The genetics of monarch butterfly migration and warning colouration

Journal name:
Nature
Volume:
514,
Pages:
317–321
Date published:
DOI:
doi:10.1038/nature13812
Received
Accepted
Published online

Abstract

The monarch butterfly, Danaus plexippus, is famous for its spectacular annual migration across North America, recent worldwide dispersal, and orange warning colouration. Despite decades of study and broad public interest, we know little about the genetic basis of these hallmark traits. Here we uncover the history of the monarch’s evolutionary origin and global dispersal, characterize the genes and pathways associated with migratory behaviour, and identify the discrete genetic basis of warning colouration by sequencing 101 Danaus genomes from around the globe. The results rewrite our understanding of this classic system, showing that D. plexippus was ancestrally migratory and dispersed out of North America to occupy its broad distribution. We find the strongest signatures of selection associated with migration centre on flight muscle function, resulting in greater flight efficiency among migratory monarchs, and that variation in monarch warning colouration is controlled by a single myosin gene not previously implicated in insect pigmentation.

At a glance

Figures

  1. Global dispersal of the monarch butterfly.
    Figure 1: Global dispersal of the monarch butterfly.

    a, Monarch butterfly sampling locations. b, Inferred phylogeny among Danaus species based on maximum likelihood analysis of 3,714 single-copy genes. c, Neighbour-joining phylogeny of all D. plexippus individuals, based on genome-wide SNP data. ATL, Atlantic crossing; CEN, Central America (including south Florida); NOR, North America (including Mexico); PAC, Pacific crossing. d, Neighbour-joining consensus tree based on 1,000 bootstrap replicates. e, Principal component analysis (PCA) plots based on the first two principal components; inset shows separation between North America and south Florida. f, Genetic structure and individual ancestry; colours in each column represent ancestry proportion over range of population sizes K =  2–11. ABW, Aruba; AUS, Australia; BLZ, Belize; BMU, Bermuda; CRC, Costa Rica; ECU, Ecuador; ESP, Spain; FJI, Fiji; HI, Hawaii; MAR, Morocco; NZL, New Zealand; NCL, New Caledonia; PRI, Puerto Rico; PRT, Portugal; s.FL, south Florida; WSM, Samoa.

  2. A selective sweep associated with migration.
    Figure 2: A selective sweep associated with migration.

    a, Distribution of PBS and polymorphism in North America (πNOR), calculated in 5-kb sliding windows. Migration-associated genomic regions were identified as the points above the dashed line (P < 0.01) and to the left of the vertical green dashed line (lower quartile). Circled points consist of a single 21-kb region. b, Population genetic statistics were plotted across DPSCF300190 in 5-kb sliding windows. c, Gene models and SNP allele: white represents homozygous for the reference allele; red, homozygous for alternative allele; yellow, heterozygous; grey, masked site.

  3. Divergent selection on collagen IV [agr]-1.
    Figure 3: Divergent selection on collagen IV α-1.

    a, Collagen IV α-1 shows elevated sequence divergence (Dxy) and differentiation (FST) between migratory and non-migratory monarchs (mean ± s.e.m.), an excess of polymorphism (Hudson–Kreitman–Aguadé test), and b, haplotype divergence. c, A maximum-likelihood tree shows that the non-migratory haplotype pre-dates species-level divergence within Danaus whereas the migratory haplotype is similar to D. erippus. d, A subsection of high polymorphism and divergence in collagen IV α-1 coincides with an amino acid experiencing positive selection, including a R1573Q substitution on the migratory haplotype. e, Expression of collagen IV α-1 and α-2 differ between migratory and non-migratory populations in flight muscle tissue. FPKM, fragments per kilobase of transcript per million fragments mapped; NS, not significant. f, Flight metabolic rates differ more than resting metabolic rates between migratory and non-migratory populations (mean ± s.e.m.).

  4. The genetic basis of warning colouration.
    Figure 4: The genetic basis of warning colouration.

    a, Although D. plexippus is generally bright orange, the nivosus morph lacks orange pigmentation. b, A comparison of 12 Hawaiian monarch genome sequences (5 wild-type, 5 nivosus and 2 F1 hybrids) reveals perfect SNP associations in one gene, the myosin gene DPOGS206617. p, probability of association. c, Comparison of DNA sequence divergence (Dxy) between D. plexippus and D. chrysippus shows strong purifying selection in exon 2, coinciding with SNP associations in modern samples, crosses and field collections from the 1980s. SNP position 785 is associated in 17/20 samples from the 1980s (P = 0.02, one-tailed Fisher’s exact test).

  5. Relationships among monarch populations inferred using the maximum likelihood method implemented in Treemix.
    Extended Data Fig. 1: Relationships among monarch populations inferred using the maximum likelihood method implemented in Treemix.

    Note, this is a fully resolved, bifurcating tree. The very short basal branches indicate little genetic drift in North American populations, not unresolved basal relationships. Colours correspond to those in Fig. 1. Treemix also inferred five migration events among populations: from Puerto Rico to Aruba, from Puerto Rico to Costa Rica, from New Caledonia to Fiji, from Belize or Costa Rica to Portugal, and from Belize to Puerto Rico.

