A multi-scale brain map derived from whole-brain volumetric reconstructions
Open accessAbstract
Animal nervous system organization is crucial for all body functions and its disruption can lead to severe cognitive and behavioural impairment 1. This organization relies on features across scales-from the localization of synapses at the nanoscale, through neurons, which possess intricate neuronal morphologies that underpin circuit organization, to stereotyped connections between different regions of the brain 2. The sheer complexity of this organ means that the feat of reconstructing and modelling the structure of a complete nervous system that is integrated across all of these scales has yet to be achieved. Here we present a complete structure-function model of the main neuropil in the nematode Caenorhabditis elegans-the nerve ring-which we derive by integrating the volumetric reconstructions from two animals with corresponding 3 synaptic and gap-junctional connectomes. Whereas previously the nerve ring was considered to be a densely packed tract of neural processes, we uncover internal organization and show how local neighbourhoods spatially constrain and support the synaptic connectome. We find that the C. elegans connectome is not invariant, but that a precisely wired core circuit is embedded in a background of variable connectivity, and identify a candidate reference connectome for the core circuit. Using this reference, we propose a modular network architecture of the C. elegans brain that supports sensory computation and integration, sensorimotor convergence and brain-wide coordination. These findings reveal scalable and robust features of brain organization that may be universal across phyla.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Of the 302 CNS neurons, 180 make synapses in the brain.
“Of the 302 CNS neurons, 180 make synapses in the brain126.”
From Neuronal wiring diagram of an adult brain (2024) · cites this paper as [126]
The section “Conserved and variable circuits overlap” describes neurons making synaptic contacts in the nerve ring, but gives no count of 180 neurons. Searches of our copy for “180,” “302,” and the claimed ratio found no passage establishing that 180 of 302 CNS neurons make synapses in the brain; page numbers were not available. (LLM, conf=0.72)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Deep Residual Learning for Image Recognition
He, K., Zhang, X., Ren, S., & Sun, J. (2016) · 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) · doi:10.1109/cvpr.2016.90 · Cited by 235,474 · see citing works
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430 · see citing works
Finding and evaluating community structure in networks
Newman, M. E. J., & Girvan, M. (2004) · Physical Review E · doi:10.1103/physreve.69.026113 · Cited by 13,931 · see citing works
The structure of the nervous system of the nematode <i>Caenorhabditis elegans</i>
White, J. G., Southgate, E., Thomson, J. N., & Brenner, S. (1986) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1986.0056 · Cited by 5,589 · cited 10× · see citing works
“Furthermore, whereas the synaptic wiring has been exhaustively characterized 3,5,13,16,17 , the spatial proximity of neurons is only partially described 18,19 .”
BackgroundMethodInfluentialWhole-animal connectomes of both Caenorhabditis elegans sexes
Cook, S. J., Jarrell, T. A., Brittin, C. A., Wang, Y., Bloniarz, A. E., Yakovlev, M. A., Nguyen, K. C. Q., Tang, L. T.-H., Bayer, E. A., Duerr, J. S., et al. (2019) · Nature · doi:10.1038/s41586-019-1352-7 · Cited by 921 · see citing works
Self-citationThe pharynx of <i>Caenorhabditis elegans</i>
Albertson, D. G., & Thompson, J. N. (1976) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1976.0085 · Cited by 649 · cited 1× · see citing works
“Furthermore, whereas the synaptic wiring has been exhaustively characterized 3,5,13,16,17 , the spatial proximity of neurons is only partially described 18,19 .”
