Whole-animal connectomes of both Caenorhabditis elegans sexes

In the paper

“Connectivity has been described previously for sections of the C. elegans nervous system that encompasses the major neural centres, including the anterior and posterior body regions and the pharynx of the adult hermaphrodite and the posterior region of the adult male1–4,18.”

What the sources say

• ?Not checked — no full text of the sourcecites [1] White, J. G., Southgate, E., Thomson, J. N. & Brenner, S. The structure of the nervous system of the nematode Caenorhabditis elegans. Phil. Trans. R. Soc. Lond. B 314, 1–340 (1986). source
• ?Not checked — no full text of the sourcecites [2] Albertson, D. G. & Thomson, J. N. The pharynx of Caenorhabditis elegans. Phil. Trans. R. Soc. Lond. B 275, 299–325 (1976). source
• ?Not checked — no full text of the sourcecites [3] Jarrell, T. A. et al. The connectome of a decision-making neural network. Science 337, 437–444 (2012). source
• Partly supported

  The paper’s opening passage says earlier reports described the anterior sensory cells, pharynx, ventral nerve cord and nerve ring; it then describes this paper’s reconstruction of synaptic interactions in the adult hermaphrodite tail. That supports the claim about connectivity in parts of the hermaphrodite nervous system, but our copy does not support the adult-male posterior-region component. (LLM, conf=0.88)

  cites [4] Hall, D. H. & Russell, R. L. The posterior nervous system of the nematode Caenorhabditis elegans: serial reconstruction of identified neurons and complete pattern of synaptic interactions. J. Neurosci. 11, 1–22 (1991). sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction and Materials and Methods (Data Acquisition; page unavailable) describe earlier reconstructions of the hermaphrodite nervous system, particularly the anterior, neck, and tail regions. The paper does not establish the claim about previously described connectivity in the adult male’s posterior region; its Results (Reconstruction) also distinguish its somatic wiring diagram from the pharyngeal nervous system. (LLM, conf=0.85)

  cites [18] Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H. & Chklovskii, D. B. Structural properties of the Caenorhabditis elegans neuronal network. PLOS Comput. Biol. 7, e1001066 (2011). sourceExperimental — accuracy not yet measured

In the paper

“As the sensory neurons of C. elegans generally respond to multiple stimuli, sensory integration begins within the sensory neurons themselves25,26.”

What the sources say

• Partly supported

  The Abstract reports that C. elegans PHA/PHB neurons respond to multiple stimuli and use intracellular and intercellular pathways to process them; the Discussion describes encoding and discrimination in those neurons. This supports sensory processing within particular sensory neurons, but the paper does not establish that C. elegans sensory neurons generally respond to multiple stimuli or that integration always begins within them. (LLM, conf=0.82)

  cites [25] Zou, W. et al. Polymodal responses in C. elegans phasmid neurons rely on multiple intracellular and intercellular signaling pathways. Sci. Rep. 7, 42295 (2017). sourceExperimental — accuracy not yet measured
• Partly supported

  The Abstract reports that ASH neurons respond to nose touch, hyperosmolarity, and volatile repellents, and distinguish stimuli through distinct signaling pathways within the neurons. This supports stimulus processing within ASH, but the paper does not establish that C. elegans sensory neurons generally respond to multiple stimuli. (LLM, conf=0.86)

  cites [26] Hart, A. C., Kass, J., Shapiro, J. E. & Kaplan, J. M. Distinct signaling pathways mediate touch and osmosensory responses in a polymodal sensory neuron. J. Neurosci. 19, 1952–1958 (1999). sourceExperimental — accuracy not yet measured

In the paper

“Functional studies have shown that SMD encodes the amplitude of a deep ventral bend behaviour known as the Ω-turn; SMB influences the amplitude of sinusoidal movement; SAB is thought to act in proprioception; and the SIA neurons are involved in so-called ‘flipping behaviour’ during lethargus24,29,30.”

