The human brain: rewired and running hot

The extended neural architecture of human attachment: An fMRI coordinate-based meta-analysis of affiliative studies

Functional imaging studies and clinical evidence indicate that cortical areas relevant to social cognition are closely integrated with evolutionarily conserved basal forebrain structures and neighboring regions, enabling human attachment and affiliative emotions. The neural circuitry of human affiliation is continually being unraveled as functional magnetic resonance imaging (fMRI) becomes increasingly prevalent, with studies examining human brain responses to various attachment figures. However, previous fMRI meta-analyses on affiliative stimuli have encountered challenges, such as low statistical power and the absence of robustness measures. To address these issues, we conducted an exhaustive coordinate-based meta-analysis of 79 fMRI studies, focusing on personalized affiliative stimuli, including one's infants, family, romantic partners, and friends. We employed complementary coordinate-based analyses (Activation Likelihood Estimation and Signed Differential Mapping) and conducted a robustness analysis of the results. Findings revealed cluster convergence in cortical and subcortical structures related to reward and motivation, salience detection, social bonding, and cognition. Our study thoroughly explores the neural correlates underpinning affiliative responses, effectively overcoming the limitations noted in previous meta-analyses. It provides an extensive view of the neural substrates associated with affiliative stimuli, illuminating the intricate interaction between cortical and subcortical regions. Our findings significantly contribute to understanding the neurobiology of human affiliation, expanding the known human attachment circuitry beyond the traditional basal forebrain regions observed in other mammals to include uniquely human isocortical structures.

Characterization of the three-dimensional synaptic and mitochondrial nanoarchitecture within glutamatergic synaptic complexes in postmortem human brain via focused ion beam-scanning electron microscopy

Glutamatergic synapses are the primary site of excitatory synaptic signaling and neural communication in the cerebral cortex. Electron microscopy (EM) studies in non-human model organisms have demonstrated that glutamate synaptic activity and functioning are directly reflected in quantifiable ultrastructural features. Thus, quantitative EM analysis of glutamate synapses in ex vivo preserved human brain tissue has the potential to provide novel insight into in vivo synaptic functioning. However, factors associated with the acquisition and preservation of human brain tissue have resulted in persistent concerns regarding the potential confounding effects of antemortem and postmortem biological processes on synaptic and sub-synaptic ultrastructural features. Thus, we sought to determine how well glutamate synaptic relationships and nanoarchitecture are preserved in postmortem human dorsolateral prefrontal cortex (DLPFC), a region that substantially differs in size and architecture from model systems. Focused ion beam-scanning electron microscopy (FIB-SEM), a powerful volume EM (VEM) approach, was employed to generate high-fidelity, fine-resolution, three-dimensional (3D) micrographic datasets appropriate for quantitative analyses. Using postmortem human DLPFC with a 6-hour postmortem interval, we optimized a tissue preservation and staining workflow that generated samples of excellent ultrastructural preservation and the high-contrast staining intensity required for FIB-SEM imaging. Quantitative analysis of sub-cellular, sub-synaptic and organelle components within glutamate axo-spinous synapses revealed that ultrastructural features of synaptic function and activity were well-preserved within and across individual synapses in postmortem human brain tissue. The synaptic, sub-synaptic and organelle measures were highly consistent with findings from experimental models that are free from antemortem or postmortem effects. Further, dense reconstruction of neuropil revealed a unique, ultrastructurally-complex, spiny dendritic shaft that exhibited features characteristic of neuronal processes with heightened synaptic communication, integration and plasticity. Altogether, our findings provide a critical proof-of-concept that ex vivo VEM analysis provides a valuable and informative means to infer in vivo functioning of human brain.

An energy costly architecture of neuromodulators for human brain evolution and cognition

In comparison to other species, the human brain exhibits one of the highest energy demands relative to body metabolism. It remains unclear whether this heightened energy demand uniformly supports an enlarged brain or if specific signaling mechanisms necessitate greater energy. We hypothesized that the regional distribution of energy demands will reveal signaling strategies that have contributed to human cognitive development. We measured the energy distribution within the brain functional connectome using multimodal brain imaging and found that signaling pathways in evolutionarily expanded regions have up to 67% higher energetic costs than those in sensory-motor regions. Additionally, histology, transcriptomic data, and molecular imaging independently reveal an up-regulation of signaling at G-protein-coupled receptors in energy-demanding regions. Our findings indicate that neuromodulator activity is predominantly involved in cognitive functions, such as reading or memory processing. This study suggests that an up-regulation of neuromodulator activity, alongside increased brain size, is a crucial aspect of human brain evolution.

Lateralization of the hippocampus: A review of molecular, functional, and physiological properties in health and disease

The hippocampus is a part of the brain's medial temporal lobe that is located under the cortex. It belongs to the limbic system and helps to collect and transfer information from short-term to long-term memory, as well as spatial orientation in each mammalian brain hemisphere. After more than two centuries of research in brain asymmetry, the hippocampus has attracted much attention in the study of brain lateralization. The hippocampus is very important in cognitive disorders, related to seizures and dementia, such as epilepsy and Alzheimer's disease. In addition, the motivation to study the hippocampus has increased significantly due to the asymmetry in the activity of the left and right hippocampi in healthy people, and its disruption during some neurological diseases. After a general review of the hippocampal structure and its importance in related diseases, the asymmetry in the brain with a focus on the hippocampus during the growth and maturation of healthy people, as well as the differences created in patients at the molecular, functional, and physiological levels are discussed. Most previous work indicates that the hippocampus is lateralized in healthy people. Also, lateralization at different levels remarkably changes in patients, and it appears that the most complex cognitive disorder is caused by a new dominant asymmetric system.

Epigenetic regulation of human-specific gene expression in the prefrontal cortex

BACKGROUND

Changes in gene expression levels during brain development are thought to have played an important role in the evolution of human cognition. With the advent of high-throughput sequencing technologies, changes in brain developmental expression patterns, as well as human-specific brain gene expression, have been characterized. However, interpreting the origin of evolutionarily advanced cognition in human brains requires a deeper understanding of the regulation of gene expression, including the epigenomic context, along the primate genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) to measure the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), both of which are associated with transcriptional activation in the prefrontal cortex of humans, chimpanzees, and rhesus macaques.

