Skip to main content

Perspective: A New Era of Comparative Connectomics

  • Chapter
  • First Online:
Decoding Neural Circuit Structure and Function

Abstract

Morphological studies on brains have recently entered a new phase of circuit analysis identified under the newly designated area of connectomics, the study of brain wiring diagrams exact at synapse level that can now be produced by means of electron microscopy and automated reconstruction. The most comprehensive examples come from the brains of invertebrates with few neurons, which Nature provides in great abundance especially among marine larval invertebrates. Two complete examples, the nematode C. elegans and the larva of the ascidian Ciona intestinalis, are now published; others are in the pipeline. Each species has its advantages and champions, especially clearly so in Drosophila, which offers outstanding opportunities for functional analysis of complex behaviours using genetics-based methods. Collectively‚ these offer an ultimate prospect for the causal analysis of behaviour. In addition, the availability of multiple connectomes from behaviourally different species will reveal features of the network design that are common to all, and that enable comparison with networks from different levels of biological organization, as well as with those from networks that have evolved from human technologies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Bassett DS, Bullmore E (2006) Small-world brain networks. Neuroscientist 12:512–523

    Article  PubMed  Google Scholar 

  • Bezares-Calderón LA, Jékely G (2016) Think small. eLIFE 5. pii: e22497. doi:10.7554/eLife.22497

  • Borst A (2009) Drosophila’s view on insect vision. Curr Biol 19:R36–R47

    Article  CAS  PubMed  Google Scholar 

  • Borst A, Egelhaaf M (1989) Principles of visual motion detection. Trends Neurosci 12:297–306

    Article  CAS  PubMed  Google Scholar 

  • Borst A, Haag J (2002) Neural networks in the cockpit of the fly. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 188:419–437

    Article  CAS  PubMed  Google Scholar 

  • Bumbarger DJ, Riebesell M, Rödelsperger C, Sommer RJ (2013) System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes. Cell 152:109–119

    Article  CAS  PubMed  Google Scholar 

  • Butcher NJ, Friedrich AB, Lu Z, Tanimoto H, Meinertzhagen IA (2012) Different classes of input and output neurons reveal new features in microglomeruli of the adult Drosophila mushroom body calyx. J Comp Neurol 520:2185–2201

    Article  PubMed  Google Scholar 

  • Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, Shih CT, Wu JJ, Wang GT, Chen YC, Wu CC, Chen GY, Ching YT, Lee PC, Lin CY, Lin HH, Wu CC, Hsu HW, Huang YA, Chen JY, Chiang HJ, Lu CF, Ni RF, Yeh CY, Hwang JK (2011) Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol 21:1–11. doi:10.1016/j.cub.2010.11.056

    Article  CAS  PubMed  Google Scholar 

  • Denk W, Heinz H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2:e329. doi:10.1371/journal.pbio.0020329

    Article  PubMed  PubMed Central  Google Scholar 

  • Ding H, Smith RG, Poleg-Polsky A, Diamond JS, Briggman KL (2016) Species-specific wiring for direction selectivity in the mammalian retina. Nature 535:105–110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Douglass JK, Strausfeld NJ (2003) Anatomical organization of retinotopic motion-sensitive pathways in the optic lobes of flies. Microsc Res Tech 62:132–150

    Article  PubMed  Google Scholar 

  • Durbin RM (1987) Studies on the development and organisation of the nervous system of Caernorhabditis elegans. Doctoral thesis, University of Cambridge

    Google Scholar 

  • Fahrenbach WH (1984) Continuous serial thin sectioning for electron microscopy. J Electron Microsc Techn 1:387–398

    Article  Google Scholar 

  • Fahrenbach WH (1985) Anatomical circuitry of lateral inhibition in the eye of the horseshoe crab, Limulus polyphemus. Proc R Soc Lond B 225:219–249

    Article  CAS  PubMed  Google Scholar 

  • Feng L, Zhao T, Kim J (2015) neuTube 1.0: a new design for efficient neuron reconstruction software based on the SWC format. eNeuro 2(1). pii: ENEURO.0049-14.2014

    Google Scholar 

  • Fischbach K-F, Dittrich APM (1989) The optic lobe of Drosophila melanogaster. I. A Golgi analysis of wild-type structure. Cell Tiss Res 258:441–475

