Neocortical Evolution: Neuronal Circuits Arise Independently of Lamination

Evolutionary convergence of sensory circuits in the pallium of amniotes

The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko), and mammals (mouse). We reveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species and found an early developmental divergence in the transcriptomic progression of glutamatergic neurons. Our research highlights developmental distinctions and functional similarities in the sensory circuit between birds and mammals, suggesting the convergence of high-order sensory processing across amniote lineages.

Parallel development of object recognition in newborn chicks and deep neural networks

How do newborns learn to see? We propose that visual systems are space-time fitters, meaning visual development can be understood as a blind fitting process (akin to evolution) in which visual systems gradually adapt to the spatiotemporal data distributions in the newborn's environment. To test whether space-time fitting is a viable theory for learning how to see, we performed parallel controlled-rearing experiments on newborn chicks and deep neural networks (DNNs), including CNNs and transformers. First, we raised newborn chicks in impoverished environments containing a single object, then simulated those environments in a video game engine. Second, we recorded first-person images from agents moving through the virtual animal chambers and used those images to train DNNs. Third, we compared the viewpoint-invariant object recognition performance of the chicks and DNNs. When DNNs received the same visual diet (training data) as chicks, the models developed common object recognition skills as chicks. DNNs that used time as a teaching signal-space-time fitters-also showed common patterns of successes and failures across the test viewpoints as chicks. Thus, DNNs can learn object recognition in the same impoverished environments as newborn animals. We argue that space-time fitters can serve as formal scientific models of newborn visual systems, providing image-computable models for studying how newborns learn to see from raw visual experiences.

Analysis of Shannon's entropy to contrast between the Embodied and Neurocentrist hypothesis of conscious experience

We usually accept that consciousness is in the brain. This statement corresponds to a Neurocentrist view. However, with all the physical and physiological data currently available, a convincing explanation of how consciousness emerges has not been given this topic is aborded by Anil Seth (2021). Because of this, a natural question arises: Is consciousness really in the brain or not? If the answer is no, this corresponds to the Embodied perspective. We cannot discriminate between these two points of view because we cannot identify how the organism processes the information. If we try to measure information processing in the brain, then the Neurocentrist view is unavoidable. For example, the information integration theory of Tononi's research group and the global work area theory developed by Dehaene and Baars, focus solely on the brain without considering aspects of Embodied vision (See Tononi, 2021; Dehaene, 2021). In this article, we propose an index based on Shannon's entropy, capable of identifying the leading processing elements acting: Are they mainly inner or external? In order to validate it, we performed simulations with networks accounting for different amounts of internal and outer layers. Since Shannon's entropy is an abstract measure of the information content, this index is not dependent on the physical network nor the proportion of different layers. Therefore, we validate the index as free of bias. This index is a way to discriminate between Embodied from Neurocentrist hypotheses.

Digital Twin Studies for Reverse Engineering the Origins of Visual Intelligence

What are the core learning algorithms in brains? Nativists propose that intelligence emerges from innate domain-specific knowledge systems, whereas empiricists propose that intelligence emerges from domain-general systems that learn domain-specific knowledge from experience. We address this debate by reviewing digital twin studies designed to reverse engineer the learning algorithms in newborn brains. In digital twin studies, newborn animals and artificial agents are raised in the same environments and tested with the same tasks, permitting direct comparison of their learning abilities. Supporting empiricism, digital twin studies show that domain-general algorithms learn animal-like object perception when trained on the first-person visual experiences of newborn animals. Supporting nativism, digital twin studies show that domain-general algorithms produce innate domain-specific knowledge when trained on prenatal experiences (retinal waves). We argue that learning across humans, animals, and machines can be explained by a universal principle, which we call space-time fitting. Space-time fitting explains both empiricist and nativist phenomena, providing a unified framework for understanding the origins of intelligence.

Genomic loss of GPR108 disrupts AAV transduction in birds

The G protein-coupled receptor 108 (GPR108) gene encodes a protein factor identified as critical for adeno-associated virus (AAV) entry into mammalian cells, but whether it is universally involved in AAV transduction is unknown. Remarkably, we have discovered that GPR108 is absent in the genomes of birds and in most other sauropsids, providing a likely explanation for the overall lower AAV transduction efficacy of common AAV serotypes in birds compared to mammals. Importantly, transgenic expression of human GPR108 and manipulation of related glycan binding sites in the viral capsid significantly boost AAV transduction in zebra finch cells. These findings contribute to a more in depth understanding of the mechanisms and evolution of AAV transduction, with potential implications for the design of efficient tools for gene manipulation in experimental animal models, and a range of gene therapy applications in humans.