BackgroundThe Rich Club of the<i>C. elegans</i>Neuronal Connectome
Towlson, E. K., Vértes, P. E., Ahnert, S. E., Schafer, W. R., & Bullmore, E. T. (2013) · The Journal of Neuroscience · doi:10.1523/jneurosci.3784-12.2013 · Cited by 343 · see citing works
Dense connectomic reconstruction in layer 4 of the somatosensory cortex
Motta, A., Berning, M., Boergens, K. M., Staffler, B., Beining, M., Loomba, S., Hennig, P., Wissler, H., & Helmstaedter, M. (2019) · Science · doi:10.1126/science.aay3134 · Cited by 333 · see citing works
Hall, D., & Russell, R. (1991) · The Journal of Neuroscience · doi:10.1523/jneurosci.11-01-00001.1991 · Cited by 268 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 42
- [1]Hahamy A, Behrmann M. & Malach R. The idiosyncratic brain: Distortion of spontaneous connectivity patterns in autism spectrum disorder. Nat. Neurosci 18, 302– 309 (2015). 25599222
- [2]Swanson LW & Lichtman JW From Cajal to connectome and beyond. Ann. Rev. Neurosci 39, 197– 216 (2016). 27442070
- [4]Ryan K, Lu Z. & Meinertzhagen IA The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling. eLife 5, e16962 (2016). PMC5140270 27921996
- [7]Jarrell TA The connectome of a decision-making neural network. Science 337, 437– 444 (2012). 22837521
- [8]Bumbarger DJ, Riebesell M, Rodelsperger C. & Sommer RJ System-wide rewiring underlies¨ behavioral differences in predatory and bacterial-feeding nematodes. Cell 152, 109– 119 (2013). 23332749
- [9]Ohyama T. A multilevel multimodal circuit enhances action selection in Drosophila. Nature 520, 633– 639 (2015). 25896325
- [10]Zheng Z. A complete electron microscopy volume of the brain of adult Drosophila melanogaster. Cell 174, 730– 743 (2018). 30033368 PMC6063995
- [11]Kasthuri N. Saturated reconstruction of a volume of neocortex. Cell 162, 648– 61 (2015). 26232230
- [13]Varshney LR, Chen BL, Paniagua E, Hall DH & Chklovskii DB Structural properties of the Caenorhabditis elegans neuronal network. PLoS Comput. Biol 7, 21 (2011). PMC3033362 21304930
- [14]Sulston JE, Schierenberg E, White JG & Thomson JN The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol 100, 64– 119 (1983). 6684600
- [15]Barabási DL & Barabási A-L A genetic model of the connectome. Neuron 105, 435– 445 (2020). 31806491 PMC7007360
- [17]Cook SJ The connectome of the Caenorhabditis elegans pharynx. J. Comp. Neurol 528, 2767– 2784 (2020). 32352566 PMC7601127
- [18]White J, Southgate E, Thomson J. & Brenner S. Factors that determine connectivity in the nervous system of Caenorhabditis elegans. Cold Spring Harb. Symp. Quant. Biol 48, 633– 640 (1983). 6586380
- [19]Durbin RM Studies on the development and organisation of the nervous system of Caenorhabditis elegans. Ph.D. thesis, University of Cambridge (1987).
- [20]Witvliet D. Connectomes across development reveal principles of brain maturation in C. elegans. Preprint at https://www.biorxiv.org/content/10.1101/2020.04.30.066209v1 (2020). PMC8756380 34349261 · DOI
- [21]Blondel VD, Guillaume J-L, Lambiotte R. & Lefebvre E. Fast unfolding of communities in large networks. J. Stat. Mech 2008, P10008 (2008).