    Article  Google Scholar 

  • Gao S, Takemura S-Y, Ting C-Y, Huang S, Lu Z, Luan H, Rister J, Yang M, Hong S-T, Wang JW, Odenwald W, White B, Meinertzhagen IA, Lee C-H (2008) Neural substrate of spectral discrimination in Drosophila. Neuron 60:328–342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goldschmidt R (1908) Das Nervensystem von Ascaris lumbricoides und megalocephala, I. Z wissenschaftliche Zool 90:73–136

    Google Scholar 

  • Goldschmidt R (1909) Das Nervensystem von Ascaris lumbricoides und megalocephala, II. Z wissenschaftliche Zool 92:306–357

    Google Scholar 

  • Hale ME (2014) Mapping circuits beyond the models: integrating connectomics and comparative neuroscience. Neuron 83:1256–1258

    Article  CAS  PubMed  Google Scholar 

  • Hall DH (1995) Electron microscopy and three-dimensional image reconstruction. Methods Cell Biol 48:395–436

    Article  CAS  PubMed  Google Scholar 

  • Harris KM, Perry E, Bourne J, Feinberg M, Ostroff L, Hurlburt J (2006) Uniform serial sectioning for transmission electron microscopy. J Neurosci 26:12101–12103

    Article  CAS  PubMed  Google Scholar 

  • Hayworth KJ, Xu CS, Lu Z, Knott GW, Fetter RD, Tapia JC, Lichtman JW, Hess HF (2015) Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics. Nat Methods 12:319–322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heisenberg M, Wolf R (1984) Vision in Drosophila. Springer, Berlin

    Book  Google Scholar 

  • Helmstaedter M, Briggman KL, Turaga SC, Jain V, Seung HS, Denk W (2013) Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature 500:168–174

    Article  CAS  PubMed  Google Scholar 

  • Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW (2012) The connectome of a decision-making neural network. Science 337:437–444

    Article  CAS  PubMed  Google Scholar 

  • Jenett A, Rubin GM, Ngo TT, Shepherd D, Murphy C, Dionne H, Pfeiffer BD, Cavallaro A, Hall D, Myers EW, Iwinski ZR, Aso Y, DePasquale GM, Enos A, Hulamm P, Lam SC, Li HH, Laverty TR, Long F, Qu L, Murphy SD, Rokicki K, Safford T, Shaw K, Simpson JH, Sowell A, Tae S, Yu Y, Zugates CT (2012) A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2:991–1001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jovanic T, Schneider-Mizell CM, Shao M, Masson JB, Denisov G, Fetter RD, Mensh BD, Truman JW, Cardona A, Zlatic M (2016) Competitive disinhibition mediates behavioral choice and sequences in Drosophila. Cell 167(858–870):e19. doi:10.1016/j.cell.2016.09.009

    Google Scholar 

  • Knott G, Marchman H, Wall D, Lich B (2008) Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J Neurosci 28:2959–2964

    Article  CAS  PubMed  Google Scholar 

  • Knott G, Rosset S, Cantoni M (2011) Focussed ion beam milling and scanning electron microscopy of brain tissue. J Vis Exp 53:e2588. doi:10.3791/2588

    Google Scholar 

  • Lacalli TC (1984) Structure and organization of the nervous system in the trochophore larva of Spirobranchus. Philos Trans R Soc Lond B Biol Sci 306:79–135

    Article  Google Scholar 

  • Lichtman JW, Sanes JR (2008) Ome sweet ome: what can the genome tell us about the connectome? Curr Opin Neurobiol 18:346–353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luan H, Peabody NC, Vinson CR, White BH (2006) Refined spatial manipulation of neuronal function by combinatorial restriction of transgene expression. Neuron 52:425–436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Macagno ER, Lopresti V, Levinthal C (1973) Structure and development of neuronal connections in isogenic organisms: variations and similarities in the optic system of Daphnia magna. Proc Natl Acad Sci USA 70:57–61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meinertzhagen IA (2001) Plasticity in the insect nervous system. Adv Insect Physiol 28:84–167

    Article  Google Scholar 

  • Meinertzhagen IA (2014) The anatomical organization of the compound eye visual system. In: Dubnau J (ed) Handbook of behavior genetics of Drosophila melanogaster, vol 1. University Press, Cambridge, pp 1–19

    Google Scholar 

  • Meinertzhagen IA (2016a) Morphology of invertebrate neurons and synapses. In: Byrne JH (ed) Handbook of invertebrate neurobiology. Oxford University Press