The Development of Object Recognition Requires Experience with the Surface Features of Objects

What role does visual experience play in the development of object recognition? Prior controlled-rearing studies suggest that newborn animals require slow and smooth visual experiences to develop object recognition. Here, we examined whether the development of object recognition also requires experience with the surface features of objects. We raised newborn chicks in automated controlled-rearing chambers that contained a single virtual object, then tested their ability to recognize that object from familiar and novel viewpoints. When chicks were reared with an object that had surface features, the chicks developed view-invariant object recognition. In contrast, when chicks were reared with a line drawing of an object, the chicks failed to develop object recognition. The chicks reared with line drawings performed at chance level, despite acquiring over 100 h of visual experience with the object. These results indicate that the development of object recognition requires experience with the surface features of objects.

Convergent Circuit Computation for Categorization in the Brains of Primates and Songbirds

Categorization is crucial for behavioral flexibility because it enables animals to group stimuli into meaningful classes that can easily be generalized to new circumstances. A most abstract quantitative category is set size, the number of elements in a set. This review explores how categorical number representations are realized by the operations of excitatory and inhibitory neurons in associative telencephalic microcircuits in primates and songbirds. Despite the independent evolution of the primate prefrontal cortex and the avian nidopallium caudolaterale, the neuronal computations of these associative pallial circuits show surprising correspondence. Comparing cellular functions in distantly related taxa can inform about the evolutionary principles of circuit computations for cognition in distinctly but convergently realized brain structures.

Cell type specializations of the vocal-motor cortex in songbirds

Identifying molecular specializations in cortical circuitry supporting complex behaviors, like learned vocalizations, requires understanding of the neuroanatomical context from which these circuits arise. In songbirds, the robust arcopallial nucleus (RA) provides descending cortical projections for fine vocal-motor control. Using single-nuclei transcriptomics and spatial gene expression mapping in zebra finches, we have defined cell types and molecular specializations that distinguish RA from adjacent regions involved in non-vocal motor and sensory processing. We describe an RA-specific projection neuron, differential inhibitory subtypes, and glia specializations and have probed predicted GABAergic interneuron subtypes electrophysiologically within RA. Several cell-specific markers arise developmentally in a sex-dependent manner. Our interactive apps integrate cellular data with developmental and spatial distribution data from the gene expression brain atlas ZEBrA. Users can explore molecular specializations of vocal-motor neurons and support cells that likely reflect adaptations key to the physiology and evolution of vocal control circuits and refined motor skills.

Eagle eyed or bird brained?

The importance of the visual system to birds for behaviours from feeding, mate choice, flying, navigation and determination of seasons, together with the presence of photoreceptors in the retina, the pineal and the brain, render the avian visual system a particularly fruitful model for understanding of eye-brain interactions. In this review we will particularly focus on the pigeon, since here we have a brain stereotactically mapped and a genome fully sequenced, together with a particular bird, the homing pigeon, with remarkable ability to navigate over hundreds of miles and return to exactly the same roosting site with exceptional precision. We might denigrate the avian species by the term bird brained, but here are animals with phenomenal abilities to use their exceptional vision, their eagle eyedness, to best advantage.

Molecular biology of serotonergic systems in avian brains

Serotonin (5-hydroxytryptamine, 5-HT) is a phylogenetically conserved neurotransmitter and modulator. Neurons utilizing serotonin have been identified in the central nervous systems of all vertebrates. In the central serotonergic system of vertebrate species examined so far, serotonergic neurons have been confirmed to exist in clusters in the brainstem. Although many serotonin-regulated cognitive, behavioral, and emotional functions have been elucidated in mammals, equivalents remain poorly understood in non-mammalian vertebrates. The purpose of this review is to summarize current knowledge of the anatomical organization and molecular features of the avian central serotonergic system. In addition, selected key functions of serotonin are briefly reviewed. Gene association studies between serotonergic system related genes and behaviors in birds have elucidated that the serotonergic system is involved in the regulation of behavior in birds similar to that observed in mammals. The widespread distribution of serotonergic modulation in the central nervous system and the evolutionary conservation of the serotonergic system provide a strong foundation for understanding and comparing the evolutionary continuity of neural circuits controlling corresponding brain functions within vertebrates. The main focus of this review is the chicken brain, with this type of poultry used as a model bird. The chicken is widely used not only as a model for answering questions in developmental biology and as a model for agriculturally useful breeding, but also in research relating to cognitive, behavioral, and emotional processes. In addition to a wealth of prior research on the projection relationships of avian brain regions, detailed subdivision similarities between avian and mammalian brains have recently been identified. Therefore, identifying the neural circuits modulated by the serotonergic system in avian brains may provide an interesting opportunity for detailed comparative studies of the function of serotonergic systems in mammals.