- [22]Gray JM, Hill JJ & Bargmann CI A circuit for navigation in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 102, 3184– 91 (2005). 15689400 PMC546636
- [23]Kato S. Global brain dynamics embed the motor command sequence of Caenorhabditis elegans. Cell 163, 656– 669 (2015). 26478179
- [26]Milo R. Network motifs: simple building blocks of complex networks. Science 298, 824– 827 (2002). 12399590
- [28]Thomson AM Neocortical layer 6, a review. Front. Neuroanat 4 (2010). PMC2885865 20556241
- [29]Rapti G, Li C, Shan A, Lu Y. & Shaham S. Glia initiate brain assembly through noncanonical Chimaerin–Furin axon guidance in C. elegans. Nat. Neurosci 20, 1350– 1360 (2017). 28846083 PMC5614858
- [30]Morgan JL & Lichtman JW An individual interneuron participates in many kinds of inhibition and innervates much of the mouse visual thalamus. Neuron 106, 468– 481 (2020). 32142646 PMC7295017
- [31]Chen X. Brain-wide organization of neuronal activity and convergent sensorimotor transformations in larval zebrafish. Neuron 100, 876– 890 (2018). 30473013 PMC6543271
- [32]Stern S, Kirst C. & Bargmann CI Neuromodulatory control of long-term behavioral patterns and individuality across development. Cell 171, 1649– 1662 (2017). 29198526
- [33]Wang L. & Marquardt T. What axons tell each other: Axon-axon signaling in nerve and circuit assembly. Curr. Opin. Neurobiol 23, 974– 982 (2013). 23973157
- [34]Moyle MW Structural and developmental principles of neuropil assembly in C. elegans Preprint at https://www.biorxiv.org/content/10.1101/2020.03.15.992222v1 (2020). PMC8385650 33627875 · DOI
- [37]Peachey LD Thin sections. I. A study of section thickness and physical distortion produced during microtomy. J. Biophys. Biochem. Cyt 4, 233– 242 (1958). PMC2224471 13549493
- [38]Cardona A. TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE 7, e38011 (2012). PMC3378562 22723842
- [39]Xu M. Computer assisted assembly of connectomes from electron micrographs: Application to Caenorhabditis elegans. PLoS ONE 8, e54050 (2013). PMC3546938 23342070
- [41]Rosvall M. & Bergstrom CT Maps of random walks on complex networks reveal community structure. Proc. Natl. Acad. Sci. USA 105, 1118– 1123 (2008). 18216267 PMC2234100
- [44]Chang AJ, Chronis N, Karow DS, Marletta MA & Bargmann CI A distributed chemosensory circuit for oxygen preference in C. elegans. PLoS Biol. 4, e274 (2006). 16903785 PMC1540710
- [45]Zimmer M. Neurons detect increases and decreases in oxygen levels using distinct guanylate cyclases. Neuron 61, 865– 879 (2009). 19323996 PMC2760494
- [46]Tomioka M. The Insulin/PI 3-Kinase pathway regulates salt chemotaxis learning in Caenorhabditis elegans. Neuron 51, 613– 625 (2006). 16950159
- [47]Hendricks M, Ha H, Maffey N. & Zhang Y. Compartmentalized calcium dynamics in a C. elegans interneuron encode head movement. Nature 487, 99– 103 (2012). 22722842 PMC3393794
- [48]Perkins LA, Hedgecock EM, Thomson JN & Culotti JG Mutant sensory cilia in the nematode Caenorhabditis elegans. Dev. Biol 117, 456– 487 (1986). 2428682
- [49]Sawin ER, Ranganathan R. & Horvitz HR C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway. Neuron 26, 619– 631 (2000). 10896158
- [50]Kang L, Gao J, Schafer WR, Xie Z. & Xu XZ C. elegans TRP family protein TRP-4 is apore-forming subunit of a native mechanotransduction channel. Neuron 67, 381– 391 (2010). 20696377 PMC2928144
- [51]Chalfie M. & Sulston J. Developmental genetics of the mechanosensory neurons of Caenorhabditis elegans. Dev. Biol 82, 358– 370 (1981). 7227647
- [52]Suzuki H. In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the MEC-4 channel in the process of gentle touch sensation. Neuron 39, 1005– 1017 (2003). 12971899
- [53]Chalfie M. The neural circuit for touch sensitivity in Caenorhabditis elegans. J. Neurosci 5, 956– 964 (1985). 3981252 PMC6565008
- [54]Li C. The FMRFamide-related neuropeptide FLP-20 is required in the mechanosensory neurons during memory for massed training in C. elegans. Learn. Mem 20, 103– 108 (2013). 23325727 PMC3549060
- [55]Hukema RK, Rademakers S, Dekkers MPJ, Burghoorn J. & Jansen G. Antagonistic sensory cues generate gustatory plasticity in Caenorhabditis elegans. EMBO J. 25, 312– 322 (2006). 16407969 PMC1383522
Cited by
Sorted by citations
Neuronal wiring diagram of an adult brain
Dorkenwald, S., Matsliah, A., Sterling, A. R., Schlegel, P., Yu, S.-C., McKellar, C. E., Lin, A., Costa, M., Eichler, K., Yin, Y., et al. (2024) · Nature · doi:10.1038/s41586-024-07558-y · Cited by 570 · see citing works
“Of the 302 CNS neurons, 180 make synapses in the brain 126 .”