    Google Scholar 

  • Meinertzhagen IA (2016b) Connectome studies on Drosophila: a short perspective on a tiny brain. J Neurogenet 30:62–68

    Article  CAS  PubMed  Google Scholar 

  • Meinertzhagen IA, Lee C-H (2012) The genetic analysis of functional connectomics in Drosophila. Adv Genet 80:99–151

    PubMed  PubMed Central  Google Scholar 

  • Meinertzhagen IA, O’Neil SD (1991) Synaptic organization of columnar elements in the lamina of the wild type in Drosophila melanogaster. J Comp Neurol 305:232–263

    Article  CAS  PubMed  Google Scholar 

  • Meinertzhagen IA, Sorra KE (2001) Synaptic organisation in the fly’s optic lamina: few cells, many synapses and divergent microcircuits. Progr Brain Res 131:53–69

    Article  CAS  Google Scholar 

  • Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298:824–827

    Article  CAS  PubMed  Google Scholar 

  • Morgan JL, Lichtman JW (2013) Why not connectomics? Nat Methods 10:494–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohyama T, Schneider-Mizell CM, Fetter RD, Aleman JV, Franconville R, Rivera-Alba M, Mensh BD, Branson KM, Simpson JH, Truman JW, Cardona A, Zlatic M (2015) A multilevel multimodal circuit enhances action selection in Drosophila. Nature 520:633–639

    Article  CAS  PubMed  Google Scholar 

  • Peng H, Chung P, Long F, Qu L, Jenett A, Seeds AM, Myers EW, Simpson JH (2011) BrainAligner: 3D registration atlases of Drosophila brains. Nat Methods 8:493–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM (2008) Tools for neuroanatomy and neurogenetics in Drosophila. P Natl Acad Sci USA 105:9715-9720

    Google Scholar 

  • Pfeiffer BD, Ngo TT, Hibbard KL, Murphy C, Jenett A, Truman JW, Rubin GM (2010) Refinement of tools for targeted gene expression in Drosophila. Genetics 186:735–755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Randel N, Asadulina A, Bezares-Calderón LA, Verasztó C, Williams EA, Conzelmann M, Shahidi R, Jékely G (2014) Neuronal connectome of a sensory-motor circuit for visual navigation. eLIFE 3. doi:10.7554/eLife.02730

  • Randel N, Shahidi R, Verasztó C, Bezares-Calderón LA, Schmidt S, Jékely G (2015) Inter-individual stereotypy of the Platynereis larval visual connectome. eLIFE 4:e08069. doi:10.7554/eLife.08069

    Article  PubMed  PubMed Central  Google Scholar 

  • Ryan K, Lu Z, Meinertzhagen IA (2016) The CNS connectome of a tadpole larva of Ciona intestinalis highlights sidedness in the brain of a chordate sibling. eLIFE 5:e16962

    Google Scholar 

  • Rybak J, Talarico G, Ruiz S, Arnold C, Cantera R, Hansson BS (2016) Synaptic circuitry of identified neurons in the antennal lobe of Drosophila melanogaster. J Comp Neurol 524:1920–1956

    Article  CAS  PubMed  Google Scholar 

  • Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li F, Zwart MF, Champion A, Midgley FM, Fetter RD, Saalfeld S, Cardona A (2016) Quantitative neuroanatomy for connectomics in Drosophila. eLIFE 5. pii: e12059

    Google Scholar 

  • Shih CT, Sporns O, Yuan SL, Su TS, Lin YJ, Chuang CC, Wang TY, Lo CC, Greenspan RJ, Chiang AS (2015) Connectomics-based analysis of information flow in the Drosophila brain. Curr Biol 25:1249–1258

    Article  CAS  PubMed  Google Scholar 

  • Shinomiya K, Karuppudurai T, Lin T-Y, Lu Z, Lee C-H, Meinertzhagen IA (2014) Candidate neural substrates for off-edge motion detection in Drosophila. Curr Biol 24:1–9

    Article  Google Scholar 

  • Silies M, Gohl DM, Clandinin TR (2014) Motion-detecting circuits in flies: coming into view. Ann Rev Neurosci 37:307–327

    Article  CAS  PubMed  Google Scholar 

  • Simpson JH (2009) Mapping and manipulating neural circuits in the fly brain. Adv Genet 65:79–143

    CAS  PubMed  Google Scholar 

  • Sterling P, Laughlin S (2015) Principles of neural design. The MIT Press, London