RESULTS

We found a discrete functional association, in which ^H3K4me3HP gain was significantly associated with myelination assembly and signaling transmission, while ^H3K4me3HP loss played a vital role in synaptic activity. Moreover, ^H3K27acHP gain was enriched in interneuron and oligodendrocyte markers, and ^H3K27acHP loss was enriched in CA1 pyramidal neuron markers. Using strand-specific RNA sequencing (ssRNA-seq), we first demonstrated that approximately 7 and 2% of human-specific expressed genes were epigenetically marked by ^H3K4me3HP and ^H3K27acHP, respectively, providing robust support for causal involvement of histones in gene expression. We also revealed the co-activation role of epigenetic modification and transcription factors in human-specific transcriptome evolution. Mechanistically, histone-modifying enzymes at least partially contribute to an epigenetic disturbance among primates, especially for the H3K27ac epigenomic marker. In line with this, peaks enriched in the macaque lineage were found to be driven by upregulated acetyl enzymes.

CONCLUSIONS

Our results comprehensively elucidated a causal species-specific gene-histone-enzyme landscape in the prefrontal cortex and highlighted the regulatory interaction that drove transcriptional activation.

The energetics of childhood: Current knowledge and insights into human variation, evolution, and health

How organisms capture and ultimately use metabolic energy-a limiting resource of life-has profound implications for understanding evolutionary legacies and current patterns of phenotypic variation, adaptation, and health. Energetics research among humans has a rich history in biological anthropology and beyond. The energetics of childhood, however, remains relatively underexplored. This shortcoming is notable given the accepted importance of childhood in the evolution of the unique human life history pattern as well as the known sensitivity of childhood development to local environments and lived experiences. In this review, I have three objectives: (1) To overview current knowledge regarding how children acquire and use energy, highlighting work among diverse human populations and pointing to recent advances and remaining areas of uncertainty; (2) To discuss key applications of this knowledge for understanding human variation, evolution, and health; (3) To recommend future avenues for research. A growing body of evidence supports a model of trade-offs and constraint in childhood energy expenditure. This model, combined with advancements on topics such as the energetics of immune activity, the brain, and the gut, provides insights into the evolution of extended human subadulthood and the nature of variation in childhood development, lifetime phenotype, and health.

Evolution of the Human Brain Can Help Determine Pathophysiology of Neurodevelopmental Disorders

The evolution of humans brought about a co-occurring evolution of the human brain, which is far larger and more complex than that of many other organisms. The brain has evolved characteristically in humans in many respects, including macro-and micro-anatomical changes in the brain structure, changes in gene expression, and cell populations and ratios. These characteristics are essential for the execution of higher functions, such as sociality, language, and cognition, which express humanity, and are thought to have been acquired over evolutionary time. However, with the acquisition of higher functions also comes the risk of the disease in which they fail. This review focuses on human brain evolution and neurodevelopmental disorders (NDDs) and discusses brain development, molecular evolution, and human brain evolution. Discussing the potential for the development and pathophysiology of NDDs acquired by human brain evolution will provide insights into the acquisition and breakdown of higher functions from a new perspective.

Integration of Vestibular and Auditory Information in Ontogenesis

Background: We analyzed the hypothesis that the vestibular and auditory systems are integrative functions. Methods: The study involved 383 children (5.5 ± 2.4 years old). We assessed the conduct of auditory information by recording the auditory brain stem response (ABR), post-rotational nystagmus (PRN), and cervical vestibular evoked myogenic potentials (cVEMP), and calculated the integration of the parameters. All procedures were carried out using the JACOBI 4 software package. Results: We have found out that PRN, ABR, and cVEMP represent three different groups of integrative functions, each of which is conditioned by its own integrative mechanism. We have proven that PRN and ABR are associated with age, but no relationship was found between cVEMP and age. Conclusion: According to our data, the severity of ABR and PRN depended on age, while cVEMP was not associated with age. The functional immaturity of the child’s vestibular system, which probably arose in utero, often becomes apparent only at school when reading and writing must be mastered. These skills require maturity of both the vestibule ocular and vestibule spinal functions of the vestibular system.

My Fear Is Not, and Never Will Be, Your Fear: On Emotions and Feelings in Animals

Do nonhuman animals (henceforth, animals) have emotions, and if so, are these similar to ours? This opinion piece aims to add to the recent debate about this question and provides a critical re-evaluation of what can be concluded about animal and human emotions. Emotions, and their cognitive interpretation, i.e., feelings, serve important survival functions. Emotions, we believe, can exist without feelings and are unconsciously influencing our behavior more than we think, and possibly more so than feelings do. Given that emotions are expressed in body and brain, they can be inferred from these measures. We view feelings primarily as private states, which may be similar across closely related species but remain mostly inaccessible to science. Still, combining data acquired through behavioral observation with data obtained from noninvasive techniques (e.g., eyetracking, thermography, hormonal samples) and from cognitive tasks (e.g., decision-making paradigms, cognitive bias, attentional bias) provides new information about the inner states of animals, and possibly about their feelings as well. Given that many other species show behavioral, neurophysiological, hormonal, and cognitive responses to valenced stimuli equivalent to human responses, it seems logical to speak of animal emotions and sometimes even of animal feelings. At the very least, the contemporary multi-method approach allows us to get closer than ever before. We conclude with recommendations on how the field should move forward.

As soon as there was life, there was danger: the deep history of survival behaviours and the shallower history of consciousness

It is often said that fear is a universal innate emotion that we humans have inherited from our mammalian ancestors by virtue of having inherited conserved features of their nervous systems. Contrary to this common sense-based scientific point of view, I have argued that what we have inherited from our mammalian ancestors, and they from their distal vertebrate ancestors, and they from their chordate ancestors, and so forth, is not a fear circuit. It is, instead, a defensive survival circuit that detects threats, and in response, initiates defensive survival behaviours and supporting physiological adjustments. Seen in this light, the defensive survival circuits of humans and other mammals can be conceptualized as manifestations of an ancient survival function-the ability to detect danger and respond to it-that may in fact predate animals and their nervous systems, and perhaps may go back to the beginning of life. Fear, on the other hand, from my perspective, is a product of cortical cognitive circuits. This conception is not just of academic interest. It also has practical implications, offering clues as to why efforts to treat problems related to fear and anxiety are not more effective, and what might make them better. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.

Genetic Mechanisms Underlying the Evolution of Connectivity in the Human Cortex

One of the most salient features defining modern humans is our remarkable cognitive capacity, which is unrivaled by any other species. Although we still lack a complete understanding of how the human brain gives rise to these unique abilities, the past several decades have witnessed significant progress in uncovering some of the genetic, cellular, and molecular mechanisms shaping the development and function of the human brain. These features include an expansion of brain size and in particular cortical expansion, distinct physiological properties of human neurons, and modified synaptic development. Together they specify the human brain as a large primate brain with a unique underlying neuronal circuit architecture. Here, we review some of the known human-specific features of neuronal connectivity, and we outline how novel insights into the human genome led to the identification of human-specific genetic modifiers that played a role in the evolution of human brain development and function. Novel experimental paradigms are starting to provide a framework for understanding how the emergence of these human-specific genomic innovations shaped the structure and function of neuronal circuits in the human brain.

