Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

Effects of deafening on vocal production learning in the Egyptian fruit-bat

Some species have evolved the ability to use the sense of hearing to modify existing vocalizations, or even create new ones. This ability corresponds to various forms of vocal production learning that are all possessed by humans, and independently displayed by distantly related species. Among mammals, a few species, including the Egyptian fruit-bat, would possess such vocal production learning abilities. Yet the necessity of an intact auditory system for the development of the Egyptian fruit-bat typical vocal repertoire has not been tested. Here we addressed this gap by eliminating pups' sense of hearing at birth and assessing its effects on vocal production in adulthood. The deafening treatment enabled us to both causally test these bats vocal learning ability and discern learned from innate aspects of their vocalizations. Leveraging wireless individual audio recordings from freely interacting adults, we show that a subset of the Egyptian fruit-bat vocal repertoire necessitates auditory feedback. Intriguingly, these affected vocalizations belong to different acoustic groups in the vocal repertoire of males and females. These findings open the possibilities for targeted studies of the mammalian neural circuits that enable sexually dimorphic forms of vocal learning.

Significance

Vocal production learning is the rare capacity amongst animals where hearing is used to modify or create new vocalizations. The Egyptian fruit-bat is believed to possess this capacity, yet whether they need audition to achieve a mature vocal repertoire is unknown. Furthermore, a systematic causal examination of learned and innate aspects of the entire repertoire has never been performed in a vocal learner. Here, we addressed these major gaps directly by abolishing hearing in Egyptian fruit-bats at birth and investigating its effects on the vocal production in adulthood. Leveraging simultaneous individual wireless audio-recordings from freely interacting adult bats, we identify the subset of learned vocalizations and provide evidence that vocal learning is sexually dimorphic in that species.

Hippocampal representation during collective spatial behaviour in bats

Social animals live and move through spaces shaped by the presence, motion and sensory cues of multiple other individuals1-6. Neural activity in the hippocampus is known to reflect spatial behaviour7-9 yet its study is lacking in such dynamic group settings, which are ubiquitous in natural environments. Here we studied hippocampal activity in groups of bats engaged in collective spatial behaviour. We find that, under spontaneous conditions, a robust spatial structure emerges at the group level whereby behaviour is anchored to specific locations, movement patterns and individual social preferences. Using wireless electrophysiological recordings from both stationary and flying bats, we find that many hippocampal neurons are tuned to key features of group dynamics. These include the presence or absence of a conspecific, but not typically of an object, at landing sites, shared spatial locations, individual identities and sensory signals that are broadcasted in the group setting. Finally, using wireless calcium imaging, we find that social responses are anatomically distributed and robustly represented at the population level. Combined, our findings reveal that hippocampal activity contains a rich representation of naturally emerging spatial behaviours in animal groups that could in turn support the complex feat of collective behaviour.

Coevolution of motor cortex and behavioral specializations associated with flight and echolocation in bats

Bats have evolved behavioral specializations that are unique among mammals, including self-propelled flight and echolocation. However, areas of motor cortex that are critical in the generation and fine control of these unique behaviors have never been fully characterized in any bat species, despite the fact that bats compose ∼25% of extant mammalian species. Using intracortical microstimulation, we examined the organization of motor cortex in Egyptian fruit bats (Rousettus aegyptiacus), a species that has evolved a novel form of tongue-based echolocation.^1,2 We found that movement representations include an enlarged tongue region containing discrete subregions devoted to generating distinct tongue movement types, consistent with their behavioral specialization generating active sonar using tongue clicks. This magnification of the tongue in motor cortex is comparable to the enlargement of somatosensory representations in species with sensory specializations.^3-5 We also found a novel degree of coactivation between the forelimbs and hindlimbs, both of which are involved in altering the shape and tension of wing membranes during flight. Together, these findings suggest that the organization of motor cortex has coevolved with peripheral morphology in bats to support the unique motor demands of flight and echolocation.

A stable hippocampal code in freely flying bats

Neural activity in the hippocampus is known to reflect how animals move through an environment1,2. Although navigational behaviour may show considerable stability3-6, the tuning stability of individual hippocampal neurons remains unclear7-12. Here we used wireless calcium imaging to longitudinally monitor the activity of dorsal CA1 hippocampal neurons in freely flying bats performing highly reproducible flights in a familiar environment. We find that both the participation and the spatial selectivity of most neurons remain stable over days and weeks. We also find that apparent changes in tuning can be largely attributed to variations in the flight behaviour of the bats. Finally, we show that bats navigating in the same environment under different room lighting conditions (lights on versus lights off) exhibit substantial changes in flight behaviour that can give the illusion of neuronal instability. However, when similar flight paths are compared across conditions, the stability of the hippocampal code persists. Taken together, we show that the underlying hippocampal code is highly stable over days and across contexts if behaviour is taken into account.

