Eye movement kinematics reveal novel circadian organization of sleep substates.

Overview

1. Max Planck Institute for Biological Cybernetics, Tübingen, Germany

Abstract

In most non-mammalian model organisms, sleep is operationally defined as persistent locomotor quiescence (e.g., ≥1 min) associated with decreased arousal1–3. In contrast to the long-established subdivision of mammalian sleep by eye movements4–9, the existence of sleep-associated eye movements and, more broadly, discrete sleep substates in non-mammalian organisms remains actively debated10–14. Here we present the first systematic investigation of fish eye movements during naturally occurring sleep across the full circadian cycle, under light–dark cycles as well as constant light and constant darkness. Across Danio species (Danio rerio, Danio nigrofasciatus and Danio aesculapii), we identify four discrete, conserved sleep substates with circadian organization: three sleep states with distinct eye-movement kinematics (QEM-1, QEM-2 and QEM-3) and one sleep state with no eye movements (QNEM). QNEM predominates at night, QEM-2 increases toward morning, and unexpectedly, QEM-1 occurs almost exclusively during the day. QEM-1 fulfills multiple criteria for sleep in zebrafish, including elevated arousal thresholds, partial loss of postural control, homeostatic rebound after deprivation, noradrenergic suppression, and brain-wide neural dynamics that encode state progression. Altogether, these findings uncover a previously unrecognized sleep architecture in larval fish, in which multiple substates with distinct eye-movement kinematics are conserved across Danio species and gated by circadian time and ambient light.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

No file of the authors' code could be read here: it is described below, and read at its source.

Code availability

Code used to generate the findings and figures of this study is available at https://github.com/crheller/saccade-ms.git.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

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Data availability

Source data for all graphs generated in this study are provided as a Source Data file with this paper. Raw imaging data are available from the corresponding authors upon request due to their large file size ( > 20TB). Source data are provided with this paper.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 2 keywords, 8 MeSH terms, 1 funder, 59 references.

Cite

This paper

Choudhary, V., Heller, C. R., Aimon, S., de Sardenberg Schmid, L., Li, J. M., & Robson, D. N. (2026). Eye movement kinematics reveal novel circadian organization of sleep substates. Nature communications, 17(1), 4068. https://doi.org/10.1038/s41467-026-72222-0

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