Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns

Consciousness makes sense in the light of evolution

I believe consciousness is a property of advanced nervous systems, and as such a product of evolution. Thus, to understand consciousness we need to describe the trajectory leading to its evolution and the selective advantages conferred. A deeper understanding of the neurology would be a significant contribution, but other advanced functions, such as hearing and vision, are explained with a comparable lack of detailed knowledge of the brain processes responsible. In this paper, I try to add details and credence to a previously suggested, evolution-based model of consciousness. According to this model, the feature started to evolve in early amniotes (reptiles, birds, and mammals) some 320 million years ago. The reason was the introduction of feelings as a strategy for making behavioral decisions.

The putative role of the habenula in animal migration

BACKGROUND

When an addicted animal seeks a specific substance, it is based on the perception of internal and external cues that strongly motivate to pursue the acquisition of that compound. In essence, a similar process acts out when an animal leaves its present area to begin its circannual migration. This review article examines the existence of scientific evidence for possible relatedness of migration and addiction by influencing Dorsal Diencephalic Conduction System (DDCS) including the habenula.

METHODS

For this review especially the databases of Pubmed and Embase were frequently and non-systematically searched.

RESULTS

The mechanisms of bird migration have been thoroughly investigated. Especially the mechanism of the circannual biorhythm and its associated endocrine regulation has been well elucidated. A typical behavior called "Zugunruhe" marks the moment of leaving in migratory birds. The role of magnetoreception in navigation has also been clarified in recent years. However, how bird migration is regulated at the neuronal level in the forebrain is not well understood. Among mammals, marine mammals are most similar to birds. They use terrestrial magnetic field when navigating and often bridge long distances between breeding and foraging areas. Population migration is further often seen among the large hoofed mammals in different parts of the world. Importantly, learning processes and social interactions with conspecifics play a major role in these ungulates. Considering the evolutionary development of the forebrain in vertebrates, it can be postulated that the DDCS plays a central role in regulating the readiness and intensity of essential (emotional) behaviors. There is manifold evidence that this DDCS plays an important role in relapse to abuse after prolonged periods of abstinence from addictive behavior. It is also possible that the DDCS plays a role in navigation.

CONCLUSIONS

The role of the DDCS in the neurobiological regulation of bird migration has hardly been investigated. The involvement of this system in relapse to addiction in mammals might suggest to change this. It is recommended that particularly during "Zugunruhe" the role of neuronal regulation via the DDCS will be further investigated.

Variations in touch representation in the hummingbird and zebra finch forebrain

Somatosensation is essential for animals to perceive the external world through touch, allowing them to detect physical contact, temperature, pain, and body position. Studies on rodent vibrissae have highlighted the organization and processing in mammalian somatosensory pathways.1,2 Comparative research across vertebrates is vital for understanding evolutionary influences and ecological specialization on somatosensory systems. Birds, with their diverse morphologies, sensory abilities, and behaviors, serve as ideal models for investigating the evolution of somatosensation. Prior studies have uncovered tactile-responsive areas within the avian telencephalon, particularly in pigeons,3,4,5,6 parrots,7 and finches,8 but variations in somatosensory maps and responses across avian species are not fully understood. This study aims to explore somatotopic organization and neural coding in the telencephalon of Anna's hummingbirds (Calypte anna) and zebra finches (Taeniopygia guttata) by using in vivo extracellular electrophysiology to record activity in response to controlled tactile stimuli on various body regions. These findings reveal unique representations of body regions across distinct forebrain somatosensory nuclei, indicating significant differences in the extent of areas dedicated to certain body surfaces, which may correlate with their behavioral importance.

The role of lateral hypothalamic nucleus in mediating locomotive behaviors in pigeons (Columba livia)

The lateral hypothalamic nucleus (LHy) is located in the dorsolateral hypothalamus of birds, and it is essential to many life processes. However, limited information is available about the role of LHy in mediating locomotive behaviors. In this work, we investigated the structure and function of LHy in pigeons (Columba livia) by Nissl staining, immunohistochemical (IHC) staining, insituhybridization (ISH) staining and constant current stimulation methods. The results showed that LHy appears crescent in shape, and three-dimensional coordinate value range of LHy is: A: 5.0-8.0 mm, L: 0.7-1.2 mm, D: 9.5-10.3 mm. The dopaminergic neurons in LHy were distributed in small amount and concentrated manner, while the glutamatergic neurons were distributed in a large number and uniform manner. The distribution of the above two neurons at each coronal level showed a significant positive correlation (R2 = 0.7516, P < 0.001). Our work demonstrated that LHy mainly mediates forward movement (P < 0.01) and ipsilateral lateral movement (P < 0.001), and these movements were significantly effected by electrical stimulation intensity. Our results showed that LHy can mediate the generation of directional behavior and this will provide technical support for the study of locomotor behavior regulation in birds.

Auditory discrimination learning and acoustic cue weighing in female zebra finches with localized FoxP1 knockdowns

Rare disruptions of the transcription factor FOXP1 are implicated in a human neurodevelopmental disorder characterized by autism and/or intellectual disability with prominent problems in speech and language abilities. Avian orthologues of this transcription factor are evolutionarily conserved and highly expressed in specific regions of songbird brains, including areas associated with vocal production learning and auditory perception. Here, we investigated possible contributions of FoxP1 to song discrimination and auditory perception in juvenile and adult female zebra finches. They received lentiviral knockdowns of FoxP1 in one of two brain areas involved in auditory stimulus processing, HVC (proper name) or CMM (caudomedial mesopallium). Ninety-six females, distributed over different experimental and control groups were trained to discriminate between two stimulus songs in an operant Go/Nogo paradigm and subsequently tested with an array of stimuli. This made it possible to assess how well they recognized and categorized altered versions of training stimuli and whether localized FoxP1 knockdowns affected the role of different features during discrimination and categorization of song. Although FoxP1 expression was significantly reduced by the knockdowns, neither discrimination of the stimulus songs nor categorization of songs modified in pitch, sequential order of syllables or by reversed playback were affected. Subsequently, we analyzed the full dataset to assess the impact of the different stimulus manipulations for cue weighing in song discrimination. Our findings show that zebra finches rely on multiple parameters for song discrimination, but with relatively more prominent roles for spectral parameters and syllable sequencing as cues for song discrimination.NEW & NOTEWORTHY In humans, mutations of the transcription factor FoxP1 are implicated in speech and language problems. In songbirds, FoxP1 has been linked to male song learning and female preference strength. We found that FoxP1 knockdowns in female HVC and caudomedial mesopallium (CMM) did not alter song discrimination or categorization based on spectral and temporal information. However, this large dataset allowed to validate different cue weights for spectral over temporal information for song recognition.