What the sources say

• ?Not checked — no full text of the sourcecites [24] Gray, J. M., Hill, J. J. & Bargmann, C. I. A circuit for navigation in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 102, 3184–3191 (2005). source
• Supported

  The cited paper is pertinent to the SAB clause of the multiply cited sentence. In Results, “Other neuronal signaling features are also unc-3-dependent” (page not supplied), it describes a putative proprioceptive function for SAB neurons, matching the claim’s cautious wording that SAB is thought to act in proprioception. (LLM, conf=0.91)

  cites [29] Kratsios, P. et al. Transcriptional coordination of synaptogenesis and neurotransmitter signaling. Curr. Biol. 25, 1282–1295 (2015). source
• Supported

  The Results section (‘Optogenetic activation of sublateral neurons can induce flipping during lethargus’; page unavailable) reports that activating SIA neurons can trigger flipping and that this is more likely during lethargus. This directly supports the SIA clause attributable to this paper; the other neuron functions in the multiply cited sentence are not treated as claims attributed to this source. (LLM, conf=0.93)

  cites [30] Schwarz, J. & Bringmann, H. Analysis of the NK2 homeobox gene ceh-24 reveals sublateral motor neuron control of left–right turning during sleep. eLife 6, e24846 (2017). source

In the paper

“The notable similarity in the placement of the nodes to the neuroanatomy of the worm reflects economical wiring, a property commonly found for nervous systems, including in C. elegans19–22.”

What the sources say

• Supported

  The opening summary (p. 1) says neuron positions in C. elegans are organized to reduce total wiring cost. The introduction (p. 1) describes cost as a constraint on nervous-system organization, supporting the citing sentence’s broader characterization. The paper does not evaluate the citing authors’ particular node placement, but that similarity is their own observation. (LLM, conf=0.88)

  cites [19] Ahn, Y.-Y., Jeong, H. & Kim, B. J. Wiring cost in the organization of a biological neuronal network. Physica A 367, 531–537 (2006). source
• Supported

  The opening section (p. 1) describes wiring economy as a general principle with many successful applications. It also reports that minimizing wiring cost predicts the positions of most C. elegans neurons; the comparison section (p. 2) says most predicted positions lie close to their actual locations. (LLM, conf=0.90)

  cites [20] Chen, B. L., Hall, D. H. & Chklovskii, D. B. Wiring optimization can relate neuronal structure and function. Proc. Natl Acad. Sci. USA 103, 4723–4728 (2006). source
• ?Not checked — no full text of the sourcecites [21] Wang, I. E. & Clandinin, T. R. The influence of wiring economy on nervous system evolution. Curr. Biol. 26, R1101–R1108 (2016). source
• Partly supported

  The Conclusions (page unavailable) say that total wiring-length minimization has a large influence on C. elegans interneuron placement, supporting the economical-wiring interpretation. But they also note discrepancies between real and optimal positions; the Results report that optimal layouts could reduce real wiring length substantially. The paper does not establish that economical wiring is a common property of nervous systems generally. (LLM, conf=0.84)

  cites [22] Gushchin, A. & Tang, A. Total wiring length minimization of C. elegans neural network: a constrained optimization approach. PLoS ONE 10, e0145029 (2015). sourceExperimental — accuracy not yet measured

In the paper

“The ASEL-ASER pair is known to be lateralized in its ability to sense chemosensory cues34,35.”

What the sources say

• ?Not checked — no full text of the sourcecites [34] Pierce-Shimomura, J. T., Faumont, S., Gaston, M. R., Pearson, B. J. & Lockery, S. R. The homeobox gene lim-6 is required for distinct chemosensory representations in C. elegans. Nature 410, 694–698 (2001). source
• Supported

  The Abstract states that ASEL and ASER express distinct sets of chemoreceptors, giving the gustatory system the capacity to sense and discriminate environmental inputs. The Results also report left–right-specific expression of receptor genes, supporting the claimed lateralization of chemosensory function. (LLM, conf=0.92)

  cites [35] Johnston, R. J. Jr, Chang, S., Etchberger, J. F., Ortiz, C. O. & Hobert, O. MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl Acad. Sci. USA 102, 12449–12454 (2005). sourceExperimental — accuracy not yet measured

In the paper

“For example, the major layer 1 pre-motor interneurons AVA and AVB, which promote backward and forward locomotion, respectively, are targeted by three major male-specific interneurons, PVV, PVX and PVY, that regulate the locomotion of the male during copulation37,38.”