BackgroundNeuronal wiring diagram of an adult brain
Dorkenwald, S., Matsliah, A., Sterling, A. R., Schlegel, P., Yu, S.-C., McKellar, C. E., Lin, A., Costa, M., Eichler, K., Yin, Y., et al. (2023) · doi:10.1101/2023.06.27.546656 · Cited by 149 · see citing works
BRAIN 2.0: Transforming neuroscience
Ngai, J. (2022) · Cell · doi:10.1016/j.cell.2021.11.037 · Cited by 77 · see citing works
“All animals are conscious”: Shifting the null hypothesis in consciousness science
Andrews, K. (2024) · Mind & Language · doi:10.1111/mila.12498 · Cited by 40 · see citing works
An integrative data-driven model simulating C. elegans brain, body and environment interactions
Zhao, M., Wang, N., Jiang, X., Ma, X., Ma, H., He, G., Du, K., Ma, L., & Huang, T. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00738-w · Cited by 29 · see citing works
“It has completely mapped morphologies of all 302 neurons 14,15 (in adult hermaphrodite), along with the connectome and synapse-level structure 16–18 .”
Cyclic structure with cellular precision in a vertebrate sensorimotor neural circuit
Yang, R., Vishwanathan, A., Wu, J., Kemnitz, N., Ih, D., Turner, N., Lee, K., Tartavull, I., Silversmith, W. M., Jordan, C. S., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.05.010 · Cited by 11 · see citing works
Zalucki, O., Brown, D. J., & Key, B. (2023) · Biology & Philosophy · doi:10.1007/s10539-023-09924-y · Cited by 7 · see citing works
Principles of synaptogenesis: Insights from Caenorhabditis elegans
Frankel, E. B., & Kurshan, P. T. (2025) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2025.103056 · Cited by 7 · see citing works
Birch, J. (2024) · The Edge of Sentience · doi:10.1093/9780191966729.003.0003 · Cited by 1 · see citing works
- Authors
- Brittin, C. A., Cook, S. J., Hall, D. H., Emmons, S. W., & Cohen, N.
- Affiliations
- Albert Einstein College of Medicine (US)
- University of Leeds (GB)
- Corresponding author
- Cohen, Netta
- Venue
- Nature
- Published
- 2021-02-24
- Volume
- 591
- Issue
- 7848
- Pages
- 105-110
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC11648602
- OpenAlex
- W3131776733
- Cited by
- 116
- References
- 9
- Citations by year
- 2026: 9 · 2025: 14 · 2024: 45 · 2023: 20 · 2022: 16 · 2021: 12
- FWCI
- 10.72
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health (R24OD010943)
- Engineering and Physical Sciences Research Council (EP/J004057/1)
- National Institute of Mental Health (R01MH112689, F32MH115438)
- National Center for Research Resources (R24RR012596)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P30HD071593)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neurobiology and Insect Physiology Research
- Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- Caenorhabditis elegans, nerve ring, connectome, volumetric reconstruction, synaptic connectivity, gap junctions, structural-functional model, modular network architecture, nervous system evolution
- MeSH terms
- Animals, Brain, Models, Biological, Neural Pathways, Synapses, Neurites, Caenorhabditis elegans, Gap Junctions, Neuropil, Connectome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review