A 3D MRI-based atlas of a lizard brain

The SmARTR pipeline: A modular workflow for the cinematic rendering of 3D scientific imaging data

Advancements in noninvasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology-enhancing research, medical anatomical analysis, and facilitating the preservation and digital archiving of scientific specimens. We introduce the SmARTR pipeline (Small Animal Realistic Three-dimensional Rendering), a comprehensive workflow integrating wet lab procedures, 3D data acquisition, and processing to produce photorealistic scientific data through 3D cinematic rendering. This versatile pipeline supports multiscale visualizations-from tissue-level to whole-organism details across diverse living organisms-and is adaptable to various imaging sources. Its modular design and customizable rendering scenarios, enabled by the global illumination modeling and programming modules available in the free MeVisLab software and seamlessly integrated into detailed SmARTR networks, make it a powerful tool for 3D data analysis. Accessible to a broad audience, the SmARTR pipeline serves as a valuable resource across multiple life science research fields and for education, diagnosis, outreach, and artistic endeavors.

Seasonal mRNA Expression of Circadian Clock Genes in the Lizard Brain

Seasonally breeding animals undergo physiological and behavioral changes to time reproduction to occur during specific seasons. These changes are regulated by changing environmental conditions, which may be communicated to the brain using the central circadian clock. This clock consists of a daily oscillation in the expression of several core genes, including period (per), cryptochrome (cry), circadian locomotor output cycles kaput (clock), and basic helix-loop-helix ARNT-like protein 1 (bmal1). We began to examine seasonal regulation of four core circadian clock genes in a dissection of the reptile brain containing the hypothalamus-per1, cry1, bmal1 and clock. Our study focused on examining mRNA expression in the morning and compared levels between breeding and nonbreeding animals. We found that per1 and bmal1 mRNA expression was highest in the nonbreeding compared to breeding season in the anole hypothalamus. We also found that cry1 mRNA expression was higher in the female compared to the male anole hypothalamus. We found support for the idea that core circadian genes play a role in regulating changes between the seasons and/or sexes, although more work is needed to elucidate what processes might be differentially regulated. To our knowledge, this is the first examination of the expression of these four genes in the reptilian brain.

Expanding understanding of chick embryo's nervous system development at HH22-HH41 embryonic stages using X-ray microcomputed tomography

Assessing the embryotoxicity and teratogenicity of various substances and processes is crucial due to their complexity and resource intensity. The chicken embryo (CE) serves an ideal model for simulating the first months of mammalian embryonic development. This makes the CE a reliable model for testing teratogenic effects, particularly in relation to the nervous system (NS), which experiences developmental abnormalities second in frequency only to cardiovascular teratogenic disorders. Microcomputed tomography (μCT) is a promising method for studying these processes. The advantages of μCT include relatively high research speed, diagnostic accuracy, high resolution and the ability to visualize the entire internal 3D structure of an object while preserving for other types of research. At the same time, there are practically no available databases of normative μCT data, both qualitative and quantitative, which would act as a starting point for screening detection of abnormalities in the development of the NS. In this study, we present a simple method for obtaining very detailed quantitative sets of 2D and 3D μCT data of NS structures of the CE (Gallus Gallus domesticus) at HH22-HH41 embryonic stages with contrasting by 1% phosphotungstic acid. The results of μCT demonstrate the exact boundaries, high general and differentiated contrast of the main and specific structures of the NS of CE, which are quantitatively and qualitatively similar to results of histological analysis. Calculations of the X-ray density and volume of the main structures of the NS at constant exponential growth are presented. In addition to the increase in linear dimensions, significant changes in the structures of various parts of the brain were identified and visualized during the CE development at HH22 to HH41 embryonic stages. The data presented establish the first methodology for obtaining normative data, including subtle localized differences in the NS in CE embryogenesis. The data obtained open up new opportunities for modern embryology, teratology, pharmacology and toxicology.