A unifying mechanism governing inter-brain neural relationship during social interactions

A key goal of social neuroscience is to understand the inter-brain neural relationship-the relationship between the neural activity of socially interacting individuals. Decades of research investigating this relationship have focused on the similarity in neural activity across brains. Here, we instead asked how neural activity differs between brains, and how that difference evolves alongside activity patterns shared between brains. Applying this framework to bats engaged in spontaneous social interactions revealed two complementary phenomena characterizing the inter-brain neural relationship: fast fluctuations of activity difference across brains unfolding in parallel with slow activity covariation across brains. A model reproduced these observations and generated multiple predictions that we confirmed using experimental data involving pairs of bats and a larger social group of bats. The model suggests that a simple computational mechanism involving positive and negative feedback could explain diverse experimental observations regarding the inter-brain neural relationship.

Cortical representation of group social communication in bats

Social interactions occur in group settings and are mediated by communication signals that are exchanged between individuals, often using vocalizations. The neural representation of group social communication remains largely unexplored. We conducted simultaneous wireless electrophysiological recordings from the frontal cortices of groups of Egyptian fruit bats engaged in both spontaneous and task-induced vocal interactions. We found that the activity of single neurons distinguished between vocalizations produced by self and by others, as well as among specific individuals. Coordinated neural activity among group members exhibited stable bidirectional interbrain correlation patterns specific to spontaneous communicative interactions. Tracking social and spatial arrangements within a group revealed a relationship between social preferences and intra- and interbrain activity patterns. Combined, these findings reveal a dedicated neural repertoire for group social communication within and across the brains of freely communicating groups of bats.

Nonlocal spatiotemporal representation in the hippocampus of freely flying bats

Navigation occurs through a continuum of space and time. The hippocampus is known to encode the immediate position of moving animals. However, active navigation, especially at high speeds, may require representing navigational information beyond the present moment. Using wireless electrophysiological recordings in freely flying bats, we demonstrate that neural activity in area CA1 predominantly encodes nonlocal spatial information up to meters away from the bat's present position. This spatiotemporal representation extends both forward and backward in time, with an emphasis on future locations, and is found during both random exploration and goal-directed navigation. The representation of position thus extends along a continuum, with each moment containing information about past, present, and future, and may provide a key mechanism for navigating along self-selected and remembered paths.

The fully automated bat (FAB) flight room: A human-free environment for studying navigation in flying bats and its initial application to the retrosplenial cortex

BACKGROUND

Bats can offer important insight into the neural computations underlying complex forms of navigation. Up to now, this had been done with the confound of the human experimenter being present in the same environment the bat was navigating in.

NEW METHOD

We, therefore, developed a novel behavioral setup, the fully automated bat (FAB) flight room, to obtain a detailed and quantitative understanding of bat navigation flight behavior while studying its relevant neural circuits, but importantly without human intervention. As a demonstration of the FAB flight room utility we trained bats on a four-target, visually-guided, foraging task and recorded neural activity from the retrosplenial cortex (RSC).

RESULTS

We find that bats can be efficiently trained and engaged in complex, multi-target, visuospatial behavior in the FAB flight room. Wireless neural recordings from the bat RSC during the task confirm the multiplexed characteristics of single RSC neurons encoding spatial positional information, target selection, reward obtainment and the intensity of visual cues used to guide navigation.

COMPARISON WITH EXISTING METHODS

In contrast to the methods introduced in previous studies, we now can investigate spatial navigation in bats without potential experimental biases that can be easily introduced by active physical involvement and presence of experimenters in the room.

CONCLUSIONS

Combined, we describe a novel experimental approach for studying spatial navigation in freely flying bats and provide support for the involvement of bat RSC in aerial visuospatial foraging behavior.