Where is the error? Hierarchical predictive coding through dendritic error computation

Top-down feedback in cortex is critical for guiding sensory processing, which has prominently been formalized in the theory of hierarchical predictive coding (hPC). However, experimental evidence for error units, which are central to the theory, is inconclusive and it remains unclear how hPC can be implemented with spiking neurons. To address this, we connect hPC to existing work on efficient coding in balanced networks with lateral inhibition and predictive computation at apical dendrites. Together, this work points to an efficient implementation of hPC with spiking neurons, where prediction errors are computed not in separate units, but locally in dendritic compartments. We then discuss the correspondence of this model to experimentally observed connectivity patterns, plasticity, and dynamics in cortex.

Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution

The evolution of advanced cognition in vertebrates is associated with two independent innovations in the forebrain: the six-layered neocortex in mammals and the dorsal ventricular ridge (DVR) in sauropsids (reptiles and birds). How these innovations arose in vertebrate ancestors remains unclear. To reconstruct forebrain evolution in tetrapods, we built a cell-type atlas of the telencephalon of the salamander Pleurodeles waltl. Our molecular, developmental, and connectivity data indicate that parts of the sauropsid DVR trace back to tetrapod ancestors. By contrast, the salamander dorsal pallium is devoid of cellular and molecular characteristics of the mammalian neocortex yet shares similarities with the entorhinal cortex and subiculum. Our findings chart the series of innovations that resulted in the emergence of the mammalian six-layered neocortex and the sauropsid DVR.

Consciousness without cortex

Sensory consciousness - the awareness and ability to report subjective experiences - is a property of biological nervous systems that has evolved out of unconscious processing over hundreds of millions of years. From which brain structures and based on which mechanisms can conscious experience emerge? Based on the body of work in human and nonhuman primates, the emergence of consciousness is intimately associated with the workings of the mammalian cerebral cortex with its specific cell types and layered structure. However, recent neurophysiological recordings demonstrate a neuronal correlate of consciousness in the pallial endbrain of crows. These telencephalic integration centers in birds originate embryonically from other pallial territories, lack a layered architecture characteristic for the cerebral cortex, and exhibit independently evolved pallial cell types. This argues that the mammalian cerebral cortex is not a prerequisite for consciousness to emerge in all vertebrates. Rather, it seems that the anatomical and physiological principles of the telencephalic pallium offer this structure as a brain substrate for consciousness to evolve independently across vertebrate phylogeny.

From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex

With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution.

Multiple Routes to Animal Consciousness: Constrained Multiple Realizability Rather Than Modest Identity Theory

The multiple realizability thesis (MRT) is an important philosophical and psychological concept. It says any mental state can be constructed by multiple realizability (MR), meaning in many distinct ways from different physical parts. The goal of our study is to find if the MRT applies to the mental state of consciousness among animals. Many things have been written about MRT but the ones most applicable to animal consciousness are by Shapiro in a 2004 book called The Mind Incarnate and by Polger and Shapiro in their 2016 work, The Multiple Realization Book. Standard, classical MRT has been around since 1967 and it says that a mental state can have very many different physical realizations, in a nearly unlimited manner. To the contrary, Shapiro's book reasoned that physical, physiological, and historical constraints force mental traits to evolve in just a few, limited directions, which is seen as convergent evolution of the associated neural traits in different animal lineages. This is his mental constraint thesis (MCT). We examined the evolution of consciousness in animals and found that it arose independently in just three animal clades-vertebrates, arthropods, and cephalopod mollusks-all of which share many consciousness-associated traits: elaborate sensory organs and brains, high capacity for memory, directed mobility, etc. These three constrained, convergently evolved routes to consciousness fit Shapiro's original MCT. More recently, Polger and Shapiro's book presented much the same thesis but changed its name from MCT to a "modest identity thesis." Furthermore, they argued against almost all the classically offered instances of MR in animal evolution, especially against the evidence of neural plasticity and the differently expanded cerebrums of mammals and birds. In contrast, we argue that some of these classical examples of MR are indeed valid and that Shapiro's original MCT correction of MRT is the better account of the evolution of consciousness in animal clades. And we still agree that constraints and convergence refute the standard, nearly unconstrained, MRT.

Fate restrictions in embryonic neural progenitors

The vertebrate central nervous system (CNS) is a fantastically complex organ composed of dozens of cell types within the neural and glial lineages. Its organization is laid down during development, through the localized and sequential production of subsets of neurons with specific identities. The principles and mechanisms that underlie the timely production of adequate classes of cells are only partially understood. Recent advances in molecular profiling describe the developmental trajectories leading to this amazing cellular diversity and provide us with cell atlases of an unprecedented level of precision. Yet, some long-standing questions pertaining to lineage relationships between neural progenitor cells and their differentiated progeny remain unanswered. Here, we discuss questions related to proliferation potential, timing of fate choices and restriction of neuronal output potential of individual CNS progenitors through the lens of lineage relationship. Unlocking methodological barriers will be essential to accurately describe CNS development at a cellular resolution.

