The written record

A Hippocampal Digital Twin Reveals Latent Structure in Freely Flying Bats

Adam S. Lowet†, Yongrong Qiu†, Angelo Forli, Krishna C. Kasuba, Yang Lin, Andreas S. Tolias‡ and Michael M. Yartsev‡ († Equal contribution; ‡ Co-last authors)

A digital twin of the hippocampus: an AI model trained jointly on neural activity and free flight that predicts both. Although trained only on flight, it generalizes to data it never saw, including new recording sessions and even activity during rest and sleep. Its internal representations also revealed a hidden organizing principle, confirmed in the recorded neurons: spatially distinct paths between the same origin and destination share one underlying firing sequence.

A Two-Dimensional Grid-Cell Code for Three-Dimensional Navigation in Freely Flying Bats

Kevin K Qi, Michael M Yartsev

Grid cells in freely flying bats preserve a two-dimensional toroidal code that aligns with the planar structure of flight paths, offering a parsimonious solution for navigating three-dimensional space.

A High-Dimensional Population Code in the Bat Motor Cortex During Natural Dexterous Flight

Boaz Styr, Kevin K. Qi, Xing Chen, William A. Liberti III and Michael M. Yartsev

Bats fly with their hands: their scientific name, Chiroptera, literally means hand-wing. Their flight is like playing piano in mid-air, reshaping the wing from moment to moment through roughly 30 joints across both wings, a natural behavior of extremely dexterous motor control. The wing motor cortex supporting it operates in a high-dimensional regime rarely seen in simpler, more reduced preparations, with sparsely active neurons combining mixed kinematic selectivity and millisecond-precise entrainment to the wingbeat. bioRxiv preprint →

Coverage:Berkeley Engineering News

Ultrafast Frame-Free Imaging of Neural Activity with Event Cameras

Angelo Forli†, Krishna Chaitanya Kasuba†, Katharine Henn, Deborah Lee, Miriam Hernández-Morales, Chunlei Liu, Evan Miller, and Michael M. Yartsev († Equal contribution)

Event cameras report fluorescence changes as sparse asynchronous events rather than frames, resolving single action potentials at kilohertz rates and opening a new path toward large-scale voltage imaging in freely behaving, even flying, animals.

Natural behavior is what you do, not just where you are

Yartsev, M.M.

Naturalistic environments can create an illusion of ecological relevance: studying natural behavior demands an ethological focus on what animals actually do, not only on where experiments take place.

Replay and representation dynamics in the hippocampus of freely flying bats

Angelo Forli, Wudi Fan, Kevin K. Qi, Michael M. Yartsev

Hippocampal ensembles in flying bats replay entire flight trajectories at rest and sweep ahead of the animal in flight, locked to the wing-beat rhythm rather than theta oscillations.

Coverage:UC Berkeley News · Behind the Paper, Springer Nature

Understanding the Neural Basis of Natural Intelligence

Angelo Forli & Michael M Yartsev

Understanding natural intelligence requires moving beyond strict reductionism: new tools now give access to neural dynamics and behavior across timescales, contexts, and species, bringing real-world principles within reach.

Coverage:Berkeley Neuroscience News

Role of auditory feedback for vocal production learning in the Egyptian fruit-bat

Julie E Elie, Sandra E Muroy, Daria Genzel, Tong Na, Lisa A Beyer, Donald L Swiderski, Yehoash Raphael & Michael M Yartsev

A subset of the Egyptian fruit bat vocal repertoire requires auditory feedback to develop, and the affected vocalizations differ between males and females, revealing sexually dimorphic vocal learning.

Neural Representation of Human Experimenters in the Bat Hippocampus

Madeleine C. Snyder, Kevin K. Qi & Michael M. Yartsev

Hippocampal neurons in bats encode the presence, position, and identity of human experimenters, indicating that researchers themselves shape the neural dynamics of the animals they study: a gentle case for letting animals behave naturally, without a human in the room.

Coverage:Nature Neuroscience Research Briefing · The Transmitter · PsyPost

Vocal Learning-Associated Convergent Evolution in Mammalian Proteins and Regulatory Elements

Morgan E. Wirthlin^, Tobias A. Schmid^, Julie E. Elie^, Xiaomeng Zhang, Varvara A. Shvareva, Ashley Rakuljuc, Maria B. Ji, Ninad S. Bhat, Irene M. Kaplow, Daniel E. Schaffer, Alyssa J. Lawler, Siddharth Annaldasula, Byungkook Lim, Eiman Azim, Zoonomia Consortium, Wynn K. Meter, Michael M. Yartsev*, Andreas P. Pfenning* (^ co-first authors, * co-last & corresponding authors)

Comparative genomics across 215 mammals, anchored by a newly identified vocal motor cortical region in Egyptian fruit bats, implicates convergent losses of motor cortex regulatory elements in vocal learning evolution.

Coverage:UC Berkeley News

Hippocampal Representation During Collective Spatial Behavior in Bats

Angelo Forli & Michael M. Yartsev

In groups of bats engaged in collective spatial behavior, hippocampal neurons are tuned to conspecific presence, shared locations, individual identities, and sensory signals broadcast within the group.

Coverage:UC Berkeley News · Quanta Magazine · Nature Research Briefing

Natural behavior is the language of the brain

Cory T. Miller, David Gire, Kim Hoke, Alexander C. Huk, Darcy Kelley, David A. Leopold, Matthew C. Smear, Frederic Theunissen, Michael Yartsev, Cristopher M. Niell

A roadmap for grounding neuroscience in naturally occurring behavior: harnessing behavioral variability, rather than eliminating it, links neural activity to the everyday challenges animals evolved to solve.