Parallel executive pallio-motor loops in the pigeon brain

A core component of the avian pallial cognitive network is the multimodal nidopallium caudolaterale (NCL) that is considered to be analogous to the mammalian prefrontal cortex (PFC). The NCL plays a key role in a multitude of executive tasks such as working memory, decision-making during navigation, and extinction learning in complex learning environments. Like the PFC, the NCL is positioned at the transition from ascending sensory to descending motor systems. For the latter, it sends descending premotor projections to the intermediate arcopallium (AI) and the medial striatum (MSt). To gain detailed insight into the organization of these projections, we conducted several retrograde and anterograde tracing experiments. First, we tested whether NCL neurons projecting to AI (NCLarco neurons) and MSt (NCLMSt neurons) are constituted by a single neuronal population with bifurcating neurons, or whether they form two distinct populations. Here, we found two distinct projection patterns to both target areas that were associated with different morphologies. Second, we revealed a weak topographic projection toward the medial and lateral striatum and a strong topographic projection toward AI with clearly distinguishable sensory termination fields. Third, we investigated the relationship between the descending NCL pathways to the arcopallium with those from the hyperpallium apicale, which harbors a second major descending pathway of the avian pallium. We embed our findings within a system of parallel pallio-motor loops that carry information from separate sensory modalities to different subpallial systems. Our results also provide insights into the evolution of the avian motor system from which, possibly, the song system has emerged.

Brain surface morphology and ecological and macroevolutionary inferences of avian New World suboscines (Aves, Passeriformes, Tyrannides)

The New World suboscines (Passeriformes and Tyrannides) are one of the biggest endemic vertebrate radiations in South America, including the families Furnariidae and Tyrannidae. Avian brain morphology is a reliable proxy to study their evolution. The aim of this work is to elucidate whether the brains of these families reflect the ecological differences (e.g., feeding behavior) and to clarify macroevolutionary aspects of their neuroanatomy. Our hypotheses are as follows: Brain size is similar between both families and with other Passeriformes; brain morphology in Tyrannides is the result of the pressure of ecological factors; and brain disparity is low since they share ecological traits. Skulls of Furnariidae and Tyrannidae were micro-computed tomography-scanned, and three-dimensional models of the endocast were generated. Regression analyses were performed between brain volume and body mass. Linear and surface measurements were used to build phylomorphospaces and to calculate the amount of phylogenetic signal. Tyrannidae showed a larger brain disparity than Furnariidae, although it is not shaped by phylogeny in the Tyrannides. Furnariidae present enlarged Wulsts (eminentiae sagittales) but smaller optic lobes, while in Tyrannidae, it is the opposite. This could indicate that in Tyrannides there is a trade-off between the size of these two visual-related brain structures.

Input and Output Connections of the Crow Nidopallium Caudolaterale

The avian telencephalic structure nidopallium caudolaterale (NCL) functions as an analog to the mammalian prefrontal cortex. In crows, corvid songbirds, it plays a crucial role in higher cognitive and executive functions. These functions rely on the NCL's extensive telencephalic connections. However, systematic investigations into the brain-wide connectivity of the NCL in crows or other songbirds are lacking. Here, we studied its input and output connections by injecting retrograde and anterograde tracers into the carrion crow NCL. Our results, mapped onto a published carrion crow brain atlas, confirm NCL multisensory connections and extend prior pigeon findings by identifying a novel input from the hippocampal formation. Furthermore, we analyze crow NCL efferent projections to the arcopallium and report newly identified arcopallial neurons projecting bilaterally to the NCL. These findings help to clarify the role of the NCL as central executive hub in the corvid songbird brain.

Why birds are smart

Many cognitive neuroscientists believe that both a large brain and an isocortex are crucial for complex cognition. Yet corvids and parrots possess non-cortical brains of just 1-25 g, and these birds exhibit cognitive abilities comparable with those of great apes such as chimpanzees, which have brains of about 400 g. This opinion explores how this cognitive equivalence is possible. We propose four features that may be required for complex cognition: a large number of associative pallial neurons, a prefrontal cortex (PFC)-like area, a dense dopaminergic innervation of association areas, and dynamic neurophysiological fundaments for working memory. These four neural features have convergently evolved and may therefore represent 'hard to replace' mechanisms enabling complex cognition.

Nano-selenium alleviates cadmium-induced neurotoxicity in cerebrum via inhibiting gap junction protein connexin 43 phosphorylation

Cadmium (Cd) as a ubiquitous toxic heavy metal is reported to affect the nervous system. Selenium (Se) has been shown to have antagonistic effects against heavy metal toxicity. In addition, it shows potential antioxidant and anti-inflammatory properties. Thus, the purpose of this study was to determine the possible mechanism of brain injury after high Cd exposure and the mitigation of Nano-selenium (Nano-Se) against Cd-induced brain injury. In this study, the Cd-treated group showed a decrease in the number of neurons in brain tissue, swelling of the endoplasmic reticulum and mitochondria, and the formation of autophagosomes. Nano-Se intervention restored Cd-caused alterations in neuronal morphology, endoplasmic reticulum, and mitochondrial structure, thereby reducing neuronal damage. Furthermore, we found that some differentially expressed genes were involved in cell junction and molecular functions. Subsequently, we selected eleven (11) related differentially expressed genes for verification. The qRT-PCR results revealed the same trend of results as determined by RNA-Seq. Our findings also showed that Nano-Se supplementation alleviated Cx43 phosphorylation induced by Cd exposure. Based on immunofluorescence colocalization it was demonstrated that higher expression of GFAP and lower expressions of Cx43 were restored by Nano-Se supplementation. In conclusion, the data presented in this study establish a direct association between the phosphorylation of Cx43 and the occurrence of autophagy and neuroinflammation. However, it is noteworthy that the introduction of Nano-Se supplementation has been observed to mitigate these alterations. These results elucidate the relieving effect of Nano-Se on Cd exposure-induced brain injury.

Different ways of evolving tool-using brains in teleosts and amniotes

In mammals and birds, tool-using species are characterized by their relatively large telencephalon containing a higher proportion of total brain neurons compared to other species. Some teleost species in the wrasse family have evolved tool-using abilities. In this study, we compared the brains of tool-using wrasses with various teleost species. We show that in the tool-using wrasses, the telencephalon and the ventral part of the forebrain and midbrain are significantly enlarged compared to other teleost species but do not contain a larger proportion of cells. Instead, this size difference is due to large fiber tracts connecting the dorsal part of the telencephalon (pallium) to the inferior lobe, a ventral mesencephalic structure absent in amniotes. The high degree of connectivity between these structures in tool-using wrasses suggests that the inferior lobe could contribute to higher-order cognitive functions. We conclude that the evolution of non-telencephalic structures might have been key in the emergence of these cognitive functions in teleosts.

