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

• Main Author: De Jong, Menno
• Format: Dataset
• Language: English
• Published: Dryad 2022
• Subjects: FOS Biological sciences; 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; The ''Y''
• Online Access: https://dx.doi.org/10.5061/dryad.qbzkh18n6; https://datadryad.org/stash/dataset/doi: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. ... : 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 converted into artificial ...