Skip to main content

Thank you for visiting nature.com. 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.

Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds

Abstract

Morphological characters are the result of developmental gene expression. The identity of a character is ultimately grounded in the gene regulatory network directing development and thus whole-genome gene expression data can provide evidence about character identity. This approach has been successfully used to assess cell-type identity1,2,3. Here we use transcriptomic data to address a long-standing uncertainty in evolutionary biology, the identity of avian wing digits4,5. Embryological evidence clearly identifies the three wing digits as developing from digit positions 2, 3 and 4 (ref. 6), whereas palaeontological data suggest that they are digits I, II and III7. We compare the transcriptomes of the wing and foot digits and find a strong signal that unites the first wing digit with the first foot digit, even though the first wing digit develops from embryological position 2. Interestingly, our transcriptomic data of the posterior digits show a higher degree of differentiation among forelimb digits compared with hindlimb digits. These data show that in the stem lineage of birds the first digit underwent a translocation from digit position 1 to position 2, and further indicate that the posterior wing digits have unique identities contrary to any model of avian digit identity proposed so far5,8.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Chicken embryonic digit transcriptomes identify forelimb and hindlimb digits I but no clear correspondence between posterior forelimbs and hindlimbs.
Figure 2: Expression of Zic3.
Figure 3: Expression of Socs2.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All mRNA-seq data are deposited in the Gene Expression Omnibus under accession number GSE28156.

References

  1. Novershtern, N. et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296–309 (2011)

    CAS  Article  Google Scholar 

  2. Cherbas, L. et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. 21, 301–314 (2011)

    CAS  Article  Google Scholar 

  3. Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511 (2000)

    ADS  CAS  Article  Google Scholar 

  4. Wagner, G. P. The developmental evolution of avian digit homology: an update. Theory Biosci. 124, 165–183 (2005)

    Article  Google Scholar 

  5. Young, R. L., Bever, G. S., Wang, Z. & Wagner, G. P. Identity of the avian wing digits: problems resolved and unsolved. Dev. Dyn. 240, 1042–1053 (2011)

    Article  Google Scholar 

  6. Burke, A. C. & Feduccia, A. Developmental patterns and the identification of homologies in the avian hand. Science 278, 666–668 (1997)

    ADS  CAS  Article  Google Scholar 

  7. Wagner, G. P. & Gauthier, J. A. 1,2,3 = 2,3,4: a solution to the problem of the homology of the digits in the avian hand. Proc. Natl Acad. Sci. USA 96, 5111–5116 (1999)

    ADS  CAS  Article  Google Scholar 

  8. Tamura, K. et al. Embryological evidence identifies wing digits in birds as digits 1, 2, and 3. Science 331, 753–757 (2011)

    ADS  CAS  Article  Google Scholar 

  9. Burke, A. C., Nelson, C. E., Morgan, B. A. & Tabin, C. Hox genes and the evolution of vertebrate axial morphology. Development 121, 333–346 (1995)

    CAS  Google Scholar 

  10. Mansfield, J. H. & Abzhanov, A. Hox expression in the American alligator and evolution of archosaurian axial patterning. J. Exp. Zool. B 314, 629–644 (2010)

    Article  Google Scholar 

  11. Averof, M. & Akam, M. Hox genes and the diversification of insect and crustacean body plans. Nature 376, 420–423 (1995)

    ADS  CAS  Article  Google Scholar 

  12. Arendt, D. The evolution of cell types in animals: emerging principles from molecular studies. Nature Rev. Genet. 9, 868–882 (2008)

    CAS  Article  Google Scholar 

  13. Sugino, K. et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nature Neurosci. 9, 99–107 (2006)

    CAS  Article  Google Scholar 

  14. Palmer, C., Diehn, M., Alizadeh, A. A. & Brown, P. O. Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 7, 115 (2006)

    Article  Google Scholar 

  15. Wagner, G. P. The developmental genetics of homology. Nature Rev. Genet. 8, 473–479 (2007)

    CAS  Article  Google Scholar 

  16. Young, R. L. & Wagner, G. P. Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations. J. Exp. Zool. B 316B, 165–170 (2011)

    Article  Google Scholar 

  17. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010)

    CAS  Article  Google Scholar 

  18. Welten, M. C., Verbeek, F. J., Meijer, A. H. & Richardson, M. K. Gene expression and digit homology in the chicken embryo wing. Evol. Dev. 7, 18–28 (2005)

