Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Ancient deuterostome origins of vertebrate brain signalling centres


Neuroectodermal signalling centres induce and pattern many novel vertebrate brain structures but are absent, or divergent, in invertebrate chordates. This has led to the idea that signalling-centre genetic programs were first assembled in stem vertebrates and potentially drove morphological innovations of the brain. However, this scenario presumes that extant cephalochordates accurately represent ancestral chordate characters, which has not been tested using close chordate outgroups. Here we report that genetic programs homologous to three vertebrate signalling centresthe anterior neural ridge, zona limitans intrathalamica and isthmic organizerare present in the hemichordate Saccoglossus kowalevskii. Fgf8/17/18 (a single gene homologous to vertebrate Fgf8, Fgf17 and Fgf18), sfrp1/5, hh and wnt1 are expressed in vertebrate-like arrangements in hemichordate ectoderm, and homologous genetic mechanisms regulate ectodermal patterning in both animals. We propose that these genetic programs were components of an unexpectedly complex, ancient genetic regulatory scaffold for deuterostome body patterning that degenerated in amphioxus and ascidians, but was retained to pattern divergent structures in hemichordates and vertebrates.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: An ANR-like signalling centre in S. kowalevskii.
Figure 2: A ZLI-like signalling centre in S. kowalevskii.
Figure 3: An IsO-like signalling centre in S. kowalevskii.
Figure 4: Evolutionary gain and loss of ANR, ZLI and IsO-like genetic programs.

Accession codes

Data deposits

S. kowalevskii gene sequences have been deposited in GenBank, and accession numbers are provided in Supplementary Table 2.


  1. 1

    Echevarria, D., Vieira, C., Gimeno, L. & Martinez, S. Neuroepithelial secondary organizers and cell fate specification in the developing brain. Brain Res. Brain Res. Rev. 43, 179–191 (2003)

    CAS  Article  Google Scholar 

  2. 2

    Wilson, S. W. & Houart, C. Early steps in the development of the forebrain. Dev. Cell 6, 167–181 (2004)

    CAS  Article  Google Scholar 

  3. 3

    Wurst, W. & Bally-Cuif, L. Neural plate patterning: upstream and downstream of the isthmic organizer. Nature Rev. Neurosci. 2, 99–108 (2001)

    CAS  Article  Google Scholar 

  4. 4

    Wicht, H. & Lacalli, T. C. The nervous system of amphioxus: structure, development, and evolutionary significance. Can. J. Zool. 150, 122–150 (2005)

    Article  Google Scholar 

  5. 5

    Lacalli, T. C. Prospective protochordate homologs of vertebrate midbrain and MHB, with some thoughts on MHB origins. Int. J. Biol. Sci. 2, 104–109 (2006)

    CAS  Article  Google Scholar 

  6. 6

    Meinertzhagen, I. A., Lemaire, P. & Okamura, Y. The neurobiology of the ascidian tadpole larva: recent developments in an ancient chordate. Annu. Rev. Neurosci. 27, 453–485 (2004)

    CAS  Article  Google Scholar 

  7. 7

    Lowe, C. J. et al. Anteroposterior patterning in hemichordates and the origins of the chordate nervous system. Cell 113, 853–865 (2003)

    CAS  Article  Google Scholar 

  8. 8

    Holland, L. Z. & Short, S. Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain. Brain Behav. Evol. 72, (2008)

  9. 9

    Holland, L. Z. Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nature Rev. Neurosci. 10, 736–746 (2009)

    CAS  Article  Google Scholar 

  10. 10

    Irimia, M. et al. Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer. Evodevo. 1, 7 (2010)

    CAS  Article  Google Scholar 

  11. 11

    Tomer, R., Denes, A. S., Tessmar-Raible, K. & Arendt, D. Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell 142, 800–809 (2010)

    CAS  Article  Google Scholar 

  12. 12

    Urbach, R. A procephalic territory in Drosophila exhibiting similarities and dissimilarities compared to the vertebrate midbrain/hindbrain boundary region. Neural Dev. 2, 23 (2007)

    Article  Google Scholar 

  13. 13

    Crossley, P. H., Martinez, S. & Martin, G. R. Midbrain development induced by FGF8 in the chick embryo. Nature 380, 66–68 (1996)

    ADS  CAS  Article  Google Scholar 

  14. 14

    Reifers, F. et al. Fgf8 is mutated in zebrafish acerebellar (ace) mutants and is required for maintenance of midbrain-hindbrain boundary development and somitogenesis. Development 125, 2381–2395 (1998)

    CAS  PubMed  Google Scholar 

  15. 15

    Houart, C. et al. Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron 35, 255–265 (2002)

