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doublesex is a mimicry supergene


One of the most striking examples of sexual dimorphism is sex-limited mimicry in butterflies, a phenomenon in which one sex—usually the female—mimics a toxic model species, whereas the other sex displays a different wing pattern1. Sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio, in which it is often associated with female mimetic polymorphism1,2,3. In multiple polymorphic species, the entire wing pattern phenotype is controlled by a single Mendelian ‘supergene’4. Although theoretical work has explored the evolutionary dynamics of supergene mimicry5,6,7,8,9, there are almost no empirical data that address the critical issue of what a mimicry supergene actually is at a functional level. Using an integrative approach combining genetic and association mapping, transcriptome and genome sequencing, and gene expression analyses, we show that a single gene, doublesex, controls supergene mimicry in Papilio polytes. This is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci4. Analysis of gene expression and DNA sequence variation indicates that isoform expression differences contribute to the functional differences between dsx mimicry alleles, and protein sequence evolution may also have a role. Our results combine elements from different hypotheses for the identity of supergenes, showing that a single gene can switch the entire wing pattern among mimicry phenotypes but may require multiple, tightly linked mutations to do so.

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Figure 1: Polymorphic, sex-limited mimicry in Papilio polytes.
Figure 2: Mapping the mimicry supergene.
Figure 3: Expression of doublesex in P. polytes.

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  1. Joron, M. & Mallet, J. L. Diversity in mimicry: paradox or paradigm? Trends Ecol. Evol. 13, 461–466 (1998)

    CAS  PubMed  Google Scholar 

  2. Kunte, K. The diversity and evolution of batesian mimicry in Papilio swallowtail butterflies. Evolution 63, 2707–2716 (2009)

    PubMed  Google Scholar 

  3. Kunte, K. Female-limited mimetic polymorphism: a review of theories and a critique of sexual selection as balancing selection. Anim. Behav. 78, 1029–1036 (2009)

    Google Scholar 

  4. Clarke, C. A. & Sheppard, P. M. Super-genes and mimicry. Heredity 14, 175–185 (1960)

    Google Scholar 

  5. Charlesworth, D. & Charlesworth, B. Theoretical genetics of Batesian mimicry II. Evolution of supergenes. J. Theor. Biol. 55, 305–324 (1975)

    CAS  PubMed  Google Scholar 

  6. Charlesworth, D. & Charlesworth, B. Mimicry: the hunting of the supergene. Curr. Biol. 21, R846–R848 (2011)

    CAS  PubMed  Google Scholar 

  7. Fisher, R. A. The Genetical Theory of Natural Selection (Clarendon Press, 1930)

    MATH  Google Scholar 

  8. Sheppard, P. M. The evolution of mimicry: a problem in ecology and genetics. Cold Spring Harb. Symp. Quant. Biol. 24, 131–140 (1959)

    CAS  PubMed  Google Scholar 

  9. Turner, J. R. G. in The Biology of Butterflies (eds Vane-Wright, R. I. & Ackery, P. R. ) 141–161 (Academic, 1984)

    Google Scholar 

  10. Bates, H. W. Contributions to an insect fauna of the Amazon valley (Lepidoptera: Heliconidae). Trans. Linn. Soc. (Lond.) 23, 495–566 (1862)

    Google Scholar 

  11. Ford, E. B. The genetics of polymorphism in the Lepidoptera. Adv. Genet. 5, 43–87 (1953)

    CAS  PubMed  Google Scholar 

  12. Mallet, J. & Joron, M. Evolution of diversity in warning color and mimicry: Polymorphisms, shifting balance, and speciation. Annu. Rev. Ecol. Syst. 30, 201–233 (1999)

    Google Scholar 

  13. Clarke, C. A. & Sheppard, P. M. The genetics of the mimetic butterfly Papilio polytes L. Phil. Trans. R. Soc. Lond. B 263, 431–458 (1972)

    ADS  CAS  Google Scholar 

  14. Clarke, C. A., Sheppard, P. M. & Thornton, I. W. B. The genetics of the mimetic butterfly Papilio memnon L. Phil. Trans. R. Soc. Lond. B 254, 37–89 (1968)