Species and individual differences and connectional asymmetry of Broca's area in humans and macaques

To reveal the connectional specialization of the Broca's area (or its homologue), voxel-wise inter-species and individual differences, and inter-hemispheric asymmetry were respectively inspected in humans and macaques at both whole-brain connectivity and single tract levels. It was discovered that the developed connectivity blueprint approach is able to localize connectionally comparable voxels between the two species in Broca's area, whereas the quantitative differences between blueprints of locationally or connectionally corresponding voxels enable us to generate inter-hemispheric, inter-subject, and inter-species connectional variabilities, respectively. More importantly, the inter-species and inter-subject variabilities exhibited positive correlation in both two primates, and relatively higher variabilities were detected in the anatomically defined pars triangularis. By contrast, negative relationship was identified between the inter-species variability and hemispheric asymmetry in human brain. In particular, relatively higher asymmetry was revealed in the anatomically defined pars opercularis. Therefore, our novel findings demonstrated that pars triangularis, as compared to pars opercularis, might be a more active area during primate evolution, in which the brain connectivity and possible functions of pars triangularis show relatively higher degree in species specialization, yet lower in hemispheric specialization. Meanwhile, brain connectivity and possible functions of pars opercularis manifested an opposite pattern. At the tract level, functional roles related to the ventral stream in speech comprehension were relatively conservative and bilaterally organized, while those related to the dorsal stream in speech production show relatively higher species and hemispheric specializations.

Unraveling Human Brain Development and Evolution Using Organoid Models

Brain organoids are proving to be physiologically relevant models for studying human brain development in terms of temporal transcriptional signature recapitulation, dynamic cytoarchitectural development, and functional electrophysiological maturation. Several studies have employed brain organoid technologies to elucidate human-specific processes of brain development, gene expression, and cellular maturation by comparing human-derived brain organoids to those of non-human primates (NHPs). Brain organoids have been established from a variety of NHP pluripotent stem cell (PSC) lines and many protocols are now available for generating brain organoids capable of reproducibly representing specific brain region identities. Innumerous combinations of brain region specific organoids derived from different human and NHP PSCs, with CRISPR-Cas9 gene editing techniques and strategies to promote advanced stages of maturation, will successfully establish complex brain model systems for the accurate representation and elucidation of human brain development. Identified human-specific processes of brain development are likely vulnerable to dysregulation and could result in the identification of therapeutic targets or disease prevention strategies. Here, we discuss the potential of brain organoids to successfully model human-specific processes of brain development and explore current strategies for pinpointing these differences.

Divergent connectomic organization delineates genetic evolutionary traits in the human brain

The relationship between human brain connectomics and genetic evolutionary traits remains elusive due to the inherent challenges in combining complex associations within cerebral tissue. In this study, insights are provided about the relationship between connectomics, gene expression and divergent evolutionary pathways from non-human primates to humans. Using in vivo human brain resting-state data, we detected two co-existing idiosyncratic functional systems: the segregation network, in charge of module specialization, and the integration network, responsible for information flow. Their topology was approximated to whole-brain genetic expression (Allen Human Brain Atlas) and the co-localization patterns yielded that neuron communication functionalities-linked to Neuron Projection-were overrepresented cell traits. Homologue-orthologue comparisons using dN/dS-ratios bridged the gap between neurogenetic outcomes and biological data, summarizing the known evolutionary divergent pathways within the Homo Sapiens lineage. Evidence suggests that a crosstalk between functional specialization and information flow reflects putative biological qualities of brain architecture, such as neurite cellular functions like axonal or dendrite processes, hypothesized to have been selectively conserved in the species through positive selection. These findings expand our understanding of human brain function and unveil aspects of our cognitive trajectory in relation to our simian ancestors previously left unexplored.

The Radically Embodied Conscious Cybernetic Bayesian Brain: From Free Energy to Free Will and Back Again

Drawing from both enactivist and cognitivist perspectives on mind, I propose that explaining teleological phenomena may require reappraising both "Cartesian theaters" and mental homunculi in terms of embodied self-models (ESMs), understood as body maps with agentic properties, functioning as predictive-memory systems and cybernetic controllers. Quasi-homuncular ESMs are suggested to constitute a major organizing principle for neural architectures due to their initial and ongoing significance for solutions to inference problems in cognitive (and affective) development. Embodied experiences provide foundational lessons in learning curriculums in which agents explore increasingly challenging problem spaces, so answering an unresolved question in Bayesian cognitive science: what are biologically plausible mechanisms for equipping learners with sufficiently powerful inductive biases to adequately constrain inference spaces? Drawing on models from neurophysiology, psychology, and developmental robotics, I describe how embodiment provides fundamental sources of empirical priors (as reliably learnable posterior expectations). If ESMs play this kind of foundational role in cognitive development, then bidirectional linkages will be found between all sensory modalities and frontal-parietal control hierarchies, so infusing all senses with somatic-motoric properties, thereby structuring all perception by relevant affordances, so solving frame problems for embodied agents. Drawing upon the Free Energy Principle and Active Inference framework, I describe a particular mechanism for intentional action selection via consciously imagined (and explicitly represented) goal realization, where contrasts between desired and present states influence ongoing policy selection via predictive coding mechanisms and backward-chained imaginings (as self-realizing predictions). This embodied developmental legacy suggests a mechanism by which imaginings can be intentionally shaped by (internalized) partially-expressed motor acts, so providing means of agentic control for attention, working memory, imagination, and behavior. I further describe the nature(s) of mental causation and self-control, and also provide an account of readiness potentials in Libet paradigms wherein conscious intentions shape causal streams leading to enaction. Finally, I provide neurophenomenological handlings of prototypical qualia including pleasure, pain, and desire in terms of self-annihilating free energy gradients via quasi-synesthetic interoceptive active inference. In brief, this manuscript is intended to illustrate how radically embodied minds may create foundations for intelligence (as capacity for learning and inference), consciousness (as somatically-grounded self-world modeling), and will (as deployment of predictive models for enacting valued goals).

Evolution of DNA methylation in the human brain

DNA methylation is a critical regulatory mechanism implicated in development, learning, memory, and disease in the human brain. Here we have elucidated DNA methylation changes during recent human brain evolution. We demonstrate dynamic evolutionary trajectories of DNA methylation in cell-type and cytosine-context specific manner. Specifically, DNA methylation in non-CG context, namely CH methylation, has increased (hypermethylation) in neuronal gene bodies during human brain evolution, contributing to human-specific down-regulation of genes and co-expression modules. The effects of CH hypermethylation is particularly pronounced in early development and neuronal subtypes. In contrast, DNA methylation in CG context shows pronounced reduction (hypomethylation) in human brains, notably in cis-regulatory regions, leading to upregulation of downstream genes. We show that the majority of differential CG methylation between neurons and oligodendrocytes originated before the divergence of hominoids and catarrhine monkeys, and harbors strong signal for genetic risk for schizophrenia. Remarkably, a substantial portion of differential CG methylation between neurons and oligodendrocytes emerged in the human lineage since the divergence from the chimpanzee lineage and carries significant genetic risk for schizophrenia. Therefore, recent epigenetic evolution of human cortex has shaped the cellular regulatory landscape and contributed to the increased vulnerability to neuropsychiatric diseases.

Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective

The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.

Evolution of regulatory signatures in primate cortical neurons at cell-type resolution

The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type-specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype-specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergoes subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type-dependent gene-expression programs, and provides a resource for further exploration of human brain evolution and function.

Longitudinal connections and the organization of the temporal cortex in macaques, great apes, and humans

The temporal association cortex is considered a primate specialization and is involved in complex behaviors, with some, such as language, particularly characteristic of humans. The emergence of these behaviors has been linked to major differences in temporal lobe white matter in humans compared with monkeys. It is unknown, however, how the organization of the temporal lobe differs across several anthropoid primates. Therefore, we systematically compared the organization of the major temporal lobe white matter tracts in the human, gorilla, and chimpanzee great apes and in the macaque monkey. We show that humans and great apes, in particular the chimpanzee, exhibit an expanded and more complex occipital-temporal white matter system; additionally, in humans, the invasion of dorsal tracts into the temporal lobe provides a further specialization. We demonstrate the reorganization of different tracts along the primate evolutionary tree, including distinctive connectivity of human temporal gray matter.

Sex differences in the brains of capuchin monkeys (Sapajus [Cebus] apella)

This study reports an analysis of 20 T1-weighted magnetic resonance imaging scans from tufted capuchin monkeys (5 male, 15 female). We carried out a data-driven, whole-brain volumetric analysis on regional gray matter anatomy using voxel-based morphometry. This revealed that males showed statistically significant expansion of a region of the hypothalamus, while females showed significant expansion in a distributed set of regions, including the cerebellum, early visual cortex, and higher-order visual regions spanning occipital and temporal cortex. In order to elucidate the network connectivity of these regions, we employed probabilistic tractography on diffusion tensor imaging data. This showed that the female-enlarged regions connect with distributed association networks across the brain. Notably, this contrasts with rodent studies, where sex differences are focused in deep, ancestral limbic regions involved in the control of reproductive behavior. Additionally, in our data set, for several regions, male and female volumetric measures were completely nonoverlapping. This contrasts with human studies, where sex differences in cortical regions have been reported but are characterized by overlapping rather than divergent male and female values. We suggest that these results can be understood in the context of the different lifetime experiences of males and females, which may produce increased experience-dependent cortical plasticity in capuchins compared to rodents, and in humans compared to capuchins.

Metabolic changes in human brain evolution

Because the human brain is considerably larger than those of other primates, it is not surprising that its energy requirements would far exceed that of any of the species within the order. Recently, the development of stem cell technologies and single-cell transcriptomics provides novel ways to address the question of what specific genomic changes underlie the human brain's unique phenotype. In this review, we consider what is currently known about human brain metabolism using a variety of methods from brain imaging and stereology to transcriptomics. Next, we examine novel opportunities that stem cell technologies and single-cell transcriptomics provide to further our knowledge of human brain energetics. These new experimental approaches provide the ability to elucidate the functional effects of changes in genetic sequence and expression levels that potentially had a profound impact on the evolution of the human brain.

In vivo-assessment of the human temporal network: Evidence for asymmetrical effective connectivity

The human temporal lobe is a multimodal association area which plays a key role in various aspects of cognition, particularly in memory formation and spatial navigation. Functional and anatomical connectivity of temporal structures is thus a subject of intense research, yet by far underexplored in humans due to ethical and technical limitations. We assessed intratemporal cortico-cortical interactions in the living human brain by means of single pulse electrical stimulation, an invasive method allowing mapping effective intracortical connectivity with a high spatiotemporal resolution. Eighteen subjects with normal anterior-mesial temporal MR imaging undergoing intracranial presurgical epilepsy diagnostics with multiple depth electrodes were included. The investigated structures were temporal pole, hippocampus, amygdala and parahippocampal gyrus. Intratemporal cortical connectivity was assessed as a function of amplitude of the early component of the cortico-cortical evoked potentials (CCEP). While the analysis revealed robust interconnectivity between all explored structures, a clear asymmetry in bidirectional connectivity was detected for the hippocampal network and for the connections between the temporal pole and parahippocampal gyrus. The amygdala showed bidirectional asymmetry only to the hippocampus. The provided evidence of asymmetrically weighed intratemporal effective connectivity in humans in vivo is important for understanding of functional interactions within the temporal lobe since asymmetries in the brain connectivity define hierarchies in information processing. The findings are in exact accord with the anatomical tracing studies in non-human primates and open a translational route for interventions employing modulation of temporal lobe function.

Reverse engineering human brain evolution using organoid models

Primate brains vary dramatically in size and organization, but the genetic and developmental basis for these differences has been difficult to study due to lack of experimental models. Pluripotent stem cells and brain organoids provide a potential opportunity for comparative and functional studies of evolutionary differences, particularly during the early stages of neurogenesis. However, many challenges remain, including isolating stem cell lines from additional great ape individuals and species to capture the breadth of ape genetic diversity, improving the reproducibility of organoid models to study evolved differences in cell composition and combining multiple brain regions to capture connectivity relationships. Here, we describe strategies for identifying evolved developmental differences between humans and non-human primates and for isolating the underlying cellular and genetic mechanisms using comparative analyses, chimeric organoid culture, and genome engineering. In particular, we focus on how organoid models could ultimately be applied beyond studies of progenitor cell evolution to decode the origin of recent changes in cellular organization, connectivity patterns, myelination, synaptic development, and physiology that have been implicated in human cognition.

Structural Variability Across the Primate Brain: A Cross-Species Comparison

A large amount of variability exists across human brains; revealed initially on a small scale by postmortem studies and, more recently, on a larger scale with the advent of neuroimaging. Here we compared structural variability between human and macaque monkey brains using grey and white matter magnetic resonance imaging measures. The monkey brain was overall structurally as variable as the human brain, but variability had a distinct distribution pattern, with some key areas showing high variability. We also report the first evidence of a relationship between anatomical variability and evolutionary expansion in the primate brain. This suggests a relationship between variability and stability, where areas of low variability may have evolved less recently and have more stability, while areas of high variability may have evolved more recently and be less similar across individuals. We showed specific differences between the species in key areas, including the amount of hemispheric asymmetry in variability, which was left-lateralized in the human brain across several phylogenetically recent regions. This suggests that cerebral variability may be another useful measure for comparison between species and may add another dimension to our understanding of evolutionary mechanisms.

Genes with human-specific features are primarily involved with brain, immune and metabolic evolution

Background

Humans have adapted to widespread changes during the past 2 million years in both environmental and lifestyle factors. This is evident in overall body alterations such as average height and brain size. Although we can appreciate the uniqueness of our species in many aspects, molecular variations that drive such changes are far from being fully known and explained. Comparative genomics is able to determine variations in genomic sequence that may provide functional information to better understand species-specific adaptations. A large number of human-specific genomic variations have been reported but no currently available dataset comprises all of these, a problem which contributes to hinder progress in the field.

Results

Here we critically update high confidence human-specific genomic variants that mostly associate with protein-coding regions and find 856 related genes. Events that create such human-specificity are mainly gene duplications, the emergence of novel gene regions and sequence and structural alterations. Functional analysis of these human-specific genes identifies adaptations to brain, immune and metabolic systems to be highly involved. We further show that many of these genes may be functionally associated with neural activity and generating the expanded human cortex in dynamic spatial and temporal contexts.

Conclusions

This comprehensive study contributes to the current knowledge by considerably updating the number of human-specific genes following a critical bibliographic survey. Human-specific genes were functionally assessed for the first time to such extent, thus providing unique information. Our results are consistent with environmental changes, such as immune challenges and alterations in diet, as well as neural sophistication, as significant contributors to recent human evolution.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2886-2) contains supplementary material, which is available to authorized users.

Organization of extrastriate and temporal cortex in chimpanzees compared to humans and macaques

There is evidence for enlargement of association cortex in humans compared to other primate species. Expansion of temporal association cortex appears to have displaced extrastriate cortex posteriorly and inferiorly in humans compared to macaques. However, the details of the organization of these recently expanded areas are still being uncovered. Here, we used diffusion tractography to examine the organization of extrastriate and temporal association cortex in chimpanzees, humans, and macaques. Our goal was to characterize the organization of visual and auditory association areas with respect to their corresponding primary areas (primary visual cortex and auditory core) in humans and chimpanzees. We report three results: (1) Humans, chimpanzees, and macaques show expected retinotopic organization of primary visual cortex (V1) connectivity to V2 and to areas immediately anterior to V2; (2) In contrast to macaques, chimpanzee and human V1 shows apparent connectivity with lateral, inferior, and anterior temporal regions, beyond the retinotopically organized extrastriate areas; (3) Also in contrast to macaques, chimpanzee and human auditory core shows apparent connectivity with temporal association areas, with some important differences between humans and chimpanzees. Diffusion tractography reconstructs diffusion patterns that reflect white matter organization, but does not definitively represent direct anatomical connectivity. Therefore, it is important to recognize that our findings are suggestive of species differences in long-distance white matter organization rather than demonstrations of direct connections. Our data support the conclusion that expansion of temporal association cortex, and the resulting posterior displacement of extrastriate cortex, occurred in the human lineage after its separation from the chimpanzee lineage. It is possible, however, that some expansion of the temporal lobe occurred prior to the separation of humans and chimpanzees, reflected in the reorganization of long white matter tracts in the temporal lobe that connect occipital areas to the fusiform gyrus, middle temporal gyrus, and anterior temporal lobe.

Commercial Rodents in America: Standard Animals, Model Animals, and Biological Diversity

Rodents as standardized test animals were developed for commercial distribution in the USA between 1910 and the 1930s. The selective breeding of rats (Rattus norvegicus) and pure-bred mice (Mus musculus) at the Wistar Institute and the Jackson Memorial Laboratories eventually led to a decline in the diversity of species used in American medical and life sciences. The early driving figures, science administrator Milton Greenman and the scientists Henry Donaldson and Clarence Little, sought to standardize animals to render science and its application to humanity more precise. But their efforts were exaggerated in the USA through an expanding industrial and engineering ideal, culminating in a preference for Big Science. I explore the nineteenth century origins of this ideal in Emil Du Bois-Reymond's neurophysiology. This foundation later merged with increasing standardization, American commercialism, and the success of Big Science to transform animal laboratory "standards" into "model animals." Recent accounts of research with commercially bred mice reveal how findings can be co-constructed using human clinical data, as animal research is applied to humans. The neglect of evolutionary perspectives and the dominance of "models" may even have begun with the government's post-war emphasis on funding greater species access for large-scale biomedical research.

Understanding the Higher-Order Approach to Consciousness

The higher-order theory (HOT) of consciousness has often been misunderstood by critics. Here, we clarify its position on several issues, and distinguish it from other views, such as the global workspace theory (GWT) and early sensory models (e.g., first-order local recurrency theories). For example, HOT has been criticized for overintellectualizing consciousness. We show that, while higher-order states are cognitively assembled, the requirements are in fact considerably less than often presumed. In this sense, HOT may be viewed as an intermediate position between GWT and early sensory views. We also clarify that most proponents of HOT do not stipulate consciousness as equivalent to metacognition or confidence. Furthermore, compared with other existing theories, HOT can arguably account better for complex everyday experiences, such as emotions and episodic memories. This makes HOT particularly useful as a framework for conceptualizing pathological mental states.