    CAS  Article  Google Scholar 

  16. 16

    Paek, H., Gutin, G. & Hebert, J. M. FGF signaling is strictly required to maintain early telencephalic precursor cell survival. Development 136, 2457–2465 (2009)

    CAS  Article  Google Scholar 

  17. 17

    Kiecker, C. & Lumsden, A. Hedgehog signaling from the ZLI regulates diencephalic regional identity. Nature Neurosci. 7, 1242–1249 (2004)

    CAS  Article  Google Scholar 

  18. 18

    Scholpp, S., Wolf, O., Brand, M. & Lumsden, A. Hedgehog signalling from the zona limitans intrathalamica orchestrates patterning of the zebrafish diencephalon. Development 133, 855–864 (2006)

    CAS  Article  Google Scholar 

  19. 19

    Meulemans, D. & Bronner-Fraser, M. Insights from amphioxus into the evolution of vertebrate cartilage. PLoS ONE 2, e787 (2007)

    ADS  Article  Google Scholar 

  20. 20

    Imai, K. S., Stolfi, A., Levine, M. & Satou, Y. Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system. Development 136, 285–293 (2009)

    CAS  Article  Google Scholar 

  21. 21

    Shimeld, S. M. The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev. Genes Evol. 209, 40–47 (1999)

    CAS  Article  Google Scholar 

  22. 22

    Takatori, N., Satou, Y. & Satoh, N. Expression of hedgehog genes in Ciona intestinalis embryos. Mech. Dev. 116, 235–238 (2002)

    CAS  Article  Google Scholar 

  23. 23

    Scholpp, S. & Lumsden, A. Building a bridal chamber: development of the thalamus. Trends Neurosci. 33, 373–380 (2010)

    CAS  Article  Google Scholar 

  24. 24

    Bertrand, S. et al. Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits. Proc. Natl Acad. Sci. USA 108, 9160–9165 (2011)

    ADS  CAS  Article  Google Scholar 

  25. 25

    Holland, L. Z., Holland, N. N. & Schubert, M. Developmental expression of AmphiWnt1, an amphioxus gene in the Wnt1/wingless subfamily. Dev. Genes Evol. 210, 522–524 (2000)

    CAS  Article  Google Scholar 

  26. 26

    Bourlat, S. J. et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85–88 (2006)

    ADS  CAS  Article  Google Scholar 

  27. 27

    Darras, S., Gerhart, J., Terasaki, M., Kirschner, M. & Lowe, C. J. β-catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii. Development 138, 959–970 (2011)

    CAS  Article  Google Scholar 

  28. 28

    Gillis, J. A., Fritzenwanker, J. H. & Lowe, C. J. A stem-deuterostome origin of the vertebrate pharyngeal transcriptional network. Proc. R. Soc. B 279, 237–246 (2012)

    Article  Google Scholar 

  29. 29

    Lowe, C. J. et al. Dorsoventral patterning in hemichordates: insights into early chordate evolution. PLoS Biol. 4, e291 (2006)

    Article  Google Scholar 

  30. 30

    Shimamura, K. & Rubenstein, J. L. Inductive interactions direct early regionalization of the mouse forebrain. Development 124, 2709–2718 (1997)

    CAS  PubMed  Google Scholar 

  31. 31

    Fukuchi-Shimogori, T. & Grove, E. A. Neocortex patterning by the secreted signaling molecule FGF8. Science 294, 1071–1074 (2001)

    ADS  CAS  Article  Google Scholar 

  32. 32

    Walshe, J. & Mason, I. Unique and combinatorial functions of Fgf3 and Fgf8 during zebrafish forebrain development. Development 130, 4337–4349 (2003)

    CAS  Article  Google Scholar 

  33. 33

    Garel, S., Huffman, K. J. & Rubenstein, J. L. Molecular regionalization of the neocortex is disrupted in Fgf8 hypomorphic mutants. Development 130, 1903–1914 (2003)

    CAS  Article  Google Scholar 

  34. 34

    Mohammadi, M. et al. Structures of the tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors. Science 276, 955–960 (1997)

    CAS  Article  Google Scholar 

  35. 35

    Lagutin, O. V. et al. Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development. Genes Dev. 17, 368–379 (2003)

    CAS  Article  Google Scholar 

  36. 36

    Crossley, P. H., Martinez, S., Ohkubo, Y. & Rubenstein, J. L. Coordinate expression of Fgf8, Otx2, Bmp4, and Shh in the rostral prosencephalon during development of the telencephalic and optic vesicles. Neuroscience 108, 183–206 (2001)

    CAS  Article  Google Scholar 

  37. 37

    Hébert, J. M. & Fishell, G. The genetics of early telencephalon patterning: some assembly required. Nature Rev. Neurosci. 9, 678–685 (2008)

