Genomics Reveals Gradual Speciation and Intergeneric Admixture of Sea Lions in the Western North Pacific

Description of the data and file structure This data constitutes the raw data underlying the results reported in "Genomics Reveals Gradual Speciation and Intergeneric Admixture of Sea Lions in the Western North Pacific". This study analyzed newly obtained whole-genome sequencing data from one Steller Sea Lion individual alongside existing data from sea lions. In addition to fundamental genomic features, we report results from PCA, Maximum-Likelihood tree, Heterozygosity, D- and f4-statistics, and psmc analysis. Files and variables File: PCA_label-list Description: Name list of each group used to visualize a PCA plot with R script ("PCA.R"). File: RAxML_tree.support Description: Output file of the RAxML and raw data of the visualized Maximum-Likelihood tree. File: PCA_input.beagle.gz Description: Input file for "pcangsd" to conduct principal component analysis. This file was created using bam files of each individual with "angsd" command. File: Table1_TableS1-6.xlsx Description: Table 1 and TableS1~S6. File: Treemix_input.model Description: Input file for "treemix", which describe the list of individuals' name. File: Treemix_input.treemix.gz Description: Input file for "treemix", which describe the list of individuals' name. File: PCA.cov Description: Covariance matrix generated by "pcangsd". It was used to conduct PCA and to visualize a PCA plot with R script ("PCA.R"). File: Dsuite_Treemix_input.vcf.gz Description: Input VCF file for "Dsuite" and "treemix". Code/software All analyses using Rscript were performed with R v. 4.4.3. The packages required by each Rscript are listed within the script. "RAxML_tree.support" was visualized using FigTree v. 1.4.3. Access information The sequence data of a Steller Sea Lion, newly obtained in this study, are available in the GenBank SRA database with BioProject accession PRJDB38035.数据与文件结构说明 本数据集为论文《Genomics Reveals Gradual Speciation and Intergeneric Admixture of Sea Lions in the Western North Pacific》所报道研究结果的支撑原始数据。本研究分析了1头斯特勒海狮（Steller Sea Lion）的全新全基因组测序数据，以及已公开的海狮相关基因组数据。除基础基因组特征外，本研究还报告了主成分分析（PCA, Principal Component Analysis）、最大似然树（Maximum-Likelihood tree）、杂合度（Heterozygosity）、D统计量与f4统计量（D- and f4-statistics）以及psmc分析（psmc analysis）的相关结果。 文件与变量 文件：PCA_label-list 说明：用于配合R脚本"PCA.R"绘制PCA可视化图的各组样本名称列表。 文件：RAxML_tree.support 说明：RAxML软件的输出文件，以及可视化最大似然树的原始数据。 文件：PCA_input.beagle.gz 说明：用于"pcangsd"工具执行主成分分析的输入文件，该文件通过angsd命令对每个个体的BAM文件（Binary Alignment Map）处理生成。 文件：Table1_TableS1-6.xlsx 说明：包含表1及补充表S1~S6的电子表格文件。 文件：Treemix_input.model 说明："treemix"工具的输入文件，内含样本名称列表。 文件：Treemix_input.treemix.gz 说明："treemix"工具的输入文件，内含样本名称列表。 文件：PCA.cov 说明：由"pcangsd"生成的协方差矩阵，用于执行主成分分析及配合R脚本"PCA.R"绘制PCA可视化图。 文件：Dsuite_Treemix_input.vcf.gz 说明："Dsuite"与"treemix"工具的输入VCF格式（Variant Call Format）压缩文件。 代码与软件 所有基于R脚本的分析均使用R v. 4.4.3版本完成，各R脚本所需的依赖软件包已在脚本内列明。"RAxML_tree.support"文件的可视化工作使用FigTree v. 1.4.3工具完成。 数据获取说明 本研究中新获得的1头斯特勒海狮（Steller Sea Lion）的测序数据，已上传至GenBank SRA数据库，对应的BioProject收录号为PRJDB38035。