Cocaine- and Amphetamine-Regulated Transcript Peptide in the Central Nervous System of the Gecko, Hemidactylus leschenaultii: Molecular Characterization, Neuroanatomical Organization, and Regulation by Neuropeptide Y

Neuropeptide cocaine- and amphetamine-regulated transcript (CART) is widely expressed in the brains of teleosts, amphibians, birds, and mammals and has emerged as a conserved regulator of energy balance across these vertebrate phyla. However, as yet, there is no information on CART in the reptilian brain. We characterized the cDNA encoding CART and mapped CART-containing elements in the brain of gecko, Hemidactylus leschenaultii (hl) using a specific anti-CART antiserum. We report a 683-bp hlcart transcript containing a 336-bp open reading frame, which encodes a putative 111-amino acid hl-preproCART. The 89-amino acid hl-proCART generated from hl-preproCART produced two putative bioactive hl-CART-peptides. These bioactive CART-peptides were > 93% similar with those in rats/humans. Although reverse transcription-polymerase chain reaction (RT-PCR) detected hlcart-transcript in the brain, CART-containing neurons/fibers were widely distributed in the telencephalon, diencephalon, mesencephalon, rhombencephalon, spinal cord, and retina. The mitral cells in olfactory bulb, neurons in the paraventricular, periventricular, arcuate (Arc), Edinger-Westphal, and brainstem nuclei were intensely CART-positive. In view of antagonistic roles of neuropeptide Y (NPY) and CART in energy balance in the framework of mammalian hypothalamus, we probed CART-NPY interaction in the hypothalamus of H. leschenaultii. Double immunofluorescence showed a dense NPY-innervation of Arc CART neurons. Ex vivo hypothalamic slices treated with NPY/NPY-Y1-receptor agonist significantly reduced hlcart-mRNA levels in the Arc-containing tissues and CART-ir in the dorsal-Arc. However, CART-ir in ventral-Arc was unaffected. NPY via Y1-receptors may regulate energy balance by inhibiting dArc CART neurons. This study on CART in a reptilian brain fills the current void in literature and underscores the conserved feature of the neuropeptide across the entire vertebrate phyla.

Bioimaging of sense organs and the central nervous system in extant fishes and reptiles in situ: A review

Bioimaging is changing the field of sensory biology, especially for taxa that are lesser-known, rare, and logistically difficult to source. When integrated with traditional neurobiological approaches, developing an archival, digital repository of morphological images can offer the opportunity to improve our understanding of whole neural systems without the issues of surgical intervention and negate the risk of damage and artefactual interpretation. This review focuses on current approaches to bioimaging the peripheral (sense organs) and central (brain) nervous systems in extant fishes (cartilaginous and bony) and non-avian reptiles in situ. Magnetic resonance imaging (MRI), micro-computed tomography (μCT), both super-resolution track density imaging and diffusion tensor-based imaging, and a range of other new technological advances are presented, together with novel approaches in optimizing both contrast and resolution, for developing detailed neuroanatomical atlases and enhancing comparative analyses of museum specimens. For MRI, tissue preparation, including choice of fixative, impacts tissue MR responses, where both resolving power and signal-to-noise ratio improve as field strength increases. Time in fixative, concentration of contrast agent, and duration of immersion in the contrast agent can also significantly affect relaxation times, and thus image quality. For μCT, the use of contrast-enhancing stains (iodine-, non-iodine-, or nanoparticle-based) is critical, where the type of fixative used, and the concentration of stain and duration of staining time often require species-specific optimization. Advanced reconstruction algorithms to reduce noise and artifacts and post-processing techniques, such as deconvolution and filtering, are now being used to improve image quality and resolution.

Comparative MRI analysis of the forebrain of three sauropsida models

The study of the brain by magnetic resonance imaging (MRI) allows to obtain detailed anatomical images, useful to describe specific encephalic structures and to analyze possible variabilities. It is widely used in clinical practice and is becoming increasingly used in veterinary medicine, even in exotic animals; however, despite its potential, its use in comparative neuroanatomy studies is still incipient. It is a technology that in recent years has significantly improved anatomical resolution, together with the fact that it is non-invasive and allows for systematic comparative analysis. All this makes it particularly interesting and useful in evolutionary neuroscience studies, since it allows for the analysis and comparison of brains of rare or otherwise inaccessible species. In the present study, we have analyzed the prosencephalon of three representative sauropsid species, the turtle Trachemys scripta (order Testudine), the lizard Pogona vitticeps (order Squamata) and the snake Python regius (order Squamata) by MRI. In addition, we used MRI sections to analyze the total brain volume and ventricular system of these species, employing volumetric and chemometric analyses together. The raw MRI data of the sauropsida models analyzed in the present study are available for viewing and downloading and have allowed us to produce an atlas of the forebrain of each of the species analyzed, with the main brain regions. In addition, our volumetric data showed that the three groups presented clear differences in terms of total and ventricular brain volumes, particularly the turtles, which in all cases presented distinctive characteristics compared to the lizards and snakes.

