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High-density 3-D coordinate data of avian and non-avian dinosaur endocasts


Watanabe, Akinobu et al. (2021), High-density 3-D coordinate data of avian and non-avian dinosaur endocasts, Dryad, Dataset,


How do large and unique brains evolve? Historically, comparative neuroanatomical studies have attributed the evolutionary genesis of highly encephalized brains to deviations along, as well as from, conserved scaling relationships among brain regions. However, the relative contributions of these concerted (integrated) and mosaic (modular) processes as drivers of brain evolution remain unclear, especially in non-mammalian groups. While proportional brain sizes have been the predominant metric used to characterize brain morphology to date, we perform a high-density geometric morphometric analysis on the encephalized brains of crown birds (Neornithes or Aves) compared to their stem taxa—the non-avialan coelurosaurian dinosaurs. When analyzed together with developmental neuroanatomical data of model archosaurs (GallusAlligator), crown birds exhibit a distinct allometric relationship that dictates their brain evolution and development. Furthermore, analyses by neuroanatomical regions reveal that the acquisition of this derived shape-to-size scaling relationship occurred in a mosaic pattern, where the ‘avian’-grade optic lobe and cerebellum evolved first among non-avialan dinosaurs, followed by major changes to the evolutionary and developmental dynamics of cerebrum shape after the origin of Avialae. Notably, the brain of crown birds is a more integrated structure than non-avialan archosaurs, implying that diversification of brain morphologies within Neornithes proceeded in a more coordinated manner, perhaps due to spatial constraints and abbreviated growth period. Collectively, these patterns demonstrate a plurality in evolutionary processes that generate encephalized brains in archosaurs and across vertebrates.


The landmark data were collected using the program Landmark Editor v3.6 to virtually place three-dimensional (3-D) coordinate points on polygon mesh files of endocasts reconstructed from micro-computed tomography (CT) data. The landmark scheme includes a combination of discrete landmarks, curve semi-landmarks, and surface semi-landmarks that characterizes the shape of endocasts and their regions (cerebrum, optic lobe, cerebellum, medulla). Initially, coordinate data were collected from both sides of the endocasts (e.g., left and right cerebrum) which were subjected to generalized Procrustes alignment minimizing total bending energy with sliding semi-landmarks while projecting the semi-landmarks on mesh surfaces. After alignment, the median and left landmarks were extracted (i.e., right landmarks removed) from the aligned dataset to remove redundant shape information and to avoid artifacts associated with aligning one-sided data of bilaterally symmetric structures.

Usage Notes

The dataset is organized as a 2-D matrix, where rows are specimens and columns are coordinate values. The specimen sampling (n=72) comprises six non-avialan coelurosaurian dinosaurs (specimens 2,42,55,56,57,72 in dataset), Archaeopteryx (specimen 19), and 38 crown birds (specimens 1,17,18, 20–26,41,43–54,58–71), as well as developmental series of Alligator (specimens 3–16) and Gallus (specimens 27–40).

Important Note: The dataset includes 225 3-D (semi-)landmarks that encompass bilateral form of endocasts. The semi-landmarks have been slid based on minimizing total bending energy and scale has been retained so that centroid size could still be calculated. To prevent artifacts related to aligning one-sided coordinate data of bilateral structures, the dataset should first be subjected to typical generalized Procrustes alignment minimizing total Procrustes distance without sliding semilandmarks because sliding has already been conducted. After alignment, then the left and median (semi-)landmarks should be extracted: landmarks 1–54, 109–137, 168–170, 173–175, 178–180, 183–185, 188–190, 193–195, 198–200, 203–205, 208–210, 213–215, 218–220, 222–224. This left-sided dataset should include 119 3-D (semi-)landmarks. The landmark dataset is partitioned into left cerebrum (landmarks 1–54), left optic lobe (landmarks 55–83), left side of cerebellum (landmarks 84–101), and left side of medulla (102–119).


National Science Foundation, Award: Graduate Research Fellowship

National Science Foundation, Award: DEB-1406849

National Science Foundation, Award: DEB-1311790

National Science Foundation, Award: DEB-1457181

National Science Foundation, Award: DEB-1457180

National Science Foundation, Award: DEB-1754659

Society of Vertebrate Paleontology, Award: Mary R. Dawson Predoctoral Fellowship Grant

Jurassic Foundation

Macaulay Family Endowment

Newt and Callista Gingrich Endowment

American Museum of Natural History, Award: Division of Paleontology

Society of Vertebrate Paleontology, Award: Mary R. Dawson Predoctoral Fellowship Grant

Macaulay Family Endowment

Newt and Callista Gingrich Endowment