Best practices for digitally constructing endocranial casts: examples from birds and their dinosaurian relatives

Flightless birds are not neuroanatomical analogs of non-avian dinosaurs

Background

In comparative neurobiology, major transitions in behavior are thought to be associated with proportional size changes in brain regions. Bird-line theropod dinosaurs underwent a drastic locomotory shift from terrestrial to volant forms, accompanied by a suite of well-documented postcranial adaptations. To elucidate the potential impact of this locomotor shift on neuroanatomy, we first tested for a correlation between loss of flight in extant birds and whether the brain morphology of these birds resembles that of their flightless, non-avian dinosaurian ancestors. We constructed virtual endocasts of the braincase for 80 individuals of non-avian and avian theropods, including 25 flying and 19 flightless species of crown group birds. The endocasts were analyzed using a three-dimensional (3-D) geometric morphometric approach to assess changes in brain shape along the dinosaur-bird transition and secondary losses of flight in crown-group birds (Aves).

Results

While non-avian dinosaurs and crown-group birds are clearly distinct in endocranial shape, volant and flightless birds overlap considerably in brain morphology. Phylogenetically informed analyses show that locomotory mode does not significantly account for neuroanatomical variation in crown-group birds. Linear discriminant analysis (LDA) also indicates poor predictive power of neuroanatomical shape for inferring locomotory mode. Given current sampling, Archaeopteryx, typically considered the oldest known bird, is inferred to be terrestrial based on its endocranial morphology.

Conclusion

The results demonstrate that loss of flight does not correlate with an appreciable amount of neuroanatomical changes across Aves, but rather is partially constrained due to phylogenetic inertia, evident from sister taxa having similarly shaped endocasts. Although the present study does not explicitly test whether endocranial changes along the dinosaur-bird transition are due to the acquisition of powered flight, the prominent relative expansion of the cerebrum, in areas associated with flight-related cognitive capacity, suggests that the acquisition of flight may have been an important initial driver of brain shape evolution in theropods.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1312-0) contains supplementary material, which is available to authorized users.

Nocturnal giants: evolution of the sensory ecology in elephant birds and other palaeognaths inferred from digital brain reconstructions

The recently extinct Malagasy elephant birds (Palaeognathae, Aepyornithiformes) included the largest birds that ever lived. Elephant bird neuroanatomy is understudied but can shed light on the lifestyle of these enigmatic birds. Palaeoneurological studies can provide clues to the ecologies and behaviours of extinct birds because avian brain shape is correlated with neurological function. We digitally reconstruct endocasts of two elephant bird species, Aepyornis maximus and A. hildebrandti, and compare them with representatives of all major extant and recently extinct palaeognath lineages. Among palaeognaths, we find large olfactory bulbs in taxa generally occupying forested environments where visual cues used in foraging are likely to be limited. We detected variation in olfactory bulb size among elephant bird species, possibly indicating interspecific variation in habitat. Elephant birds exhibited extremely reduced optic lobes, a condition also observed in the nocturnal kiwi. Kiwi, the sister taxon of elephant birds, have effectively replaced their visual systems with hyperdeveloped olfactory, somatosensory and auditory systems useful for foraging. We interpret these results as evidence for nocturnality among elephant birds. Vision was likely deemphasized in the ancestor of elephant birds and kiwi. These results show a previously unreported trend towards decreased visual capacity apparently exclusive to flightless, nocturnal taxa endemic to predator-depauperate islands.

Neuroanatomy and inner ear labyrinths of the narwhal, Monodon monoceros, and beluga, Delphinapterus leucas (Cetacea: Monodontidae)

Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic-endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X-ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var - a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a 'direct' angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.

A new rhynchocephalian (Reptilia: Lepidosauria) from the Late Jurassic of Solnhofen (Germany) and the origin of the marine Pleurosauridae

A new rhynchocephalian is described based on a recently discovered and well-preserved specimen from the Late Jurassic (Kimmeridgian) marine limestones of Solnhofen, Bavaria. Phylogenetic analysis recovers the new taxon as the sister group to Pleurosauridae, a small radiation of rhynchocephalians representing the oldest marine invasion of crown-clade Lepidosauria. The relatively strong evidence for this taxonomically exclusive lineage, within a generally volatile rhynchocephalian tree, places the new taxon in a position to inform the early history of the pleurosaur transition to the sea. The early steps in this transition are distributed throughout the skeleton and appear to increase hydrodynamic efficiency for both swimming and aquatic feeding. This early history may also have included a global truncation of plesiomorphic ontogenetic trajectories that left a number of skeletal features with reduced levels of ossification/fusion. The exact degree to which Vadasaurus had adopted an aquatic ecology remains unclear, but the insight it provides into the origin of the enigmatic pleurosaurs exemplifies the potential of Rhynchocephalia for generating and informing broad-based questions regarding the interplay of development, morphology, ecology and macroevolutionary patterns.