Nuclei and Tracts in the Telencephalon of Crocodiles: Identification and Characterization Using an Organizational Scheme Applicable to Other Reptiles

The telencephalon of reptiles has been suggested to be the key to understanding the evolution of the forebrain. Nevertheless, a meaningful framework to organize the telencephalon in any reptile has, with rare exception, yet to be presented. To address this gap in knowledge, the telencephalon was investigated in two species of crocodiles. A variety of morphological stains were used to examine tissue in transverse, horizontal, and sagittal planes of sections. Besides providing a description of individual nuclei, brain parts were organized based on two features. One was related to two fixed, internal structures: the lateral ventricle and the dorsal medullary lamina. The other was the alignment of neurons into either layers, cortex, or not, nucleus. Viewed from this perspective, all structures, with limited exceptions, could be accurately placed within the telencephalon regardless of the plane of section. Furthermore, this framework can be applied to other reptiles. A further extension of this scheme suggests that all structures in the telencephalon could be grouped into one of two categories: pallial or basal.

Assessing brain neuroplasticity: Surface morphometric analysis of cortical changes induced by Quadrato motor training

Morphological markers for brain plasticity are still lacking and their findings are challenged by the extreme variability of cortical brain surface. Trying to overcome the "correspondence problem," we applied a landmark-free method (the generalized procrustes surface analysis (GPSA)) for investigating the shape variation of cortical surface in a group of 40 healthy volunteers (i.e., the practice group) subjected to daily motor training known as Quadrato motor training (QMT). QMT is a sensorimotor walking meditation that aims at balancing body, cognition, and emotion. More specifically, QMT requires coordination and attention and consists of moving in one of three possible directions on corners of a 50 × 50 cm2. Brain magnetic resonance images (MRIs) of practice group (acquired at baseline, as well as after 6 and 12 weeks of QMT), were 3D reconstructed and here compared with brain MRIs of six more volunteers never practicing the QMT (naïve group). Cortical regions mostly affected by morphological variations were visualized on a 3D average color-scaled brain surface indicating from higher (red) to lower (blue) levels of variation. Cortical regions interested in most of the shape variations were as follows: (1) the supplementary motor cortex; (2) the inferior frontal gyrus (pars opercolaris) and the anterior insula; (3) the visual cortex; (4) the inferior parietal lobule (supramarginal gyrus and angular gyrus). Our results show that surface morphometric analysis (i.e., GPSA) can be applied to assess brain neuroplasticity processes, such as those stimulated by QMT.

Nuclei and tracts in the thalamus of crocodiles

The thalamus is one of the most important divisions of the forebrain because it serves as the major hub for transmission of information between the brainstem and telencephalon. While many studies have investigated the thalamus in mammals, comparable analyses in reptiles are incomplete. To fill this gap in knowledge, the thalamus was investigated in crocodiles using a variety of morphological techniques. The thalamus consists of two parts: a dorsal and a ventral division. The dorsal thalamus was defined by its projections to the telencephalon, whereas the ventral thalamus lacked this circuit. The complement of nuclei in each part of the thalamus was identified and characterized. Alar and basal components of both the dorsal and ventral thalamus were distinguished. Although some alar-derived nuclei in the dorsal thalamus shared certain features, no grouping could account for all of the known nuclei. However, immunohistochemical observations suggested a subdivision of alar-derived ventral thalamic nuclei. In view of this, a different approach to the organization of the dorsal thalamus should be considered. Development of the dorsal thalamus is suggested to be one way to provide a fresh perspective on its organization.

