Letter | Published:

Digits and fin rays share common developmental histories

Nature volume 537, pages 225228 (08 September 2016) | Download Citation

Abstract

Understanding the evolutionary transformation of fish fins into tetrapod limbs is a fundamental problem in biology1. The search for antecedents of tetrapod digits in fish has remained controversial because the distal skeletons of limbs and fins differ structurally, developmentally, and histologically2,3. Moreover, comparisons of fins with limbs have been limited by a relative paucity of data on the cellular and molecular processes underlying the development of the fin skeleton. Here, we provide a functional analysis, using CRISPR/Cas9 and fate mapping, of 5′ hox genes and enhancers in zebrafish that are indispensable for the development of the wrists and digits of tetrapods4,5. We show that cells marked by the activity of an autopodial hoxa13 enhancer exclusively form elements of the fin fold, including the osteoblasts of the dermal rays. In hox13 knockout fish, we find that a marked reduction and loss of fin rays is associated with an increased number of endochondral distal radials. These discoveries reveal a cellular and genetic connection between the fin rays of fish and the digits of tetrapods and suggest that digits originated via the transition of distal cellular fates.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    Gaining Ground: The Origin and Evolution of Tetrapods. Indiana University Press, Indiana (2012)

  2. 2.

    The fin to limb transition: New data, interpretations, and hypotheses from paleontology and developmental biology. Annu. Rev. Earth Planet. Sci. 37, 163–179 (2009)

  3. 3.

    & The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet. 29, 419–426 (2013)

  4. 4.

    et al. Hoxa-13 and Hoxd-13 play a crucial role in the patterning of the limb autopod. Development 122, 2997–3011 (1996)

  5. 5.

    , , & A Hoxa13:Cre mouse strain for conditional gene manipulation in developing limb, hindgut, and urogenital system. Genesis 53, 366–376 (2015)

  6. 6.

    & The development of the paired fins in the zebrafish (Danio rerio). Mech. Dev. 79, 99–120 (1998)

  7. 7.

    , & Ever since Owen: Changing perspectives on the early evolution of tetrapods. Annu. Rev. Ecol. Evol. Syst. 39, 571–592 (2008)

  8. 8.

    The Development of the Teleost Fin and Implications for Our Understanding of Tetrapod Limb Evolution. (Springer US, 1991)

  9. 9.

    & The apical ectodermal ridge: morphological aspects and signaling pathways. Int. J. Dev. Biol. 52, 857–871 (2008)

  10. 10.

    , & Vertebrate limb bud development: moving towards integrative analysis of organogenesis. Nat. Rev. Genet. 10, 845–858 (2009)

  11. 11.

    , , , & Mechanism of pectoral fin outgrowth in zebrafish development. Development 139, 2916–2925 (2012)

  12. 12.

    , & Hox gene expression in teleost fins and the origin of vertebrate digits. Nature 375, 678–681 (1995)

  13. 13.

    & The origin of digits: expression patterns versus regulatory mechanisms. Dev. Cell 18, 526–532 (2010)

  14. 14.

    & Cis-regulatory programs in the development and evolution of vertebrate paired appendages. Semin. Cell Dev. Biol. (2016)

  15. 15.

    & The role of Hox genes during vertebrate limb development. Curr. Opin. Genet. Dev. 17, 359–366 (2007)

  16. 16.

    , & Biphasic Hoxd gene expression in shark paired fins reveals an ancient origin of the distal limb domain. PLoS One 2, e754 (2007)

  17. 17.

    , & An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature 447, 473–476 (2007)

  18. 18.

    & Tri-phasic expression of posterior Hox genes during development of pectoral fins in zebrafish: implications for the evolution of vertebrate paired appendages. Dev. Biol. 322, 220–233 (2008)

  19. 19.

    et al. HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution. Sci. Rep. 6, 22720 (2016)

  20. 20.

    , , , & Hoxd13 contribution to the evolution of vertebrate appendages. Dev. Cell 23, 1219–1229 (2012)

  21. 21.

    et al. Deep conservation of wrist and digit enhancers in fish. Proc. Natl Acad. Sci. USA 112, 803–808 (2015)

  22. 22.