A bird's eye view of the hippocampus beyond space: Behavioral, neuroanatomical, and neuroendocrine perspectives

Although the hippocampus is one of the most-studied brain regions in mammals, research on the avian hippocampus has been more limited in scope. It is generally agreed that the hippocampus is an ancient feature of the amniote brain, and therefore homologous between the two lineages. Because birds and mammals are evolutionarily not very closely related, any shared anatomy is likely to be crucial for shared functions of their hippocampi. These functions, in turn, are likely to be essential if they have been conserved for over 300 million years. Therefore, research on the avian hippocampus can help us understand how this brain region evolved and how it has changed over evolutionary time. Further, there is a strong research foundation in birds on hippocampal-supported behaviors such as spatial navigation, food caching, and brood parasitism that scientists can build upon to better understand how hippocampal anatomy, network circuitry, endocrinology, and physiology can help control these behaviors. In this review, we summarize our current understanding of the avian hippocampus in spatial cognition as well as in regulating anxiety, approach-avoidance behavior, and stress responses. Although there are still some questions about the exact number of subdivisions in the avian hippocampus and how that might vary in different avian families, there is intriguing evidence that the avian hippocampus might have complementary functional profiles along the rostral-caudal axis similar to the dorsal-ventral axis of the rodent hippocampus, where the rostral/dorsal hippocampus is more involved in cognitive processes like spatial learning and the caudal/ventral hippocampus regulates emotional states, anxiety, and the stress response. Future research should focus on elucidating the cellular and molecular mechanisms - including endocrinological - in the avian hippocampus that underlie behaviors such as spatial navigation, spatial memory, and anxiety-related behaviors, and in so doing, resolve outstanding questions about avian hippocampal function and organization.

Context-dependent activation of a social behavior brain network during learned vocal production

Neural activation in brain regions for vocal control is social context dependent. This context-dependent brain activation reflects social context-appropriate vocal behavior but has unresolved mechanisms. Studies of non-vocal social behaviors in multiple organisms suggest a functional role for several evolutionarily conserved and highly interconnected brain regions. Here, we use neural activity-dependent gene expression to evaluate the functional connectivity of this social behavior network within zebra finches in non-social and social singing contexts. We found that activity in one social behavior network region, the medial preoptic area (POM), was strongly associated with the amount of non-social undirected singing in zebra finches. In addition, in all regions of the social behavior network and the paraventricular nucleus (PVN), a higher percentage of EGR1 expression was observed during a social female-directed singing context compared to a non-social undirected singing context. Furthermore, we observed distinct patterns of significantly correlated activity between regions of the social behavior network during non-social undirected and social female-directed singing. Our results suggest that non-social vs. social contexts differentially activate this social behavior network and PVN. Moreover, neuronal activity within this social behavior network, PVN, and POM may alter context-appropriate vocal production.

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.

Lesions to Caudomedial Nidopallium Impair Individual Vocal Recognition in the Zebra Finch

Many social animals can recognize other individuals by their vocalizations. This requires a memory system capable of mapping incoming acoustic signals to one of many known individuals. Using the zebra finch, a social songbird that uses songs and distance calls to communicate individual identity (Elie and Theunissen, 2018), we tested the role of two cortical-like brain regions in a vocal recognition task. We found that the rostral region of the Cadomedial Nidopallium (NCM), a secondary auditory region of the avian pallium, was necessary for maintaining auditory memories for conspecific vocalizations in both male and female birds, whereas HVC (used as a proper name), a premotor areas that gates auditory input into the vocal motor and song learning pathways in male birds (Roberts and Mooney, 2013), was not. Both NCM and HVC have previously been implicated for processing the tutor song in the context of song learning (Sakata and Yazaki-Sugiyama, 2020). Our results suggest that NCM might not only store songs as templates for future vocal imitation but also songs and calls for perceptual discrimination of vocalizers in both male and female birds. NCM could therefore operate as a site for auditory memories for vocalizations used in various facets of communication. We also observed that new auditory memories could be acquired without intact HVC or NCM but that for these new memories NCM lesions caused deficits in either memory capacity or auditory discrimination. These results suggest that the high-capacity memory functions of the avian pallial auditory system depend on NCM.SIGNIFICANCE STATEMENT Many aspects of vocal communication require the formation of auditory memories. Voice recognition, for example, requires a memory for vocalizers to identify acoustical features. In both birds and primates, the locus and neural correlates of these high-level memories remain poorly described. Previous work suggests that this memory formation is mediated by high-level sensory areas, not traditional memory areas such as the hippocampus. Using lesion experiments, we show that one secondary auditory brain region in songbirds that had previously been implicated in storing song memories for vocal imitation is also implicated in storing vocal memories for individual recognition. The role of the neural circuits in this region in interpreting the meaning of communication calls should be investigated in the future.

Context-dependent activation of a social behavior brain network associates with learned vocal production

In zebra finches, an avian brain network for vocal control undergoes context-dependent patterning of song-dependent activation. Previous studies in zebra finches also implicate the importance of dopaminergic input in producing context-appropriate singing behavior. In mice, it has been shown that oxytocinergic neurons originated in the paraventricular nucleus of the hypothalamus (PVN) synapse directly onto dopamine neurons in the ventral tegmental area (VTA), implicating the necessity of oxytocin signaling from the PVN for producing a context-appropriate song. Both avian and non-avian axonal tract-tracing studies indicate high levels of PVN innervation by the social behavior network. Here, we hypothesize that the motivation for PVN oxytocin neurons to trigger dopamine release originates in the social behavior network, a highly conserved and interconnected collection of six regions implicated in various social and homeostatic behaviors. We found that expression of the neuronal activity marker EGR1 was not strongly correlated with song production in any of the regions of the social behavior network. However, when EGR1 expression levels were normalized to the singing rate, we found significantly higher levels of expression in the social behavior network regions except the medial preoptic area during a social female-directed singing context compared to a non-social undirected singing context. Our results suggest neuronal activity within the male zebra finch social behavior network influences the synaptic release of oxytocin from PVN onto dopaminergic projection neurons in the VTA, which in turn signals to the vocal control network to allow for context-appropriate song production.

Recent developments in parrot cognition: a quadrennial update

Psittacines, along with corvids, are commonly referred to as 'feathered apes' due to their advanced cognitive abilities. Until rather recently, the research effort on parrot cognition was lagging behind that on corvids, however current developments show that the number of parrot studies is steadily increasing. In 2018, M. L. Lambert et al. provided a comprehensive review on the status of the most important work done so far in parrot and corvid cognition. Nevertheless, only a little more than 4 years after this publication, more than 50 new parrot studies have been published, some of them chartering completely new territory. On the 25th anniversary of Animal Cognition we think this warrants a detailed review of parrot cognition research over the last 4 years. We aim to capture recent developments and current trends in this rapidly expanding and diversifying field.

Sex differences in myelination of the zebra finch vocal control system emerge relatively late in development

The role of myelination in the development of motor control is widely known, but its role in the development of cognitive abilities is less understood. Here, we examined sex differences in the development of myelination of structures and tracts that support song learning and production in songbirds. We collected brains from 63 young male and female zebra finches (Taeniopygia guttata) over four stages of development that correspond to different stages of song learning. Using a myelination marker (myelin basic protein), we measured the development of myelination in three different nuclei of the vocal control system (HVC, RA, and lateral magnocellular nucleus of the anterior nidopallium [LMAN]) and two tracts (HVC-RA and lamina mesopallium ventralis [LMV]). We found that the myelination of the vocal control nuclei and tracts is sex related and male biased. In males, the patterns of myelination were age-dependent, asynchronous in rate and progression and associated with the development of song learning and production. In females, myelination of vocal control nuclei was low or absent and did not significantly change with age. Sex differences in myelination of the HVC-RA tract were large and emerged late in development well after sex differences in the size of vocal control brain regions are established. Myelination of this tract in males coincides with the age of song crystallization. Overall, the changes in myelination in the vocal control areas and tracts measured are region-, age-, and sex-specific and are consistent with sex differences in song development.

Forebrain nuclei linked to woodpecker territorial drum displays mirror those that enable vocal learning in songbirds

Vocal learning is thought to have evolved in 3 orders of birds (songbirds, parrots, and hummingbirds), with each showing similar brain regions that have comparable gene expression specializations relative to the surrounding forebrain motor circuitry. Here, we searched for signatures of these same gene expression specializations in previously uncharacterized brains of 7 assumed vocal non-learning bird lineages across the early branches of the avian family tree. Our findings using a conserved marker for the song system found little evidence of specializations in these taxa, except for woodpeckers. Instead, woodpeckers possessed forebrain regions that were anatomically similar to the pallial song nuclei of vocal learning birds. Field studies of free-living downy woodpeckers revealed that these brain nuclei showed increased expression of immediate early genes (IEGs) when males produce their iconic drum displays, the elaborate bill-hammering behavior that individuals use to compete for territories, much like birdsong. However, these specialized areas did not show increased IEG expression with vocalization or flight. We further confirmed that other woodpecker species contain these brain nuclei, suggesting that these brain regions are a common feature of the woodpecker brain. We therefore hypothesize that ancient forebrain nuclei for refined motor control may have given rise to not only the song control systems of vocal learning birds, but also the drumming system of woodpeckers.

Vocal learning is thought to have evolved in three orders of birds (songbirds, parrots, and hummingbirds). This study shows that woodpeckers have evolved a set of brain nuclei to mediate their drum displays, and these regions closely mirror those that underlie song learning in songbirds.

Morphology, biochemistry and connectivity of Cluster N and the hippocampal formation in a migratory bird

The exceptional navigational capabilities of migrating birds are based on the perception and integration of a variety of natural orientation cues. The “Wulst” in the forebrain of night-migratory songbirds contains a brain area named “Cluster N”, which is involved in processing directional navigational information derived from the Earth´s magnetic field. Cluster N is medially joined by the hippocampal formation, known to retrieve and utilise navigational information. To investigate the connectivity and neurochemical characteristics of Cluster N and the hippocampal formation of migratory birds, we performed morphological and histochemical analyses based on the expression of calbindin, calretinin, parvalbumin, glutamate receptor type 1 and early growth response protein-1 in the night-migratory Garden warbler (Sylvia borin) and mapped their mutual connections using neuronal tract tracing. The resulting expression patterns revealed regionally restricted neurochemical features, which mapped well onto the hippocampal and hyperpallial substructures known from other avian species. Magnetic field-induced neuronal activation covered caudal parts of the hyperpallium and the medially adjacent hippocampal dorsomedial/dorsolateral subdivisions. Neuronal tract tracings revealed connections between Cluster N and the hippocampal formation with the vast majority originating from the densocellular hyperpallium, either directly or indirectly via the area corticoidea dorsolateralis. Our data indicate that the densocellular hyperpallium could represent a central relay for the transmission of magnetic compass information to the hippocampal formation where it might be integrated with other navigational cues in night-migratory songbirds.

A brain atlas of the carrion crow (Corvus corone)

Corvidae, passerine songbirds such as jays, crows, and ravens known as corvids, have become model systems for the study of avian cognition. The superior cognitive capabilities of corvids mainly emerge from a disproportionally large telencephalon found in these species. However, a systematic mapping of the neuroanatomy of the corvid brain, and the telencephalon in particular, is lacking so far. Here, we present a brain atlas of the carrion crow, Corvus corone, with special emphasis on the telencephalic pallium. We applied four staining techniques to brain slices (Nissl, myelin, combination of Nissl and myelin, and tyrosine hydroxylase targeting catecholaminergic neurons). This allowed us to identify brain nuclei throughout the brain and delineate the known pallial subdivisions termed hyperpallium, entopallium, mesopallium, nidopallium, arcopallium, and hippocampal complex. The extent of these subdivisions and brain nuclei are described according to stereotaxic coordinates. In addition, 3D depictions of pallial regions were reconstructed from these slices. While the overall organization of the carrion crow's brain matches other songbird brains, the relative proportions and expansions of associative pallial areas differ considerably in agreement with enhanced cognitive skills found in corvids. The presented global organization of the crow brain in stereotaxic coordinates will help to guide future neurobiological studies in corvids.

Neuronal satellitosis is a common finding in the avian brain

AbstractPerineuronal or neuronal satellitosis is the term describing the presence of glial cells in the satellite space surrounding the neuronal perikaryon. Confusingly, this finding has been described both as a physiologic and pathologic condition in humans and animals. In animals, neuronal satellitosis has been described in mammals, as well as in avian species. For the latter, authors wondered whether this finding can be expressed in the normal telencephalon of different avian orders and families and whether this pattern in different species shows a specific brain-region association. For these aims, this study explored the presence of neuronal satellitosis in the major areas of the healthy telencephalon in wild avian species of different orders and families, evaluating its grade in different brain regions. Neuronal satellitosis was seen in the Hyperpallium and Mesopallium as areas with the highest grade. Passeriformes showed the highest grade of neuronal satellitosis compared to Diurnal, Nocturnal raptors, and Charadriiformes. To clarify the exact role of neuronal satellitosis in animals without neurological disease further studies are needed.

Chick Hippocampal Formation Displays Subdivision- and Layer-Selective Expression Patterns of Serotonin Receptor Subfamily Genes

Hippocampal formation (HF) plays a key role in cognitive and emotional processing in mammals. In HF neural circuits, serotonin receptors (5-HTRs) modulate functions related to cognition and emotion. To understand the phylogenetic continuity of the neural basis for cognition and emotion, it is important to identify the neural circuits that regulate cognitive and emotional processing in animals. In birds, HF has been shown to be related to cognitive functions and emotion-related behaviors. However, details regarding the distribution of 5-HTRs in the avian brain are very sparse, and 5-HTRs, which are potentially involved in cognitive functions and emotion-related behaviors, are poorly understood. Previously, we showed that 5-HTR1B and 5-HTR3A were expressed in chick HF. To identify additional 5-HTRs that are potentially involved in cognitive and emotional functions in avian HF, we selected the chick orthologs of 5-HTR1D, 5-HTR1E, 5-HTR1F, 5-HTR2B, 5-HTR5A, and 5-HTR7 and performed in situ hybridization in the chick telencephalon. We found that 5-HTR1D, 5-HTR1E, 5-HTR5A, and 5-HTR7 were expressed in the chick HF, especially 5-HTR1D and 5-HTR1E, which showed subdivision- and layer-selective expression patterns, suggesting that the characteristic 5-HT regulation is involved in cognitive functions and emotion-related behaviors in these HF regions. These findings can facilitate the understanding of serotonin regulation in avian HF and the correspondence between the HF subdivisions of birds and mammals.

Nicotinic acetylcholine receptors in a songbird brain

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that mediate fast synaptic transmission and cell signaling, which contribute to learning, memory, and the execution of motor skills. Birdsong is a complex learned motor skill in songbirds. Although the existence of 15 nAChR subunits has been predicted in the avian genome, their expression patterns and potential contributions to song learning and production have not been comprehensively investigated. Here, we cloned all the 15 nAChR subunits (ChrnA1-10, B2-4, D, and G) from the zebra finch brain and investigated the mRNA expression patterns in the neural pathways responsible for the learning and production of birdsong during a critical period of song learning. Although there were no detectable hybridization signals for ChrnA1, A6, A9, and A10, the other 11 nAChR subunits were uniquely expressed in one or more major subdivisions in the song nuclei of the songbird brain. Of these 11 subunits, ChrnA3-5, A7, and B2 were differentially regulated in the song nuclei compared with the surrounding anatomically related regions. ChrnA5 was upregulated during the critical period of song learning in the lateral magnocellular nucleus of the anterior nidopallium. Furthermore, single-cell RNA sequencing revealed ChrnA7 and B2 to be the major subunits expressed in neurons of the vocal motor nuclei HVC and robust nucleus of the arcopallium, indicating the potential existence of ChrnA7-homomeric and ChrnB2-heteromeric nAChRs in limited cell populations. These results suggest that relatively limited types of nAChR subunits provide functional contributions to song learning and production in songbirds.

Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9

The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line, designated CFS414, from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we disrupted endogenous gene sequences using S.aureus Cas9 and confirmed a stress-dependent localization response of a song system specialized gene, SAP30L. The utility of CFS414 cells enhances the comprehensive molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.

Striatal Injury Induces Overall Brain Alteration at the Pallial, Thalamic, and Cerebellar Levels

Simple Summary

Magnetic resonance imaging showed that striatal injury leads to structural changes within several brain areas. Here, we specify these changes via gene expression of synaptic plasticity markers, neuronal markers, assessing the number of newborn cells as well as cell densities. We found that the injury resulted in long-lasting modifications involving plasticity and neural protection mechanisms in areas directly as well as indirectly connected with the damaged striatum, including the cerebellum.

Abstract

The striatal region Area X plays an important role during song learning, sequencing, and variability in songbirds. A previous study revealed that neurotoxic damage within Area X results in micro and macrostructural changes across the entire brain, including the downstream dorsal thalamus and both the upstream pallial nucleus HVC (proper name) and the deep cerebellar nuclei (DCN). Here, we specify these changes on cellular and gene expression levels. We found decreased cell density in the thalamic and cerebellar areas and HVC, but it was not related to neuronal loss. On the contrary, perineuronal nets (PNNs) in HVC increased for up to 2 months post-lesion, suggesting their protecting role. The synaptic plasticity marker Forkhead box protein P2 (FoxP2) showed a bi-phasic increase at 8 days and 3 months post-lesion, indicating a massive synaptic rebuilding. The later increase in HVC was associated with the increased number of new neurons. These data suggest that the damage in the striatal vocal nucleus induces cellular and gene expression alterations in both the efferent and afferent destinations. These changes may be long-lasting and involve plasticity and neural protection mechanisms in the areas directly connected to the injury site and also to distant areas, such as the cerebellum.

The evolution of brain neuron numbers in amniotes

The evolution of brain processing capacity has traditionally been inferred from data on brain size. However, similarly sized brains of distantly related species can differ in the number and distribution of neurons, their basic computational units. Therefore, a finer-grained approach is needed to reveal the evolutionary paths to increased cognitive capacity. Using a new, comprehensive dataset, we analyzed brain cellular composition across amniotes. Compared to reptiles, mammals and birds have dramatically increased neuron numbers in the telencephalon and cerebellum, which are brain parts associated with higher cognition. Astoundingly, a phylogenetic analysis suggests that as few as four major changes in neuron–brain scaling in over 300 million years of evolution pave the way to intelligence in endothermic land vertebrates.

Reconstructing the evolution of brain information-processing capacity is paramount for understanding the rise of complex cognition. Comparative studies of brain evolution typically use brain size as a proxy. However, to get a less biased picture of the evolutionary paths leading to high cognitive power, we need to compare brains not by mass but by numbers of neurons, which are their basic computational units. This study reconstructs the evolution of brains across amniotes by directly analyzing neuron numbers by using the largest dataset of its kind and including essential data on reptiles. We show that reptiles have not only small brains relative to body size but also low neuronal densities, resulting in average neuron numbers over 20 times lower than those in birds and mammals of similar body size. Amniote brain evolution is characterized by the following four major shifts in neuron–brain scaling. The most dramatic increases in brain neurons occurred independently with the appearance of birds and mammals, resulting in convergent neuron scaling in the two endotherm lineages. The other two major increases in the number of neurons happened in core land birds and anthropoid primates, which are two groups known for their cognitive prowess. Interestingly, relative brain size is associated with relative neuronal cell density in reptiles, birds, and primates but not in other mammals. This has important implications for studies using relative brain size as a proxy when looking for evolutionary drivers of animal cognition.

Historical museum samples enable the examination of divergent and parallel evolution during invasion

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

High associative neuron numbers could drive cognitive performance in corvid species

Corvids possess cognitive skills, matching those of non-human primates. However, how these species with their small brains achieve such feats remains elusive. Recent studies suggest that cognitive capabilities could be based on the total numbers of telencephalic neurons. Here we extend this hypothesis further and posit that especially high neuron counts in associative pallial areas drive flexible, complex cognition. If true, avian species like corvids should specifically accumulate neurons in the avian associative areas meso- and nidopallium. To test the hypothesis, we analyzed the neuronal composition of telencephalic areas in corvids and non-corvids (chicken, pigeons, and ostriches - the species with the largest bird brain). The overall number of pallial neurons in corvids was much higher than in chicken and pigeons and comparable to those of ostriches. However, neuron numbers in the associative mesopallium and nidopallium were twice as high in corvids and, in correlation with these associative areas, the corvid subpallium also contained high neuron numbers. These findings support our hypothesis that large absolute numbers of associative pallial neurons contribute to cognitive flexibility and complexity and are key to explain why crows are smart. Since meso/nidopallial and subpallial areas scale jointly, it is conceivable that associative pallio-striatal loops play a similar role in executive decision-making as described in primates. This article is protected by copyright. All rights reserved.