Anatomical Description of Rhinoceros Iguana (Cyclura cornuta cornuta) Head by Computed Tomography, Magnetic Resonance Imaging and Gross-Sections

In this paper, we attempted to elaborate on an atlas of the head of the rhinoceros iguana, applying modern imaging techniques such as CT and MRI. Furthermore, by combining the images acquired through these techniques with macroscopic anatomical sections, we obtained an adequate description of the relevant structures that form the head of this species. This anatomical information could provide a valuable diagnostic tool for the clinical evaluation of different pathological processes in iguanas such as abscesses and osteodystrophy secondary to nutrient imbalances, skull malformations, fractures, and neoplasia.

Macro- and microscopic brain anatomy of the amazon lava lizard (Tropidurus torquatus) (WIED, 1820)

Abstract Reptiles have a key role in understanding amniotes’ reproductive independence of water. Many adaptations arose, including in locomotor patterns and behaviours, and the nervous system adapted to those new habits. We have described the macroscopic anatomy and cytoarchitecture of the Amazon Lava Lizard brain (Tropidurus torquatus), an abundant lizard in South America. Fifteen specimens were captured, euthanized and their brains were dissected, eight of these were processed and stained in haematoxylin-eosin. Their main areas of the brain are the telencephalon and diencephalon, in the forebrain, tectum and tegmentum, in the midbrain and medulla oblongata and cerebellum, in the hindbrain. The main and accessory olfactory bulbs are the most rostral structure of the brain and are composed of six layers. Brain hemispheres compose the telencephalon and are divided in pallium and subpallium. Medial, dorsomedial, lateral and dorsal cortices are part of the pallium. Striatum, pallidum and septum compose the subpallium. The diencephalon is composed of thalamus, epithalamus and hypothalamus. The midbrain has a ventral tegmentum, composed of torus semicircularis and a dorsal 14 layered optic tectum. Most part of the hindbrain is composed of the medulla oblongata, and the cerebellum arises from it, forming a three-layered plate like structure. In general, the brain of Tropidurus torquatus resembles those of other lizards, with its own adaptations.

Anatomia macro- e microscópica do encéfalo do calango (Tropidurus torquatus) (WIED, 1820)

Resumo Os répteis têm um papel fundamental para a compreensão da independência reprodutiva da água que surgiu nos amniotas. Várias adaptações ocorreram, inclusive em padrões e comportamentos locomotores, e o sistema nervoso se adaptou a esses novos hábitos. Descrevemos a anatomia macroscópica e a citoarquitetura do encéfalo do calango (Tropidurus torquatus), um lagarto abundante na América do Sul. Quinze espécimes foram capturados, eutanasiados e seus encéfalos dissecados, oito destes foram processados e corados em hematoxilina-eosina. As principais áreas do cérebro são o telencéfalo e o diencéfalo, na parte anterior do encéfalo, teto e tegmento, no mesencéfalo e bulbo e cerebelo, na parte posterior do encéfalo. Os bulbos olfatórios principais e acessórios são as estruturas mais rostrais do cérebro e são compostos por seis camadas. Os hemisférios cerebrais compõem o telencéfalo e são divididos em pálio e subpálio. Os córtices medial, dorsomedial, lateral e dorsal fazem parte do pálio. Estriado, pálido e septo compõem o subpálio. O diencéfalo é composto pelo tálamo, epitálamo e hipotálamo. O mesencéfalo possui um tegmento ventral, composto de torus semicircularis e um tecto óptico dorsal com 14 camadas. A maior parte da parte posterior do encéfalo é composta pelo bulbo, e o cerebelo surge como uma projeção dessa estrutura, em formato plano, com três camadas. Em geral, o encéfalo de Tropidurus torquatus se assemelha ao de outros lagartos, com suas próprias adaptações.

Nuclei and tracts in the pretectum and associated tegmentum of crocodiles

In all vertebrates, the pretectum and associated tegmentum arise from prosomere 1, but the adult derivatives of these embryonic regions are not well defined in reptiles-especially in crocodiles, the reptilian group most closely related to birds. Despite its importance in vision and visuomotor behavior, descriptions of the pretectum in crocodiles are brief and photographs are lacking. To fill this gap in knowledge, the pretectum and associated tegmentum were examined in two crocodilians, Caiman crocodilus and Alligator mississippiensis, using a variety of histological stains in all three traditional planes of section. These observations were compared with similar studies in other reptiles and birds. These comparisons were hampered by differences in nomenclature and limited data. Nevertheless, pretectal nuclei in receipt of retinal input in crocodiles, other reptiles, and birds were the most easily identified when compared with the present analysis. Despite identifying the traditional nuclei comprising the pretectum of crocodiles, other areas remain to be characterized. Nevertheless, knowledge gained from this description will aid further investigations of this brain region in crocodiles and other reptiles as well as provide a reference for developmental studies in crocodiles.