An avian cortical circuit for chunking tutor song syllables into simple vocal-motor units

How are brain circuits constructed to achieve complex goals? The brains of young songbirds develop motor circuits that achieve the goal of imitating a specific tutor song to which they are exposed. Here, we set out to examine how song-generating circuits may be influenced early in song learning by a cortical region (NIf) at the interface between auditory and motor systems. Single-unit recordings reveal that, during juvenile babbling, NIf neurons burst at syllable onsets, with some neurons exhibiting selectivity for particular emerging syllable types. When juvenile birds listen to their tutor, NIf neurons are also activated at tutor syllable onsets, and are often selective for particular syllable types. We examine a simple computational model in which tutor exposure imprints the correct number of syllable patterns as ensembles in an interconnected NIf network. These ensembles are then reactivated during singing to train a set of syllable sequences in the motor network.

Young songbirds learn to imitate their parents’ songs. Here, the authors find that, in baby birds, neurons in a brain region at the interface of auditory and motor circuits signal the onsets of song syllables during both tutoring and babbling, suggesting a specific neural mechanism for vocal imitation.

Multidimensional Tuning in Motor Cortical Neurons during Active Behavior

A region within songbird cortex, dorsal intermediate arcopallium (AId), is functionally analogous to motor cortex in mammals and has been implicated in song learning during development. Non-vocal factors such as visual and social cues are known to mediate song learning and performance, yet previous chronic-recording studies of regions important for song behavior have focused exclusively on neural activity in relation to song production. Thus, we have little understanding of the range of non-vocal information that single neurons may encode. We made chronic recordings in AId of freely behaving juvenile zebra finches and evaluated neural activity during diverse motor behaviors throughout entire recording sessions, including song production as well as hopping, pecking, preening, fluff-ups, beak interactions, scratching, and stretching. These movements are part of natural behavioral repertoires and are important components of both song learning and courtship behavior. A large population of AId neurons showed significant modulation of activity during singing. In addition, single neurons demonstrated heterogeneous response patterns during multiple movements (including excitation during one movement type and suppression during another), and some neurons showed differential activity depending on the context in which movements occurred. Moreover, we found evidence of neurons that did not respond during discrete movements but were nonetheless modulated during active behavioral states compared with quiescence. Our results suggest that AId neurons process both vocal and non-vocal information, highlighting the importance of considering the variety of multimodal factors that can contribute to vocal motor learning during development.

Molecular and cellular evolution of corticogenesis in amniotes

The cerebral cortex varies dramatically in size and complexity between amniotes due to differences in neuron number and composition. These differences emerge during embryonic development as a result of variations in neurogenesis, which are thought to recapitulate modifications occurred during evolution that culminated in the human neocortex. Here, we review work from the last few decades leading to our current understanding of the evolution of neurogenesis and size of the cerebral cortex. Focused on specific examples across vertebrate and amniote phylogeny, we discuss developmental mechanisms regulating the emergence, lineage, complexification and fate of cortical germinal layers and progenitor cell types. At the cellular level, we discuss the fundamental impact of basal progenitor cells and the advent of indirect neurogenesis on the increased number and diversity of cortical neurons and layers in mammals, and on cortex folding. Finally, we discuss recent work that unveils genetic and molecular mechanisms underlying this progressive expansion and increased complexity of the amniote cerebral cortex during evolution, with a particular focus on those leading to human-specific features. Whereas new genes important in human brain development emerged the recent hominid lineage, regulation of the patterns and levels of activity of highly conserved signaling pathways are beginning to emerge as mechanisms of central importance in the evolutionary increase in cortical size and complexity across amniotes.

One-shot learning of view-invariant object representations in newborn chicks

Can newborn brains perform one-shot learning? To address this question, we reared newborn chicks in strictly controlled environments containing a single view of a single object, then tested their object recognition performance across 24 uniformly-spaced viewpoints. We found that chicks can build view-invariant object representations from a single view of an object: a case of one-shot learning in newborn brains. Chicks can also build the same view-invariant object representation from different views of an object, showing that newborn brains converge on common object representations from different sets of sensory inputs. Finally, by rearing chicks with larger numbers of object views, we found that chicks develop enhanced recognition for familiar views. These results illuminate the earliest stages of object recognition, revealing (1) powerful one-shot learning that builds invariant object representations from the first views of an object and (2) view-based learning that enriches object representations, producing enhanced recognition for familiar views.

ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies

An in-depth understanding of the genetics and evolution of brain function and behavior requires a detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species and a first for any sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among many fundamental themes.

