Summary: What did the first complex vertebrate brain look like? To answer this central evolutionary question, researchers have produced the first three-dimensional, single-cell transcriptomic atlas of an entire lamprey brain. The lamprey—a jawless, eel-like fish whose basic body plan has remained largely unchanged for roughly 360 million years—serves as a living window into early vertebrate brain organization.
Using high-resolution spatial and single-nucleus RNA sequencing, the team mapped the precise locations and gene-expression profiles of individual cells across the whole lamprey brain. By comparing this primitive blueprint with modern mammalian brains, they found deeply conserved molecular patterns across many core brain regions. These results indicate that the vertebrate common ancestor already possessed a highly organized and molecularly distinct brain architecture rather than an undifferentiated nerve mass.
Key Facts
- First 3D single-cell map: The study delivers the first comprehensive three-dimensional cellular blueprint of a jawless vertebrate brain, combining spatial positioning with active gene-expression data for individual cells.
- Deep evolutionary homology: Core frontostriatal and subcortical networks in lampreys show conserved molecular and genetic signatures when compared with mouse brain regions, pushing the origin of organized vertebrate brain architecture back more than 450 million years.
- “Moonlighting” neurons: The atlas identifies anamniote-enriched neurons (AENs), versatile cells that carry both excitatory and inhibitory signals, performing multiple roles within ancestral neural circuits.
- Duplication and specialization: These multifunctional AENs are common in lampreys and zebrafish but rare in amniotes (reptiles, birds, and mammals), which instead predominantly use specialist neurons—a shift likely linked to ancient whole-genome duplication events.
- Lineage-specific innovations: The lamprey exhibits unique midbrain neurons and very large Müller-like cells, while mammalian evolution produced a multilayered neocortex and other derived architectures.
- Primitive cerebellar roots: The atlas uncovers a dispersed population of cells with cerebellar molecular signatures, indicating an early, diffuse cerebellum-like region present before the evolution of jaws.
Source: Chinese Academy of Sciences
Why the lamprey? The lamprey occupies a pivotal evolutionary position. Having split from jawed vertebrates roughly 450 million years ago and retaining many ancestral features, it provides a comparative baseline for reconstructing the earliest vertebrate brain blueprint.
Published in Science on June 18, the study was led by SU Bing of the Kunming Institute of Zoology, Chinese Academy of Sciences, with collaborators from BGI-Research and Liaoning Normal University. The researchers combined single-nucleus RNA sequencing with high-resolution spatial transcriptomics to build a complete 3D molecular atlas of the adult lamprey brain—locating every major cell population and profiling active genes across the entire nervous system.
Despite evolving separately from jawed vertebrates for over 450 million years, lamprey brain regions such as the olfactory bulb, thalamus, and hindbrain share similar cellular compositions and spatial arrangements with those of mice. These conserved molecular signatures support the idea that a complex, regionally organized brain existed in the last common ancestor of all vertebrates.
At the same time, the study highlights evolutionary divergence: the lamprey shows lineage-specific midbrain neurons and oversized Müller cells, while mammals evolved elaborate cortical layering and other derived specializations. The data also illuminate how neuronal specialization unfolded: ancestral multifunctional neurons gradually resolved into more specialized cell types in later lineages.
One notable finding is the presence of anamniote-enriched neurons (AENs) in lampreys—cells that can simultaneously mediate excitatory and inhibitory signaling. These “moonlighting” neurons are common in lampreys and zebrafish but are largely absent in amniotes, where gene duplication and divergence produced distinct excitatory and inhibitory neuron classes. This shift toward specialization likely contributed to more complex and segregated neural circuits in terrestrial vertebrates.
The atlas also detects dispersed cell types with cerebellar molecular profiles, revealing that the developmental and molecular foundations of the cerebellum predate jawed vertebrates. These primitive cerebellum-like cells suggest that motor coordination networks were already emerging in early vertebrate evolution.
Taken together, the 3D single-cell atlas reconstructs key elements of the ancestral vertebrate brain and clarifies how ancient, multifunctional cell types were reorganized and specialized over evolutionary time to create the diverse and regionally complex brains seen across modern vertebrates.
Key Questions Answered:
A: The lamprey split from jawed vertebrates around 450 million years ago and has retained many ancestral anatomical and molecular features. Because it lacks many derived innovations found in modern fish, reptiles, and mammals, its brain preserves an earlier organizational state and serves as a comparative reference for reconstructing the ancestral vertebrate brain blueprint.
A: “Moonlighting” neurons, identified here as anamniote-enriched neurons (AENs), are versatile cells that combine excitatory and inhibitory signaling capabilities. In early vertebrates such cells were common, but in amniote lineages they largely disappeared as genome duplications and subsequent specialization produced separate, dedicated excitatory and inhibitory neuron classes.
A: The evidence indicates an embryonic or diffuse form of cerebellum was present. While lampreys lack the compact, layered cerebellum of mammals, the atlas identifies cells with cerebellar gene-expression signatures, supporting the existence of a primitive cerebellum-like region in early vertebrates.
Editorial Notes:
- This article was edited by a Neuroscience News editor.
- The original journal paper was reviewed in full.
- Additional context was added by editorial staff.
About this brain-mapping and evolutionary neuroscience research
Author: SU Bing (Kunming Institute of Zoology) and collaborators
Source: Kunming Institute of Zoology, Chinese Academy of Sciences
Contact: SU Bing – Kunming Institute of Zoology
Image credit: Neuroscience News
Original Research: Open access.
Paper: Lamprey 3D single-cell transcriptomics reveals ancestral and specialized features of the vertebrate brain. DOI: 10.1126/science.aea2535
Abstract
Lamprey 3D single-cell transcriptomics reveals ancestral and specialized features of the vertebrate brain
INTRODUCTION
The vertebrate brain is organized into distinct regions and diverse cell types that together support complex behaviors. Reconstructing how this complexity arose requires comparative analyses across deep evolutionary time. The lamprey, a basal jawless vertebrate that diverged from jawed vertebrates around 450 million years ago, retains many ancestral brain features and lacks several derived specializations such as a layered neocortex, making it an ideal model for separating ancestral traits from later innovations.
RATIONALE
Previous single-cell studies cataloged brain cell types in several species, but a complete three-dimensional spatial map for a jawless vertebrate was lacking. To fill this gap, researchers combined single-nucleus RNA sequencing with high-resolution spatial transcriptomics to assemble a full 3D molecular atlas of the adult lamprey brain. They then compared these data with new zebrafish profiles and existing datasets from reptiles, birds, and mammals to trace evolutionary changes in brain structure, cell composition, spatial layout, and molecular identity.
RESULTS
The 3D atlas identifies 209 distinct cell populations across 14 major brain regions in the lamprey. Many core structures—including the olfactory bulb, thalamus, and hindbrain—display conserved cellular organization and molecular signatures when compared with mouse. At the same time, the atlas reveals lineage-specific differences, such as unique midbrain neurons and oversized Müller cells in lamprey, and the layered forebrain architecture that evolved in mammals. The data show a pronounced evolutionary shift from multifunctional ancestral neurons toward specialized neuronal types, as well as the presence of primitive cerebellar-like cells in lamprey that prefigure the vertebrate cerebellum.
CONCLUSION
This 3D single-cell atlas demonstrates that the last common ancestor of vertebrates already possessed a sophisticated, regionally organized brain. Subsequent evolution increased complexity not only by adding new structures but by refining and specializing ancient cell types and reorganizing their spatial relationships. The shift from broadly functioning ancestral neurons to specialized, segregated circuits underlies much of the functional diversification observed across modern vertebrate brains.