FORGOTTEN LINEAGES AND RECURRENT HYBRIDIZATIONS WITHIN THE KELP GENUS ALARIA (PHAEOPHYCEAE) REVEALED BY WHOLE GENOME SEQUENCING

Provided in this project are vcf files and occurrence data related to phylogenomic analysis of the kelp <i>Alaria</i>. All detailed methods, including filtering parameters, can be found in the article sharing this project title (article currently in review).<br>Alaria_occurence_data_2iv20.csv: occurrence data used for Fig. 1 map, sourced from records from Luning 1990 (Biogeography of Seaweeds), Barcode of Life Data Systems, and Macroalgal Portal.<br><br>Alaria_phylogenomics_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to KU-791D_nuclear_scaffolds.fasta. This file has no SNP filters applied to it.<br><br>Alaria_Undaria_final_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to Undaria pinnatifida genome (Shan et al. 2020). This file has no SNP filters applied to it.<br><br>Alaria_Undaria_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>Alaria_Undaria_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>KU-791D_nuclear_scaffolds.fasta: reference nuclear scaffolds for Alaria esculenta used for mapping reads from various species of Alaria.<br>

本项目提供与翅藻属（Alaria）系统发育基因组学分析相关的VCF（Variant Call Format，变异呼叫格式）文件及物种出现记录数据。本项目同名论文目前处于审稿阶段，所有详细方法（包括过滤参数）均可在该论文中查阅。
Alaria_occurence_data_2iv20.csv：用于绘制图1的物种出现记录数据，数据来源包括Luning于1990年发表的《海藻生物地理学》（Biogeography of Seaweeds）、生命条形码数据系统（Barcode of Life Data Systems）以及大型藻类门户网站（Macroalgal Portal）。
Alaria_phylogenomics_SNP_final.fasta：用于翅藻属系统发育分析的最终单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集，格式为FASTA，测序读段比对至参考核支架序列（KU-791D_nuclear_scaffolds_fasta）。
Alaria_phylogenomics_SNP_final.vcf.gz：用于翅藻属系统发育分析的最终单核苷酸多态性数据集，格式为VCF，测序读段比对至参考核支架序列（KU-791D_nuclear_scaffolds_fasta）。
Alaria_phylogenomics_SNP_final_LD.fasta：用于翅藻属系统发育分析的最终单核苷酸多态性数据集，格式为FASTA，且额外经过连锁不平衡（Linkage Disequilibrium, LD）过滤，测序读段比对至参考核支架序列（KU-791D_nuclear_scaffolds_fasta）。
Alaria_phylogenomics_SNP_final_LD.vcf.gz：用于翅藻属系统发育分析的最终单核苷酸多态性数据集，格式为VCF，且额外经过连锁不平衡过滤，测序读段比对至参考核支架序列（KU-791D_nuclear_scaffolds_fasta）。
Alaria_phylogenomics_SNP_raw.vcf.gz：原始VCF文件，由翅藻属样本的测序读段比对至KU-791D_nuclear_scaffolds.fasta序列后，经BAM（Binary Alignment Map，二进制比对映射）文件合并与单核苷酸多态性调用步骤生成，该文件未应用任何SNP过滤规则。
Alaria_Undaria_final_raw.vcf.gz：原始VCF文件，由翅藻属样本的测序读段比对至裙带菜（Undaria pinnatifida）参考基因组（Shan等人2020年发表）后，经BAM文件合并与单核苷酸多态性调用步骤生成，该文件未应用任何SNP过滤规则。
Alaria_Undaria_SNP_final.fasta：用于翅藻属系统发育分析的最终单核苷酸多态性数据集，格式为FASTA，以裙带菜作为外类群，测序读段比对至裙带菜参考基因组（Shan等人2020年发表）。
Alaria_Undaria_SNP_final.vcf.gz：用于翅藻属系统发育分析的最终单核苷酸多态性数据集，格式为VCF，以裙带菜作为外类群，测序读段比对至裙带菜参考基因组（Shan等人2020年发表）。
KU-791D_nuclear_scaffolds.fasta：用于翅藻属各物种测序读段比对的参考核支架序列，源自鹅掌翅藻（Alaria esculenta）。