast of mature alligators. Any statistical test that could support\nyour statement?\nWe have calculated Procrustes shape distance between each non-avian dinosaur to adult\nAlligator, then plotted and regressed distances against centroid size, showing that larger and\nmore mature dinosaurs gradually converge to the adult endocast shape of Alligator. We do\nnot include this finding in the study because centroid size should not be used as proxy for\nmaturity. However, it strengthens the case that larger, generally more mature non-avialan\ndinosaur endocast has lower shape distance to Alligator endocast.\n4. Lines 99-100: “These neuroanatomical changes collectively result in an endocast that is\nanatomically distinct and is arranged all along the same plane.” I don’t understand this\nsentence. Anatomically distinct from what?\nHere, we are specifically referencing crown birds. This statement is now clarified to say\n“…the anatomical arrangement of the endocast more closely resembles crown birds than the\narrangement found in a juvenile specimen of the early avialan Archaeopteryx does along\nPC1.” (Ln 100-102)\n5. Lines 100-102: “Notably, P. lujiatunensis follows this trend between the perinatal (sub-\nyearling) and subadult (7 and 8-years-old) stages but reverts towards a more juvenile-like\nform between the inferred ages of 8 and 10 years old.” The other sub-adult specimen does\nnot show such a trend. Could you clarify/interpret such a difference?\nThe most likely explanation is that one of the two subadults exhibits some kind of\ndorsomedial deformation that is bilaterally distributed, particularly around the midbrain.\nThere is difficulty in interpreting which would be the more likely culprit considering that PKUP\n1053 and PKUP 1054 are the only subadult Psittacosaurus lujiatunensis endocrania\ncurrently segmented. From personal observation, the endocast of PKUP 1053 preserves\nmore anatomy and was interpreted to have a better-defined dorsal eminence than PKUP\n1054, particularly anterior of the cerebellar area. Regardless of the potential issues with\nPKUP 1054, we interpret that the re-organization of the endocranium to be true considering\nthat the endocast that we interpret to be less deformed, PKUP 1053, still maintains a visual\nand statistical difference from the perinate and adult specimens. We have added the\nfollowing to help explain the difference pointed out by the reviewer: “The seemingly strange\nposition of 7-year-old Psittacosaurus may be due to the dorsoventrally shallower morphology\n(which result in more anteroposteriorly elongated, less flexed profile) compared to the three\nother Psittacosaurus endocasts, which may be due to moderate degree of deformation” (Ln\n109-112)\n6. Lines 103-104: “Among the morphospace partitions of the brain, juvenile non-avialan\ndinosaurs reliably overlapped the crown birds or lay near the avian morphospace in a\nmanner similar to oviraptors and troodontids.” I disagree, the results considering the\nbrainstem morphology (Fig. 2e) is not showing such a distribution (see perinate\nPsittacosaurus and juvenile T-rex). Please rephrase your statement in order to indicate that\nvariability may exist.\nThis section has been reworded to say “The morphospace for brainstem shape visually\nseparates crown birds and all other taxa sampled in this study along PC2 (Fig. 2e). The PC1\naxis largely documents the ontogenetic shape changes in alligator and chicken, from a\nmediolaterally expanded and dorsoventrally curved brainstem in perinatal specimens to\nanteroposteriorly elongated and weaker dorsoventral flexion in adults. Along PC2, crown\nbirds and the chicken ontogenetic series cluster together, while non-avialan dinosaurs\noverlap considerably with adult and subadult alligators. More immature alligators were\ngrouped with Archaeopteryx, relatively immature Psittacosaurus specimens (IVPP V15451,\nPKUP V1053, and PKUP V1054), and the immature troodontid IGM 100/1126 (Fig. 2e)..” (Ln\n150-157)\n7. Lines 105-107: “The exception to this is the juvenile Lambeosaurus (ROM 758), as the\ntotal endocranial form and cerebrum and brainstem partitions of the closely related juvenile\nCorythosaurus (ROM 759) plotted more closely to crown birds” I am not sure of the meaning\nof this sentence. Based on the results in Fig. 2 (please clearly indicate the juvenile\nCorythosaurus (ROM 759) on the different figures), I rather see the opposite and the juvenile\nCorythosaurus plots more closely to alligators (you are saying that in the following\nsentence). Please clarify.