Neuroethology of bat navigation

Once a year about 15 million Mexican free-tailed bats (Tadarida brasiliensis) migrate up to 1,500 kilometers from wintering grounds, seamlessly flying over the Mexican border to enter the United States. Their destination is the Bracken Cave in southern Texas, which will be their summer home between the months of March through October. While residing there, these bats emerge every night at dusk from the narrow 100-foot-wide opening of this enormous cave and begin their nightly commute to foraging grounds located up to 50 kilometers away. Upon arrival, they will spend the night hunting for insects in mid-air while providing a valuable service to local farmers by keeping crop pests in check. Close to the break of dawn, as the night of hunting comes to an end, these bats will begin making their trip back to the roost.

A Modular Approach to Vocal Learning: Disentangling the Diversity of a Complex Behavioral Trait

Vocal learning is a behavioral trait in which the social and acoustic environment shapes the vocal repertoire of individuals. Over the past century, the study of vocal learning has progressed at the intersection of ecology, physiology, neuroscience, molecular biology, genomics, and evolution. Yet, despite the complexity of this trait, vocal learning is frequently described as a binary trait, with species being classified as either vocal learners or vocal non-learners. As a result, studies have largely focused on a handful of species for which strong evidence for vocal learning exists. Recent studies, however, suggest a continuum in vocal learning capacity across taxa. Here, we further suggest that vocal learning is a multi-component behavioral phenotype comprised of distinct yet interconnected modules. Discretizing the vocal learning phenotype into its constituent modules would facilitate integration of findings across a wider diversity of species, taking advantage of the ways in which each excels in a particular module, or in a specific combination of features. Such comparative studies can improve understanding of the mechanisms and evolutionary origins of vocal learning. We propose an initial set of vocal learning modules supported by behavioral and neurobiological data and highlight the need for diversifying the field in order to disentangle the complexity of the vocal learning phenotype.

Long-term and persistent vocal plasticity in adult bats

Bats exhibit a diverse and complex vocabulary of social communication calls some of which are believed to be learned during development. This ability to produce learned, species-specific vocalizations – a rare trait in the animal kingdom – requires a high-degree of vocal plasticity. Bats live extremely long lives in highly complex and dynamic social environments, which suggests that they might also retain a high degree of vocal plasticity in adulthood, much as humans do. Here, we report persistent vocal plasticity in adult bats (Rousettus aegyptiacus) following exposure to broad-band, acoustic perturbation. Our results show that adult bats can not only modify distinct parameters of their vocalizations, but that these changes persist even after noise cessation – in some cases lasting several weeks or months. Combined, these findings underscore the potential importance of bats as a model organism for studies of vocal plasticity, including in adulthood.

Bats are long-lived animals that can produce a complex vocabulary of social communication calls. Here, the authors show that even in adulthood, bats retain the ability to adaptively introduce long-term modifications to their vocalizations, showing persistent vocal plasticity.

Correlated Neural Activity across the Brains of Socially Interacting Bats

Social interactions occur between multiple individuals, but what is the detailed relationship between the neural dynamics across their brains? To address this question across timescales and levels of neural activity, we used wireless electrophysiology to simultaneously record from pairs of bats engaged in a wide range of natural social interactions. We found that neural activity was remarkably correlated between their brains over timescales from seconds to hours. The correlation depended on a shared social environment and was most prominent in high frequency local field potentials (>30 Hz), followed by local spiking activity. Furthermore, the degree of neural correlation covaried with the extent of social interactions, and an increase in correlation preceded their initiation. These results show that inter-brain correlation is an inherent feature of natural social interactions, reveal the domain of neural activity where it is most prominent, and provide a foundation for studying its functional role in social behaviors.

Evidence for hormonal control of heart regenerative capacity during endothermy acquisition

Tissue regenerative potential displays striking divergence across phylogeny and ontogeny, but the underlying mechanisms remain enigmatic. Loss of mammalian cardiac regenerative potential correlates with cardiomyocyte cell-cycle arrest and polyploidization as well as the development of postnatal endothermy. We reveal that diploid cardiomyocyte abundance across 41 species conforms to Kleiber's law-the ¾-power law scaling of metabolism with bodyweight-and inversely correlates with standard metabolic rate, body temperature, and serum thyroxine level. Inactivation of thyroid hormone signaling reduces mouse cardiomyocyte polyploidization, delays cell-cycle exit, and retains cardiac regenerative potential in adults. Conversely, exogenous thyroid hormones inhibit zebrafish heart regeneration. Thus, our findings suggest that loss of heart regenerative capacity in adult mammals is triggered by increasing thyroid hormones and may be a trade-off for the acquisition of endothermy.

