Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (Cuculus canorus) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species. Here, we show that female plumage dichromatism maps to the female-restricted genome. We further demonstrate that, consistent with balancing selection, ancestry of the rufous phenotype is shared with the likewise female dichromatic sister species, the oriental cuckoo (Cuculus optatus). This study shows that sex-specific polymorphism in trait variation can be resolved by genetic variation residing on a sex-limited chromosome and be maintained across species boundaries.

Advanced Science Research Center and Program in Psychology Graduate Center of the City University of New York New York NY 10031 USA

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal

British Trust for Ornithology Thetford UK

Centre for Biodiversity Genetics Norwegian Institute for Nature Research Trondheim Norway

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal

Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal

Departamento de Ecología Evolutiva Museo Nacional de Ciencias Naturales CSIC Madrid Spain

Department of Evolutionary Zoology and Human Biology University of Debrecen Debrecen Hungary

Department of Genetics University of Cambridge Cambridge CB2 3EH UK

Department of Life Sciences MARE Marine and Environmental Sciences Centre ARNET Aquatic Research Network University of Coimbra Coimbra Portugal

Department of Ornithology Max Planck Institute for Biological Intelligence Seewiesen Germany

Division of Evolutionary Biology LMU Munich Planegg Martinsried Germany

Evolutionary Ecology Group Faculty of Biology and Geology Babeș Bolyai University Cluj Napoca Romania

Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş Bolyai University Cluj Napoca Romania

HUN REN UD Behavioral Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Debrecen Hungary

Hungarian Natural History Museum Budapest Hungary

Institute of Plant and Animal Ecology Ural Branch Russian Academy of Sciences Yekaterinburg Russia

Institute of Vertebrate Biology Czech Academy of Sciences Brno Czech Republic

Palaeogenomics and Bio Archaeology Research Network School of Archaeology University of Oxford Oxford OX1 3QY UK

Scientific and Practical Center of Biodiversity Irbit Russia

STAR UBB Institute of Advanced Studies in Science and Technology Babeş Bolyai University Cluj Napoca Romania

The Vertebrate Genome Lab Rockefeller University New York NY 10065 USA

Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK

Zoological Museum Moscow State University Moscow Russia

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