    ADS  Google Scholar 

  15. Joron, M. et al. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature 477, 203–206 (2011)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Larracuente, A. M. & Presgraves, D. C. The selfish Segregation Distorter gene complex of Drosophila melanogaster. Genetics 192, 33–53 (2012)

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Takayama, S. & Isogai, A. Self-incompatibility in plants. Annu. Rev. Plant Biol. 56, 467–489 (2005)

    CAS  PubMed  Google Scholar 

  18. Nijhout, H. F. Developmental perspectives on evolution of butterfly mimicry. Bioscience 44, 148–157 (1994)

    Google Scholar 

  19. Burtis, K. C. & Baker, B. S. Drosophila doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. Cell 56, 997–1010 (1989)

    CAS  PubMed  Google Scholar 

  20. Williams, T. M. & Carroll, S. B. Genetic and molecular insights into the development and evolution of sexual dimorphism. Nature Rev. Genet. 10, 797–804 (2009)

    CAS  PubMed  Google Scholar 

  21. Kopp, A. Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 28, 175–184 (2012)

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Cho, S., Huang, Z. Y. & Zhang, J. Z. Sex-specific splicing of the honeybee doublesex gene reveals 300 million years of evolution at the bottom of the insect sex-determination pathway. Genetics 177, 1733–1741 (2007)

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Kijimoto, T., Moczek, A. P. & Andrews, J. Diversification of doublesex function underlies morph-, sex-, and species-specific development of beetle horns. Proc. Natl Acad. Sci. USA 109, 20526–20531 (2012)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Tanaka, K., Barmina, O., Sanders, L. E., Arbeitman, M. N. & Kopp, A. Evolution of sex-specific traits through changes in HOX-dependent doublesex expression. PLoS Biol. 9, e1001131 (2011)

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Williams, T. M. et al. The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. Cell 134, 610–623 (2008)

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Loehlin, D. W. et al. Non-coding changes cause sex-specific wing size differences between closely related species of Nasonia. PLoS Genet. 6, e1000821 (2010)

    PubMed  PubMed Central  Google Scholar 

  27. Charlesworth, B. & Charlesworth, D. Elements of Evolutionary Genetics (Roberts & Co., 2010)

    MATH  Google Scholar 

  28. Hoffmann, A. A., Sgro, C. M. & Weeks, A. R. Chromosomal inversion polymorphisms and adaptation. Trends Ecol. Evol. 19, 482–488 (2004)

    PubMed  Google Scholar 

  29. Clark, R. et al. Colour pattern specification in the Mocker swallowtail Papilio dardanus: the transcription factor invected is a candidate for the mimicry locus H. Proc. R. Soc. Lond. B 275, 1181–1188 (2008)

    Google Scholar 

  30. Scriber, J. M., Hagen, R. H. & Lederhouse, R. C. Genetics of mimicry in the tiger swallowtail butterflies, Papilio glaucus and P. canadensis (Lepidoptera: Papilionidae). Evolution 50, 222–236 (1996)

    PubMed  Google Scholar 

  31. Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012)

    PubMed  PubMed Central  Google Scholar 

  32. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359 (2012)

    CAS  PubMed  PubMed Central  Google Scholar 

  33. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  34. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011)

    CAS  PubMed  Google Scholar 

  35. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011)

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165–1188 (2001)

    MathSciNet  MATH  Google Scholar 

  37. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007)

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Hudson, R. R., Kreitman, M. & Aguade, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987)

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhang, W., Kunte, K. & Kronforst, M. R. Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies. Genome Biol. Evol. 5, 1233–1245 (2013)

    PubMed  PubMed Central  Google Scholar 

  40. Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009)

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol. 29, 644–652 (2011)

    CAS  Google Scholar 

  42. Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Kelley, L. A. & Sternberg, M. J. Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4, 363–371 (2009)

    CAS  PubMed  Google Scholar 

  44. Mellert, D. J., Robinett, C. C. & Baker, B. S. doublesex functions early and late in gustatory sense organ development. PLoS ONE 7, e51489 (2012)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

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We thank W. Wang for sharing genome sequence data, C. Robinett for providing the Dsx-DM monoclonal antibody, and E. Westerman, S. Nallu, M. Zhang, G. Garcia and N. Pierce for assistance and discussion. This project was funded by National Science Foundation grant DEB-1316037 to M.R.K.