Gene expression profiles of the muscarinic acetylcholine receptors in brain regions relating to filial imprinting of newly-hatched domestic chicks

Muscarinic acetylcholine receptors (mAChRs) in the central nervous system play an important role in regulating complex functions such as learning, memory, and selective attention. Five subtypes of the mAChRs (M₁-M₅) have been identified in mammals, and are classified into two subfamilies: excitatory (M₁, M₃, and M₅) and inhibitory (M₂ and M₄) subfamilies. Filial imprinting of domestic chicks is a useful model in the laboratory to investigate the mechanisms of memory formation in early learning. We recently found that mAChRs in the intermediate medial mesopallium (IMM) are involved in the memory formation of imprinting. However, expression profiles of each mAChR subtype in the brain regions including the IMM remain unexplored. Here we show the unique gene expression of each mAChR subtype in the pallial regions involved in imprinting. In terms of the excitatory mAChRs, M₅ was expressed in the IMM region and other parts of the pallium, whereas M₃ was less expressed in the IMM but highly expressed in the hyperpallium and nidopallium. Regarding the inhibitory mAChRs, M₂ was sparsely distributed but clearly in some cells throughout the pallial regions. M₄ was highly expressed in the IMM region and other parts of the pallium. These expression profiles can be used as a basis for understanding cholinergic modulation in the memory formation of imprinting and other learning processes in birds, and compared to those of mammals.

Evolving Views on the Pallium

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

Nonhuman and Nonhuman-Human Communication: Some Issues and Questions

Deciphering nonhuman communication – particularly nonhuman vocal communication – has been a longstanding human quest. We are, for example, fascinated by the songs of birds and whales, the grunts of apes, the barks of dogs, and the croaks of frogs; we wonder about their potential meaning and their relationship to human language. Do these utterances express little more than emotional states, or do they convey actual bits and bytes of concrete information? Humans’ numerous attempts to decipher nonhuman systems have, however, progressed slowly. We still wonder why only a small number of species are capable of vocal learning, a trait that, because it allows for innovation and adaptation, would seem to be a prerequisite for most language-like abilities. Humans have also attempted to teach nonhumans elements of our system, using both vocal and nonvocal systems. The rationale for such training is that the extent of success in instilling symbolic reference provides some evidence for, at the very least, the cognitive underpinnings of parallels between human and nonhuman communication systems. However, separating acquisition of reference from simple object-label association is not a simple matter, as reference begins with such associations, and the point at which true reference emerges is not always obvious. I begin by discussing these points and questions, predominantly from the viewpoint of someone studying avian abilities. I end by examining the question posed by Premack: do nonhumans that have achieved some level of symbolic reference then process information differently from those that have not? I suggest the answer is likely “yes,” giving examples from my research on Grey parrots (Psittacus erithacus).

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.

Avian pallial circuits and cognition: A comparison to mammals

Cognitive functions are similar in birds and mammals. So, are therefore pallial cellular circuits and neuronal computations also alike? In search of answers, we move in from bird's pallial connectomes, to cortex-like sensory canonical circuits and connections, to forebrain micro-circuitries and finally to the avian "prefrontal" area. This voyage from macro- to micro-scale networks and areas reveals that both birds and mammals evolved similar neural and computational properties in either convergent or parallel manner, based upon circuitries inherited from common ancestry. Thus, these two vertebrate classes evolved separately within 315 million years with highly similar pallial architectures that produce comparable cognitive functions.

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.

A canonical interlaminar circuit in the sensory dorsal ventricular ridge of birds: The anatomical organization of the trigeminal pallium

The dorsal ventricular ridge (DVR), which is the largest component of the avian pallium, contains discrete partitions receiving tectovisual, auditory, and trigeminal ascending projections. Recent studies have shown that the auditory and the tectovisual regions can be regarded as complexes composed of three highly interconnected layers: an internal senso-recipient one, an intermediate afferent/efferent one, and a more external re-entrant one. Cells located in homotopic positions in each of these layers are reciprocally linked by an interlaminar loop of axonal processes, forming columnar-like local circuits. Whether this type of organization also extends to the trigemino-recipient DVR is, at present, not known. This question is of interest, since afferents forming this sensory pathway, exceptional among amniotes, are not thalamic but rhombencephalic in origin. We investigated this question by placing minute injections of neural tracers into selected locations of vital slices of the chicken telencephalon. We found that neurons of the trigemino-recipient nucleus basorostralis pallii (Bas) establish reciprocal, columnar and homotopical projections with cells located in the overlying ventral mesopallium (MV). "Column-forming" axons originated in B and MV terminate also in the intermediate strip, the fronto-trigeminal nidopallium (NFT), in a restricted manner. We also found that the NFT and an internal partition of B originate substantial, coarse-topographic projections to the underlying portion of the lateral striatum. We conclude that all sensory areas of the DVR are organized according to a common neuroarchitectonic motif, which bears a striking resemblance to that of the radial/laminar intrinsic circuits of the sensory cortices of mammals.

Songbirds can learn flexible contextual control over syllable sequencing

The flexible control of sequential behavior is a fundamental aspect of speech, enabling endless reordering of a limited set of learned vocal elements (syllables or words). Songbirds are phylogenetically distant from humans but share both the capacity for vocal learning and neural circuitry for vocal control that includes direct pallial-brainstem projections. Based on these similarities, we hypothesized that songbirds might likewise be able to learn flexible, moment-by-moment control over vocalizations. Here, we demonstrate that Bengalese finches (Lonchura striata domestica), which sing variable syllable sequences, can learn to rapidly modify the probability of specific sequences (e.g. ‘ab-c’ versus ‘ab-d’) in response to arbitrary visual cues. Moreover, once learned, this modulation of sequencing occurs immediately following changes in contextual cues and persists without external reinforcement. Our findings reveal a capacity in songbirds for learned contextual control over syllable sequencing that parallels human cognitive control over syllable sequencing in speech.

Human speech and birdsong share numerous parallels. Both humans and birds learn their vocalizations during critical phases early in life, and both learn by imitating adults. Moreover, both humans and songbirds possess specific circuits in the brain that connect the forebrain to midbrain vocal centers.

Humans can flexibly control what they say and how by reordering a fixed set of syllables into endless combinations, an ability critical to human speech and language. Birdsongs also vary depending on their context, and melodies to seduce a mate will be different from aggressive songs to warn other males to stay away. However, so far it was unclear whether songbirds are also capable of modifying songs independent of social or other naturally relevant contexts.

To test whether birds can control their songs in a purposeful way, Veit et al. trained adult male Bengalese finches to change the sequence of their songs in response to random colored lights that had no natural meaning to the birds. A specific computer program was used to detect different variations on a theme that the bird naturally produced (for example, “ab-c” versus “ab-d”), and rewarded birds for singing one sequence when the light was yellow, and the other when it was green. Gradually, the finches learned to modify their songs and were able to switch between the appropriate sequences as soon as the light cues changed. This ability persisted for days, even without any further training.

This suggests that songbirds can learn to flexibly and purposefully modify the way in which they sequence the notes in their songs, in a manner that parallels how humans control syllable sequencing in speech. Moreover, birds can learn to do this ‘on command’ in response to an arbitrarily chosen signal, even if it is not something that would impact their song in nature.

Songbirds are an important model to study brain circuits involved in vocal learning. They are one of the few animals that, like humans, learn their vocalizations by imitating conspecifics. The finding that they can also flexibly control vocalizations may help shed light on the interactions between cognitive processing and sophisticated vocal learning abilities.

