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.

附加文件3：补充表S1。本研究用于全基因组测序的狮、豹样本及测序运行结果。
补充表S2：各染色体上发现的狮子单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数量及虎的估算染色体大小（数据源自Cho等人2013年的研究）。
补充表S3：狮子SNP面板中常染色体及线粒体DNA（mitochondrial DNA, mtDNA）单核苷酸多态性的坐标信息。
补充表S4：使用该SNP面板（包含125个常染色体SNP与14个mtDNA SNP）完成基因分型的所有个体的基因型分型结果。
补充表S5：基于SNP面板的SNP分型赋值结果。本研究针对125个核单核苷酸多态性，分别使用完整数据集（样本量N=211）及剔除缺失数据占比>25%的样本后的缩减数据集（样本量N=171，分型赋值为“-”的样本表示该样本已被排除）开展STRUCTURE群体结构分析；单倍群通过SNP面板中纳入的14个mtDNA SNP的分型结果推断得到，单倍群的判定依据参考Bertola等人2016年的研究；若40%及以上的mtDNA SNP分型失败，则该样本的单倍群字段标记为“?”；若分型赋值后带有“?”，则表示该样本中60%~85%的纳入mtDNA SNP成功完成分型。
补充表S6：狮子的观测杂合度相关结果，分别基于全基因组测序SNP数据（针对个体，涵盖全部SNP及覆盖至少5只狮子的SNP）或SNP面板检测结果（针对种群）计算得到，并与基于微卫星数据得到的观测杂合度（针对种群）进行对比。表格底纹按杂合度从低到高依次以红色至绿色表示排名。需注意：由于贝宁样本的测序覆盖度较低，其杂合度可能被低估。针对SNP面板的分析，仅纳入此前已完成微卫星分型的同批次样本。左侧散点图展示了基于全部SNP与基于覆盖至少5只狮子的SNP得到的观测杂合度之间的相关性；右侧散点图分别展示了基于全部SNP与基于SNP面板数据（灰色）得到的观测杂合度，以及基于已发表微卫星数据（红色）得到的观测杂合度之间的相关性；柱状图则展示了各数据集下每个个体/种群的观测杂合度。
补充表S7：用于过滤贝宁与南非（RSA）地区污染狮子样本中细菌读段的GenBank（基因银行）条目。
补充表S8：经Cho等人2013年研究鉴定的、疑似属于Y染色体的虎基因组支架（scaffold）。