Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae)

Abstract Aposematism and crypsis are contrasting antipredator strategies widespread across animal taxa, yet their genetic basis remains poorly understood in amphibians. Aposematic species advertise toxicity through conspicuous coloration, whereas cryptic species rely on concealment to avoid predators. The granular poison frog, Oophaga granulifera, with allopatric aposematic (red) and cryptic (green) morphs, provides an excellent system to explore the molecular mechanisms underlying transitions between these strategies. We used a comparative genomic approach, mapping RNA-seq reads to the Oophaga sylvatica reference genome and a de novo assembled O. granulifera superTranscriptome, to characterize its population genetics and detect genes with single nucleotide polymorphisms under positive selection. We identified two main genetic clusters with strong divergence between green and red populations. We found 283 SNPs showing signatures compatible with positive selection using the reference genome and 749 SNPs using the reference superTranscriptome, indicating greater sensitivity of the latter approach in capturing species-specific genetic variation. Some of these SNPs occur in coloration-related genes, including genes involved in melanin synthesis (DVL2, FZD7, GNAI1), pteridine synthesis (MYCBP2), iridophore development (IMPDH1, PSAT1), carotenoid metabolism (BCO1, RARG, RETSAT), and pigmentation variation. Our findings highlight the complex genetic basis of color diversity in anurans and the value of generating species-specific genomic resources for non-model organism’s research. Subjects Acknowledgements The authors gratefully acknowledge the computing time granted by the Resource Allocation Board and provided on the supercomputer Emmy/Grete at NHR-Nord@Göttingen as part of the NHR infrastructure. The calculations for this research were conducted with computing resources under the project (project ID: nib00033). We acknowledge financial support by the Open Access Publication Fund of the University of Veterinary Medicine Hannover Foundation. Special thanks to Evan Twomey for his comments on an early version of the manuscript, and to Sebastian Wöhle for his help with bibliographic references. Funding Open Access funding enabled and organized by Projekt DEAL. Anaisa Cajigas is supported by a Doctoral scholarship from the Deutscher Akademischer Austauschdienst (DAAD). This project was funded by grants from the Deutsche Forschung Gemeinschaft to Heike Pröhl (DFG: PR 626/10 − 1) and to Ariel Rodríguez (DFG: RO 5508/2 − 1). Author information Authors and Affiliations Corresponding authors Ethics declarations Competing interests The authors declare no competing interests. Additional information Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Supplementary Information Below is the link to the electronic supplementary material. Rights and permissions Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. About this article Cite this article Cajigas Gandia, A., Pröhl, H., Metzger, J. et al. Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae). Sci Rep (2026). https://doi.org/10.1038/s41598-026-66654-3 Received: Accepted: Published: DOI: https://doi.org/10.1038/s41598-026-66654-3