ArticleNature ecology & evolution2025
Deep learning reveals the complex genetic architecture of male guppy colouration.
Article in Nature ecology & evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Conserved sex-biased DNA methylation patterns target key developmental genes and reproductive function in two Poeciliidae species.G3 (Bethesda, Md.) · 2026Article
- Color patterns as a model for connecting developmental mechanisms to phenotypic evolution.Nature communications · 2026Review
- Ancient inversion polymorphisms associate with sexually selected traits across natural guppy populations.PLoS biology · 2026Article
- Beyond the Classics: The Synergy of AI and Genomics Reveals an Expanded Repertoire of Pigmentation Genes.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2026Review
- Immediate Background Color Choice in Male and FemaleAnimals : an open access journal from MDPI · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Hypotheses for the Adaptive Maintenance of Phenotypic Polymorphisms.Ecology and evolution · 2026Review
- Machine learning for evolutionary genetics and molecular evolution.Trends in genetics : TIG · 2026Review
- Social Interaction With Females Modulates Context-Dependent Male Guppy Mating Tactics for Female Receptivity.Ecology and evolution · 2025Article
- Genome Architecture and Speciation in Plants and Animals.Molecular ecology · 2025Review
- Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.G3 (Bethesda, Md.) · 2025Article
- Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly.Genome research · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
The extraordinary variation in male guppy (Poecilia reticulata) colouration is a powerful model for studying the interplay of natural and sexual selection. However, the complexity of this variation has hampered the high-resolution characterization and determination of the genetic architecture underlying male guppy colour and clouded our understanding of how this exceptional level of diversity is maintained. Here we identify the heritability and genetic basis of male colour variation using convolutional neural networks for high-resolution phenotyping coupled with selection experiments, controlled pedigrees and whole-genome resequencing for a genome-wide association study of colour traits. Our phenotypic and genomic results converge to show that colour patterning in guppies is a combination of many heritable features, each with a largely independent genetic architecture spanning the entire genome. Autosomally inherited ornaments are polygenic, with significant contributions from loci involved in neural crest cell migration. Unusually, the results of our genome-wide association study suggest that gene duplicates from the autosomes to the Y chromosome are responsible for much of the sex-linked variation in colour in guppies, providing a potential mechanism for the maintenance of variation of this classic model trait.
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