The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
Bibliographic record
Abstract
Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [ 1–6 1. Reed, R.D. ∙ Papa, R. ∙ Martin, A. ... optix drives the repeated convergent evolution of butterfly wing pattern mimicry Science. 2011; 333 :1137-1141 Crossref Scopus (327) PubMed Google Scholar 2. Kunte, K. ∙ Zhang, W. ∙ Tenger-Trolander, A. ... doublesex is a mimicry supergene Nature. 2014; 507 :229-232 Crossref Scopus (253) PubMed Google Scholar 3. Nadeau, N.J. ∙ Pardo-Diaz, C. ∙ Whibley, A. ... The gene cortex controls mimicry and crypsis in butterflies and moths Nature. 2016; 534 :106-110 Crossref Scopus (156) PubMed Google Scholar 4. Van’t Hof, A.E. ∙ Campagne, P. ∙ Rigden, D.J. ... The industrial melanism mutation in British peppered moths is a transposable element Nature. 2016; 534 :102-105 Crossref Scopus (285) PubMed Google Scholar 5. Yassin, A. ∙ Delaney, E.K. ∙ Reddiex, A.J. ... The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila Curr. Biol. 2016; 26 :2412-2422 Full Text Full Text (PDF) Scopus (42) PubMed Google Scholar 6. Jay, P. ∙ Whibley, A. ∙ Frézal, L. ... Supergene evolution triggered by the introgression of a chromosomal inversion Curr. Biol. 2018; 28 :1839-1845.e3 Full Text Full Text (PDF) Scopus (91) PubMed Google Scholar ]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [ 7, 8 7. Majerus, M.E.N. Ladybirds Collins New Naturalist, 1994 Google Scholar 8. Majerus, M.E.N. Melanism: Evolution in Action Oxford University Press, 1998 Crossref Google Scholar ]. In the harlequin ladybird, Harmonia axyridis , more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [ 9, 10 9. Tan, C. ∙ Li, J. Inheritance of the elytral color patterns of the lady-bird beetle, Harmonia axyridis Pallas Am. Nat. 1934; 68 :252-265 Crossref Google Scholar 10. Komai, T. Genetics of ladybirds Adv. Genet. 1956; 8 :155-188 Crossref Scopus (92) Google Scholar ]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis . We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis . Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis -regulatory regions of pannier , with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis -regulatory allelic variation of a single gene.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".