Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

The brown bear is a textbook example species of the effect of Quaternary glaciation cycles on the present-day geographical distribution of mtDNA haplotypes. We compiled and analysed a range-wide whole-genome dataset of 128 brown bear individuals in order to re-evaluate brown bear population structure and genetic diversity using nuclear markers from autosomes and sex chromosomes. The file 'PLOTCOMMANDS.txt' contains detailed instructions on how to recreate the figures presented within the paper.  , VCF-FILES WITH BIALLELIC SNPS
The four gzipped vcf-files contain information for biallelic single nucleotide polymorphisms (SNPs) found either on autosomes, the Y chromosome, the X-chromosome or the mitogenome (mtDNA), for a collection of 128 brown bears (1 Norwegian individual sequenced duplex), 4 polar bears, and 2 American black bears. The datasets were generated by mapping whole-genome sequencing reads against a brown bear reference genome (either nuclear or mtDNA genome), and by subsequent genotype calling using the samtools/bcftools pipeline. All samples were genotyped independently, i.e., not considering the data available for other individuals. The autosomal and X-chromosomal vcf-files were randomly thinned to retain at maximum one site every 20 Kb and 10 Kb respectively, using the thin command of the software vcftools. Diploidy levels are according to genomic region.
The haploid datasets (Y chromosome and mtDNA), as well as the haplodiploid dataset (X chromosome), can be conver..., To reproduce the figures presented within the paper, download all files from this Dryad repository, and run the R-commands listed in the file 'PLOTCOMMANDS.txt'. Â

棕熊是第四纪冰期循环对现今线粒体DNA（mtDNA）单倍型地理分布产生影响的典型模式物种。我们整合并分析了覆盖全分布范围的128只棕熊个体的全基因组数据集，旨在利用常染色体与性染色体的核标记重新评估棕熊的种群结构及遗传多样性。文件"PLOTCOMMANDS.txt"包含了复现论文中图表的详细操作指南。

含双等位基因单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的VCF文件
四个经gzip压缩的VCF文件涵盖了128只棕熊（其中1只挪威个体经双链测序）、4只北极熊以及2只美洲黑熊的双等位基因单核苷酸多态性信息，这些位点分布于常染色体、Y染色体、X染色体或线粒体基因组（mtDNA）中。本数据集通过将全基因组测序reads比对至棕熊参考基因组（核基因组或线粒体基因组），并借助samtools/bcftools流程完成后续基因型分型生成。所有样本均为独立分型，未考虑其他个体的测序数据。利用VCFtools软件的thin命令，常染色体与X染色体的VCF文件被随机稀疏化，分别保留每20 Kb和每10 Kb范围内最多一个位点。倍性水平依据所属基因组区域而定。

单倍型数据集（Y染色体与mtDNA）以及单倍二倍体数据集（X染色体）可进行转换……若要复现论文中的图表，请从该Dryad知识库下载全部文件，并运行文件"PLOTCOMMANDS.txt"中列出的R命令。