Comparative morphology of snake (Squamata) endocasts: evidence of phylogenetic and ecological signals

Brain endocasts obtained from computed tomography (CT) are now widely used in the field of comparative neuroanatomy. They provide an overview of the morphology of the brain and associated tissues located in the cranial cavity. Through anatomical comparisons between species, insights on the senses, the behavior, and the lifestyle can be gained. Although there are many studies dealing with mammal and bird endocasts, those performed on the brain endocasts of squamates are comparatively rare, thus limiting our understanding of their morphological variability and interpretations. Here, we provide the first comparative study of snake brain endocasts in order to bring new information about the morphology of these structures. Additionally, we test if the snake brain endocast encompasses a phylogenetic and/or an ecological signal. For this purpose, the digital endocasts of 45 snake specimens, including a wide diversity in terms of phylogeny and ecology, were digitized using CT, and compared both qualitatively and quantitatively. Snake endocasts exhibit a great variability. The different methods performed from descriptive characters, linear measurements and the outline curves provided complementary information. All these methods have shown that the shape of the snake brain endocast contains, as in mammals and birds, a phylogenetic signal but also an ecological one. Although phylogenetically related taxa share several similarities between each other, the brain endocast morphology reflects some notable ecological trends: e.g. (i) fossorial species possess both reduced optic tectum and pituitary gland; (ii) both fossorial and marine species have cerebral hemispheres poorly developed laterally; (iii) cerebral hemispheres and optic tectum are more developed in arboreal and terrestrial species.

Archosauriform endocranial morphology and osteological evidence for semiaquatic sensory adaptations in phytosaurs

The examination of endocranial data of archosauriforms has led to advances on the evolution of body size, nerve pathways, and sensory abilities. However, much of that research has focused on bird-line archosaurs, resulting in a skewed view of Archosauria. Phytosauria, a hypothesized sister taxon to or early-branching member of Archosauria, provides a potential outgroup condition. Most previous phytosaur endocranial studies were executed without the use of modern technology and focused on derived members of Phytosauria. We present a comparative CT examination of the internal cranial anatomy of Wannia scurriensis, the most basal known parasuchid phytosaur. Wannia scurriensis shows some overall similarity with extant crocodylians and derived phytosaurs in general endocranial shape, a large hypophyseal fossa, and trigeminal (CN V) innervation, but as a whole, the endocast has noticeable differences to crocodylians and other phytosaurs. The pineal region is expanded dorsally as in other phytosaurs but also laterally (previously unrecognized). CN V exits the pons in a more dorsal position than in Parasuchus hislopi, Machaeroprosopus mccauleyi, or Smilosuchus gregorii. Wannia scurriensis also exhibits a larger hypophyseal fossa relative to brain size than observed in P. hislopi or S. gregorii, which may indicate more rapid growth. The well-preserved semicircular canals have lateral canals that are angled more anteroventrally than in derived phytosaurs. Extensive facial innervation from the large CN V indicates increased rostrum sensitivity and mechanoreceptive abilities as in Alligator mississippiensis. These endocranial similarities among phytosaurs and with Alligator indicate conserved ecological and functional results of an aquatic lifestyle, and highlight a need for further exploration of endocranial anatomy among Archosauriformes.

Floccular fossa size is not a reliable proxy of ecology and behaviour in vertebrates

The cerebellar floccular and parafloccular lobes are housed in fossae of the periotic region of the skull of different vertebrates. Experimental evidence indicates that the lobes integrate visual and vestibular information and control the vestibulo-ocular reflex, vestibulo-collic reflex, smooth pursuit and gaze holding. Multiple paleoneuroanatomy studies have deduced the behaviour of fossil vertebrates by measuring the floccular fossae (FF). These studies assumed that there are correlations between FF volume and behaviour. However, these assumptions have not been fully tested. Here, we used micro-CT scans of extant mammals (47 species) and birds (59 species) to test six possible morphological-functional associations between FF volume and ecological/behavioural traits of extant animals. Behaviour and ecology do not explain FF volume variability in four out of six variables tested. Two variables with significant results require further empirical testing. Cerebellum plasticity may explain the lack of statistical evidence for the hypotheses tested. Therefore, variation in FF volume seems to be better explained by a combination of factors such as anatomical and phylogenetic evolutionary constraints, and further empirical testing is required.

FOSSIL SECRETS REVEALED: X-RAY CT SCANNING AND APPLICATIONS IN PALEONTOLOGY

X-ray computed tomography (CT) provides a nondestructive means of studying the inside and outside of objects. It allows accurate visualization and measurement of internal features, that are otherwise impossible to obtain nondestructively, and is a lasting digital record that can be made available to future researchers, museums, and the general public. Here, an overview of CT scanning methodologies and protocol is provided, as well as some recent examples of how this technology is allowing paleontologists to make new inroads into understanding the ecology, evolution, and development of both extant and extinct organisms. Lastly, some frontiers and outstanding questions in the acquisition, processing, and storage of digital 3-D morphological data are highlighted.

