Big cat vcf files from: Exceedingly low genetic diversity in snow leopards due to persistently small population size

Snow leopards (Panthera uncia) serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous Anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. In particular, the dearth of genetic data, unique among all big cat species, hinders a full understanding of their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer new insights into these unresolved aspects of snow leopard biology. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin–as previously identified using landscape models and fecal microsatellite markers–and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest g..., Calling SNPs in all big cat species: We included all other species in the genus Panthera (leopard, lion, tiger, jaguar) as well as cheetah and puma. Accession numbers of publicly available WGS data and reference genomes used in this analysis are listed in Supplementary Table 3 and 4, respectively. We mapped all FASTQ data to the corresponding reference genome using BWA-MEM. We sorted and indexed resulting bam files using SAMtools. We added read groups and marked duplicates using picard. We calculated depth of coverage and breadth of coverage for each sample using SAMtools. We then used GATK HaplotypeCaller to generate a GVCF file for each sample and GATK CombineGVCFs to combine the GVCF files for every species (or subgroup in the case of tigers and leopards). Lastly, we used GATK GenotypeGVCFs to create a final VCF file for every group. In order to limit the need for excessive computing power, we downsampled some samples with over 30X coverage using SAMtools view as indicated in Su..., # Big cat vcf files from: Exceedingly low genetic diversity in snow leopards due to persistently small population size Dataset DOI: [10.5061/dryad.1vhhmgr78](https://doi.org/10.5061/dryad.1vhhmgr78) ## Description of the data and file structure SNPs were called in our focal species, snow leopards (*Panthera uncia*), as well as all other big cat species using publicly available data. SNPs were called using the same pipeline in all species in order to make comparisons among the species. What we share here are the final filtered vcf files used in our analyses Additionally, in snow leopards, SNPs were also called by a service provider, Gencove Inc., so there are two vcf files for snow leopards. Sample data for snow leopard vcfs can be found in Supplementary Table 1. Sample data for other big cat vcfs can be found in Supplementary Table 3. Details regarding which reference genomes were used for each vcf can be found in Supplementary Table 4. ### Files and variables #### File: Pum...,雪豹（Panthera uncia）属于伞护种，对其开展的保护工作能够惠及其栖息的亚洲高海拔生态系统。据信，由于诸多人为威胁，雪豹种群数量正处于下降态势；然而，相关保护工作却因大量认知空白而举步维艰。尤为关键的是，相较于所有其他大型猫科动物，雪豹的遗传数据极度匮乏，这阻碍了学界对其种群结构、历史种群规模以及当前遗传多样性水平的全面认知。本研究利用41只雪豹的全基因组测序（Whole Genome Sequencing, WGS）数据（其中37只为新测序样本），为解析雪豹生物学中这些尚未解决的问题提供了全新视角。在本次研究的样本中，我们发现雪豹的分布范围以准噶尔盆地为界，存在南北两侧的首要遗传分化——这一结果与此前利用景观模型和粪便微卫星标记得出的结论一致——同时在吉尔吉斯斯坦南部、塔克拉玛干沙漠周边区域还存在次级遗传分化。值得注意的是，我们发现雪豹具有所有大型猫科动物中最低的遗传多样性（原文此处截断）。 # 所有大型猫科动物的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型流程如下： 本研究纳入了豹属（Panthera）的其余所有物种（豹、狮、虎、美洲豹）以及猎豹和美洲狮。本分析中使用的公开全基因组测序数据登录号以及参考基因组信息，分别列于补充表3和补充表4中。我们使用BWA-MEM工具将所有FASTQ数据比对至对应的参考基因组。使用SAMtools工具对生成的BAM文件进行排序和索引。使用Picard工具添加读段分组并标记重复序列。使用SAMtools工具计算每个样本的覆盖深度和覆盖广度。随后，我们使用基因组分析工具包（Genome Analysis Toolkit, GATK）的HaplotypeCaller工具为每个样本生成GVCF（Genomic Variant Call Format）文件，并使用GATK CombineGVCFs工具将所有物种（虎和豹则按亚组）的GVCF文件进行合并。最后，我们使用GATK GenotypeGVCFs工具为每个分组生成最终的VCF（Variant Call Format）文件。 为降低计算资源消耗，我们按照补充材料中的说明，使用SAMtools view工具对覆盖度超过30X的部分样本进行了降采样处理（原文此处截断）。 # 大型猫科动物VCF文件来源：因种群规模长期偏小，雪豹遗传多样性极低 数据集DOI：[10.5061/dryad.1vhhmgr78](https://doi.org/10.5061/dryad.1vhhmgr78) ## 数据与文件结构说明 本研究利用公开数据，对目标物种雪豹（Panthera uncia）以及所有其他大型猫科动物进行了SNP分型。所有物种均采用统一的分析流程进行SNP分型，以确保跨物种比较的一致性。本次共享的是本研究分析中使用的经过最终过滤的VCF文件。 此外，针对雪豹的SNP分型还由服务提供商Gencove Inc.完成，因此雪豹对应两份VCF文件。 雪豹VCF文件的样本信息详见补充表1。 其余大型猫科动物VCF文件的样本信息详见补充表3。 各VCF文件所使用的参考基因组详情见补充表4。 ### 文件与变量 #### 文件：Pum...（原文此处截断）