What the sources say

• Partly supported

  The Results section on PVY reports that PVY and PVX target the AVA backward and AVB forward command interneurons, and that PVY promotes backward movement during mating (page unavailable). It does not establish the claimed role for PVV; it also says PVX ablation had no obvious effect on vulva-search behavior, leaving its role subtle or potentially redundant. (LLM, conf=0.88)

  cites [37] Sherlekar, A. L. et al. The C. elegans male exercises directional control during mating through cholinergic regulation of sex-shared command interneurons. PLoS ONE 8, e60597 (2013). sourceExperimental — accuracy not yet measured
• Partly supported

  The section “Many male-specific ray neuron targets are not essential for ventral curling” (page unavailable) identifies PVV and PVY as male-specific interneuron/motor neurons, and the Discussion (page unavailable) mentions PVX and PVV as possible contributors to male posterior muscle control. Our copy does not establish that PVV, PVX, and PVY target AVA and AVB, or specify AVA’s and AVB’s respective roles in backward and forward locomotion. (LLM, conf=0.82)

  cites [38] Koo, P. K., Bian, X., Sherlekar, A. L., Bunkers, M. R. & Lints, R. The robustness of Caenorhabditis elegans male mating behavior depends on the distributed properties of ray sensory neurons and their output through core and male-specific targets. J. Neurosci. 31, 7497–7510 (2011). sourceExperimental — accuracy not yet measured

In the paper

“Reinforcement of connectivity by circuit activity and hence experience has been demonstrated but little studied so far45.”

What the sources say

• Partly supported

  In “DVB neurites are experience and activity-dependent” (page unavailable), the paper reports that mating experience and repeated circuit activation increase DVB neurite growth. In “DVB plasticity impacts behavior via dimorphic synaptic connectivity” (page unavailable), it reports an increase in specific synaptic connections with age. It does not directly show that activity reinforces those connections, and its statement that molecular mechanisms are not well understood does not establish that connectivity reinforcement itself has been little studied. (LLM, conf=0.83)

  cites [45] Hart, M. P. & Hobert, O. Neurexin controls plasticity of a mature, sexually dimorphic neuron. Nature 553, 165–170 (2018). sourceExperimental — accuracy not yet measured

In the paper

“the percentage uncertainty (s.d.) in the number of sections scored ranged for chemical synapses between 10% for edge weights of 10 sections or less to 2% for edge weights of 40 sections or more.”

What the sources say

• Partly supported

  The Results (page unavailable) give the claimed approximate 10% and 2% uncertainty estimates for chemical-synapse edge weights at the stated thresholds. They describe these as estimated percentage uncertainty from differences between three scorers, however, not as standard deviations. (LLM, conf=0.86)

  cites [62] Xu, M. et al. Computer assisted assembly of connectomes from electron micrographs: application to Caenorhabditis elegans. PLoS ONE 8, e54050 (2013). sourceExperimental — accuracy not yet measured

In the paper

“Although C. elegans neurons are largely isopotential48, the properties of these neurons that control activity, such as calcium levels, may be compartmentalized, as has been previously demonstrated in one example49.”

What the sources say

• ?Not checked — no full text of the sourcecites [48] Goodman, M. B., Hall, D. H., Avery, L. & Lockery, S. R. Active currents regulate sensitivity and dynamic range in C. elegans neurons. Neuron 20, 763–772 (1998). source
• Supported

  The paper reports compartmentalized calcium dynamics in the RIA interneuron: calcium activity in two axonal segments appeared independent and correlated with different directions of head movement (Abstract, passage 7). This supports the cited example of compartmentalized calcium activity; the sentence attributes the broader isopotential claim to a different citation. (LLM, conf=0.94)

  cites [49] Hendricks, M., Ha, H., Maffey, N. & Zhang, Y. Compartmentalized calcium dynamics in a C. elegans interneuron encode head movement. Nature 487, 99–103 (2012). source

In the paper

“Reproducibility of the annotation has been assessed by comparing the results of independent annotators62.”

What the sources say

• Supported

  The Results describe comparing duplicate reconstructions made by separate individuals to assess annotation uncertainty. They report differences in synapse scoring and compare three independent annotations of the PVX neuron, directly supporting the reproducibility claim. (LLM, conf=0.94)

  cites [62] Xu, M. et al. Computer assisted assembly of connectomes from electron micrographs: application to Caenorhabditis elegans. PLoS ONE 8, e54050 (2013). source

In the paper

“Outgrowth of neurites and establishment of synapses in C. elegans occurs throughout larval development and continues through the L4 larval stage and into adulthood, and ectopic neurite sprouting continues as the nervous system ages45,46.”

