Data from: Environmental variation predicts patterns of phenotypic and genomic variation in an African tropical forest frog

Morphometric data for P. auritus Sample attributes, linear morphometric and geomorphometric data, corresponding environmental data Pauritus_morphometrics.csv VCF file of SNPs generated with STACKs We used the bioinformatics software pipeline, STACKS v.1.44 (Catchen et al., 2011; Catchen, Hohenlohe, Bassham, & Amores, 2013) to process the restriction-site-associated DNA markers (RAD-tags) and generate single nucleotide polymorphism (SNP) datasets. First, we executed the “process_radtags” program in STACKS to demultiplex and trim sequence reads by the P1 barcodes and remove low quality reads (Phred quality score less than 20). After removing PCR duplicates with the “clone_filter” script, the processed reads were used to generate RAD loci without a reference genome using “denovo_map.pl” (parameter settings: m = 3 M = 5 n = 4). We empirically determined these parameters to limit the impact of over-splitting loci (see Harvey et al., 2015; Ilut, Nydam, & Hare, 2014). This involved running the de novo assembly over a wide range of values of M (1–8) with “ustacks”. From these runs, we selected a value of M = 5 since we observed that the percentage of homozygous and heterozygous loci reached a plateau at this value and thus minimized over-splitting of alleles for the final SNP calling. Stacks calls SNPs (“sstacks”) within RAD loci using a multinomial-based likelihood model that estimates the likelihood of two most frequently observed genotypes at each site and performs a standard likelihood ratio test using a chi-square distribution (Catchen et al., 2011; Hohenlohe et al., 2010). For SNP inference, we used the default alpha significance level of 0.05. Paralogous loci that stacked together were identified and removed by subsequent quality control steps built into STACKS (max number of stacks per loci (m) = 3; Harvey et al., 2015; Ilut et al., 2014). After the preliminary assembly of catalog loci using “denovo_map.pl”, we ran the STACKS correction mode (rxstacks-cstacks-sstacks) using the bounded SNP model with a 0.05 upper bound for the error rate. The “rxstacks” program made corrections to genotype and haplotype calls based on population information, rebuilt the catalog loci and filtered out loci with average log likelihood ratio of < 8.0. Pauritus_SNPs.vcf