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

Description

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.

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Funders

• Japan Society for the Promotion of Science

  Ministry of Education, Culture, Sports, Science and Technology

  Tokyo, Tokyo

  Grant ID: 23K23956

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