Blood-brain barrier and innate immunity in the pathogenesis of Alzheimer's disease

The pathogenesis of Alzheimer's disease (AD) is only partly understood. This is the probable reason why significant efforts to treat or prevent AD have been unsuccessful. In fact, as of April 2019, there have been 2094 studies registered for AD on the clinicaltrials.gov U.S. National Library of Science web page, of which only a few are still ongoing. In AD, abnormal accumulation of amyloid and tau proteins in the brain are thought to begin 10-20 years before the onset of overt symptoms, suggesting that interventions designed to prevent pathological amyloid and tau accumulation may be more effective than attempting to reverse a pathology once it is established. However, to be successful, such early interventions need to be selectively administered to individuals who will likely develop the disease long before the symptoms occur. Therefore, it is critical to identify early biomarkers that are strongly predictive of AD. Currently, patients are diagnosed on the basis of a variety of clinical scales, neuropsychological tests, imaging and laboratory modalities, but definitive diagnosis can be made only by postmortem assessment of underlying neuropathology. People suffering from AD thus may be misdiagnosed clinically with other primary causes of dementia, and vice versa, thereby also reducing the power of clinical trials. The amyloid cascade hypothesis fits well for the familial cases of AD with known mutations, but is not sufficient to explain sporadic, late-onset AD (LOAD) that accounts for over 95% of all cases. Since the earliest descriptions of AD there have been neuropathological features described other than amyloid plaques (AP) and neurofibrillary tangles (NFT), most notably gliosis and neuroinflammation. However, it is only recently that genetic and experimental studies have implicated microglial dysfunction as a causal factor for AD, as opposed to a merely biological response of its accumulation around AP. Additionally, many studies have suggested the importance of changes in blood-brain barrier (BBB) permeability in the pathogenesis of AD. Here we suggest how these less investigated aspects of the disease that have gained increased attention in recent years may contribute mechanistically to the development of lesions and symptoms of AD.

Human paleoneurology: Shaping cortical evolution in fossil hominids

Evolutionary neuroanatomy must integrate two different sources of information, namely from fossil and from living species. Fossils supply information concerning the process of evolution, whereas living species supply information on the product of evolution. Unfortunately, the fossil record is partial and fragmented, and often cannot support validations for specific evolutionary hypotheses. Living species can provide more comprehensive indications, but they do not represent ancestral groups or primitive forms. Macaques or chimpanzees are frequently used as proxy for human ancestral conditions, despite the fact they are divergent and specialized lineages, with their own biological features. Similarly, in paleoanthropology independent lineages (such as Neanderthals) should not be confused with ancestral modern human stages. In this comparative framework, paleoneurology deals with the analysis of the endocranial cavity in extinct species, in order to make inferences on brain evolution. A main target of this field is to distinguish the endocranial variations due to brain changes, from those due to cranial constraints. Digital anatomy and computed morphometrics have provided major advances in this field. However, brains and endocasts can be hard to analyze with geometrical models, because of uncertainties due to the localization of cortical landmarks and boundaries. The study of the evolution of the parietal cortex supplies an interesting case-study in which paleontological and neontological data can integrate and test evolutionary hypotheses based on multiple sources of evidence. The relationships with visuospatial functions and brain-body-tool integration stress further that the analysis of the cognitive system should go beyond the neural boundaries of the brain.

The Japan Monkey Centre Primates Brain Imaging Repository for comparative neuroscience: an archive of digital records including records for endangered species

Advances in magnetic resonance imaging (MRI) and computational analysis technology have enabled comparisons among various primate brains in a three-dimensional electronic format. Results from comparative studies provide information about common features across primates and species-specific features of neuroanatomy. Investigation of various species of non-human primates is important for understanding such features, but the majority of comparative MRI studies have been based on experimental primates, such as common marmoset, macaques, and chimpanzee. A major obstacle has been the lack of a database that includes non-experimental primates' brain MRIs. To facilitate scientific discoveries in the field of comparative neuroanatomy and brain evolution, we launched a collaborative project to develop an open-resource repository of non-human primate brain images obtained using ex vivo MRI. As an initial open resource, here we release a collection of structural MRI and diffusion tensor images obtained from 12 species: pygmy marmoset, owl monkey, white-fronted capuchin, crab-eating macaque, Japanese macaque, bonnet macaque, toque macaque, Sykes' monkey, red-tailed monkey, Schmidt's guenon, de Brazza's guenon, and lar gibbon. Sixteen postmortem brain samples from the 12 species, stored in the Japan Monkey Centre (JMC), were scanned using a 9.4-T MRI scanner and made available through the JMC collaborative research program ( http://www.j-monkey.jp/BIR/index_e.html ). The expected significant contributions of the JMC Primates Brain Imaging Repository include (1) resources for comparative neuroscience research, (2) preservation of various primate brains, including those of endangered species, in a permanent digital form, (3) resources with higher resolution for identifying neuroanatomical features, compared to previous MRI atlases, (4) resources for optimizing methods of scanning large fixed brains, and (5) references for veterinary neuroradiology. User-initiated research projects beyond these contributions are also anticipated.

Growing a social brain

It has long been assumed that social animals, such as humans, are born with a brain system that has evolved to support social affiliation. However, the evidence does not necessarily support this assumption. Alternatively, social animals can be defined as those who cannot survive alone and rely on members from their group to regulate their ongoing physiology (or allostasis). The rather simple evolutionary constraint of social dependency for survival can be sufficient to make the social environment vitally salient, and to provide the ultimate driving force for socially crafted brain development and learning. In this Perspective, we propose a framework for sociality and specify a set of hypotheses on the mechanisms of social development and underlying neural systems. The theoretical shift proposed here implies that profound human characteristics, including but not limited to sociality, are acquired at an early age, while social interactions provide key wiring instructions that determine brain development.

Hearing and orally mimicking different acoustic-semantic categories of natural sound engage distinct left hemisphere cortical regions

Oral mimicry is thought to represent an essential process for the neurodevelopment of spoken language systems in infants, the evolution of language in hominins, and a process that could possibly aid recovery in stroke patients. Using functional magnetic resonance imaging (fMRI), we previously reported a divergence of auditory cortical pathways mediating perception of specific categories of natural sounds. However, it remained unclear if or how this fundamental sensory organization by the brain might relate to motor output, such as sound mimicry. Here, using fMRI, we revealed a dissociation of activated brain regions preferential for hearing with the intent to imitate and the oral mimicry of animal action sounds versus animal vocalizations as distinct acoustic-semantic categories. This functional dissociation may reflect components of a rudimentary cortical architecture that links systems for processing acoustic-semantic universals of natural sound with motor-related systems mediating oral mimicry at a category level. The observation of different brain regions involved in different aspects of oral mimicry may inform targeted therapies for rehabilitation of functional abilities after stroke.

Quantitative assessment of prefrontal cortex in humans relative to nonhuman primates

A longstanding controversy in neuroscience pertains to differences in human prefrontal cortex (PFC) compared with other primate species; specifically, is human PFC disproportionately large? Distinctively human behavioral capacities related to higher cognition and affect presumably arose from evolutionary modifications since humans and great apes diverged from a common ancestor about 6–8 Mya. Accurate determination of regional differences in the amount of cortical gray and subcortical white matter content in humans, great apes, and Old World monkeys can further our understanding of the link between structure and function of the human brain. Using tissue volume analyses, we show a disproportionately large amount of gray and white matter corresponding to PFC in humans compared with nonhuman primates.

Humans have the largest cerebral cortex among primates. The question of whether association cortex, particularly prefrontal cortex (PFC), is disproportionately larger in humans compared with nonhuman primates is controversial: Some studies report that human PFC is relatively larger, whereas others report a more uniform PFC scaling. We address this controversy using MRI-derived cortical surfaces of many individual humans, chimpanzees, and macaques. We present two parcellation-based PFC delineations based on cytoarchitecture and function and show that a previously used morphological surrogate (cortex anterior to the genu of the corpus callosum) substantially underestimates PFC extent, especially in humans. We find that the proportion of cortical gray matter occupied by PFC in humans is up to 1.9-fold greater than in macaques and 1.2-fold greater than in chimpanzees. The disparity is even more prominent for the proportion of subcortical white matter underlying the PFC, which is 2.4-fold greater in humans than in macaques and 1.7-fold greater than in chimpanzees.

Of Men and Mice: Modeling the Fragile X Syndrome

The Fragile X Syndrome (FXS) is one of the most common forms of inherited intellectual disability in all human societies. Caused by the transcriptional silencing of a single gene, the fragile x mental retardation gene FMR1, FXS is characterized by a variety of symptoms, which range from mental disabilities to autism and epilepsy. More than 20 years ago, a first animal model was described, the Fmr1 knock-out mouse. Several other models have been developed since then, including conditional knock-out mice, knock-out rats, a zebrafish and a drosophila model. Using these model systems, various targets for potential pharmaceutical treatments have been identified and many treatments have been shown to be efficient in preclinical studies. However, all attempts to turn these findings into a therapy for patients have failed thus far. In this review, I will discuss underlying difficulties and address potential alternatives for our future research.

Know Thyself: Well-Being and Subjective Experience

The study of subjective experience represents a significant challenge to cognitive scientists, but one that is beginning to be increasingly addressed. Subjectivity renders experience less amenable to traditional objective scientific measurements than other subject matter. Our authors believe that when seeking to understand the mind, subjectivity must ultimately be investigated and understood.

Using Human iPSC-Derived Neurons to Uncover Activity-Dependent Non-Coding RNAs

Humans are arguably the most complex organisms present on Earth with their ability to imagine, create, and problem solve. As underlying mechanisms enabling these capacities reside in the brain, it is not surprising that the brain has undergone an extraordinary increase in size and complexity within the last few million years. Human induced pluripotent stem cells (hiPSCs) can be differentiated into many cell types that were virtually inaccessible historically, such as neurons. Here, we used hiPSC-derived neurons to investigate the cellular response to activation at the transcript level. Neuronal activation was performed with potassium chloride (KCl) and its effects were assessed by RNA sequencing. Our results revealed the involvement of long non-coding RNAs and human-specific genetic variants in response to neuronal activation and help validate hiPSCs as a valuable resource for the study of human neuronal networks. In summary, we find that genes affected by KCl-triggered activation are implicated in pathways that drive cell proliferation, differentiation, and the emergence of specialized morphological features. Interestingly, non-coding RNAs of various classes are amongst the most highly expressed genes in activated hiPSC-derived neurons, thus suggesting these play crucial roles in neural pathways and may significantly contribute to the unique functioning of the human brain.

Auditory object perception: A neurobiological model and prospective review

Interaction with the world is a multisensory experience, but most of what is known about the neural correlates of perception comes from studying vision. Auditory inputs enter cortex with its own set of unique qualities, and leads to use in oral communication, speech, music, and the understanding of emotional and intentional states of others, all of which are central to the human experience. To better understand how the auditory system develops, recovers after injury, and how it may have transitioned in its functions over the course of hominin evolution, advances are needed in models of how the human brain is organized to process real-world natural sounds and "auditory objects". This review presents a simple fundamental neurobiological model of hearing perception at a category level that incorporates principles of bottom-up signal processing together with top-down constraints of grounded cognition theories of knowledge representation. Though mostly derived from human neuroimaging literature, this theoretical framework highlights rudimentary principles of real-world sound processing that may apply to most if not all mammalian species with hearing and acoustic communication abilities. The model encompasses three basic categories of sound-source: (1) action sounds (non-vocalizations) produced by 'living things', with human (conspecific) and non-human animal sources representing two subcategories; (2) action sounds produced by 'non-living things', including environmental sources and human-made machinery; and (3) vocalizations ('living things'), with human versus non-human animals as two subcategories therein. The model is presented in the context of cognitive architectures relating to multisensory, sensory-motor, and spoken language organizations. The models' predictive values are further discussed in the context of anthropological theories of oral communication evolution and the neurodevelopment of spoken language proto-networks in infants/toddlers. These phylogenetic and ontogenetic frameworks both entail cortical network maturations that are proposed to at least in part be organized around a number of universal acoustic-semantic signal attributes of natural sounds, which are addressed herein.

Ultrastructural analysis of parvalbumin synapses in human dorsolateral prefrontal cortex

Coordinated activity of neural circuitry in the primate dorsolateral prefrontal cortex (DLPFC) supports a range of cognitive functions. Altered DLPFC activation is implicated in a number of human psychiatric and neurological illnesses. Proper DLPFC activity is, in part, maintained by two populations of neurons containing the calcium-binding protein parvalbumin (PV): local inhibitory interneurons that form Type II synapses, and long-range glutamatergic inputs from the thalamus that form Type I synapses. Understanding the contributions of each PV neuronal population to human DLPFC function requires a detailed examination of their anatomical properties. Consequently, we performed an electron microscopic analysis of (1) the distribution of PV immunoreactivity within the neuropil, (2) the properties of dendritic shafts of PV-IR interneurons, (3) Type II PV-IR synapses from PV interneurons, and (4) Type I PV-IR synapses from long-range projections, within the superficial and middle laminar zones of the human DLPFC. In both laminar zones, Type II PV-IR synapses from interneurons comprised ∼60% of all PV-IR synapses, and Type I PV-IR synapses from putative thalamocortical terminals comprised the remaining ∼40% of PV-IR synapses. Thus, the present study suggests that innervation from PV-containing thalamic nuclei extends across superficial and middle layers of the human DLPFC. These findings contrast with previous ultrastructural studies in monkey DLPFC where Type I PV-IR synapses were not identified in the superficial laminar zone. The presumptive added modulation of DLPFC circuitry by the thalamus in human may contribute to species-specific, higher-order functions.

The Lesion Analysis of Cholinergic Neurons in 5XFAD Mouse Model in the Three-Dimensional Level of Whole Brain

Cholinergic system is very important for many higher brain functions, including learning and memory. Cholinergic neurons, especially those in the basal forebrain, are specifically susceptible in some neurodegenerative diseases, such as in Alzheimer's disease (AD). Here, we studied the cholinergic system lesion effects of five familial AD mutations in 5XFAD mice, a transgenic mouse model of AD. Although the cholinergic system has been studied in this mouse model, the cholinergic deficits in AD mice have never been systematically mapped in a whole-brain three-dimensional (3D) reconstruction. Using the 3D reconstruction technology combined with immunohistochemistry (3D-IHC) and design-based stereology, we comprehensively compared the differences of the cholinergic neurons and fibers between the 5XFAD mice and C57BL/6 control mice at different age. Here, we found that the lesion of cholinergic fibers occurred earlier than the cholinergic neuron loss in 5XFAD mice. The cholinergic fiber lesions in the AD mice started sequentially in amygdala, cortex, hippocampus, and then basal forebrain. However, the basal forebrain was the first brain region observed with cholinergic neuron loss at the age of 9 months in 5XFAD mice, whereas such phenomenon first occurred at the age of 15 months in C57BL/6 control mice. Moreover, using 3D reconstruction to compare the lesion of cholinergic system of aged 5XFAD and C57BL/6 control mice, it is intuitive to notice the pathologic regions and severity of lesion. Therefore, the 3D-IHC provides detailed overview of the cholinergic neurons in the whole mouse brain, which will contribute to the study of the developing and pathologic mouse brain.

Divergent Human Cortical Regions for Processing Distinct Acoustic-Semantic Categories of Natural Sounds: Animal Action Sounds vs. Vocalizations

A major gap in our understanding of natural sound processing is knowledge of where or how in a cortical hierarchy differential processing leads to categorical perception at a semantic level. Here, using functional magnetic resonance imaging (fMRI) we sought to determine if and where cortical pathways in humans might diverge for processing action sounds vs. vocalizations as distinct acoustic-semantic categories of real-world sound when matched for duration and intensity. This was tested by using relatively less semantically complex natural sounds produced by non-conspecific animals rather than humans. Our results revealed a striking double-dissociation of activated networks bilaterally. This included a previously well described pathway preferential for processing vocalization signals directed laterally from functionally defined primary auditory cortices to the anterior superior temporal gyri, and a less well-described pathway preferential for processing animal action sounds directed medially to the posterior insulae. We additionally found that some of these regions and associated cortical networks showed parametric sensitivity to high-order quantifiable acoustic signal attributes and/or to perceptual features of the natural stimuli, such as the degree of perceived recognition or intentional understanding. Overall, these results supported a neurobiological theoretical framework for how the mammalian brain may be fundamentally organized to process acoustically and acoustic-semantically distinct categories of ethologically valid, real-world sounds.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions.

Fossil skulls reveal that blood flow rate to the brain increased faster than brain volume during human evolution

The evolution of human cognition has been inferred from anthropological discoveries and estimates of brain size from fossil skulls. A more direct measure of cognition would be cerebral metabolic rate, which is proportional to cerebral blood flow rate (perfusion). The hominin cerebrum is supplied almost exclusively by the internal carotid arteries. The sizes of the foramina that transmitted these vessels in life can be measured in hominin fossil skulls and used to calculate cerebral perfusion rate. Perfusion in 11 species of hominin ancestors, from Australopithecus to archaic Homo sapiens, increases disproportionately when scaled against brain volume (the allometric exponent is 1.41). The high exponent indicates an increase in the metabolic intensity of cerebral tissue in later Homo species, rather than remaining constant (1.0) as expected by a linear increase in neuron number, or decreasing according to Kleiber's Law (0.75). During 3 Myr of hominin evolution, cerebral tissue perfusion increased 1.7-fold, which, when multiplied by a 3.5-fold increase in brain size, indicates a 6.0-fold increase in total cerebral blood flow rate. This is probably associated with increased interneuron connectivity, synaptic activity and cognitive function, which all ultimately depend on cerebral metabolic rate.

Resolving the organization of the third tier visual cortex in primates: a hypothesis-based approach

As highlighted by several contributions to this special issue, there is still ongoing debate about the number, exact location, and boundaries of the visual areas located in cortex immediately rostral to the second visual area (V2), i.e., the “third tier” visual cortex, in primates. In this review, we provide a historical overview of the main ideas that have led to four models of third tier cortex organization, which are at the center of today's debate. We formulate specific predictions of these models, and compare these predictions with experimental evidence obtained primarily in New World primates. From this analysis, we conclude that only one of these models (the “multiple-areas” model) can accommodate the breadth of available experimental evidence. According to this model, most of the third tier cortex in New World primates is occupied by two distinct areas, both representing the full contralateral visual quadrant: the dorsomedial area (DM), restricted to the dorsal half of the third visual complex, and the ventrolateral posterior area (VLP), occupying its ventral half and a substantial fraction of its dorsal half. DM belongs to the dorsal stream of visual processing, and overlaps with macaque parietooccipital (PO) area (or V6), whereas VLP belongs to the ventral stream and overlaps considerably with area V3 proposed by others. In contrast, there is substantial evidence that is inconsistent with the concept of a single elongated area V3 lining much of V2. We also review the experimental evidence from macaque monkey and humans, and propose that, once the data are interpreted within an evolutionary-developmental context, these species share a homologous (but not necessarily identical) organization of the third tier cortex as that observed in New World monkeys. Finally, we identify outstanding issues, and propose experiments to resolve them, highlighting in particular the need for more extensive, hypothesis-driven investigations in macaque and humans.

Comparative Connectomics

We introduce comparative connectomics, the quantitative study of cross-species commonalities and variations in brain network topology that aims to discover general principles of network architecture of nervous systems and the identification of species-specific features of brain connectivity. By comparing connectomes derived from simple to more advanced species, we identify two conserved themes of wiring: the tendency to organize network topology into communities that serve specialized functionality and the general drive to enable high topological integration by means of investment of neural resources in short communication paths, hubs, and rich clubs. Within the space of wiring possibilities that conform to these common principles, we argue that differences in connectome organization between closely related species support adaptations in cognition and behavior.