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.

Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola


Pigmentation divergence between Drosophila species has emerged as a model trait for studying the genetic basis of phenotypic evolution, with genetic changes contributing to pigmentation differences often mapping to genes in the pigment synthesis pathway and their regulators. These studies of Drosophila pigmentation have tended to focus on pigmentation changes in one body part for a particular pair of species, but changes in pigmentation are often observed in multiple body parts between the same pair of species. The similarities and differences of genetic changes responsible for divergent pigmentation in different body parts of the same species thus remain largely unknown. Here we compare the genetic basis of pigmentation divergence between Drosophila elegans and D. gunungcola in the wing, legs, and thorax. Prior work has shown that regions of the genome containing the pigmentation genes yellow and ebony influence the size of divergent male-specific wing spots between these two species. We find that these same two regions of the genome underlie differences in leg and thorax pigmentation; however, divergent alleles in these regions show differences in allelic dominance and epistasis among the three body parts. These complex patterns of inheritance can be explained by a model of evolution involving tissue-specific changes in the expression of Yellow and Ebony between D. elegans and D. gunungcola.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Insect sclerotization and pigmentation synthesis pathway and pigmentation differences between Drosophila elegans HK and D. gunungcola SK.
Fig. 2: Quantitative trait locus (QTL) mapping of thorax, leg, and wing pigmentation divergence.
Fig. 3: Genetic interactions among QTL on the X chromosome and Muller element E differ among body parts.
Fig. 4: D. gunungcola SK alleles linked to ebony on Muller element E have varied effects on thorax, leg, and wing pigmentation divergence.
Fig. 5: Model of pigmentation divergence connecting genotypes to gene expression to phenotypes.

Data availability

All supporting data can be accessed at University of Michigan Deep Blue ( and Dryad


  1. Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21(4):610–617

    CAS  Article  Google Scholar 

  2. Arnoult L, Su KF, Manoel D, Minervino C, Magriña J, Gompel N, Prud’homme B (2013) Emergence and diversification of fly pigmentation through evolution of a gene regulatory module. Science 339(6126):1423–1426

    CAS  Article  Google Scholar 

  3. Bassett AR, Tibbit C, Ponting CP, Liu J-L (2014) Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 6(6):1178–1179

    CAS  Article  Google Scholar 

  4. Broman KW, Sen S (2009) A Guide to QTL Mapping with R/qtl. Springer, New York, NY

  5. Carbone MA, Llopart A, deAngelis M, Coyne JA, Mackay TFC (2005) Quantitative trait loci affecting the difference in pigmentation between Drosophila yakuba and D. santomea. Genetics 171(1):211–225

    CAS  Article  Google Scholar 

  6. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69(4):315–324

    CAS  Article  Google Scholar 

  7. Hirai Y, Kimura MT (1997) Incipient reproductive isolation between two morphs of Drosophila elegans (Diptera: Drosophilidae). Biol J Linn Soc Linn Soc Lond 61(4):501–513

    Google Scholar 

  8. Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB (2008) The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132(5):783–793

    CAS  Article  Google Scholar 

  9. Kopp A (2009) Metamodels and phylogenetic replication: a systematic approach to the evolution of developmental pathways. Evolution; Int J Org Evolution 63(11):2771–2789

    Article  Google Scholar 

  10. Kronforst MR, Barsh GS, Kopp A, Mallet J, Monteiro A, Mullen SP et al. (2012) Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation. Pigment Cell Melanoma Res 25(4):411–433

    CAS  Article  Google Scholar 

  11. Lafuente E, Alves F, King JG, Peralta CM, Beldade P (2020) Many ways to make darker flies: Intra- and inter-specific variation in Drosophila body pigmentation components (p. 2020.08.26.268615).