Author information

Authors and Affiliations



K.K. conceived the project and helped design the study, reared mapping families and samples for gene expression analysis and genome sequencing, performed bulk-segregant analysis and RAD mapping, and contributed to drafting the manuscript. W.Z. generated the reference genome sequences and transcriptome assemblies, performed association mapping, GWAS analysis, HKA tests, structural variant detection and linkage disequilibrium analyses, analysis of protein structure and synonymous/non-synonymous calculations, and contributed to drafting the manuscript. A.T.-T. assisted with butterfly husbandry, performed fine mapping, cDNA sequencing and qRT–PCR analyses. D.H.P. performed qRT–PCR analyses. A.M. and R.D.R. performed Dsx immunohistochemistry. S.P.M. helped design the project and contributed to drafting the manuscript. M.R.K. designed and directed the project, analysed data and wrote the manuscript.

Corresponding authors

Correspondence to K. Kunte or M. R. Kronforst.

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Competing interests

The authors declare no competing financial interests.

Additional information

Sequence data are available from NCBI SRA (SRP035394) and GenBank (KJ150616KJ150623).

Extended data figures and tables

Extended Data Figure 1 Amino acid substitutions in dsx.

The position of all amino acid substitutions fixed between cyrus and polytes alleles are shown relative to the DM and dimerization domains of dsx. doublesex is a transcription factor that binds DNA as a dimer. The DM domain is responsible for DNA binding and the dimerization domain is responsible for Dsx protein dimerization.

Extended Data Figure 2 Inferred effect of amino acid substitutions on Dsx protein structure.

a, Inferred secondary structure of the Doublesex protein from the cyrus allele of P. polytes, the polytes allele of P. polytes and Bombyx mori. Green helices represent alpha helix structure and blue arrows represent beta sheet structure. b, Inferred tertiary structure of the Doublesex protein from the cyrus allele of P. polytes, the polytes allele of P. polytes and Bombyx mori. Only female isoform 1 is pictured although all protein isoforms differ between cyrus and polytes in a similar way.

Extended Data Figure 3 Analyses of linkage disequilibrium around dsx.

af, Linkage disequilibrium, measured as r2, is elevated in the 1 Mb surrounding dsx in the analysis of all samples (first 1 Mb of the 4-Mb scaffold), compared to a 2-Mb region outside of dsx (last 2 Mb of the 4-Mb scaffold), but this pattern is not evident when analysing cyrus and polytes morph samples separately. g, Linkage disequilibrium heat map, measured as D′, across the 300-kb focal interval shows elevated linkage disequilibrium across dsx but not outside of the gene. Standard colour scheme: D′ < 1, LOD <2 (white); D′ = 1, LOD <2 (blue); D′ = 1, LOD ≥ 2 (pink and red).

Extended Data Figure 4 PCR assay for dsx inversion.

a, Analysis of genome sequence data indicated the presence of an inversion containing the gene dsx. PCR primers that span the breakpoints are expected to produce a product from samples that contain the ancestral, non-inverted sequence, but these should produce no PCR product from samples containing an inversion because the forward priming site is far away and in the opposite orientation. b, Using a series of partially overlapping PCR products, we located the likely 3′ breakpoint approximately 2 kb downstream of the dsx 3′ untranslated region. A second set of breakpoint and control primers produced identical results. All primers were located in regions of no polymorphism, based on genome re-sequencing data, and were tested with ten homozygous females of each phenotype.

Extended Data Table 1 Individuals used for genome re-sequencing
Extended Data Table 2 Candidate scaffolds identified from genome-wide association study
Extended Data Table 3 Results of HKA tests
Extended Data Table 4 De novo polytes scaffolds spanning possible inversion breakpoints

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Kunte, K., Zhang, W., Tenger-Trolander, A. et al. doublesex is a mimicry supergene. Nature 507, 229–232 (2014).

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