Genetically identified neurons in avian auditory pallium mirror core principles of their mammalian counterparts

In vertebrates, advanced cognitive abilities are typically associated with the telencephalic pallium. In mammals, the pallium is a layered mixture of excitatory and inhibitory neuronal populations with distinct molecular, physiological, and network phenotypes. This cortical architecture is proposed to support efficient, high-level information processing. Comparative perspectives across vertebrates provide a lens to understand the common features of pallium that are important for advanced cognition. Studies in songbirds have established strikingly parallel features of neuronal types between mammalian and avian pallium. However, lack of genetic access to defined pallial cell types in non-mammalian vertebrates has hindered progress in resolving connections between molecular and physiological phenotypes. A definitive mapping of the physiology of pallial cells onto their molecular identities in birds is critical for understanding how synaptic and computational properties depend on underlying molecular phenotypes. Using viral tools to target excitatory versus inhibitory neurons in the zebra finch auditory association pallium (calmodulin-dependent kinase alpha [CaMKIIα] and glutamate decarboxylase 1 [GAD1] promoters, respectively), we systematically tested predictions derived from mammalian pallium. We identified two genetically distinct neuronal populations that exhibit profound physiological and computational similarities with mammalian excitatory and inhibitory pallial cells, definitively aligning putative cell types in avian caudal nidopallium with these molecular identities. Specifically, genetically identified CaMKIIα and GAD1 cell types in avian auditory association pallium exhibit distinct intrinsic physiological parameters, distinct auditory coding principles, and inhibitory-dependent pallial synchrony, gamma oscillations, and local suppression. The retention, or convergence, of these molecular and physiological features in both birds and mammals clarifies the characteristics of pallial circuits for advanced cognitive abilities.

As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions

Over the last two decades, beginning with the Avian Brain Nomenclature Forum in 2000, major revisions have been made to our understanding of the organization and nomenclature of the avian brain. However, there are still unresolved questions on avian pallial organization, particularly whether the cells above the vestigial ventricle represent distinct populations to those below it or similar populations. To test these two hypotheses, we profiled the transcriptomes of the major avian pallial subdivisions dorsal and ventral to the vestigial ventricle boundary using RNA sequencing and a new zebra finch genome assembly containing about 22,000 annotated, complete genes. We found that the transcriptomes of neural populations above and below the ventricle were remarkably similar. Each subdivision in dorsal pallium (Wulst) had a corresponding molecular counterpart in the ventral pallium (dorsal ventricular ridge). In turn, each corresponding subdivision exhibited shared gene co‐expression modules that contained gene sets enriched in functional specializations, such as anatomical structure development, synaptic transmission, signaling, and neurogenesis. These findings are more in line with the continuum hypothesis of avian brain subdivision organization above and below the vestigial ventricle space, with the pallium as a whole consisting of four major cell populations (intercalated pallium, mesopallium, hyper‐nidopallium, and arcopallium) instead of seven (hyperpallium apicale, interstitial hyperpallium apicale, intercalated hyperpallium, hyperpallium densocellare, mesopallium, nidopallium, and arcopallium). We suggest adopting a more streamlined hierarchical naming system that reflects the robust similarities in gene expression, neural connectivity motifs, and function. These findings have important implications for our understanding of overall vertebrate brain evolution.

Controlling for activity-dependent genes and behavioral states is critical for determining brain relationships within and across species

The genetic profile of vertebrate pallia has long driven debate on homology across distantly related clades. Based on an expression profile of the orphan nuclear receptor NR4A2 in mouse and chicken brains, Puelles et al. (The Journal of Comparative Neurology, 2016, 524, 665–703) concluded that the avian lateral mesopallium is homologous to the mammalian claustrum, and the medial mesopallium homologous to the insula cortex. They argued that their findings contradict conclusions by Jarvis et al. (The Journal of Comparative Neurology, 2013, 521, 3614–3665) and Chen et al. (The Journal of Comparative Neurology, 2013, 521, 3666–3701) that the hyperpallium densocellare is instead a mesopallium cell population, and by Suzuki and Hirata (Frontiers in Neuroanatomy, 2014, 8, 783) that the avian mesopallium is homologous to mammalian cortical layers 2/3. Here, we find that NR4A2 is an activity‐dependent gene and cannot be used to determine brain organization or species relationships without considering behavioral state. Activity‐dependent NR4A2 expression has been previously demonstrated in the rodent brain, with the highest induction occurring within the claustrum, amygdala, deep and superficial cortical layers, and hippocampus. In the zebra finch, we find that NR4A2 is constitutively expressed in the arcopallium, but induced in parts of the mesopallium, and in sparse cells within the hyperpallium, depending on animal stimulus or behavioral state. Basal and induced NR4A2 expression patterns do not discount the previously named avian hyperpallium densocellare as dorsal mesopallium and conflict with proposed homology between the avian mesopallium and mammalian claustrum/insula at the exclusion of other brain regions. Broadly, these findings highlight the importance of controlling for behavioral state and neural activity to genetically define brain cell population relationships within and across species.

Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Neuroethology of number sense across the animal kingdom

Many species from diverse and often distantly related animal groups (e.g. monkeys, crows, fish and bees) have a sense of number. This means that they can assess the number of items in a set - its 'numerosity'. The brains of these phylogenetically distant species are markedly diverse. This Review examines the fundamentally different types of brains and neural mechanisms that give rise to numerical competence across the animal tree of life. Neural correlates of the number sense so far exist only for specific vertebrate species: the richest data concerning explicit and abstract number representations have been collected from the cerebral cortex of mammals, most notably human and nonhuman primates, but also from the pallium of corvid songbirds, which evolved independently of the mammalian cortex. In contrast, the neural data relating to implicit and reflexive numerical representations in amphibians and fish is limited. The neural basis of a number sense has not been explored in any protostome so far. However, promising candidate regions in the brains of insects, spiders and cephalopods - all of which are known to have number skills - are identified in this Review. A comparative neuroscientific approach will be indispensable for identifying evolutionarily stable neuronal circuits and deciphering codes that give rise to a sense of number across phylogeny.

Estrogen and sex-dependent loss of the vocal learning system in female zebra finches

Sex hormones alter the organization of the brain during early development and coordinate various behaviors throughout life. In zebra finches, song learning is limited to males, with the associated song learning brain pathways only maturing in males and atrophying in females. While this atrophy can be prevented by treating females with exogenous estrogen during early post-hatch development, the requirement of estrogen during normal male song system development is uncertain. For the first time in songbirds, we administered exemestane, a potent third generation estrogen synthesis inhibitor, from the day of hatching until adulthood in order to reassess the role of estrogen in song circuit development. We examined the behavior, brain anatomy, and transcriptomes of individual song nuclei in these pharmacologically manipulated animals. We found that males with long-term exemestane treatment had diminished male-specific plumage and impaired song learning, but minimal effect on song nuclei sizes and their specialized transcriptome. Consistent with prior findings, females with long-term estrogen treatment retained a functional song system with song nuclei that had specialized gene expression similar, but not identical to males. We also observed that different song nuclei responded to estrogen manipulation differently, with Area X in the striatum being the most altered by estrogen modulation. These findings support the hypothesis that song learning is an ancestral trait in both sexes that was subsequently suppressed in females of some species and that estrogen has come to play a critical role in modulating this suppression as well as refinement of song learning.

