Polygenic selection shapes warning and cryptic coloration in Oophaga granulifera (Anura: Dendrobatidae)

Supplementary material in support of the manuscript " Signatures of polygenic selection in the evolution of aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae)" Aposematism and crypsis are widespread but opposing defensive strategies that enable survival, either by advertising toxicity through conspicuous coloration or by minimizing detection through camouflage (1). In amphibians, the genomic foundations that facilitate shifts between these strategies are still poorly understood. Oophaga granulifera, a poison frog species that displays both warning and cryptic colorations (2), represents a powerful system for investigating the evolution of complex phenotypes in non-model vertebrates. To examine population-level divergence and detect signals of positive selection between green (cryptic) and red (aposematic) phenotypes, we genotyped thousands of exonic SNPs from RNA-seq data, aligning reads against the Oophaga sylvatica reference genome as well as a species-specific superTranscriptome. Further, we performed haplotype calling using GATK software (3), and used three different methods to look for signatures of selection. We used two haplotype files (the ones obtained with each reference) to estimate population genetic parameters such as population structure and genetic diversity, and to detect selection signatures. Additionally, we filtered those files, to only keep the neutral SNPs, as obtained by BayeScan (4), to further verify if population genetic structure was influenced by selection. Here we provide: 1- The built superTranscriptome of Oophaga granulifera: SuperDuper.sorted.fasta 2- Transcripts annotation: ST_transcripts_annotation.csv 3- Haplotype file with all SNPs identified when using a reference genome: granulifera_GATK_variants.filtered.biallelic.SNPs.minDP3mac3maxmissing8.LDpruned.PLINK.vcf, and its related PLINK files 4- Filtered haplotype file with only neutral SNPs when using a reference genome: granulifera_GATK_variants.filtered.biallelic.SNPs.minDP3mac3maxmissing8.LDpruned.only-neutral.PLINK.vcf, and its related PLINK files 5- Haplotype file with all SNPs identified when using a reference superTranscriptome: granulifera_Supertranscriptome_variants.filtered.biallelic.SNPs.minDP3mac3maxmissing8.LDpruned.PLINK.vcf, and its related PLINK files 6- Filtered haplotype file with only neutral SNPs identified when using a reference superTranscriptome: granulifera_Supertranscriptome_variants.filtered.biallelic.SNPs.minDP3mac3maxmissing8.LDpruned.only-neutral.PLINK.vcf, and its related PLINK files