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

• Main Author: de Jong, Menno
• Format: Dataset
• Language: unknown
• Published: 2023
• Subjects: brown bear; Ursus arctos; whole-genome sequencing; single nucleotide polymorphisms (SNPs); postglacial recolonisation; Population connectivity; admixture analyses; single nucleotide variants (SNVs); X chromosome; Y chromosome; mtDNA; Autosome; population genomics; Loewe; The ''Y''
• Online Access: https://zenodo.org/record/7613159; https://doi.org/10.5061/dryad.qbzkh18n6

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. 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'. Funding provided by: Leibniz-GemeinschaftCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001664Award Number: Funding provided by: Estonian Ministry of Education and Research*Crossref Funder Registry ID: Award Number: IUT20-32Funding provided by: Estonian Ministry of Education and Research*Crossref Funder Registry ID: Award Number: PRG1209Funding provided by: Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE)*Crossref Funder Registry ID: Award Number: 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 ...