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Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

Nature volume 474, pages 598–603 (2011)Cite this article

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Abstract

Morphology evolves often through changes in developmental genes, but the causal mutations, and their effects, remain largely unknown. The evolution of naked cuticle on larvae of Drosophila sechellia resulted from changes in five transcriptional enhancers of shavenbaby (svb), a transcript of the ovo locus that encodes a transcription factor that governs morphogenesis of microtrichiae, hereafter called ‘trichomes’. Here we show that the function of one of these enhancers evolved through multiple single-nucleotide substitutions that altered both the timing and level of svb expression. The consequences of these nucleotide substitutions on larval morphology were quantified with a novel functional assay. We found that each substitution had a relatively small phenotypic effect, and that many nucleotide changes account for this large morphological difference. In addition, we observed that the substitutions had non-additive effects. These data provide unprecedented resolution of the phenotypic effects of substitutions and show how individual nucleotide changes in a transcriptional enhancer have caused morphological evolution.

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Figure 1: The pattern of trichomes has evolved between Drosophila species owing to changes in the enhancers of the svb gene.
Figure 2: D. sechellia E6 shows decreased and delayed expression relative to D. melanogaster E6.
Figure 3: Sequence conservation of the E6 region and location of the D. sechellia -specific substitutions.
Figure 4: Evolutionary engineering of the E10 enhancer reveals the role of evolved substitutions in altering the levels and timing of expression.
Figure 5: Effect of the engineered substitutions on trichome rescue in dorsal and lateral regions of the sixth abdominal segment of first instar larvae.

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Acknowledgements

We thank G. Davis, P. Parikh and P. Valenti for assistance with cloning and the Drosophila Species Stock Center for fly stocks. This work was supported by the Pew Charitable Trusts Latin American Fellows Program in the Biomedical Sciences Fellowship to N.F., a Ruth L. Kirschstein National Research Service Award to D.F.E. (F32 GM 83546-02), Agence Nationale de la Recherche (Blanc 2008, Netoshape) to F.P., and NIH (GM063622-06A1) and NSF (IOS-0640339) grants to D.L.S.

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Author notes

  1. Nicolás Frankel and Deniz F. Erezyilmaz: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, 08544, New Jersey, USA

    Nicolás Frankel, Deniz F. Erezyilmaz, Shu Wang & David L. Stern

  2. Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, A-1210 Vienna, Austria

    Alistair P. McGregor

  3. Université de Toulouse and Centre National de la Recherche Scientifique, Centre de Biologie du Développement, UMR5547, Toulouse, F-31062, France

    François Payre

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  1. Nicolás Frankel
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Contributions

N.F., D.F.E., A.P.M. and D.L.S. designed the experiments and analysed the data. N.F., D.F.E., A.P.M., S.W. and F.P. performed the experimental work. N.F. and D.L.S. wrote the manuscript. D.F.E., A.P.M. and F.P. commented on the manuscript at all stages.

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Correspondence to David L. Stern.

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The authors declare no competing financial interests.

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Frankel, N., Erezyilmaz, D., McGregor, A. et al. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474, 598–603 (2011). https://doi.org/10.1038/nature10200

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