Ontogenetic Shape Change in the Chicken Brain: Implications for Paleontology

Paleoneurology of stem palaeognaths clarifies the plesiomorphic condition of the crown bird central nervous system

Lithornithidae, an assemblage of volant Palaeogene fossil birds, provide our clearest insights into the early evolutionary history of Palaeognathae, the clade that today includes the flightless ratites and volant tinamous. The neotype specimen of Lithornis vulturinus, from the early Eocene (approximately 53 million years ago) of Europe, includes a partial neurocranium that has never been thoroughly investigated. Here, we describe these cranial remains including the nearly complete digital endocasts of the brain and bony labyrinth. The telencephalon of Lithornis is expanded and its optic lobes are ventrally shifted, as is typical for crown birds. The foramen magnum is positioned caudally, rather than flexed ventrally as in some crown birds, with the optic lobes, cerebellum, and foramen magnum shifted further ventrally. The overall brain shape is similar to that of tinamous, the only extant clade of flying palaeognaths, suggesting that several aspects of tinamou neuroanatomy may have been evolutionarily conserved since at least the early Cenozoic. The estimated ratio of the optic lobe's surface area relative to the total brain suggests a diurnal ecology. Lithornis may provide the clearest insights to date into the neuroanatomy of the ancestral crown bird, combining an ancestrally unflexed brain with a caudally oriented connection with the spinal cord, a moderately enlarged telencephalon, and ventrally shifted, enlarged optic lobes.

Comparative digital reconstruction of Pica pica and Struthio camelus and their cranial suture ontogenies

To date, several studies describe post-hatching ontogenetic variation in birds; however, none of these studies document and compare ontogenetic variation of the entire skull in multiple avian species. Therefore, we studied ontogenetic skull variation of two bird species with very different ecologies, Pica pica, and Struthio camelus, using μCT based 3D reconstructions. For each specimen, we performed bone-by-bone segmentation in order to visualize and describe the morphological variation of each bone during ontogeny and estimated the average sutural closure of the skulls to identify different ontogenetic stages. Although bone fusion of P. pica occurs more rapidly than that of S. camelus the general sequence of bone fusion follows a similar trend from posterior to anterior, but a more detailed analysis reveals some interspecific variation in the fusion patterns. Although growth persists over a longer period in S. camelus than in P. pica and adults of the former species are significantly larger, the skull of the most mature S. camelus is still less fused than that of P. pica. Different growth and fusion patterns of the two species indicate that the interspecific ontogenetic variation could be related to heterochronic developments. Nevertheless, this hypothesis needs to be tested in a broader phylogenetic framework in order to detect the evolutionary direction of the potential heterochronic transformations.

Differential response of the soil nutrients, soil bacterial community structure and metabolic functions to different risk areas in Lead-Zine tailings

Rapid growth in the mining industry has brought about a large formation of tailings, which result in serious destruction of the ecological environment and severe soil pollution problems. This study assesses soil nutrients, soil bacterial community and soil microbes' metabolic function in heavily polluted areas (W1), moderately polluted areas (W2), lightly polluted areas (W3) and clean areas (CK) using 16S Illumina sequencing. The results of this study showed that compared with CK, a severe loss of soil nutrients and richness of OTUs (Chao1 and ACE indices) were observed with the aggravated pollution of tailings. The Chao1 and ACE indices in the W1 group decreased significantly by 15.53 and 16.03%, respectively, (p < 0.01). Besides, the relative abundance of Actinobacteria and Proteobacteria was high whereas and relative abundance of Chloroflexi in the polluted areas. Among them, W1 groups increased significantly the relative abundance of Actinobacteria and decreased significantly the relative abundance of Chloroflexi, these can be used as indicator phyla for changes in soil community structures under polluted stress. Tax4 Fun analysis showed that W1 groups affected the soil bacterial community and altered the primary types of biological metabolism in polluted areas. Tailings have adverse impacts on soil bacterial community and metabolic functions, and the deterioration in soil quality is dependent on the levels of tailings pollution. Cumulatively, this study provides valuable information on the bacterial community structure and metabolic functions in the tailing polluted soil.