  12. Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W et al. (2019) Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution. Curr Biol 29(13):2157–2166. e6

    CAS  Article  Google Scholar 

  13. Massey JH, Wittkopp PJ (2016) The Genetic Basis of Pigmentation Differences Within and Between Drosophila Species. Curr Top Developmental Biol 119:27–61

    CAS  Article  Google Scholar 

  14. Massey JH, Rice GR, Firdaus A, Chen C-Y, Yeh S-D, Stern DL, Wittkopp PJ (2020a) Co-evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution; Int J Org Evolution 74(6):1098–1111

    CAS  Article  Google Scholar 

  15. Massey JH, Li J, Wittkopp PJ (2020b) A method using CO2 anesthesia to collect embryos for microinjection in Drosophila elegans. Drosoph Inf Serv 103:75–77

    Google Scholar 

  16. Miller DFB, Holtzman SL, Kaufman TC (2002) Customized microinjection glass capillary needles for P-element transformations in Drosophila melanogaster. BioTechniques 33(2):369–370. 366–367372 passim

    Article  Google Scholar 

  17. Pinheiro J, Bates D, DebRoy S, Sarkar DR Core Team (2016) Nlme: Linear and Nonlinear Mixed Effects Models, R package version 3.1

  18. Prud’homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh S-D et al. (2006) Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440(7087):1050–1053

    Article  Google Scholar 

  19. Rebeiz M, Pool JE, Kassner VA, Aquadro CF, Carroll SB (2009) Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science 326(5960):1663–1667

    CAS  Article  Google Scholar 

  20. Stern DL, Orgogozo V (2008) The loci of evolution: how predictable is genetic evolution? Evolution; Int J Org Evolution 62(9):2155–2177

    Article  Google Scholar 

  21. Stern DL (2014) Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Trends Genet 30(12):547–554

    CAS  Article  Google Scholar 

  22. True JR (2003) Insect melanism: the molecules matter. Trends Ecol Evolution 18(12):640–647

    Article  Google Scholar 

  23. Wittkopp PJ, True JR, Carroll SB (2002) Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns. Dev (Camb, Engl) 129(8):1849–1858

    CAS  Article  Google Scholar 

  24. Wittkopp PJ, Carroll SB, Kopp A (2003) Evolution in black and white: genetic control of pigment patterns in Drosophila. Trends Genet: TIG 19(9):495–504

    CAS  Article  Google Scholar 

  25. Wittkopp PJ (2006) Evolution of cis-regulatory sequence and function in Diptera. Heredity 97(3):139–147

    CAS  Article  Google Scholar 

  26. Wittkopp PJ, Kalay G (2011) Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet 13(1):59–69

    Article  Google Scholar 

  27. Wittkopp PJ, Stewart EE, Arnold LL, Neidert AH, Haerum BK, Thompson et al. (2009) Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science 326(5952):540–544

    CAS  Article  Google Scholar 

  28. Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8(3):206–216

    CAS  Article  Google Scholar 

  29. Yeh S-D, Liou S-R, True JR (2006) Genetics of divergence in male wing pigmentation and courtship behavior between Drosophila elegans and D. gunungcola. Heredity 96(5):383–395

    Article  Google Scholar 

  30. Yeh S-D, True JR (2014) The genetic architecture of coordinately evolving male wing pigmentation and courtship behavior in Drosophila elegans and Drosophila gunungcola. G3 4(11):2079–2093

    Article  Google Scholar 

Download references


We thank members of the Wittkopp, Stern, and Rebeiz labs for helpful discussions. For fly strains, we thank J. True (Stony Brook University). For guidance with CRISPR/Cas9 genome editing and embryo injections, we thank Abigail Lamb. For helpful advice on creating F1 hybrids, we thank Shu-Dan Yeh (National Central University). Funding was provided by University of Michigan, Department of Ecology and Evolutionary Biology, Peter Olaus Okkelberg Research Award, National Institutes of Health (NIH) training grant T32GM007544, and Howard Hughes Medical Institute Janelia Graduate Research Fellowship to JHM; NIH R01 GM089736 and 1R35GM118073 to PJW.

Author information



Corresponding author

Correspondence to Patricia J. Wittkopp.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Associate editor: Darren Obbard

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Massey, J.H., Li, J., Stern, D.L. et al. Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola. Heredity (2021).

Download citation


Quick links