Additional file 3 of Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

Additional file 3: Supplemental Table S1. Lion and leopard samples included for whole genome sequencing and results from sequencing runs. Supplemental Table S2. Number of discovered lion SNPs per chromosome and estimated chromosome size in tiger (derived from Cho et al. (2013)). Supplemental Table S3. Coordinates of autosomal and mitochondrial SNPs in lion SNP panel. Supplemental Table S4. Genotype calls for all individuals included for genotyping with the SNP panel (125 autosomal + 14 mtDNA SNPs). Supplemental Table S5. Assignment values from SNPpanel SNPs. STRUCTURE analysis was done on 125 nuclear SNPs with the complete dataset (N = 211) and a reduced dataset excluding samples with >25% missing data (N=171, '-' for assignment indicates that this sample was excluded). Haplogroups were infered from callings of 14 mtDNA SNPs which were included in the SNP panel (see Bertola et al. (2016) for reference of haplogroups). If 40% or more of the mtDNA SNPs failed, the field for the haplogroup is marked with '?'. Haplogroups marked with '?' after the assignment indicate that 60%-85% of the included mtDNA SNPs were succesfully called. Supplemental Table S6. Observed heterozygosity for lions, based on SNP data from either whole genome sequencing (individuals; all SNPs and SNPs covered in 5 or more lions) or based on results of the SNP panel (populations), and comparison with observed heterozygosity based on microsatellite data (populations). Shading indicates the ranking from low heterozygosity (red) to high heterozygosity (green). It must be noted that due to low coverage in the sample from Benin, heterozygosity may be underestimated. For the SNP panel, only results from the same samples which had previously been analyzed for the microsatellites were included. The left scatter plot shows the correlation between observed heterozygosity called based on all SNPs and based on SNPs covered in 5 or more lions. The right scatter plot shows the correlation between observed heterozygosity based on all SNPs and based on the SNP panel data (grey), and observed heterozygosity based on previously published microsatellite data (red). The bar plot shows observed heterozygosity for each dataset and per individual/population. Supplemental Table S7. Genbank entries to filter bacterial reads in contaminated lion samples Benin and RSA. Supplemental Table S8. Tiger scaffolds from Cho et al. (2013) identified as potentially of Y-chromosomal origin.