File S1 - Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

Contains: Figure S1. PCA on autosomal SNPs called from the short-read sequencing data for 10 resequenced individuals. Figure S2. Summary of SFS distribution for raw SNP counts for synonymous and non-synonymous substitutions. Figure S3. Boxplot of distribution of mtDNA coverages for the 10 previously sequenced individuals. Table S1. Distribution of SNPs by population and functional class from PolyPhen-2. Table S2. Parameters for input demographic models. Table S3. Inferred parameters for single-γ selection models. Table S4. Inferred parameters for multiple-γ selection models. Table S5. Enriched GO MF (Molecular Function) categories under negative selection. Only categories with at least 10 genes and Fisher’s exact test P-value Table S6. Enriched GO BP (Biological Process) categories under negative selection. Only categories with at least 10 genes and Fisher’s exact test P-value (PDF)