The chick pallium displays divergent expression patterns of chick orthologues of mammalian neocortical deep layer-specific genes

The avian pallium is organised into clusters of neurons and does not have layered structures such as those seen in the mammalian neocortex. The evolutionary relationship between sub-regions of avian pallium and layers of mammalian neocortex remains unclear. One hypothesis, based on the similarities in neural connections of the motor output neurons that project to sub-pallial targets, proposed the cell-type homology between brainstem projection neurons in neocortex layers 5 or 6 (L5/6) and those in the avian arcopallium. Recent studies have suggested that gene expression patterns are associated with neural connection patterns, which supports the cell-type homology hypothesis. However, a limited number of genes were used in these studies. Here, we showed that chick orthologues of mammalian L5/6-specific genes, nuclear receptor subfamily 4 group A member 2 and connective tissue growth factor, were strongly expressed in the arcopallium. However, other chick orthologues of L5/6-specific genes were primarily expressed in regions other than the arcopallium. Our results do not fully support the cell-type homology hypothesis. This suggests that the cell types of brainstem projection neurons are not conserved between the avian arcopallium and the mammalian neocortex L5/6. Our findings may help understand the evolution of pallium between birds and mammals.

Inhibitory cell populations depend on age, sex, and prior experience across a neural network for Critical Period learning

In many ways, the complement of cell subtypes determines the information processing that a local brain circuit can perform. For example, the balance of excitatory and inhibitory (E/I) signaling within a brain region contributes to response magnitude and specificity in ways that influence the effectiveness of information processing. An extreme example of response changes to sensory information occur across Critical Periods (CPs). In primary mammalian visual cortex, GAD65 and parvalbumin inhibitory cell types in particular control experience-dependent responses during a CP. Here, we test how the density of GAD65- and parvalbumin-expressing cells may inform on a CP for complex behavioral learning. Juvenile male zebra finch songbirds (females cannot sing) learn to sing through coordinated sensory, sensorimotor, and motor learning processes distributed throughout a well-defined neural network. There is a CP for sensory learning, the process by which a young male forms a memory of his “tutor’s” song, which is then used to guide the young bird’s emerging song structure. We quantified the effect of sex and experience with a tutor on the cell densities of GAD65- and parvalbumin-expressing cells across major nodes of the song network, using ages that span the CP for tutor song memorization. As a resource, we also include whole-brain mapping data for both genes. Results indicate that inhibitory cell populations differ across sex, age, and experiential conditions, but not always in the ways we predicted.

Neural architecture of the vertebrate brain: implications for the interaction between emotion and cognition

Cognition is considered a hallmark of the primate brain that requires a high degree of signal integration, such as achieved in the prefrontal cortex. Moreover, it is often assumed that cognitive capabilities imply "superior" computational mechanisms compared to those involved in emotion or motivation. In contrast to these ideas, we review data on the neural architecture across vertebrates that support the concept that association and integration are basic features of the vertebrate brain, which are needed to successfully adapt to a changing world. This property is not restricted to a few isolated brain centers, but rather resides in neuronal networks working collectively in a context-dependent manner. In different vertebrates, we identify shared large-scale connectional systems involving the midbrain, hypothalamus, thalamus, basal ganglia, and amygdala. The high degree of crosstalk and association between these systems at different levels supports the notion that cognition, emotion, and motivation cannot be separated - all of them involve a high degree of signal integration.

Evolution of the Chordate Telencephalon

The dramatic evolutionary expansion of the neocortex, together with a proliferation of specialized cortical areas, is believed to underlie the emergence of human cognitive abilities. In a broader phylogenetic context, however, neocortex evolution in mammals, including humans, is remarkably conservative, characterized largely by size variations on a shared six-layered neuronal architecture. By contrast, the telencephalon in non-mammalian vertebrates, including reptiles, amphibians, bony and cartilaginous fishes, and cyclostomes, features a great variety of very different tissue structures. Our understanding of the evolutionary relationships of these telencephalic structures, especially those of basally branching vertebrates and invertebrate chordates, remains fragmentary and is impeded by conceptual obstacles. To make sense of highly divergent anatomies requires a hierarchical view of biological organization, one that permits the recognition of homologies at multiple levels beyond neuroanatomical structure. Here we review the origin and diversification of the telencephalon with a focus on key evolutionary innovations shaping the neocortex at multiple levels of organization.

Evolution of neuronal identity in the cerebral cortex

To understand neocortex evolution, we must define a theory for the elaboration of cell types, circuits, and architectonics from an ancestral structure that is consistent with developmental, molecular, and genetic data. To this end, cross-species comparison of cortical cell types emerges as a very informative approach. We review recent results that illustrate the contribution of molecular and transcriptomic data to the construction of plausible models of cortical cell-type evolution.