Establishing an MRI-Based Protocol and Atlas of the Bearded Dragon (Pogona vitticeps) Brain

The bearded dragon (Pogona vitticeps) has become a popular companion lizard, and as such, clients have increasingly come to expect the application of advanced diagnostic and therapeutic options in their care. The purpose of this study was to establish an MRI-based protocol and brain atlas to improve diagnostic capabilities in bearded dragons presenting with neurologic dysfunction. Using a high-field 3T magnet, in vivo MRI of the brain was successfully performed in seven healthy bearded dragons utilizing an injectable anesthetic protocol utilizing intravenous alfaxalone. From this, we created an atlas of the brain in three planes, identifying nine regions of interest. A total scan time of 35 min allowed for the collection of a quality diagnostic scan and all lizards recovered without complication. This study provides practitioners a neuroanatomic reference when performing brain MRI on the bearded dragon along with a concise and rapid MRI protocol.

Higher Rate of Male Sexual Displays Correlates with Larger Ventral Posterior Amygdala Volume and Neuron Soma Volume in Wild-Caught Common Side-Blotched Lizards, Uta stansburiana

Several areas of the vertebrate brain are involved in facilitating and inhibiting the production of sexual behaviors and displays. In the laboratory, a higher rate of sexual displays is correlated with a larger ventral posterior amygdala (VPA), an area of the brain involved in the expression of sexual display behaviors, as well as larger VPA neuronal somas. However, it remains unclear if individuals in the field reflect similar patterns, as there are likely many more selective pressures in the field that may also modulate the VPA architecture. In this study, we examined variation in VPA volume and neuron soma volume in wild-caught common side-blotched lizards (Uta stansburiana) from two different populations. In a population from Nevada, males experience high predation pressure and have decreased sexual display rates during the breeding season, whereas a population in Oregon has lower levels of predation and higher rates of male sexual displays. We found that wild-caught males from the population with lower display rates also exhibited decreased VPA volume and VPA neuron cell soma volume, which may suggest that decreased display rate, possibly due to increased predation rate, covaries with VPA attributes.

Evolving Views on the Pallium

The pallium is the largest part of the telencephalon in amniotes, and comparison of its subdivisions across species has been extremely difficult and controversial due to its high divergence. Comparative embryonic genoarchitecture studies have greatly contributed to propose models of pallial fundamental divisions, which can be compared across species and be used to extract general organizing principles as well as to ask more focused and insightful research questions. The use of these models is crucial to discern between conservation, convergence or divergence in the neural populations and networks found in the pallium. Here we provide a critical review of the models proposed using this approach, including tetrapartite, hexapartite and double-ring models, and compare them to other models. While recognizing the power of these models for understanding brain architecture, development and evolution, we also highlight limitations and comment on aspects that require attention for improvement. We also discuss on the use of transcriptomic data for understanding pallial evolution and advise for better contextualization of these data by discerning between gene regulatory networks involved in the generation of specific units and cell populations versus genes expressed later, many of which are activity dependent and their expression is more likely subjected to convergent evolution.

Spatial tissue profiling by imaging-free molecular tomography

Several techniques are currently being developed for spatially resolved omics profiling, but each new method requires the setup of specific detection strategies or specialized instrumentation. Here we describe an imaging-free framework to localize high-throughput readouts within a tissue by cutting the sample into thin strips in a way that allows subsequent image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (called STRP-seq) and validated it by profiling the spatial transcriptome of the mouse brain. We applied the technique to the brain of the Australian bearded dragon, Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. We expect that STRP-seq can be used to derive spatially resolved data from a range of other omics techniques.