Nonoscillatory Phase Coding and Synchronization in the Bat Hippocampal Formation

Hippocampal theta oscillations were proposed to be important for multiple functions, including memory and temporal coding of position. However, previous findings from bats have questioned these proposals by reporting absence of theta rhythmicity in bat hippocampal formation. Does this mean that temporal coding is unique to rodent hippocampus and does not generalize to other species? Here, we report that, surprisingly, bat hippocampal neurons do exhibit temporal coding similar to rodents, albeit without any continuous oscillations at the 1-20 Hz range. Bat neurons exhibited very strong locking to the non-rhythmic fluctuations of the field potential, such that neurons were synchronized together despite the absence of oscillations. Further, some neurons exhibited "phase precession" and phase coding of the bat's position-with spike phases shifting earlier as the animal moved through the place field. This demonstrates an unexpected type of neural coding in the mammalian brain-nonoscillatory phase coding-and highlights the importance of synchrony and temporal coding for hippocampal function across species.

Causal contribution and dynamical encoding in the striatum during evidence accumulation

A broad range of decision-making processes involve gradual accumulation of evidence over time, but the neural circuits responsible for this computation are not yet established. Recent data indicate that cortical regions that are prominently associated with accumulating evidence, such as the posterior parietal cortex and the frontal orienting fields, may not be directly involved in this computation. Which, then, are the regions involved? Regions that are directly involved in evidence accumulation should directly influence the accumulation-based decision-making behavior, have a graded neural encoding of accumulated evidence and contribute throughout the accumulation process. Here, we investigated the role of the anterior dorsal striatum (ADS) in a rodent auditory evidence accumulation task using a combination of behavioral, pharmacological, optogenetic, electrophysiological and computational approaches. We find that the ADS is the first brain region known to satisfy the three criteria. Thus, the ADS may be the first identified node in the network responsible for evidence accumulation.

The emperor's new wardrobe: Rebalancing diversity of animal models in neuroscience research

The neuroscience field is steaming ahead, fueled by a revolution in cutting-edge technologies. Concurrently, another revolution has been underway-the diversity of species utilized for neuroscience research is sharply declining, as the field converges on a few selected model organisms. Here, from the perspective of a young scientist, I naively ask: Is the great diversity of questions in neuroscience best studied in only a handful of animal models? I review some of the limitations the field is facing following this convergence and how these can be rectified by increasing the diversity of appropriate model species. I propose that at this exciting time of revolution in genetics and device technologies, neuroscience might be ready to diversify again, if provided the appropriate support.

Representation of three-dimensional space in the hippocampus of flying bats

Many animals, on air, water, or land, navigate in three-dimensional (3D) environments, yet it remains unclear how brain circuits encode the animal's 3D position. We recorded single neurons in freely flying bats, using a wireless neural-telemetry system, and studied how hippocampal place cells encode 3D volumetric space during flight. Individual place cells were active in confined 3D volumes, and in >90% of the neurons, all three axes were encoded with similar resolution. The 3D place fields from different neurons spanned different locations and collectively represented uniformly the available space in the room. Theta rhythmicity was absent in the firing patterns of 3D place cells. These results suggest that the bat hippocampus represents 3D volumetric space by a uniform and nearly isotropic rate code.

Pausing purkinje cells in the cerebellum of the awake cat

A recent controversy has emerged concerning the existence of long pauses, presumably reflecting bistability of membrane potential, in the cerebellar Purkinje cells (PC) of awake animals. It is generally agreed that in the anesthetized animals and in vitro, these cells switch between two stable membrane potential states: a depolarized state (the ‘up-state’) characterized by continuous firing of simple spikes (SS) and a hyperpolarized state (the ‘down-state’) characterized by long pauses in the SS activity. To address the existence of long pauses in the neural activity of cerebellar PCs in the awake and behaving animal we used extracellular recordings in cats and find that approximately half of the recorded PCs exhibit such long pauses in the SS activity and transition between activity – periods with uninterrupted SS lasting an average of 1300 ms – and pauses up to several seconds. We called these cells pausing Purkinje cells (PPC) and they can easily be distinguished from continuous firing Purkinje cells. In most PPCs, state transitions in both directions were often associated (25% of state transitions) with complex spikes (CSs). This is consistent with intracellular findings of CS-driven state transitions. In sum, we present proof for the existence of long pauses in the PC SS activity that probably reflect underlying bistability, provide the first in-depth analysis of these pauses and show for the first time that transitions in and out of these pauses are related to CS firing in the awake and behaving animal.