Using automated controlled rearing to explore the origins of object permanence

What are the origins of object permanence? Despite widespread interest in this question, methodological barriers have prevented detailed analysis of how experience shapes the development of object permanence in newborn organisms. Here, we introduce an automated controlled-rearing method for studying the emergence of object permanence in strictly controlled virtual environments. We used newborn chicks as an animal model and recorded their behavior continuously (24/7) from the onset of vision. Across four experiments, we found that object permanence can develop rapidly, within the first few days of life. This ability developed even when chicks were reared in impoverished visual environments containing no object occlusion events. Object permanence failed to develop, however, when chicks were reared in environments containing temporally non-smooth objects (objects moving on discontinuous spatiotemporal paths). These results suggest that experience with temporally smooth objects facilitates the development of object permanence, confirming a key prediction of temporal learning models in computational neuroscience.

The expression of tyrosine hydroxylase and DARPP-32 in the house crow (Corvus splendens) brain

Birds of the family Corvidae which includes diverse species such as crows, rooks, ravens, magpies, jays, and jackdaws are known for their amazing abilities at problem-solving. Since the catecholaminergic system, especially the neurotransmitter dopamine, plays a role in cognition, we decided to study the distribution of tyrosine hydroxylase (TH), the rate-limiting enzyme in the synthesis of catecholamines in the brain of house crows (Corvus splendens). We also studied the expression of DARPP-32 (dopamine and cAMP-regulated phosphoprotein), which is expressed in dopaminoceptive neurons. Our results demonstrated that as in other avian species, the expression of both TH and DARPP-32 was highest in the house crow striatum. The caudolateral nidopallium (NCL, the avian analogue of the mammalian prefrontal cortex) could be differentiated from the surrounding pallial regions based on a larger number of TH-positive "baskets" of fibers around neurons in this region and greater intensity of DARPP-32 staining in the neuropil in this region. House crows also possessed distinct nuclei in their brains which corresponded to song control regions in other songbirds. Whereas immunoreactivity for TH was higher in the vocal control region Area X compared to the surrounding MSt (medial striatum) in house crows, staining in RA and HVC was not as prominent. Furthermore, the arcopallial song control regions RA (nucleus robustus arcopallialis) and AId (intermediate arcopallium) were strikingly negative for DARPP-32 staining, in contrast to the surrounding arcopallium. Patterns of immunoreactivity for TH and DARPP-32 in "limbic" areas such as the hippocampus, septum, and extended amygdala have also been described.

Comparative Principles for Next-Generation Neuroscience

Neuroscience is enjoying a renaissance of discovery due in large part to the implementation of next-generation molecular technologies. The advent of genetically encoded tools has complemented existing methods and provided researchers the opportunity to examine the nervous system with unprecedented precision and to reveal facets of neural function at multiple scales. The weight of these discoveries, however, has been technique-driven from a small number of species amenable to the most advanced gene-editing technologies. To deepen interpretation and build on these breakthroughs, an understanding of nervous system evolution and diversity are critical. Evolutionary change integrates advantageous variants of features into lineages, but is also constrained by pre-existing organization and function. Ultimately, each species’ neural architecture comprises both properties that are species-specific and those that are retained and shared. Understanding the evolutionary history of a nervous system provides interpretive power when examining relationships between brain structure and function. The exceptional diversity of nervous systems and their unique or unusual features can also be leveraged to advance research by providing opportunities to ask new questions and interpret findings that are not accessible in individual species. As new genetic and molecular technologies are added to the experimental toolkits utilized in diverse taxa, the field is at a key juncture to revisit the significance of evolutionary and comparative approaches for next-generation neuroscience as a foundational framework for understanding fundamental principles of neural function.

Differential developmental changes in cortical representations of auditory-vocal stimuli in songbirds

Procedural skill learning requires iterative comparisons between feedback of self-generated motor output and a goal sensorimotor pattern. In juvenile songbirds, neural representations of both self-generated behaviors (each bird's own immature song) and the goal motor pattern (each bird's adult tutor song) are essential for vocal learning, yet little is known about how these behaviorally relevant stimuli are encoded. We made extracellular recordings during song playback in anesthetized juvenile and adult zebra finches ( Taeniopygia guttata) in adjacent cortical regions RA (robust nucleus of the arcopallium), AId (dorsal intermediate arcopallium), and RA cup, each of which is well situated to integrate auditory-vocal information: RA is a motor cortical region that drives vocal output, AId is an adjoining cortical region whose projections converge with basal ganglia loops for song learning in the dorsal thalamus, and RA cup surrounds RA and receives inputs from primary and secondary auditory cortex. We found strong developmental differences in neural selectivity within RA, but not in AId or RA cup. Juvenile RA neurons were broadly responsive to multiple songs but preferred juvenile over adult vocal sounds; in addition, spiking responses lacked consistent temporal patterning. By adulthood, RA neurons responded most strongly to each bird's own song with precisely timed spiking activity. In contrast, we observed a complete lack of song responsivity in both juvenile and adult AId, even though this region receives song-responsive inputs. A surprisingly large proportion of sites in RA cup of both juveniles and adults did not respond to song playback, and responsive sites showed little evidence of song selectivity. NEW & NOTEWORTHY Motor skill learning entails changes in selectivity for behaviorally relevant stimuli across cortical regions, yet the neural representation of these stimuli remains understudied. We investigated how information important for vocal learning in zebra finches is represented in regions analogous to infragranular layers of motor and auditory cortices during vs. after the developmentally regulated learning period. The results provide insight into how neurons in higher level stages of cortical processing represent stimuli important for motor skill learning.