Social boldness correlates with brain gene expression in male green anoles

Within populations, some individuals tend to exhibit a bold or shy social behavior phenotype relative to the mean. The neural underpinnings of these differing phenotypes - also described as syndromes, personalities, and coping styles - is an area of ongoing investigation. Although a social decision-making network has been described across vertebrate taxa, most studies examining activity within this network do so in relation to exhibited differences in behavioral expression. Our study instead focuses on constitutive gene expression in bold and shy individuals by isolating baseline gene expression profiles that influence social boldness predisposition, rather than those reflecting the results of social interaction and behavioral execution. We performed this study on male green anole lizards (Anolis carolinensis), an established model organism for behavioral research, which provides a crucial comparison group to investigations of birds and mammals. After identifying subjects as bold or shy through repeated reproductive and agonistic behavior testing, we used RNA sequencing to compare gene expression profiles between these groups within various forebrain, midbrain, and hindbrain regions. The ventromedial hypothalamus had the largest group differences in gene expression, with bold males having increased expression of neuroendocrine and neurotransmitter receptor and calcium channel genes compared to shy males. Conversely, shy males express more integrin alpha-10 in the majority of examined regions. There were no significant group differences in physiology or hormone levels. Our results highlight the ventromedial hypothalamus as an important center of behavioral differences across individuals and provide novel candidates for investigations into the regulation of individual variation in social behavior phenotype.

MRI- and histologically derived neuroanatomical atlas of the Ambystoma mexicanum (axolotl)

Amphibians are an important vertebrate model system to understand anatomy, genetics and physiology. Importantly, the brain and spinal cord of adult urodels (salamanders) have an incredible regeneration capacity, contrary to anurans (frogs) and the rest of adult vertebrates. Among these amphibians, the axolotl (Ambystoma mexicanum) has gained most attention because of the surge in the understanding of central nervous system (CNS) regeneration and the recent sequencing of its whole genome. However, a complete comprehension of the brain anatomy is not available. In the present study we created a magnetic resonance imaging (MRI) atlas of the in vivo neuroanatomy of the juvenile axolotl brain. This is the first MRI atlas for this species and includes three levels: (1) 82 regions of interest (ROIs) and a version with 64 ROIs; (2) a division of the brain according to the embryological origin of the neural tube, and (3) left and right hemispheres. Additionally, we localized the myelin rich regions of the juvenile brain. The atlas, the template that the atlas was derived from, and a masking file, can be found on Zenodo at https://doi.org/10.5281/zenodo.4595016 . This MRI brain atlas aims to be an important tool for future research of the axolotl brain and that of other amphibians.

A fully segmented 3D anatomical atlas of a lizard brain

As the relevance of lizards in evolutionary neuroscience increases, so does the need for more accurate anatomical references. Moreover, the use of magnetic resonance imaging (MRI) in evolutionary neuroscience is becoming more widespread; this represents a fundamental methodological shift that opens new avenues of investigative possibility but also poses new challenges. Here, we aim to facilitate this shift by providing a three-dimensional segmentation atlas of the tawny dragon brain. The tawny dragon (Ctenophorus decresii) is an Australian lizard of increasing importance as a model system in ecology and, as a member of the agamid lizards, in evolution. Based on a consensus average 3D image generated from the MRIs of 13 male tawny dragon heads, we identify and segment 224 structures visible across the entire lizard brain. We describe the relevance of this atlas to the field of evolutionary neuroscience and propose further experiments for which this atlas can provide the foundation. This advance in defining lizard neuroanatomy will facilitate numerous studies in evolutionary neuroscience. The atlas is available for download as a supplementary material to this manuscript and through the Open Science Framework (OSF; https://doi.org/10.17605/OSF.IO/UJENQ ).

Heterochronic Developmental Shifts Underlying Squamate Cerebellar Diversity Unveil the Key Features of Amniote Cerebellogenesis

