Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

CIBIO InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto 4485 661 Vairão Portugal

CIBIO InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto 4485 661 Vairão Portugal;

Departamento de Biologia Faculdade de Ciências Universidade do Porto 4169 007 Porto Portugal

Department of Analytical Chemistry Faculty of Science Charles University 128 43 Prague 2 Czech Republic

Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences 750 07 Uppsala Sweden

Department of Biology Lund University 223 62 Lund Sweden

Department of Earth and Environmental Sciences University of Pavia 27100 Pavia Italy

Department of Food Science Faculty of Agrobiology Food and Natural Resources Czech University of Life Sciences Prague 165 21 Prague 6 Czech Republic

Department of Health Life and Environmental Sciences University of L'Aquila 67100 L'Aquila Italy

Department of Philosophy and History of Science Faculty of Science Charles University 128 00 Prague 2 Czech Republic

Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A and M University College Station TX 77843

Department of Zoology National Museum 193 00 Prague Czech Republic

Department of Zoology University of Oxford OX1 3PS Oxford United Kingdom

Ethology Laboratory Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia 469 80 Paterna Spain

School of Biological Sciences University of Tasmania Hobart TAS 7005 Tasmania Australia

Science for Life Laboratory National Bioinformatics Infrastructure Sweden 751 23 Uppsala Sweden

Science for Life Laboratory Uppsala Department of Immunology Genetics and Pathology Uppsala University 752 36 Uppsala Sweden

Science for Life Laboratory Uppsala Department of Medical Biochemistry and Microbiology Uppsala University 752 36 Uppsala Sweden

Science for Life Laboratory Uppsala Department of Medical Biochemistry and Microbiology Uppsala University 752 36 Uppsala Sweden;

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