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。纳入全基因组测序（whole genome sequencing）的狮与豹样本，以及测序运行结果。补充表S2：各染色体上已发现的狮子单核苷酸多态性（SNP）数量，以及基于Cho等人2013年研究推导的虎染色体预估大小。补充表S3：狮子SNP分型面板（SNP panel）中常染色体与线粒体DNA（mtDNA）SNP的坐标位置。补充表S4：使用SNP分型面板对所有纳入基因分型的个体进行的基因型判定结果（包含125个常染色体SNP与14个mtDNA SNP）。补充表S5：来自SNP分型面板SNP的归属值。研究基于完整数据集（样本量N=211）以及剔除了缺失数据占比>25%的样本后的缩减数据集（样本量N=171，归属值栏中用"-"表示该样本已被排除），对125个核SNP开展了STRUCTURE群体结构分析。单倍型群（haplogroup）通过SNP分型面板中纳入的14个mtDNA SNP的分型结果推断而来（单倍型群的参考标准参见Bertola等人2016年的研究）。若40%及以上的mtDNA SNP分型失败，则该样本的单倍型群字段标记为"?"；归属值后带有"?"的单倍型群，表示该样本中60%~85%的纳入mtDNA SNP成功完成分型。补充表S6：基于全基因组测序数据（针对个体：包含所有SNP以及至少在5头狮子中覆盖到的SNP）或SNP分型面板结果（针对种群）计算得到的狮子观测杂合度，以及与基于微卫星数据（针对种群）得到的观测杂合度的对比结果。着色标注表示杂合度从低到高的排序：低杂合度对应红色，高杂合度对应绿色。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分型面板的结果，仅纳入了此前已完成微卫星分析的同一样本。左侧散点图展示了基于所有SNP与基于至少在5头狮子中覆盖到的SNP计算得到的观测杂合度之间的相关性；右侧散点图展示了基于所有SNP计算的观测杂合度与基于SNP分型面板数据（灰色）、以及基于已发表微卫星数据（红色）计算的观测杂合度之间的相关性；柱状图则展示了各数据集以及每个个体/种群的观测杂合度。补充表S7：用于过滤贝宁与南非（RSA）受污染狮子样本中细菌测序读段的GenBank数据库条目。补充表S8：Cho等人2013年研究中鉴定出的、可能来源于Y染色体的虎基因组支架（scaffold）。