\nThe reviewer is correct and juvenile hadrosaurs are more similar to alligators in endocranial\nmorphology. A favourable comparison with crown birds was a miswording on the authors'\npart. We clarify this mistake with: “Juvenile hadrosaurs, such as the juvenile Lambeosaurus\n(ROM 758) and Corythosaurus (ROM 759), generally plot more closely with alligators than\ncrown birds” (Ln 112-113)\n8. Lines 124-125: “In the cerebellar morphospace, crown birds and Archaeopteryx form a\ngroup that is separated from alligators along PC2 (Fig. 2c)” Yes and no, we can see a small\noverlap.\nSection changed to read “In the cerebellum shape morphospace, crown birds and\nArchaeopteryx form a group that is almost completely separated from alligators along PC2\n(Fig. 2c)” for better accuracy (Ln 128-129)\n9. Line 133: “Apart from the hadrosaur Lambeosaurus (ROM 758),…….” And also the\nCorythosaurus specimen, right?\nCorrect. We have updated this sentence to clarify our meaning of ‘immature’: “Apart from the\njuvenile hadrosaurs, Lambeosaurus (ROM 758) and Corythosaurus (ROM 759), all juvenile\nspecimens of troodontids, the tyrannosaurid CMNH 7541, and other ornithischian dinosaurs,\noverlap with crown birds in PC2 values” (Ln 137-139)\n10. Lines 135-137: “During postnatal ontogeny, the endocranial shapes of ornithischian and\nnon-avialan dinosaurs (except Psittacosaurus) begin in the area of morphospace occupied\nby crown birds and subsequently converge to mature alligators.” You just said in the\nprevious sentence that the position of the juvenile hadrosaur Lambeosaurus (and maybe the\njuvenile Corythosaurus) overlaps the alligator distribution. Why such a sentence here? Also\nyou are talking here about the cerebellum shape, not the whole endocranial shape, please\nbe more precise.\nCorrect, our intention was to discuss trends in the cerebellar space. This section has been\nedited for precision and to reduce redundancy: “Relatively mature specimens of\ntyrannosaurids, troodontids, and hadrosaurs strongly overlap with relatively mature\nalligators. Interestingly, all the Psittacosaurus specimens lie among crown birds regardless\nof ontogenetic stage, although this similarity is likely due to the presence of a prominent\ndorsal eminence, thought to represent space occupied by non-neuronal soft tissues (e.g.,\nvenous sinus, meninges), on the cerebellum (Fig. 1a). Apart from the juvenile hadrosaurs,\nLambeosaurus (ROM 758) and Corythosaurus (ROM 759), all juvenile specimens of\ntroodontids, the tyrannosaurid CMNH 7541, and other ornithischian dinosaurs, overlap with\ncrown birds in PC2 values” (Ln 132-139)\n11. Line 174: “Notably, the immature specimens of ornithischian dinosaurs align with crown\nbirds in RSC1 values” Even the juvenile specimens of Lambeosaurus and Corythosaurus?\nCorrect. We have changed this segment to say “. Notably, the perinatal Psittacosaurus\nspecimen (IVPP V15451) aligns with crown birds in RSC1 values, whereas the juvenile\nLambeosaurus (ROM 758), juvenile Corythosaurus (ROM 159) and more mature\nornithischian dinosaurs have RSC1 values that are closer to adult Alligator” (Ln 176-179)\n12. Lines 183-185: “Immature ornithischian and non-avialan dinosaurs group within or near\ncrown birds, with juvenile Lambeosaurus (ROM 758) and relatively mature non-avialan\ndinosaurs more closely resembling adult Alligator (Fig. 3c).” The end of the sentence\ncontradicts the beginning. You are stating that immature ornithischian dinosaurs are within or\nnear crown birds whereas it is only the Psittacosaurus specimens among the ornithischians,\njuvenile Lambeosaurus and Corythosaurus are within alligators.\nCorrect. We also notice that this sentence seems a little repetitive with the next sentence.\nThe sentence commented on has been reworded as follows to incorporate the reviewer’s\ncomments and better incorporate it with the following sentence: “Psittacosaurus, immature\ntheropods, and non-avialan maniraptoran dinosaurs group within or near crown birds, with\nthe juvenile Lambeosaurus (ROM 758) and more mature non-avialan dinosaurs more closely\nresembling adult Alligator (Fig. 3c)” (Ln 186-189)\n13. Lines 186-188: “Interestingly, adult and subadult psittacosaurs plot with crown birds\nalong with Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247) specimens, while\nthe juvenile hadrosaur Lambeosaurus (ROM 758) aligns more closely with Alligator.” Please\nindicate Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247) on Fig. 3. The juvenile\nCorythosaurus also aligns with alligators right?