The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes

The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for “true” Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.

The domesticated brain: genetics of brain mass and brain structure in an avian species

As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.

Novel insights into early neuroanatomical evolution in penguins from the oldest described penguin brain endocast

Digital methodologies for rendering the gross morphology of the brain from X-ray computed tomography data have expanded our current understanding of the origin and evolution of avian neuroanatomy and provided new perspectives on the cognition and behavior of birds in deep time. However, fossil skulls germane to extracting digital endocasts from early stem members of extant avian lineages remain exceptionally rare. Data from early-diverging species of major avian subclades provide key information on ancestral morphologies in Aves and shifts in gross neuroanatomical structure that have occurred within those groups. Here we describe data on the gross morphology of the brain from a mid-to-late Paleocene penguin fossil from New Zealand. This most basal and geochronologically earliest-described endocast from the penguin clade indicates that described neuroanatomical features of early stem penguins, such as lower telencephalic lateral expansion, a relatively wider cerebellum, and lack of cerebellar folding, were present far earlier in penguin history than previously inferred. Limited dorsal expansion of the wulst in the new fossil is a feature seen in outgroup waterbird taxa such as Gaviidae (Loons) and diving Procellariiformes (Shearwaters, Diving Petrels, and allies), indicating that loss of flight may not drastically affect neuroanatomy in diving taxa. Wulst enlargement in the penguin lineage is first seen in the late Eocene, at least 25 million years after loss of flight and cooption of the flight stroke for aquatic diving. Similar to the origin of avian flight, major shifts in gross brain morphology follow, but do not appear to evolve quickly after, acquisition of a novel locomotor mode. Enlargement of the wulst shows a complex pattern across waterbirds, and may be linked to sensory modifications related to prey choice and foraging strategy.

Endocranial Morphology of the Primitive Nodosaurid Dinosaur Pawpawsaurus campbelli from the Early Cretaceous of North America

BACKGROUND

Ankylosaurs are one of the least explored clades of dinosaurs regarding endocranial anatomy, with few available descriptions of braincase anatomy and even less information on brain and inner ear morphologies. The main goal of this study is to provide a detailed description of the braincase and internal structures of the Early Cretaceous nodosaurid Pawpawsaurus campbelli, based on recently made CT scans.

METHODOLOGY/PRINCIPAL FINDINGS

The skull of Pawpawsaurus was CT scanned at University of Texas at Austin (UTCT). Three-dimensional models were constructed using Mimics 18.0 (Materialise). The digital data and further processed 3D models revealed inaccessible anatomic structures, allowing a detailed description of the lateral wall of the braincase (obscured by other bones in the articulated skull), and endocranial structures such as the cranial endocast, the most complete inner ear morphology for a nodosaurid, and the interpretation of the airflow system within the nasal cavities.

CONSLUSIONS/SIGNIFICANCE

The new information on the endocranial morphology of Pawpawsaurus adds anatomical data to the poorly understand ankylosaur paleoneurology. The new set of data has potential use not only in taxonomy and phylogeny, but also in paleobiological interpretations based on the relative development of sense organs, such as olfaction, hearing and balance.

Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues

Morphologists have historically had to rely on destructive procedures to visualize the three‐dimensional (3‐D) anatomy of animals. More recently, however, non‐destructive techniques have come to the forefront. These include X‐ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard‐tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT‐based research is the use of chemical agents to render visible, and differentiate between, soft‐tissue structures in X‐ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine‐based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine‐based, contrast‐enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting‐edge applications of diffusible iodine‐based contrast‐enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.

Brain modularity across the theropod-bird transition: testing the influence of flight on neuroanatomical variation

Living birds constitute the only vertebrate group whose brain volume relative to body size approaches the uniquely expanded values expressed by mammals. The broad suite of complex behaviors exhibited by crown-group birds, including sociality, vocal learning, parental care, and flying, suggests the origins of their encephalization was likely driven by a mosaic of selective pressures. If true, the historical pattern of brain expansion may be more complex than either a gradual expansion, as proposed by early studies of the avian brain, or a sudden expansion correlating with the appearance of flight. The origins of modern avian neuroanatomy are obscured by the more than 100 million years of evolution along their phylogenetic stem (from the origin of the modern radiation in the Middle Jurassic to the split from crocodile-line archosaurs). Here we use phylogenetic comparative approaches to explore which evolutionary scenarios best explain variation in measured volumes of digitally partitioned endocasts of modern birds and their non-avian ancestors. Our analyses suggest that variation in the relative volumes of the endocranium and cerebrum explain most of the structural variation in this lineage. Generalized multi-regime Ornstein-Uhlenbeck (OU) models suggest that powered flight does not appear to be a driver of observed variation, reinforcing the hypothesis that the deep history of the avian brain is complex, with nuances still to be discovered.