    CAS  Article  Google Scholar 

  19. Tickle, C. Making digit patterns in the vertebrate limb. Nature Rev. Mol. Cell Biol. 7, 45–53 (2006)

    CAS  Article  Google Scholar 

  20. Vargas, A. O. & Fallon, J. F. Birds have dinosaur wings: The molecular evidence. J. Exp. Zool. B 304B, 86–90 (2005)

    CAS  Article  Google Scholar 

  21. Vargas, A. O. et al. The evolution of HoxD-11 expression in the bird wing: insights from Alligator mississippiensis . PLoS ONE 3, e3325 (2008)

    ADS  Article  Google Scholar 

  22. Uejima, A. et al. Anterior shift in gene expression precedes anteriormost digit formation in amniote limbs. Dev. Growth Differ. 52, 223–234 (2010)

    CAS  Article  Google Scholar 

  23. Montavon, T., Le Garrec, J. F., Kerszberg, M. & Duboule, D. Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness. Genes Dev. 22, 346–359 (2008)

    CAS  Article  Google Scholar 

  24. Firulli, B. A. et al. Altered Twist1 and Hand2 dimerization is associated with Saethre-Chotzen syndrome and limb abnormalities. Nature Genet. 37, 373–381 (2005)

    CAS  Article  Google Scholar 

  25. Zhu, L., Zhou, G., Poole, S. & Belmont, J. W. Characterization of the interactions of human ZIC3 mutants with GLI3. Hum. Mutat. 29, 99–105 (2008)

    CAS  Article  Google Scholar 

  26. Tzchori, I. et al. LIM homeobox transcription factors integrate signaling events that control three-dimensional limb patterning and growth. Development 136, 1375–1385 (2009)

    CAS  Article  Google Scholar 

  27. Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006)

    CAS  Article  Google Scholar 

  28. Wang, L. K. et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136–138 (2010)

    Article  Google Scholar 

  29. Hargrave, M., Bowles, J. & Koopman, P. In situ hybridization of whole-mount embryos. Methods Mol. Biol. 326, 103–113 (2006)

    CAS  PubMed  Google Scholar 

  30. Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010)

    Article  Google Scholar 

  31. Dahn, R. D. & Fallon, J. F. Interdigital regulation of digit identity and homeotic transformation by modulated BMP signaling. Science 289, 438–441 (2000)

    ADS  CAS  Article  Google Scholar 

  32. Suzuki, T., Hasso, S. M. & Fallon, J. F. Unique SMAD1/5/8 activity at the phalanx-forming region determines digit identity. Proc. Natl Acad. Sci. USA 105, 4185–4190 (2008)

    ADS  CAS  Article  Google Scholar 

  33. Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49–92 (1951)

    CAS  Article  Google Scholar 

  34. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995)

    MathSciNet  MATH  Google Scholar 

  35. Young, M. D., Wakefield, M. J., Smyth, G. K. & Oshlack, A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11, R14 (2010)

    Article  Google Scholar 

  36. McMahon, A. R. & Merzdorf, C. S. Expression of the zic1, zic2, zic3, and zic4 genes in early chick embryos. BMC Res. Notes 3, 167 (2010)

    Article  Google Scholar 

  37. Abellán, A. et al. Olfactory and amygdalar structures of the chicken ventral pallium based on the combinatorial expression patterns of LIM and other developmental regulatory genes. J. Comp. Neurol. 516, 166–186 (2009)

    Article  Google Scholar 

  38. Nelson, C. E. et al. Analysis of Hox gene expression in the chick limb bud. Development 122, 1449–1466 (1996)

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank J. Noonan for discussions on this project, K. Cooper for experimental assistance and N. Carriero for read-mapping assistance and C. Tabin for providing us with the Hoxd12 probe. The authors are also grateful for the technical support for this project by the Yale Center for Genomic Analysis. The financial support by the Yale Science Development Fund is gratefully acknowledged.

Author information

Authors and Affiliations

Authors

Contributions

Z.W. performed the experiments and data analysis and participated in design of the study. R.L.Y., H.X. and G.P.W. participated in data analysis. G.P.W. conceived and designed the study and supervised the work. All authors discussed the results and made substantial contributions to the manuscript.

Corresponding author

Correspondence to Günter P. Wagner.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-10 with legends, Supplementary Table 1, a Supplementary Discussion and Supplementary References. (PDF 989 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wang, Z., Young, R., Xue, H. et al. Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds. Nature 477, 583–586 (2011). https://doi.org/10.1038/nature10391

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10391

This article is cited by

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.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing