DOI: 10.5061/dryad.pg4f4qrxq
title: Genotyping by sequencing data for thirty-six modern and two historic populations of Arctic Bell-Heather (<em>Cassiope tetragona</em>)

description: We sequenced C. tetragona from 36 extant pan-Arctic populations, two
 historic (250- to 500-year-old) populations sampled from under glacial ice
 in the Canadian High Arctic, and an outgroup (C. mertensiana) with
 genotyping by sequencing. We found 26,350 single-nucleotide polymorphisms
 (SNPs) (shared in a vcf file) when calling genetic variants from a de novo
 reference genome that we assembled.
description: We built genotyping-by-sequencing (GBS) libraries using
 <em>Cassiope tetragona</em> tissue from 36 Arctic locations,
 including two ∼250-500-year-old populations collected under glacial ice on
 Ellesmere Island, Canada. We assembled a <em>de novo</em> GBS
 reference and called variants in dDocent. <br> <br> Detailed
 methods can be found here: https://doi.org/10.1111/jbi.14961
description: # Genotyping by sequencing data for thirty-six modern and two historic
 populations of Arctic Bell-Heather (*Cassiope tetragona*)
 [https://doi.org/10.5061/dryad.pg4f4qrxq](https://doi.org/10.5061/dryad.pg4f4qrxq) #### Data Summary The raw single-nucleotide polymorphisms from genotyping-by-sequencing (GBS) libraries of *Cassiope tetragona* plants from 36 circumpolar Arctic research sites and ~250-500-year-old samples collected under glacial ice on Ellesmere Island, Canada. Data was used in "Multiple Pleistocene refugia for Arctic Bell-Heather revealed with genomic analyses of modern and historic plants" to determine the demographic history of *Cassiope tetragona* populations around the Arctic. #### **Data processing**  All code and analyses for generating and then working with this vcf file can be found on Github here: [https://github.com/celphin/Population_genomics_Cassiope](https://github.com/celphin/Population_genomics_Cassiope) #### Description of the data and file structure * Cassiope_Population_information_Dryad.txt: Text file including sample details for each sample in the vcf file. Columns include: * Sampling location code * Location lat and long * Number of samples from that location * TotalRawSNPs.vcf: Variant call file (vcf) with all SNPs found prior to any filtering. Built using dDocent. The VCF file includes the following columns standard to the format: ``` #CHROM: contig number from the de novo reference.fasta assembly (see below) POS: Position of the SNP on the contig ID: Identifier of the SNP REF: Reference nucleotide ALT: Alternate nucleotide(s) QUAL: Quality score of the SNP FILTER: Filtering information INFO: Additional information (e.g., allele frequency, number of samples) Sample columns: One per individual, contain genotype information for that individual, individuals are identified by their location ID from Cassiope_Population_information_Dryad.txt ``` * reference.fasta: De novo GBS reference assembly (fasta file) made in Rainbow (through dDocent). Fasta files have a header line for every contig sequence starting with "&gt;" that contains the contig name\ The line(s) directly following the header contain the nucleotide sequence for that contig #### Sharing/Access information Raw sequence data are available in the GenBank/SRA database under accession number SUB11222726 and BioProject ID PRJNA824830. Related manuscript: [https://doi.org/10.1111/jbi.14961](https://doi.org/10.1111/jbi.14961)