Dumbbell-shaped brains of Polish crested chickens as a model system for the evolution of novel brain morphologies

The evolutionary history of vertebrates is replete with emergence of novel brain morphologies, including the origin of the human brain. Existing model organisms and toolkits for investigating drivers of neuroanatomical innovations have largely proceeded on mammals. As such, a compelling non-mammalian model system would facilitate our understanding of how unique brain morphologies evolve across vertebrates. Here, we present the domestic chicken breed, white crested Polish chickens, as an avian model for investigating how novel brain morphologies originate. Most notably, these crested chickens exhibit cerebral herniation from anterodorsal displacement of the telencephalon, which results in a prominent protuberance on the dorsal aspect of the skull. We use a high-density geometric morphometric approach on cephalic endocasts to characterize their brain morphology. Compared with standard white Leghorn chickens (WLCs) and modern avian diversity, the results demonstrate that crested chickens possess a highly variable and unique overall brain configuration. Proportional sizes of neuroanatomical regions are within the observed range of extant birds sampled in this study, but Polish chickens differ from WLCs in possessing a relatively larger cerebrum and smaller cerebellum and medulla. Given their accessibility, phylogenetic proximity, and unique neuroanatomy, we propose that crested breeds, combined with standard chickens, form a promising comparative system for investigating the emergence of novel brain morphologies.

Ontogenetic variation in the crocodylian vestibular system

Crocodylians today live in tropical to subtropical environments, occupying mostly shallow waters. Their body size changes drastically during ontogeny, as do their skull dimensions and bite forces, which are associated with changes in prey preferences. Endocranial neurosensory structures have also shown to change ontogenetically, but less is known about the vestibular system of the inner ear. Here we use 30 high-resolution computed tomography (CT) scans and three-dimensional geometric morphometrics to investigate the size and shape changes of crocodylian endosseous labyrinths throughout ontogeny, across four stages (hatchling, juvenile, subadult and adult). We find two major patterns of ontogenetic change. First, the labyrinth increases in size during ontogeny, with negative allometry in relation to skull size. Second, labyrinth shape changes significantly, with hatchlings having shorter semicircular canal radii, with thicker diameters and an overall dorsoventrally shorter labyrinth than those of more mature individuals. We argue that the modification of the labyrinth during crocodylian ontogeny is related to constraints imposed by skull growth, due to fundamental changes in the crocodylian braincase during ontogeny (e.g. verticalisation of the basicranium), rather than changes in locomotion, diet, or other biological functions or behaviours.

Ontogeny and variation of the pachycephalosaurine dinosaur Sphaerotholus buchholtzae, and its systematics within the genus

The ontogeny and taxonomy of the dome-headed pachycephalosaurs are topics of continued debate. Pachycephalosaurid diversity in the Maastrichtian of North America is particularly controversial, and the validity and composition within the genus Sphaerotholus remains unresolved. While the type species, S. goodwini, is generally considered valid, debate has centred around the validity and taxonomy of S. buchholtzae and S. edmontonensis. Here we employ morphometrics, histology and phylogenetic analysis to resolve these issues.

An ontogenetic assessment of S. buchholtzae (N &gt; 20) confirms previously observed ontogenetic morphologies: inflation of the frontoparietal dome, obliteration of tesserate surface texture, blunting of the peripheral nodes and decreasing void space within the dome. While linear bivariate analysis finds S. edmontonensis nested within S. buchholtzae, three-dimensional geometric morphometrics supports S. edmontonensis and S. buchholtzae as distinct species. Phylogenetic analysis recovers a Sphaerotholus lineage with S. goodwini as sister-taxon to a clade formed by S. edmontonensis and S. buchholtzae.

The stratigraphic, phylogenetic, morphometric and ontogenetic data support the validity of both S. edmontonensis and S. buchholtzae, and their placement within the genus Sphaerotholus. The morphological similarities of S. edmontonensis to immature S. buchholtzae, and the slightly older geological age of S. edmontonensis, suggest that S. edmontonensis and S. buchholtzae may be part of an anagenetic lineage.

Ontogenetic endocranial shape change in alligators and ostriches and implications for the development of the non-avian dinosaur endocranium

Birds and crocodiles show radically different patterns of brain development, and it is of interest to compare these to determine the pattern of brain growth expected in dinosaurs. Here we provide atlases of 3D brain (endocast) reconstructions for Alligator mississippiensis (alligator) and Struthio camelus (ostrich) through ontogeny, prepared as digital restorations from CT scans of stained head and dry skull specimens. Our morphometric analysis confirms that ostrich brains do not change significantly in shape during postnatal growth, whereas alligator brains unfold from a cramped bird-like shape in the hatchling to an elongate, straight structure in the adult. We confirm that birds exhibit paedomorphic dinosaur endocranial traits such as retaining an enlarged and compact brain shape in the adult, whereas crocodiles show peramorphic traits where the brain elongates with growth as the skull elongates. These atlases of ontogenetic stages of modern bird and crocodilian endocrania provide a basis for comparison of non-avian dinosaur endocasts and consideration of the divergence of the "avian" and "crocodilian" modes of brain development and heterochronic change on phylogenies.