A Stable Hippocampal Code in Freely Flying Bats

William A. Liberti III*, Tobias A. Schmid*, Angelo Forli, Madeleine Snyder & Michael M. Yartsev (* Equal contribution)

The spatial tuning of hippocampal neurons in freely flying bats remains stable over days and weeks: apparent instability largely reflects variation in the animals' flight behavior.

Coverage:Berkeley Neuroscience News · Berkeley Engineering News

A Unifying Mechanism Governing Inter-Brain Neural Relationship During Social Interactions

Wujie Zhang & Michael M. Yartsev

A single feedback mechanism explains both the fast fluctuations in neural activity differences between interacting brains and the slow covariation in the activity they share.

Cortical Representation of Group Social Communication in Bats

Maimon C. Rose*, Boaz Styr*, Tobias A. Schmid, Julie E. Elie & Michael M. Yartsev (* Equal contribution)

Frontal cortical neurons in freely communicating groups of bats distinguish vocalizations of self from others and among individuals, with interbrain correlations shaped by each bat's social preferences.

Coverage:UC Berkeley News · Scientific American · Science Perspective · Aeon essay

Nonlocal Spatiotemporal Representation in the Hippocampus of Freely Flying Bats

Nicholas M. Dotson & Michael M. Yartsev

Hippocampal activity in freely flying bats predominantly encodes positions meters away from the animal's current location, extending backward and forward in time with an emphasis on the future.

Coverage:UC Berkeley News · MIT Technology Review

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

Daria Genzel & Michael M. Yartsev

A human-free, fully automated flight room enables complex natural behaviors in flying bats, with initial recordings revealing retrosplenial neurons that multiplex position, target choice, reward, and visual cues.

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

Morgan Wirthlin, Edward F. Chang, Mirjam Knornschild, Leah A. Krubitzer, Claudio V. Mello, Cory T. Miller, Andreas R. Pfenning, Sonja C. Vernes, Ofer Tchernichovski & Michael M. Yartsev

Vocal learning is not a binary trait but a multi-component phenotype of distinct, interconnected modules, a framework that enables comparative study across a wider diversity of species.

Long-term and persistent vocal plasticity in adult bats

Daria Genzel, Janki Desai, Elana Paras and Michael M. Yartsev

Adult Egyptian fruit bats exposed to broad-band acoustic perturbation modify distinct parameters of their vocalizations, and these changes persist for weeks to months after the noise ceases.

Correlated Neural Activity Across the Brains of Socially Interacting Bats

Wujie Zhang and Michael M. Yartsev

Neural activity in the brains of socially interacting bats is correlated across timescales from seconds to hours, and this inter-brain correlation rises before social interactions begin.

Coverage:UC Berkeley News · Cell Preview by Omer, Zilkha & Kimchi

A Hierarchical Anti-Hebbian Network Model for the Formation of Spatial Cells in Three-Dimensional Space

Karthik Soman, Srinivasa Chakravarthy and Michael M. Yartsev

A hierarchical anti-Hebbian network model accounts for the emergence of three-dimensional place, border, and grid cells, and predicts a previously undescribed spatial cell type: plane cells.

Nonoscillatory phase-coding and synchronization in the bat hippocampal formation

Tamir Eliav, Maya Geva-Sagiv, Michael M. Yartsev, Arseny Finkelstein, Alon Rubin, Liora Las, Nachum Ulanovsky

Bat hippocampal neurons lock to nonrhythmic field-potential fluctuations and exhibit phase coding of position, demonstrating that temporal coding and synchrony do not require continuous theta oscillations.

Neuroethology of Bat Navigation

Daria Genzel, Yosef Yovel and Michael M. Yartsev

Bats solve navigational challenges ranging from nightly foraging commutes to continent-scale migration: a review of the behavioral strategies and neural mechanisms enabling flight through three-dimensional environments.

Causal contribution and dynamical encoding in the striatum during evidence accumulation

Michael M. Yartsev*, Timothy D Hanks*, Alice M Yoon, Carlos D Brody

The anterior dorsal striatum satisfies all three criteria for direct involvement in evidence accumulation: causal influence on decisions, graded encoding of accumulated evidence, and contribution throughout the accumulation process.

The Emperor's New Wardrobe: Rebalancing Diversity of Animal Models in Neuroscience Research

Michael Yartsev

Species diversity in neuroscience research is sharply declining even as technologies advance: the limitations of converging on a few model organisms, and how broader species choice rectifies them.

Coverage:F1000 Prime recommendation

Space Bats: Multi-dimensional spatial representation in the bat

Michael Yartsev

A prize essay on the bat as a model for multidimensional spatial coding: place cells map three-dimensional space in flight through neural mechanisms distinct from those described in rodents.

Coverage:AAAS News

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

Michael Yartsev & Nachum Ulanovsky

Wireless recordings from freely flying bats reveal hippocampal place cells with confined three-dimensional firing fields, encoding volumetric space through a uniform, nearly isotropic rate code without theta rhythmicity.

Coverage:Science Perspective · F1000 Prime recommendation

Reply to Models of grid cells and theta oscillations

Michael Yartsev, Menno Witter and Nachum Ulanovsky

A response to Barry and colleagues: even accounting for slow movement and low firing rates, bat grid cells lack theta rhythmicity, upholding the challenge to oscillatory interference models.

Grid cells without theta oscillations in the entorhinal cortex of bats

Michael Yartsev, Menno Witter and Nachum Ulanovsky

Grid cells exist in the bat entorhinal cortex without continuous theta oscillations, arguing against oscillatory interference models of how the brain's spatial map is generated.

Coverage:Nature News & Views · Current Biology Dispatch · F1000 Prime recommendation