    , , & An exclusively mesodermal origin of fin mesenchyme demonstrates that zebrafish trunk neural crest does not generate ectomesenchyme. Development 140, 2923–2932 (2013)

  23. 23.

    , & Dermal fin rays and scales derive from mesoderm, not neural crest. Curr. Biol. 23, R336–R337 (2013)

  24. 24.

    , , , & Trunk neural crest origin of caudal fin mesenchyme in the zebrafish Brachydanio rerio. Proc. R. Soc. Lond. B 256, 137–145 (1994)

  25. 25.

    et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat. Genet. 48, 427–437 (2016)

  26. 26.

    et al. Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish. Development 138, 169–177 (2011)

  27. 27.

    et al. Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet. 9, e1004018 (2013)

  28. 28.

    et al. Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature 466, 234–237 (2010)

  29. 29.

    , & Expression of snail2, a second member of the zebrafish snail family, in cephalic mesendoderm and presumptive neural crest of wild-type and spadetail mutant embryos. Dev. Biol. 172, 86–99 (1995)

  30. 30.

    et al. Attenuated BMP1 function compromises osteogenesis, leading to bone fragility in humans and zebrafish. Am. J. Hum. Genet. 90, 661–674 (2012)

  31. 31.

    et al. Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis 51, 835–843 (2013)

  32. 32.

    , & Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 13904–13909 (2013)

  33. 33.

    ZFIN: Zebrafish Book. 4th ed. (Univ. of Oregon Press, 2000)

Download references

Acknowledgements

We thank J. Westlund for figure preparation and construction, as well as maintenance of zebrafish facilities. M. Coates, M. Davis, R. Ho, I. Ruvinsky, J-L. Gomez Skarmeta, and C. Tabin provided comments and advice. We thank L. I. Zon, C. Mosimann, and C. Lawrence for Tg(ubi:Switch) fish, M. L. Suster for the pCR8GW-Cre-pA-FRT-kan-FRT plasmid, R. Ho and S. Briscoe for insights regarding lineage-tracing experiments, V. Bindokas and the University of Chicago Integrated Light Microscopy Core Facility for assistance with imaging, L. Zhexi for use of the high-energy CT scanning facility of University of Chicago, M. E. Horb and M. C. Salanga of the National Xenopus Resource (RRID:SCR-013731) of the Marine Biological Laboratories for tutelage in applying CRISPR/Cas9, J. Gitlin, A. Latimer and R. Thomason for providing space for zebrafish CRISPR/Cas9 experiments and also maintaining juveniles, and the Marine Resource Center of the Marine Biological Laboratories for assistance with the transfer of mutant zebrafish between University of Chicago and the MBL. This study was supported by the Uehara Memorial Foundation Research Fellowship 2013, Japan Society for the Promotion of Science Postdoctoral Research Fellowship 2012-127, and Marine Biological Laboratory Research Award 2014 (to T.N.); National Institutes of Health Grant T32 HD055164 and National Science Foundation Doctoral Dissertation Improvement Grant 1311436 (to A.R.G.); and the Brinson Foundation and the University of Chicago Biological Sciences Division (to N.H.S.).

Author information

Author notes

    • Tetsuya Nakamura
    •  & Andrew R. Gehrke

    These authors contributed equally to this work.

Affiliations

  1. Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois 60637, USA

    • Tetsuya Nakamura
    • , Andrew R. Gehrke
    • , Justin Lemberg
    • , Julie Szymaszek
    •  & Neil H. Shubin

Authors

  1. Search for Tetsuya Nakamura in:

  2. Search for Andrew R. Gehrke in:

  3. Search for Justin Lemberg in:

  4. Search for Julie Szymaszek in:

  5. Search for Neil H. Shubin in:

Contributions

T.N., A.R.G. and N.H.S. designed research; T.N. and J.S. performed in situ hybridization and CRISPR experiments; A.R.G. did fate mapping of the hox enhancers; T.N. and J.L. obtained CT scanning data; T.N., A.R.G., J.L. and N.H.S. analyzed data; and T.N., A.R.G., J.L. and N.H.S. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Neil H. Shubin.

Reviewer Information Nature thanks S. Burgess and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figure

    This file contains a 3D pdf of wild-type and double mutant fin.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature19322

Further reading

Comments

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.