3.0 Tesla magnetic resonance imaging anatomy of the central nervous system, eye, and inner ear in birds of prey

Despite the increasing interest in the clinical neurology of birds, little is known about the magnetic resonance imaging (MRI) appearance of the avian central nervous system, eye, and inner ear. The objective of this cadaveric study was to document the MRI anatomic features of the aforementioned structures using a high-resolution 3.0 Tesla MRI system. The final study group consisted of 13 cadavers of the diurnal birds of prey belonging to six species. Images were acquired in sagittal, dorsal, and transverse planes using T1-weighted and T2-weighted turbo spin echo sequences. A necropsy with macroscopic analysis of the brain and spinal cord was performed on all cadavers. Microscopic examination of the brain was performed on one cadaver of each species; the spinal cord was examined in three subjects. Anatomic structures were identified on the magnetic resonance images based on histologic slices and available literature. Very good resolution of anatomic detail was obtained. The olfactory bulbs; cerebral hemispheres; diencephalon; optic lobe; cerebellum; pons; ventricular system; optic, trigeminal, and facial nerves; pineal and pituitary glands; as well as the semicircular canals of the inner ear were identified. Exquisite detail was achieved on the ocular structures. In the spinal cord, the gray and white matter differentiation and the glycogen body were identified. This study establishes normal MRI anatomy of the central nervous system, eye, and inner ear of the birds of prey; and may be used as a reference in the assessment of neurologic disorders or visual impairment in this group of birds.

A complex mTOR response in habituation paradigms for a social signal in adult songbirds

Nonassociative learning is considered simple because it depends on presentation of a single stimulus, but it likely reflects complex molecular signaling. To advance understanding of the molecular mechanisms of one form of nonassociative learning, habituation, for ethologically relevant signals we examined song recognition learning in adult zebra finches. These colonial songbirds learn the unique song of individuals, which helps establish and maintain mate and other social bonds, and informs appropriate behavioral interactions with specific birds. We leveraged prior work demonstrating behavioral habituation for individual songs, and extended the molecular framework correlated with this behavior by investigating the mechanistic Target of Rapamycin (mTOR) signaling cascade. We hypothesized that mTOR may contribute to habituation because it integrates a variety of upstream signals and enhances associative learning, and it crosstalks with another cascade previously associated with habituation, ERK/ZENK. To begin probing for a possible role for mTOR in song recognition learning, we used a combination of song playback paradigms and bidirectional dysregulation of mTORC1 activation. We found that mTOR demonstrates the molecular signatures of a habituation mechanism, and that its manipulation reveals the complexity of processes that may be invoked during nonassociative learning. These results thus expand the molecular targets for habituation studies and raise new questions about neural processing of complex natural signals.

Effects of noxious stimuli on the electroencephalogram of anaesthetised chickens (Gallus gallus domesticus)

The reliable assessment and management of avian pain is important in the context of animal welfare. Overtly expressed signs of pain vary substantially between and within species, strains and individuals, limiting the use of behaviour in pain studies. Similarly, physiological indices of pain can also vary and may be confounded by influence from non-painful stimuli. In mammals, changes in the frequency spectrum of the electroencephalogram (EEG) recorded under light anaesthesia (the minimal anaesthesia model; MAM) have been shown to reliably indicate cerebral responses to noxious stimuli in a range of species. The aim of the current study was to determine whether the MAM can be applied to the study of nociception in birds. Ten chickens were lightly anaesthetised with halothane and their EEG recorded using surface electrodes during the application of supramaximal mechanical, thermal and electrical noxious stimuli. Spectral analysis revealed no EEG responses to any of these stimuli. Given that birds possess the neural apparatus to detect and process pain, and that the applied noxious stimuli elicit behavioural signs of pain in conscious chickens, this lack of response probably relates to methodological limitations. Anatomical differences between the avian and mammalian brains, along with a paucity of knowledge regarding specific sites of pain processing in the avian brain, could mean that EEG recorded from the head surface is insensitive to changes in neural activity in the pain processing regions of the avian brain. Future investigations should examine alternative electrode placement sites, based on avian homologues of the mammalian brain regions involved in pain processing.

