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

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.