    Article  Google Scholar 

  38. 38

    Zeltser, L. M., Larsen, C. W. & Lumsden, A. A new developmental compartment in the forebrain regulated by Lunatic fringe. Nature Neurosci. 4, 683–684 (2001)

    CAS  Article  Google Scholar 

  39. 39

    Scholpp, S. et al. Otx1l, Otx2 and Irx1b establish and position the ZLI in the diencephalon. Development 134, 3167–3176 (2007)

    CAS  Article  Google Scholar 

  40. 40

    Chen, J. K., Taipale, J., Cooper, M. K. & Beachy, P. A. Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened. Genes Dev. 16, 2743–2748 (2002)

    CAS  Article  Google Scholar 

  41. 41

    Simon, H. H., Thuret, S. & &Alberi, L. Midbrain dopaminergic neurons: control of their cell fate by the engrailed transcription factors. Cell Tissue Res. 318, 53–61 (2004)

    CAS  Article  Google Scholar 

  42. 42

    McMahon, A. P., Joyner, A. L., Bradley, A. & McMahon, J. A. The midbrain-hindbrain phenotype of Wnt-1Wnt-1 mice results from stepwise deletion of engrailed-expressing cells by 9.5 days postcoitum. Cell 69, 581–595 (1992)

    CAS  Article  Google Scholar 

  43. 43

    Nomaksteinsky, M. et al. Centralization of the deuterostome nervous system predates chordates. Curr. Biol. 19, 1264–1269 (2009)

    CAS  Article  Google Scholar 

  44. 44

    Gavino, M. A., Reddien, P. W. & A Bmp/Admp regulatory circuit controls maintenance and regeneration of dorsal-ventral polarity in planarians. Curr. biol. 21, 294–299 (2011)

    CAS  Article  Google Scholar 

  45. 45

    Grande, C. & Patel, N. H. Nodal signalling is involved in left–right asymmetry in snails. Nature 457, 1007–1011 (2009)

    ADS  CAS  Article  Google Scholar 

  46. 46

    Campo-Paysaa, F., Marletaz, F., Laudet, V. & Schubert, M. Retinoic acid signaling in development: tissue-specific functions and evolutionary origins. Genesis 46, 640–656 (2008)

    CAS  Article  Google Scholar 

  47. 47

    Freeman, R. M., Jr et al. cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism. Biol. Bull. 214, 284–302 (2008)

    CAS  Article  Google Scholar 

  48. 48

    Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)

    CAS  Article  Google Scholar 

  49. 49

    Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)

    CAS  Article  Google Scholar 

  50. 50

    Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755 (2001)

    CAS  Article  Google Scholar 

Download references


We thank J. Gerhart and M. Kirschner for assistance and support, R. Freeman for bioinformatics assistance, E. Farrelly, M. Terasaki and S. Darras for technical guidance, the members of the Lowe laboratory for discussions, and G. Wray and J. Gerhart for comments on drafts of the manuscript. We also thank the staff of the Marine Biological Laboratory, the Waquoit Bay National Estuarine Research Reserve, Carl Zeiss and Nikon for assistance during our field season. This work was funded by the Searle Kinship Foundation, Brain Research Foundation and National Science Foundation grant 1049106 (C.J.L.), National Institutes of Health grant R01 HD42330 (E.A.G.) and the University of Chicago Hinds Fund (A.M.P). A.M.P. was supported by a Marine Biological Laboratory Frank R. Lillie Fellowship, National Institute of Child Health and Development institutional training grant 1T32HD055164-01A1, and National Institute of Neurological Disorders and Stroke pre-doctoral fellowship 1F31NS074738-01A1. J.A. was supported by a National Science and Engineering Research Council of Canada pre-doctoral grant.

Author information




A.M.P., C.J.L. and J.A. conceived the project. A.M.P. and C.J.L. performed the hemichordate experiments and wrote the paper. E.E.M. and S.A. performed mouse experiments, and E.A.G. edited the paper. All authors discussed and commented on the data.

Corresponding author

Correspondence to Christopher J. Lowe.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-4 and Supplementary Tables 1-2. Please note that Supplementary Figure 1 shows that fz5/8 siRNA affects proboscis patterning specifically and that Supplementary Figure 2 shows Ptch expression in wild-type S. kowalevskii embryos and spectrum of phenotypes after hh siRNA injection. Ptch expression indicates that hh can signal to numerous body regions. Hh siRNA injection causes pleiotropic effects on AP and DV patterning. (PDF 2369 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Pani, A., Mullarkey, E., Aronowicz, J. et al. Ancient deuterostome origins of vertebrate brain signalling centres. Nature 483, 289–294 (2012).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links