Beyond Endocasts: Using Predicted Brain-Structure Volumes of Extinct Birds to Assess Neuroanatomical and Behavioral Inferences

The shape of the brain influences skull morphology in birds, and both traits are driven by phylogenetic and functional constraints. Studies on avian cranial and neuroanatomical evolution are strengthened by data on extinct birds, but complete, 3D-preserved vertebrate brains are not known from the fossil record, so brain endocasts often serve as proxies. Recent work on extant birds shows that the Wulst and optic lobe faithfully represent the size of their underlying brain structures, both of which are involved in avian visual pathways. The endocasts of seven extinct birds were generated from microCT scans of their skulls to add to an existing sample of endocasts of extant birds, and the surface areas of their Wulsts and optic lobes were measured. A phylogenetic prediction method based on Bayesian inference was used to calculate the volumes of the brain structures of these extinct birds based on the surface areas of their overlying endocast structures. This analysis resulted in hyperpallium volumes of five of these extinct birds and optic tectum volumes of all seven extinct birds. Phylogenetic ANCOVA (phyANCOVA) were performed on regressions of the brain-structure volumes and endocast structure surface areas on various brain size metrics to determine if the relative sizes of these structures in any extinct birds were significantly different from those of the extant birds in the sample. Phylogenetic ANCOVA indicated that no extinct birds studied had relative hyperpallial volumes that were significantly different from the extant sample, nor were any of their optic tecta relatively hypertrophied. The optic tectum of Dinornis robustus was significantly smaller relative to brain size than any of the extant birds in our sample. This study provides an analytical framework for testing the hypotheses of potential functional behavioral capabilities of other extinct birds based on their endocasts.

Are endocasts good proxies for brain size and shape in archosaurs throughout ontogeny?

Cranial endocasts, or the internal molds of the braincase, are a crucial correlate for investigating the neuroanatomy of extinct vertebrates and tracking brain evolution through deep time. Nevertheless, the validity of such studies pivots on the reliability of endocasts as a proxy for brain morphology. Here, we employ micro-computed tomography imaging, including diffusible iodine-based contrast-enhanced CT, and a three-dimensional geometric morphometric framework to examine both size and shape differences between brains and endocasts of two exemplar archosaur taxa - the American alligator (Alligator mississippiensis) and the domestic chicken (Gallus gallus). With ontogenetic sampling, we quantitatively evaluate how endocasts differ from brains and whether this deviation changes during development. We find strong size and shape correlations between brains and endocasts, divergent ontogenetic trends in the brain-to-endocast correspondence between alligators and chickens, and a comparable magnitude between brain-endocast shape differences and intraspecific neuroanatomical variation. The results have important implications for paleoneurological studies in archosaurs. Notably, we demonstrate that the pattern of endocranial shape variation closely reflects brain shape variation. Therefore, analyses of endocranial morphology are unlikely to generate spurious conclusions about large-scale trends in brain size and shape. To mitigate any artifacts, however, paleoneurological studies should consider the lower brain-endocast correspondence in the hindbrain relative to the forebrain; higher size and shape correspondences in chickens than alligators throughout postnatal ontogeny; artificially 'pedomorphic' shape of endocasts relative to their corresponding brains; and potential biases in both size and shape data due to the lack of control for ontogenetic stages in endocranial sampling.

Morphological variation under domestication: how variable are chickens?

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.

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.

Sensitive Periods, Vasotocin-Family Peptides, and the Evolution and Development of Social Behavior

Nonapeptides, by modulating the activity of neural circuits in specific social contexts, provide an important mechanism underlying the evolution of diverse behavioral phenotypes across vertebrate taxa. Vasotocin-family nonapeptides, in particular, have been found to be involved in behavioral plasticity and diversity in social behavior, including seasonal variation, sexual dimorphism, and species differences. Although nonapeptides have been the focus of a great deal of research over the last several decades, the vast majority of this work has focused on adults. However, behavioral diversity may also be explained by the ways in which these peptides shape neural circuits and influence social processes during development. In this review, I synthesize comparative work on vasotocin-family peptides during development and classic work on early forms of social learning in developmental psychobiology. I also summarize recent work demonstrating that early life manipulations of the nonapeptide system alter attachment, affiliation, and vocal learning in zebra finches. I thus hypothesize that vasotocin-family peptides are involved in the evolution of social behaviors through their influence on learning during sensitive periods in social development.

