Population genetics of the endangered poison frog Oophaga vicentei (Anura: Dendrobatidae)

Supplementary data in support of the manuscript " Transcriptomic genotyping elucidates the population structure and demographic history of the endangered poison frog Oophaga vicentei (Anura: Dendrobatidae)" Amphibians are experiencing a global biodiversity crisis and now represent one of the most imperiled vertebrate groups with 41% of the species classified as threatened with extinction (1). The genus Oophaga mirrors this pattern, as the majority of its species hold threat designations under the IUCN Red List. Among them, Oophaga vicentei, a species restricted to central Panama, is recognized as Endangered due to accelerating environmental disturbances, including landscape alteration, patchy habitat connectivity, and expanding mining operations (2). While the species is known to be at high risk, fundamental demographic parameters, such as population genetic diversity and population size, remain largely unresolved. Transcriptome-derived SNP genotyping provides a practical and scalable avenue for examining genomic variation in species lacking established genetic resources. In this study, we analyzed RNA-seq datasets to delineate the genetic architecture and infer the effective population size of O. vicentei across its native distribution. In order to conduct the haplotype calling of Oophaga vicentei, we used as reference the published genome of Oophaga sylvatica (NCBI accession: GCA_033576555.1). This is the most complete genome assembly of the genus Oophaga to date, but it lacks annotation. Details on the methods used to make the annotation can be seen in the related publication. We performed adapter removal and quality trimming of RNA reads with FastP 0.23.4 (3). Then, we aligned all RNA-seq reads using the two-pass mode of STAR (4) and default settings. After, we used the GATK pipeline (5) following the best practices workflow and recommendations, for RNA-seq based haplotype calling (6). Details of the steps followed in this pipeline and the settings in each step can be found in the related publication. Here we present: 1- The annotation of Oophaga sylvatica genome: galba_func.sorted.gff3 2- The vcf file with haplotypes of Oophaga vicentei before last filtering steps: vicentei_GATK_variants.filtered.biallelic.SNPs.vcf 3- The vcf file with haplotypes of Oophaga vicentei: vicentei_GATK_variants.filtered.biallelic.SNPs.minDP3mac3maxmissing8.nonCoding.LDpruned.PLINK.vcf 4- The associated PLINK files: .bed, .bim, .fam, .map, .ped, .raw