Despite a remarkable conservation of architecture and function, the cerebellum of vertebrates shows extensive variation in morphology, size, and foliation pattern. These features make this brain subdivision a powerful model to investigate the evolutionary developmental mechanisms underlying neuroanatomical complexity both within and between anamniote and amniote species. Here, we fill a major evolutionary gap by characterizing the developing cerebellum in two non-avian reptile species-bearded dragon lizard and African house snake-representative of extreme cerebellar morphologies and neuronal arrangement patterns found in squamates. Our data suggest that developmental strategies regarded as exclusive hallmark of birds and mammals, including transit amplification in an external granule layer (EGL) and Sonic hedgehog expression by underlying Purkinje cells (PCs), contribute to squamate cerebellogenesis independently from foliation pattern. Furthermore, direct comparison of our models suggests the key importance of spatiotemporal patterning and dynamic interaction between granule cells and PCs in defining cortical organization. Especially, the observed heterochronic shifts in early cerebellogenesis events, including upper rhombic lip progenitor activity and EGL maintenance, are strongly expected to affect the dynamics of molecular interaction between neuronal cell types in snakes. Altogether, these findings help clarifying some of the morphogenetic and molecular underpinnings of amniote cerebellar corticogenesis, but also suggest new potential molecular mechanisms underlying cerebellar complexity in squamates. Furthermore, squamate models analyzed here are revealed as key animal models to further understand mechanisms of brain organization.

A three-dimensional digital atlas of the Nile crocodile (Crocodylus niloticus) forebrain

The phylogenetic position of crocodilians in relation to birds and mammals makes them an interesting animal model for investigating the evolution of the nervous system in amniote vertebrates. A few neuroanatomical atlases are available for reptiles, but with a growing interest in these animals within the comparative neurosciences, a need for these anatomical reference templates is becoming apparent. With the advent of MRI being used more frequently in comparative neuroscience, the aim of this study was to create a three-dimensional MRI-based atlas of the Nile crocodile (Crocodylus niloticus) brain to provide a common reference template for the interpretation of the crocodilian, and more broadly reptilian, brain. Ex vivo MRI acquisitions in combination with histological data were used to delineate crocodilian brain areas at telencephalic, diencephalic, mesencephalic, and rhombencephalic levels. A total of 50 anatomical structures were successfully identified and outlined to create a 3-D model of the Nile crocodile brain. The majority of structures were more readily discerned within the forebrain of the crocodile with the methods used to produce this atlas. The anatomy outlined herein corresponds with both classical and recent crocodilian anatomical analyses, barring a few areas of contention predominantly related to a lack of functional data and conflicting nomenclature.

Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization

Ecomorphological studies evaluating the impact of environmental and biological factors on the brain have so far focused on morphology or size measurements, and the ecological relevance of potential multi-level variations in brain architecture remains unclear in vertebrates. Here, we exploit the extraordinary ecomorphological diversity of squamates to assess brain phenotypic diversification with respect to locomotor specialization, by integrating single-cell distribution and transcriptomic data along with geometric morphometric, phylogenetic, and volumetric analysis of high-definition 3D models. We reveal significant changes in cerebellar shape and size as well as alternative spatial layouts of cortical neurons and dynamic gene expression that all correlate with locomotor behaviours. These findings show that locomotor mode is a strong predictor of cerebellar structure and pattern, suggesting that major behavioural transitions in squamates are evolutionarily correlated with mosaic brain changes. Furthermore, our study amplifies the concept of ‘cerebrotype’, initially proposed for vertebrate brain proportions, towards additional shape characters.

The cerebellum is critical in sensory-motor control and is structurally diverse across vertebrates. Here, the authors investigate the evolutionary relationship between locomotory mode and cerebellum architecture across squamates by integrating study of gene expression, cell distribution, and 3D morphology.

Reptilian Cognition: A More Complex Picture via Integration of Neurological Mechanisms, Behavioral Constraints, and Evolutionary Context

Unlike birds and mammals, reptiles are commonly thought to possess only the most rudimentary means of interacting with their environments, reflexively responding to sensory information to the near exclusion of higher cognitive function. However, reptilian brains, though structurally somewhat different from those of mammals and birds, use many of the same cellular and molecular processes to support complex behaviors in homologous brain regions. Here, the neurological mechanisms supporting reptilian cognition are reviewed, focusing specifically on spatial cognition and the hippocampus. These processes are compared to those seen in mammals and birds within an ecologically and evolutionarily relevant context. By viewing reptilian cognition through an integrative framework, a more robust understanding of reptile cognition is gleaned. Doing so yields a broader view of the evolutionarily conserved molecular and cellular mechanisms that underlie cognitive function and a better understanding of the factors that led to the evolution of complex cognition.