Morphological variation in brain through domestication of fowl

Great variations in the size, shape, color, feather structure and behavior are observed among fowl breeds. Because many types of domestic fowls have been bred for various purposes, they are ideal to assess the relationship between brain morphology and avian biology. However, little is known about changes in brain shape that may have occurred during fowl domestication. We analyzed the brains of red jungle fowl and domestic fowl to clarify differences in the brain shape between these breeds, as well as the shape changes associated with size enlargement using three-dimensional geometric morphometrics. Principal component and multivariate regression analyses showed that ventrodorsal bending, anteroposterior elongation and width reduction were significantly correlated with brain size. According to the size-dependent analysis, the red jungle fowl brain has an intermediate shape between the brain of young broilers and that of large domestic fowl and adult broilers. After the size effect is removed, geometric morphometric analyses show that the brain of red jungle fowl is different from that of domestic fowl, with large round cerebral hemispheres. Significant correlations exist between the skull length and brain volume among fowl, while the brain volume relative to the skull length is distinctly larger in red jungle fowl compared with domestic fowl. The distinct brain shape and increased relative brain size of red jungle fowl may be driven by the presence of large, rounded cerebral hemispheres.

Volume of the crocodilian brain and endocast during ontogeny

Understanding complex situations and planning difficult actions require a brain of appropriate size. Animal encephalisation provides an indirect information about these abilities. The brain is entirely composed of soft tissue and, as such, rarely fossilises. As a consequence, the brain proportions and morphology of some extinct vertebrates are usually only inferred from their neurocranial endocasts. However, because the morphological configuration of the brain is not fully reflected in the endocast, knowledge of the brain/endocast relationship is essential (especially the ratio of brain volume to endocast volume or the equivalent proportion of interstitial tissue) for studying the endocasts of extinct animals. Here we assess the encephalic volume and structure of modern crocodilians. The results we obtained using ex vivo magnetic resonance imaging reveal how the endoneurocranial cavity and brain compartments of crocodilians change configuration during ontogeny. We conclude that the endocasts of adult crocodilians are elongated and expanded while their brains are more linearly organised. The highest proportion of brain tissue to endocast volume is in the prosencephalon at over 50% in all but the largest animals, whereas the proportion in other brain segments is under 50% in all but the smallest animals and embryos. Our results may enrich the field of palaeontological study by offering more precise phylogenetic interpretations of the neuroanatomic characteristics of extinct vertebrates at various ontogenetic stages.

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

The rapidly expanding interest in, and availability of, digital tomography data to visualize casts of the vertebrate endocranial cavity housing the brain (endocasts) presents new opportunities and challenges to the field of comparative neuroanatomy. The opportunities are many, ranging from the relatively rapid acquisition of data to the unprecedented ability to integrate critically important fossil taxa. The challenges consist of navigating the logistical barriers that often separate a researcher from high-quality data and minimizing the amount of non-biological variation expressed in endocasts - variation that may confound meaningful and synthetic results. Our purpose here is to outline preferred approaches for acquiring digital tomographic data, converting those data to an endocast, and making those endocasts as meaningful as possible when considered in a comparative context. This review is intended to benefit those just getting started in the field but also serves to initiate further discussion between active endocast researchers regarding the best practices for advancing the discipline. Congruent with the theme of this volume, we draw our examples from birds and the highly encephalized non-avian dinosaurs that comprise closely related outgroups along their phylogenetic stem lineage.

Studying avian encephalization with geometric morphometrics

Encephalization is a core concept in comparative neurobiology, aiming to quantify the neurological capacity of organisms. For measuring encephalization, many studies have employed relative brain sizes corrected for expected allometric scaling to body size. Here we highlight the utility of a multivariate geometric morphometric (GM) approach for visualizing and analyzing neuroanatomical shape variation associated with encephalization. GM readily allows the statistical evaluation of covariates, such as size, and many software tools exist for visualizing their effects on shape. Thus far, however, studies using GM have not attempted to translate the meaning of encephalization to shape data. As such, we tested the statistical relationship between size and encephalization quotients (EQs) to brain shape utilizing a broad interspecific sample of avian endocranial data. Although statistically significant, the analyses indicate that allometry accounts for <10% of total neuroanatomical shape variation. Notably, we find that EQs, despite being corrected for allometric scaling based on size, contain size-related neuroanatomical shape changes. In addition, much of what is traditionally considered encephalization comprises clade-specific trends in relative forebrain expansion, particularly driven by landbirds. EQs, therefore, fail to capture 90% of the total neuroanatomical variation after correcting for allometry and shared phylogenetic history. Moving forward, GM techniques provide crucial tools for investigating key drivers of this vast, largely unexplored aspect of avian brain morphology.