Unraveling the Evolutionary Determinants of Sleep

Despite decades of intense study, the functions of sleep are still shrouded in mystery. The difficulty in understanding these functions can be at least partly attributed to the varied manifestations of sleep in different animals. Daily sleep duration can range from 4-20 hrs among mammals, and sleep can manifest throughout the brain, or it can alternate over time between cerebral hemispheres, depending on the species. Ecological factors are likely to have shaped these and other sleep behaviors during evolution by altering the properties of conserved arousal circuits in the brain. Nonetheless, core functions of sleep are likely to have arisen early and to have persisted to the present day in diverse organisms. This review will discuss the evolutionary forces that may be responsible for phylogenetic differences in sleep and the potential core functions that sleep fulfills.

Building a state space for song learning

The songbird system has shed light on how the brain produces precisely timed behavioral sequences, and how the brain implements reinforcement learning (RL). RL is a powerful strategy for learning what action to produce in each state, but requires a unique representation of the states involved in the task. Songbird RL circuitry is thought to operate using a representation of each moment within song syllables, consistent with the sparse sequential bursting of neurons in premotor cortical nucleus HVC. However, such sparse sequences are not present in very young birds, which sing highly variable syllables of random lengths. Here, we review and expand upon a model for how the songbird brain could construct latent sequences to support RL, in light of new data elucidating connections between HVC and auditory cortical areas. We hypothesize that learning occurs via four distinct plasticity processes: 1) formation of 'tutor memory' sequences in auditory areas; 2) formation of appropriately-timed latent HVC sequences, seeded by inputs from auditory areas spontaneously replaying the tutor song; 3) strengthening, during spontaneous replay, of connections from HVC to auditory neurons of corresponding timing in the 'tutor memory' sequence, aligning auditory and motor representations for subsequent song evaluation; and 4) strengthening of connections from premotor neurons to motor output neurons that produce the desired sounds, via well-described song RL circuitry.

Life-Long Neurogenic Activity of Individual Neural Stem Cells and Continuous Growth Establish an Outside-In Architecture in the Teleost Pallium

Spatiotemporal variations of neurogenesis are thought to account for the evolution of brain shape. In the dorsal telencephalon (pallium) of vertebrates, it remains unresolved which ancestral neurogenesis mode prefigures the highly divergent cytoarchitectures that are seen in extant species. To gain insight into this question, we developed genetic tools to generate here the first 4-dimensional (3D + birthdating time) map of pallium construction in the adult teleost zebrafish. Using a Tet-On-based genetic birthdating strategy, we identify a “sequential stacking” construction mode where neurons derived from the zebrafish pallial germinal zone arrange in outside-in, age-related layers from a central core generated during embryogenesis. We obtained no evidence for overt radial or tangential neuronal migrations. Cre-lox-mediated tracing, which included following Brainbow clones, further demonstrates that this process is sustained by the persistent neurogenic activity of individual pallial neural stem cells (NSCs) from embryo to adult. Together, these data demonstrate that the spatiotemporal control of NSC activity is an important driver of the macroarchitecture of the zebrafish adult pallium. This simple mode of pallium construction shares distinct traits with pallial genesis in mammals and non-mammalian amniotes such as birds or reptiles, suggesting that it may exemplify the basal layout from which vertebrate pallial architectures were elaborated.

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Neurons of the teleost pallium are arranged in concentric age-dependent layers

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Neurons of the central pallial domain, Dc, are born during embryogenesis

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Most pallial neurons are generated from ventricular her4-positive radial glia

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The majority of individual pallial radial glia are neurogenic throughout life

Spontaneous Preference for Slowly Moving Objects in Visually Naïve Animals

To perceive the world successfully, newborns need certain types of visual experiences. The development of object recognition, for example, requires visual experience with slowly moving objects. To date, however, it is unknown whether newborns actively seek out the best visual experiences for developing object recognition. To address this question, I used an automated controlled-rearing method to examine whether visually naïve animals (newborn chicks) seek out slowly moving objects. Despite receiving equal exposure to slowly and to quickly rotating objects, the majority of the chicks developed a preference for slowly rotating objects. This preference was robust, producing large effect sizes across objects, experiments, and successive test days. These results indicate that newborn brains rapidly develop mechanisms for orienting young animals toward optimal visual experiences, thus facilitating the development of object recognition. This study also demonstrates that automation can be a valuable tool for studying the origins and development of visual preferences.

Modification of feeding circuits in the evolution of social behavior

Adaptive trade-offs between foraging and social behavior intuitively explain many aspects of individual decision-making. Given the intimate connection between social behavior and feeding/foraging at the behavioral level, we propose that social behaviors are linked to foraging on a mechanistic level, and that modifications of feeding circuits are crucial in the evolution of complex social behaviors. In this Review, we first highlight the overlap between mechanisms underlying foraging and parental care and then expand this argument to consider the manipulation of feeding-related pathways in the evolution of other complex social behaviors. We include examples from diverse taxa to highlight that the independent evolution of complex social behaviors is a variation on the theme of feeding circuit modification.