Additional materials for the journal article titled "Survey of anatomical organization of archosaurian skulls reveals major evolutionary and ontogenetic transformations in modern birds."

The skull is a hallmark of Vertebrata clade critical both for their phylogenetic success and taxonomic nomenclature. The evolution of vertebrate skull morphology is characterized by changes in skull shape and topology. Cranial skeleton topology traits tend to be less understood and include the number cranial bones and their relative arrangement, believed to be important for biomechanical and other functions. Rearrangement and co-option of pre-existing bones occur as the skeletal morphology of tetrapods evolves to produce new functions or structures. During development, evolutionary rearrangement of a given bone is limited by heterochrony and the development of neighbouring bones. Cranial rearrangement was previously explored in archosaurs using Anatomical Network Analysis (AnNA) but unable to reconstruct their vast diversity, nor pinpoint these rearrangements in time. To address this, we compiled the most comprehensive dataset to date, including 109 species of non-archosaurian archosauriformes, pseudosuchians, Paleogene birds, and modern birds. To identify the ontogenetic stage during which topological disparity is initiated, we used juvenile theropods, and for the first time, late-stage embryos, juvenile, and subadult pseudosuchians, and constructed the topological morphospace using AnNA. Specialization via fusion of cranial bones in archosaurs could be traced from crown archosaurs with subtle changes throughout the Mesozoic, when pseudosuchians and avemetatarsalians overlapped with non-archosaurian archosauriforms in the morphospace. The morphospace subsequently expanded with the rise of Aves, which were remarkably distinct from their predecessors. Interestingly, juvenile birds from different orders were not significantly different from each other, or non-avian dinosaurs, whereas their adult stages demonstrated remarkable differences. In contrast, extant crocodylians were different from non-crocodylian pseudosuchians since young. Ancestral state reconstruction analysis by maximum-likelihood showed the last common ancestor of Aves and Ichthyornis had an intermediately fused skull and kinetic closest to waterfowls (Anseriforms). Observations from bird skulls suggested that functional limitations from cranial arrangement may be compensated by morphological modification to adapt to similar environmental stimuli. When trends on skull shape and topological changes are combined, it becomes evident that these two dimensions of archosaur skull morphology are largely independent and are both needed to explain the observed diversity.