What the sources say

• Partly supported

  The ‘Morphologic plasticity displayed by adult male DVB neuron’ section reports progressive neurite outgrowth from adult days 1 to 5, and ‘DVB plasticity impacts behavior via dimorphic synaptic connectivity’ reports an increase in specific synaptic connections over that period (page numbers not supplied). The paper does not establish continued outgrowth and synapse formation throughout larval development or the L4 stage, or general ectopic sprouting across the aging nervous system; its adult finding concerns the male DVB neuron. (LLM, conf=0.87)

  cites [45] Hart, M. P. & Hobert, O. Neurexin controls plasticity of a mature, sexually dimorphic neuron. Nature 553, 165–170 (2018). sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section, “C. elegans touch receptor neurons exhibit new neurite outgrowth with age” (page unavailable), reports new branches that become more frequent in aging adults, supporting the ectopic-sprouting portion. Our copy does not establish that neurite outgrowth and synapse formation continue throughout larval development, through L4, and into adulthood; its aging-synapse findings concern deterioration rather than new synapse formation. (LLM, conf=0.86)

  cites [46] Toth, M. L. et al. Neurite sprouting and synapse deterioration in the aging Caenorhabditis elegans nervous system. J. Neurosci. 32, 8778–8790 (2012). sourceExperimental — accuracy not yet measured

In the paper

“Other shared neurons that participate in the male circuits are extensively differentiated in the adult male compared to the adult hermaphrodite and larval stages, and serve different functions in the two sexes (Fig. 6a–f).”

In the paper

“Gap junctions were more variable.”

In the paper

“Although sparse, if all edges for both sexes are considered to be undirected, both chemical and gap junction graphs are connected, meaning that there is a path connecting every pair of nodes (weakly connected).”

In the paper

“and 5,315 chemical and 1,755 gap junction edges in the male”

In the paper

“Two-dimensional layouts of the connectivity graphs based on computational arrangement reveal the pathways of sensory information flow, the small number (1–5) of synaptic steps between the sensory neurons and the end organs, and the feedforward nature of the networks”

In the paper

“Reciprocally, 54% of the shared neuron classes (50 out of 93 classes) have output onto the sex-specific component, constituting 18% of the input of the sex-specific neurons.”

In the paper

“Of these neurons, we classify 108 neurons in 17 classes—accounting for 91% of input to the body-wall muscles—as motor neurons, because a large fraction of their output is to muscle, and muscle control appears to be their primary function”

In the paper

“In total 8 neurons and 16 sex muscles are specific to the hermaphrodite; 91 neurons and 39 sex muscles are specific to the male.”

In the paper

“The primary sex differences are in reproductive functions, the vulval and uterine muscles and the motor neurons that control them in the hermaphrodite and—in the male—the large number of additional neurons, sex muscles and connections in the tail that generate the circuits for copulation3.”

What the sources say

• ?Not checked — no full text of the sourcecites [3] Jarrell, T. A. et al. The connectome of a decision-making neural network. Science 337, 437–444 (2012). source

In the paper

“They are sparse graphs with respectively 3.2% (for the hermaphrodite) and 2.4% (for the male) of all possible edges.”

In the paper

“Considering the graph of connectivity between cell classes, median degree values of around 19 illustrate the extensive cross-connectivity and thus indicate both convergence and divergence throughout the nervous system.”

In the paper

“In the hermaphrodite, 37% of the neuron classes are targeted by the two sex-specific neuron classes, HSN and VC, but this constitutes only 1.4% of total input of the shared component.”

In the paper

“The respective graphs have 4,887 chemical (or directed) edges and 1,447 gap junction (or undirected) edges in the hermaphrodite”

In the paper

“Of7,446 synapses (chemical plus gap junctions), the synapses fell roughly equally into these three regions (2,578 not nerve ring, 2,472 nerve ring 45°, 2,396 nerve ring in-plane).”

In the paper

“We scored more synapses compared to the previous papers for two reasons (Extended Data Fig. 1).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Extended Data Fig. 1

In the paper

“In the hermaphrodite, the best anterior series (N2U) ends around the midbody vulva whereas the best posterior series (JSE) extends anteriorly only as far as the junction between the ventral cord and the pre-anal ganglion”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Supplementary Information 10

In the paper

“In the male, the anterior series (N930) extends posteriorly through the ventral ganglion, whereas the posterior series (N2Y) extends anteriorly to a position near the border between the seminal vesicle and the vas deferens”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Supplementary Information 10

In the paper

“This gap includes gap junctions between adjacent muscles, neuromuscular junctions between the ventral cord motor neurons and dorsal and ventral body-wall muscles, connections from one ventral cord motor neuron to the next, and connections between the major premotor interneurons AVA and AVB and ventral cord motor neurons.”

In the paper

“N2U includes only the anterior portion of the dorsal nerve cord where the neuromuscular junctions to the dorsal muscle quadrants are located.”

