<em>Scutellaria floridana</em> ddRAD-Seq vcf files

The threatened mint Florida skullcap (Scutellaria floridana) is endemic to four counties in&nbsp;the Florida panhandle. Because development and habitat modification extirpated several historical&nbsp;occurrences, only 19 remain to date. To inform conservation management and delisting decisions, a&nbsp;comprehensive investigation of the genetic diversity and relatedness, population structure, and&nbsp;clonal diversity was conducted using SNP data generated by ddRAD. Compared with other Lamiaceae, we detected low genetic diversity (HE = 0.125‐0.145), low to moderate evidence of inbreeding&nbsp;(FIS = ‐0.02‐0.555), and moderate divergence (FST = 0.05‐0.15). We identified eight populations with most of the genetic diversity, which should be protected in situ, and four populations with low genetic diversity and high clonality. Clonal reproduction in our circular plots and in 92% of the sites examined was substantial, with average clonal richness of 0.07 and 0.59, respectively. Scutellaria&nb..., We extracted total genomic DNA from our plant material samples. Briefly, frozen samples were finely ground in liquid N2 and&nbsp;dissolved in an extraction buffer containing 100mM Tris, pH 8.0, 50 mM EDTA, 500 mM&nbsp;NaCl, and 0.1% W:V PVP 40, followed by 5M potassium acetate precipitation of cellular debris and isopropanol precipitation of genomic DNA. We assessed the quality of the&nbsp;DNA from the samples using gel electrophoresis on a 1.5% agarose gel in Tris‐Acetate‐EDTA buffer to ensure there was little to no DNA degradation. We estimated the quantity&nbsp;of DNA in our samples using a Qubit 4 fluorometer (Thermo Fisher Scientific, Waltham,&nbsp;MA). Samples that displayed adequate quality and reached a minimum DNA concentration of 20 ng/ul were then sent to Floragenex (Floragenex, Inc, 4640 SW Macadam Ave, Portland, OR), where double‐digest restriction site associated DNA sequencing (ddRAD-Seq) was carried out. To summarize, DNA was first digested using the restriction endonucl..., , # *Scutellaria floridana* ddRAD-Seq vcf files --- These are haplotype and SNP vcf files derived from ddRAD-seq of 284 individuals across 17 populations of Scutellaria floridana, the Florida skullcap, in the Lamiaceae. The final dataset that we used for downstream analysis included 10,223 loci and 28,210 variable sites that were each present in at least 60% of individuals. ## Description of the data and file structure `populations.haps.vcf`: Individual genotypes by haplotype, organized by chromosome number (ddRadseq sequenced fragment). Individuals are labeled by population and individual number. For example, Sf31.2 is Population 31, individual 2. Some populations had multiple sites within a population. In this case, the site number is also included. For example, Sf9.1.1 is Population 9, site 1, individual 1. `populations.snps.vcf`: Individual genotypes by SNP. Individuals are labeled by population and individual number. For example, Sf31.2 is Population 31, individual 2. Some p...,受威胁的佛罗里达薄荷状黄芩（*Scutellaria floridana*）为特有物种，仅分布于佛罗里达狭长地带的四个县。由于开发活动与栖息地改造导致多个历史记录的种群消失，截至目前仅存19个种群。为给保护管理与物种除名决策提供科学依据，研究人员利用双酶切限制性位点关联DNA测序（double-digest restriction site associated DNA sequencing, ddRAD）产生的单核苷酸多态性（single nucleotide polymorphism, SNP）数据，对其遗传多样性与亲缘关系、种群结构以及克隆多样性开展了全面调查。 与唇形科（Lamiaceae）其他类群相比，本研究检测到较低的遗传多样性（HE=0.125~0.145）、中低度的近交证据（FIS=-0.02~0.555）以及中度的种群遗传分化（FST=0.05~0.15）。研究鉴定出8个承载了绝大多数遗传多样性的种群，应进行就地保护；另有4个种群遗传多样性较低且克隆繁殖占比高。在圆形样地与92%的调查样点中，克隆繁殖现象显著，平均克隆丰富度分别为0.07与0.59。 研究人员从植物材料样本中提取总基因组DNA：简要流程为将冷冻样本在液氮中充分研磨后，溶解于含100mM Tris（pH 8.0）、50mM EDTA、500mM NaCl及0.1% W/V PVP 40的提取缓冲液中，随后通过5M醋酸钾沉淀去除细胞碎片，再用异丙醇沉淀基因组DNA。采用1.5%琼脂糖凝胶在Tris-乙酸-EDTA（TAE）缓冲液中进行凝胶电泳，以评估样本DNA质量，确保DNA几乎无降解。使用Qubit 4荧光计（赛默飞世尔科技，马萨诸塞州沃尔瑟姆市）估算样本DNA浓度。 质量达标且DNA浓度不低于20ng/μl的样本，被送至Floragenex公司（Floragenex, Inc，俄勒冈州波特兰市SW Macadam大道4640号）开展ddRAD测序。首先使用限制性内切酶对DNA进行酶切…… --- # *Scutellaria floridana* ddRAD-seq 变异识别格式（Variant Call Format, VCF）数据集 本数据集包含来自佛罗里达黄芩（*Scutellaria floridana*）17个种群共284个个体的ddRAD-seq测序得到的单倍型与SNP的VCF文件。本研究用于下游分析的最终数据集包含10223个位点与28210个可变位点，每个位点在至少60%的个体中均存在。 ## 数据与文件结构说明 `populations.haps.vcf`：基于单倍型的个体基因型文件，按染色体编号（ddRADseq测序片段）组织。个体编号由种群号与个体号组成，例如`Sf31.2`代表种群31的第2号个体。部分种群内包含多个样点，此时编号中还会包含样点号，例如`Sf9.1.1`代表种群9、样点1的第1号个体。 `populations.snps.vcf`：基于SNP的个体基因型文件，个体编号规则同上，例如`Sf31.2`代表种群31的第2号个体。部分种群……