  6. Demographic history of the monarch butterfly.
    Extended Data Fig. 2: Demographic history of the monarch butterfly.

    a, Patterns of linkage-disequilibrium decay across the genome in different geographic populations. b, Genome-wide distribution of minor allele frequencies. c, Heterozygosity across populations, estimated as the ratio of heterozygous SNPs to homozygous SNPs/individual. d, Demographic history inferred using PSMC. This analysis includes representative individuals of high sequencing depth for each geographic location. The period of the last glacial maximum (LGM; ~20,000 years ago) is shaded in grey.

  7. [part]a[part]i analysis parameter estimates.
    Extended Data Fig. 3: ∂a∂i analysis parameter estimates.

    a, Schematic of demographic scenario modelled in ∂a∂i labelled with parameters being estimated. Nu, effective population size (individuals); m, migration rate (individuals/year); T, time (years). b, Inferred parameter estimates. c, One-dimensional model-data comparison considering North America population only. In the left panel, the model is plotted in red and the data in blue. In the right panel, the residuals between model and data are plotted. d, Two-dimensional comparison for joint estimation of North America and dispersal populations (Central/South America, Pacific, Atlantic). The left two panels are marginal spectra for data and the maximum-likelihood model, respectively. The right two panels show the residuals.

Tables

  1. Inferring the monarch range expansion
    Extended Data Table 1: Inferring the monarch range expansion
  2. Top 20 migration-associated genomic regions
    Extended Data Table 2: Top 20 migration-associated genomic regions

Accession codes

Primary accessions

Sequence Read Archive

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Author information

Affiliations

  1. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China

    • Shuai Zhan
  2. Department of Ecology & Evolution, University of Chicago, Chicago, Illinois 60637, USA

    • Shuai Zhan,
    • Wei Zhang &
    • Marcus R. Kronforst
  3. Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA

    • Shuai Zhan &
    • Steven M. Reppert
  4. Department of Biology, Stanford University, Stanford, California 94305, USA

    • Kristjan Niitepõld &
    • Jeremy Hsu
  5. Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland

    • Kristjan Niitepõld
  6. Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, 14071 Córdoba, Spain

    • Juan Fernández Haeger
  7. School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia

    • Myron P. Zalucki
  8. Odum School of Ecology, University of Georgia, Athens, Georgia 30602, USA

    • Sonia Altizer
  9. Department of Biology, Emory University, Atlanta, Georgia 30322, USA

    • Jacobus C. de Roode

Contributions

S.Z. designed and implemented analyses of dispersal and migration and co-wrote the manuscript. W.Z. performed wing colour analyses. K.N. performed respirometry experiments. J.H. helped design the project and collected and prepared samples for sequencing. J.F.H. and M.P.Z. provided samples and interpreted results. S.A., J.C.d.R. and S.M.R. helped design the project, provided samples, and interpreted results. M.R.K. conceived and directed the project, performed targeted population genetic analyses, and co-wrote the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Sequence data are deposited in the NCBI Short Read Archive (SRA) database (accession numbers SRP045457 and SRP045468).

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Relationships among monarch populations inferred using the maximum likelihood method implemented in Treemix. (233 KB)

    Note, this is a fully resolved, bifurcating tree. The very short basal branches indicate little genetic drift in North American populations, not unresolved basal relationships. Colours correspond to those in Fig. 1. Treemix also inferred five migration events among populations: from Puerto Rico to Aruba, from Puerto Rico to Costa Rica, from New Caledonia to Fiji, from Belize or Costa Rica to Portugal, and from Belize to Puerto Rico.

  2. Extended Data Figure 2: Demographic history of the monarch butterfly. (422 KB)

    a, Patterns of linkage-disequilibrium decay across the genome in different geographic populations. b, Genome-wide distribution of minor allele frequencies. c, Heterozygosity across populations, estimated as the ratio of heterozygous SNPs to homozygous SNPs/individual. d, Demographic history inferred using PSMC. This analysis includes representative individuals of high sequencing depth for each geographic location. The period of the last glacial maximum (LGM; ~20,000 years ago) is shaded in grey.

  3. Extended Data Figure 3: ∂a∂i analysis parameter estimates. (551 KB)

    a, Schematic of demographic scenario modelled in ∂a∂i labelled with parameters being estimated. Nu, effective population size (individuals); m, migration rate (individuals/year); T, time (years). b, Inferred parameter estimates. c, One-dimensional model-data comparison considering North America population only. In the left panel, the model is plotted in red and the data in blue. In the right panel, the residuals between model and data are plotted. d, Two-dimensional comparison for joint estimation of North America and dispersal populations (Central/South America, Pacific, Atlantic). The left two panels are marginal spectra for data and the maximum-likelihood model, respectively. The right two panels show the residuals.

Extended Data Tables

  1. Extended Data Table 1: Inferring the monarch range expansion (63 KB)
  2. Extended Data Table 2: Top 20 migration-associated genomic regions (447 KB)

Supplementary information

PDF files

  1. Supplementary Information (422 KB)

    This file contains Supplementary Tables 1-14.

Additional data