Convergent evolution of complex cognition: Insights from the field of avian cognition into the study of self-awareness

Pioneering research on avian behaviour and cognitive neuroscience have highlighted that avian species, mainly corvids and parrots, have a cognitive tool kit comparable with apes and other large-brained mammals, despite conspicuous differences in their neuroarchitecture. This cognitive tool kit is driven by convergent evolution, and consists of complex processes such as casual reasoning, behavioural flexibility, imagination, and prospection. Here, we review experimental studies in corvids and parrots that tested complex cognitive processes within this tool kit. We then provide experimental examples for the potential involvement of metacognitive skills in the expression of the cognitive tool kit. We further expand the discussion of cognitive and metacognitive abilities in avian species, suggesting that an integrated assessment of these processes, together with revised and multiple tasks of mirror self-recognition, might shed light on one of the most highly debated topics in the literature-self-awareness in animals. Comparing the use of multiple assessments of self-awareness within species and across taxa will provide a more informative, richer picture of the level of consciousness in different organisms.

Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits

Birds display advanced behaviors, including vocal learning and problem-solving, yet lack a layered neocortex, a structure associated with complex behavior in mammals. To determine whether these behavioral similarities result from shared or distinct neural circuits, we used single-cell RNA sequencing to characterize the neuronal repertoire of the songbird song motor pathway. Glutamatergic vocal neurons had considerable transcriptional similarity to neocortical projection neurons; however, they displayed regulatory gene expression patterns more closely related to neurons in the ventral pallium. Moreover, while γ-aminobutyric acid-releasing neurons in this pathway appeared homologous to those in mammals and other amniotes, the most abundant avian class is largely absent in the neocortex. These data suggest that songbird vocal circuits and the mammalian neocortex have distinct developmental origins yet contain transcriptionally similar neurons.

Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex

Neurons exhibit diverse intrinsic dynamics, which govern how they integrate synaptic inputs to produce spikes. Intrinsic dynamics are often plastic during development and learning, but the effects of these changes on stimulus encoding properties are not well known. To examine this relationship, we simulated auditory responses to zebra finch song using a linear-dynamical cascade model, which combines a linear spectrotemporal receptive field with a dynamical, conductance-based neuron model, then used generalized linear models to estimate encoding properties from the resulting spike trains. We focused on the effects of a low-threshold potassium current (K_LT) that is present in a subset of cells in the zebra finch caudal mesopallium and is affected by early auditory experience. We found that K_LT affects both spike adaptation and the temporal filtering properties of the receptive field. The direction of the effects depended on the temporal modulation tuning of the linear (input) stage of the cascade model, indicating a strongly nonlinear relationship. These results suggest that small changes in intrinsic dynamics in tandem with differences in synaptic connectivity can have dramatic effects on the tuning of auditory neurons.

Experience-dependent developmental plasticity involves changes not only to synaptic connections, but to voltage-gated currents as well. Using biophysical models, it is straightforward to predict the effects of this intrinsic plasticity on the firing patterns of individual neurons, but it remains difficult to understand the consequences for sensory coding. We investigated this in the context of the zebra finch auditory cortex, where early exposure to a complex acoustic environment causes increased expression of a low-threshold potassium current. We simulated responses to song using a detailed biophysical model and then characterized encoding properties using generalized linear models. This analysis revealed that this potassium current has strong, nonlinear effects on how the model encodes the song’s temporal structure, and that the sign of these effects depend on the temporal tuning of the synaptic inputs. This nonlinearity gives intrinsic plasticity broad scope as a mechanism for developmental learning in the auditory system.

A histological study of the song system of the carrion crow (Corvus corone)

The song system of songbirds (oscines) is one of the best studied neuroethological model systems. So far, it has been treated as a relatively constrained sensorimotor system. Songbirds such as crows, however, are also known for their capability to cognitively control their audio-vocal system. Yet, the neuroanatomy of the corvid song system has never been explored systematically. We aim to close this scientific gap by presenting a stereotactic investigation of the extended song system of the carrion crow (Corvus corone), an oscine songbird of the corvid family that has become an interesting model system for cognitive neuroscience. In order to identify and delineate the song nuclei, the ascending auditory nuclei, and the descending vocal-motor nuclei, four stains were applied. In addition to the classical Nissl-, myelin-, and a combination of Nissl-and-myelin staining, staining for tyrosine hydroxylase was used to reveal the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the song system. We show that the crow brain contains the important song-related nuclei, including auditory input and motor output structures, and map them throughout the brain. Fiber-stained sections reveal putative connection patterns between the crow's song nuclei comparable to other songbirds.

Memory-specific correlated neuronal activity in higher-order auditory regions of a parrot

Male budgerigars (Melopsittacus undulatus) are open-ended learners that can learn to produce new vocalisations as adults. We investigated neuronal activation in male budgerigars using the expression of the protein products of the immediate early genes zenk and c-fos in response to exposure to conspecific contact calls (CCs: that of the mate or an unfamiliar female) in three subregions (CMM, dNCM and vNCM) of the caudomedial pallium, a higher order auditory region. Significant positive correlations of Zenk expression were found between these subregions after exposure to mate CCs. In contrast, exposure to CCs of unfamiliar females produced no such correlations. These results suggest the presence of a CC-specific association among the subregions involved in auditory memory. The caudomedial pallium of the male budgerigar may have functional subdivisions that cooperate in the neuronal representation of auditory memory.

The dorsal arcopallium of chicks displays the expression of orthologs of mammalian fear related serotonin receptor subfamily genes

Fear is an adaptive emotion that elicits defensive behavioural responses against aversive threats in animals. In mammals, serotonin receptors (5-HTRs) have been shown to modulate fear-related neural circuits in the basolateral amygdala complex (BLA). To understand the phylogenetic continuity of the neural basis for fear, it is important to identify the neural circuit that processes fear in other animals. In birds, fear-related behaviours were suggested to be processed in the arcopallium/amygdala complex and modulated by the serotonin (5-HT) system. However, details about the distribution of 5-HTRs in the avian brain are very sparsely reported, and the 5-HTR that is potentially involved in fear-related behaviour has not been elucidated. In this study, we showed that orthologs of mammalian 5-HTR genes that are expressed in the BLA, namely 5-HTR1A, 5-HTR1B, 5-HTR2A, 5-HTR2C, 5-HTR3A, and 5-HTR4, are expressed in a part of the chick arcopallium/amygdala complex called the dorsal arcopallium. This suggests that serotonergic regulation in the dorsal arcopallium may play an important role in regulating fear-related behaviour in birds. Our findings can be used as a basis for comparing the processing of fear and its serotonergic modulation in the mammalian amygdala complex and avian arcopallium/amygdala complex.