In the paper

“This varies from 1 to 23 sections in the hermaphrodite and from 1 to 41 sections in the male for chemical synapses, and from 1 to 20 sections in the hermaphrodite and from 1 to 30 sections in the male for gap junction synapses”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Supplementary Information 3

In the paper

“The completeness of the reconstructions varies and will affect the values of the weights.”

In the paper

“As none of the EM series cover an entire single animal, to generate whole-animal connectomes, data from different reconstruction series were combined and the remaining gaps were filled by extrapolating known connectivity across repetitive regions (Methods).”

In the paper

“Sex-specific neurons connect into the sex-shared central circuitry in the head with two functions: to regulate behaviour during overt reproductive activity and to mediate sex-specific, appetitive decision-making.”

In the paper

“This is most notable in the male, in which the neural network that controls copulation consists of 85 male-specific and 64 shared neurons3,36.”

What the sources say

• ?Not checked — no full text of the sourcecites [3] Jarrell, T. A. et al. The connectome of a decision-making neural network. Science 337, 437–444 (2012). source
• ?Not checked — no full text of the sourcecites [36] Emmons, S. W. Neural circuits of sexual behavior in Caenorhabditis elegans. Annu. Rev. Neurosci. 41, 349–369 (2018). source

In the paper

“The reconstructions are quantitative and based on the sizes of the synapses (Methods, Extended Data Fig. 2 and Supplementary Information 2, 3), thus making graph and network analysis possible.”

In the paper

“The sublateral motor neurons have been incompletely described heretofore, because their axons run through body regions that have not been fully imaged by EM at high magnification.”

In the paper

“The major motor neurons as well as their primary pre-motor interneurons are highly interconnected and receive some input from most of the remaining neurons, defying simple interpretation of motor output.”

In the paper

“The function of some neurons may be deduced from their connectivity, which can identify them as a previously unknown cell class.”

In the paper

“Differences arise from out-and-out errors and from differing interpretations of ambiguous structures.”

In the paper

“Differences may be due to developmental variability, as assessed above (Fig. 5a), or to age disparity, rearing conditions or experience, not to mention differences due to errors and differing degrees of completeness in the reconstructions themselves.”

In the paper

“EM-level ultrastructures can indicate neuronal functions such as sensory perception or hormone secretion.”

In the paper

“Gap junctions are more difficult to score overall, but those difficulties are similar across all animals used in this study.”

In the paper

“Such possible differences involve both chemical and gap junctional connections and occur at all levels throughout the network (Extended Data Fig. 13).”

In the paper

“If synapse size is not taken into account, judging connectivity strength by counting synapses alone will therefore underestimate the strength of strong connections and overestimate the strength of weaker connections.”

In the paper

“The connectome is too complex not to be under the control of dynamic, homeostatic mechanisms; an EM-based connectome should be considered a snapshot of a dynamic structure.”

In the paper

“It may or may not have any effect on larger synapses, depending on where they lie with respect to section boundaries; there is only a definite effect on larger synapses.”

In the paper

“How neurons signal emerges from whether they are chemically or electrically coupled.”

In the paper

“Inclusion of the end organs is important as—at least in the case of C. elegans—they are electrically coupled, which will have a marked effect on their activity.”

In the paper

“Similar results are expected for gap junctions.”

In the paper

“Thus, signalling may not be uniform or simultaneous at all synapses.”

In the paper

“These gaps in the adjacency matrices, which leave some muscle cells and some motor neurons without any innervation, precisely line up with the unreconstructed region and thus are unquestionably artefactual.”

In the paper

“However, this conclusion might not be true for a particular connection.”

In the paper

“Synaptic partnerships were not used to identify neurons.”

In the paper

“Considering that the male graph contains the same major pathways as the hermaphrodite and verifiable sex differences can be identified, the missing synapses must be distributed relatively uniformly over the connections.”

In the paper

“Notably, this has little effect on the values of the weights but it could be important for particular connections.”

In the paper

“Although our efforts failed to stain chemical synaptic features exactly as in the previously published images, they are still identifiable and measurable in size in animals from both sources.”

In the paper

“These whole-animal C. elegans connectomes should be considered a conceptualization, being constructed as they are from multiple animals and including some connections that are observed in the opposite sex and some that are not observed at all but assumed to be present based on the repetitive nature of certain regions.”

In the paper

“All anterior images were scored blind to sex.”

In the paper

“Sexually dimorphic tail anatomy precluded blinding to sex when scoring posterior images of the PAG.”

In the paper

“Use of different fluorescence markers to label the presynaptic neurite prevented blinding to genotype in most instances.”