\nUpon further review, it seems that the non-adult hadrosaurs group more closely with\nalligators. We have rephrased this sentence to say: “Adult and subadult Psittacosaurus plot\nwith crown birds along with Tyrannosaurus (AMNH 5029) and Gorgosaurus (ROM 1247)\nspecimens, while the juvenile and subadult hadrosaurs align more closely with Alligator (Fig.\n3c)” (Ln 189-191)\n14. Lines 189-190: “For the optic lobe, allometric trends group according to taxon, with\ncrown birds and Archaeopteryx grouping together along the RSC1 axis” Not sure we can say\nthat. Two mature theropod dinosaurs are grouping with crown birds, and one Psittacosaurus\nspecimen plots within alligators.\nWe agree that this sentence is only partially true as written. The original intent was to\nestablish that crown birds and Archaeopteryx, specifically, grouped together along the RSC1\naxis. We have rearranged and clarified this statement to say: “For the optic lobe, crown birds\nand Archaeopteryx group together along the RSC1 axis (Fig. 3d). Non-avialan dinosaurs\nloosely group together, with the oviraptorosaurs Incisivosaurus and Khaan closely\nresembling the optic lobe shape of crown birds and Archaeopteryx and the subadult\nPsittacosaurus (PKUP V1054) positioned with adult Alligator (Fig. 3d)” (Ln 194-197)\n15. Lines 193-194: “The perinatal Psittacosaurus (IVPP V15451) and immature troodontids\nZanabazar and unnamed troodontid (IGM 100/1126) are similar in RSC1 value to crown\nbirds” They seems to have closer RSC1 values with crown birds but not really similar\nThis is a fair point. We have clarified this statement to say “The perinatal Psittacosaurus\n(IVPP V15451) and immature troodontids Zanabazar and unnamed troodontid (IGM\n100/1126) are close to the RSC1 values of crown birds than other endocasts from non-\navialan dinosaurs” (Ln 197-199)\nDiscussion\n1. Lines 226-228: “Indeed, they begin somewhat avian-like among perinatal and juvenile\nindividuals and broadly converge to more alligator-grade endocranial morphology. Because\nthis allometric trajectory occurs in both coelurosaurian and ornithischian non-avian\ndinosaurs,….” Both sentences are a little bit oversimplified, you are not considering the\nvariability you found in your results (the other ornithischian dinosaurs for example do not\nshow such a pattern right?).\nAfter consideration, we disagree that this sections has been oversimplified. The reviewer is\nvery much correct that there is interspecific variability between the endocranial partitions.\nHowever, this particular section is discussing the results of the total endocranial shape.\nConsidering that the total shape is the sum of the granular parts, and we discuss the\nallometric shape implications for all of the specimens used in the study, we risk speculation if\nwe were to include more in this particular section. We do, however, delve deeper into the\nvariability the reviewer refers to in the following section.\n2. Lines 235-236: “In cerebrum, cerebellum, and optic lobe shapes, non-avialan dinosaurs\nresemble more those of crown birds than alligators”. You basically said in your results that\n“Based on the plot, it is uncertain whether [optic-lobes in] non-avialan dinosaurs align with\nthe allometric trajectories of alligators and/or crown birds.” (lines 195-196). Again, this\nstatement seems a little bit oversimplified to me and why are not considering other\nornithischian dinosaurs?\nLines 235-236 (now 242-244) refers to the morphometric shape of the cerebrum,\ncerebellum, and optic lobes whereas lines 195-196 (now 200-201) refer to the allometric\ntrajectories. In regards to the oversimplification, the taxonomic trends are discussed for the\ntotal shape, cerebrum, cerebellum, optic lobes, and brainstem earlier in the manuscript in\ntheir respective paragraphs under the ‘Endocranial shape morphospaces’ and ‘Allometric\ntrajectories’ subsections. The section the reviewer brings up is meant to compare all taxa\nbroadly and is therefore all inclusive of both ornithischian and saurischian specimens in the\nterm ‘‘non-avialan’ dinosaur’’\n3. Lines 239-240: “these outcomes imply that non-avialan dinosaurs underwent distinct brain\ndevelopment compared to crocodilians” At least in Psittacosaurus, not sure that such a rule\ncan be established here from the other ornithischian dinosaurs.