    Book  Google Scholar 

  • Strausfeld NJ, Campos-Ortega JA (1977) Vision in insects: pathways underlying neural adaptation and lateral inhibition. Science 195:894–897

    Article  CAS  PubMed  Google Scholar 

  • Strausfeld NJ, Nässel DR (1980) Neuroarchitectures serving compound eyes of Crustacea and insects. In: H Autrum (ed) Handbook of sensory physiology, vol VII/6B. Comparative physiology and evolution of vision in invertebrates. Springer, Berlin, pp 1–132

    Google Scholar 

  • Takemura S, Lu Z, Meinertzhagen IA (2008) Synaptic circuits of the Drosophila optic lobe: the input terminals to the medulla. J Comp Neurol 509:493–513

    Article  PubMed  PubMed Central  Google Scholar 

  • Takemura S, Bharioke A, Lu Z, Nern A, Vitaladevuni S, Rivlin PK, Katz WT, Olbris DJ, Plaza SM, Winston P, Zhao T, Horne JA, Fetter RD, Takemura S, Blazek K, Chang L-A, Ogundeyi O, Saunders MA, Shapiro V, Sigmund C, Rubin GM, Scheffer LK, Meinertzhagen IA, Chklovskii DB (2013) A visual motion detection circuit suggested by Drosophila connectomics. Nature 500:175–181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takemura S, Xu CS, Lu Z, Rivlin PK, Olbris DJ, Parag T, Plaza S, Zhao T, Katz WT, Umayam L, Weaver C, Hess H, Horne JA, Nunez J, Aniceto R, Chang L-A, Lauchie S, Nasca A, Ogundeyi O, Sigmund C, Takemura S, Tran J, Langille C, Le Lacheur K, McLin S, Shinomiya A, Chklovskii DB, Meinertzhagen IA, Scheffer LK (2015) Multi-column synaptic circuits and an analysis of their variations in the visual system of Drosophila. Proc Natl Acad Sci USA 112:13711–13716

    Google Scholar 

  • Takemura S et al (2017a) EM reconstruction of α2 and α3 lobes of the mushroom body in adult Drosophila. eLIFE (submitted)

    Google Scholar 

  • Takemura S, Nern A, Plaza S, Chklovskii DB, Scheffer LK, Rubin GM, Meinertzhagen IA (2017b) The comprehensive connectome of a neural substrate for ‘ON’ motion detection in Drosophila. Elife (under review)

    Google Scholar 

  • Tobin W, Wilson R, Lee W-C (2017) Wiring variations that enable and constrain neural computation in a sensory microcircuit. eLIFE (submitted)

    Google Scholar 

  • Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB (2011) Structural properties of the Caenorhabditis elegans neuronal network. PLoS Comput Biol 7:e1001066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ware R (1971) Computer aided nerve tracing in the brain of the rotifier, Asplanchna brightwelli. Ph.D. thesis, Massachusetts Institute of Technology, Boston, 213 pp

    Google Scholar 

  • Ware RW, LoPresti V (1975) Three-dimensional reconstruction from serial sections. Int Rev Cytol 40:325–440

    Article  CAS  PubMed  Google Scholar 

  • Watts DJ, Strogatz SH (1998) Collective dynamics of ‘small-world’ networks. Nature 393:440–442

    Article  CAS  PubMed  Google Scholar 

  • White JG, Southgate E, Thomson JN, Brenner S (1986) The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 314:1–340

    Article  CAS  PubMed  Google Scholar 

  • Windoffer R, Westheide W (1988) The nervous system of the male Dinophilus gyrociliatus (Polychaeta, Dinophilidae): II. Electron microscopical reconstruction of nervous anatomy and effector cells. J Comp Neurol 272:475–488

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The author acknowledges various sources of support for his work summarized in this review, especially grant DIS-0000065 from the Natural Sciences and Engineering Research Council, for research on the larval nervous system of Ciona, and the FlyEM team at the Janelia Research Campus of HHMI for work on Drosophila. Dr. Kerrianne Ryan read an earlier version of the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ian A. Meinertzhagen .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Meinertzhagen, I.A. (2017). Perspective: A New Era of Comparative Connectomics. In: Çelik, A., Wernet, M. (eds) Decoding Neural Circuit Structure and Function. Springer, Cham. https://doi.org/10.1007/978-3-319-57363-2_20

Download citation

Publish with us

Policies and ethics