\nWe posit that all dinosaur endocrania analysed in our manuscript show a growth pattern that\nis distinct from crocodilians. Yes, the more mature dinosaurs come very close to overlapping\nalligators in total brain shape, but the subadults and juveniles strongly diverge in form from\nalligators of a similar ontogenetic stage. In Figure 2a, this idea is displayed most clearly\nwhere non-avian dinosaurs and alligators arrive at nearly the same point in maturity but take\ndifferent routes to get there – both intraspecifically and interspecifically.\n4. Line 247: “Besides the optic lobe shape being closer to crown birds” I agree closer with\nbirds than with alligators, but also distinct from birds\nWe have rephrased this sentence to say “Besides the optic lobe shape being closer to, yet\ndistinct from, crown birds…” (Ln 254-255)\n5. Lines 248-249: “the brainstem shape of ornithischian dinosaurs visually aligns with the\nallometric trajectory of alligators (Fig. 3d), whereas that of non-avialan dinosaurs, particularly\nimmature specimens, aligns more closely with crown birds (Fig. 3e).” I think a word is\nmissing here, I mean ornithischian dinosaurs are non-avialan dinosaurs, no? Also you are\nsaying in your results about the brainstem: “As such, the results suggest that both\nornithischian and non-avialan dinosaurs resembled an alligator-grade scaling relationship in\nbrainstem shape” (lines 202-204). I am a little bit confused here\nYou are correct and this was poor word choice on our part; we should not have separated\nornithischians from the rest of the dinosaurs. We have corrected both points the reviewer\nhas made to say “the brainstem shape of ornithischian dinosaurs visually aligns with the\nallometric trajectory of alligators (Fig. 3d), whereas that of non-ornithischian dinosaurs,\nparticularly immature specimens, aligns more closely with crown birds (Fig. 3e)” (Ln 255-\n257) and “As such, the results suggest that both ornithischian and saurischian dinosaurs\nresembled an alligator-grade scaling relationship in brainstem shape”, respectively (Ln 207-\n209).\n6. Line 257, please remove the dash before “Specifically”\nRemoved\n7. Lines 276-278: “Our results suggest that paedomorphosis plays a role in the total\nendocranial form and evolution of the avian brain where the form of the bird brain more\nresembles that of juvenile non-avialan dinosaurs.” Not all non-avialan dinosaurs, only\nPsittacosaurus.\nThis is true for Psittacosaurus as well as troodontids (and to a lesser degree, Tyrannosaurus\nand Lambeosaurus) when you consider the total shape of the endocranium. Troodontidae is\nphylogenetically close to, but not part of, Avialae; thus, making our statement true for at least\none clade of ornithischian and saurischian dinosaur. Moreover – and, admittedly, more\ntenuously – most of the non-avialan dinosaurs used in this study had endocrania\nmorphologies in their juvenile forms that were closer to avians than their adult forms across\nPC1. While this does not hold the same weight as the evidence given by the juvenile\nPsittacosaurus and troodontid, it does support that the juveniles of non-avialan dinosaurs\nhad endocrania that were more ‘avian-like’ than adults\nResponse to reviewers:\nReviewer #3 (Remarks to the Author):\nDear authors,\nThank you for sending the revision of your manuscript. All my comments have been taken into\naccount and I have only one concern that should be addressed. In the introduction (line 54), if I am\ncorrect, \"However, a good developmental series of neuroanatomical\nmorphologies for non-avian dinosaurs HAS been lacking to date; AND crucial evidence IS needed for\na reliable inference of .....\". Other than that, everything is good for me.\nBest regards,\nR.A\nWe thank the author for their input! We have updated this section to say ‘However, a good\ndevelopmental series of neuroanatomical morphologies for non-avian dinosaurs has been lacking to\ndate; and crucial evidence is needed for a reliable inference of evolutionary shifts in brain\ndevelopment along the theropod-bird transition’"}]

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