Rum and Argyll red deer genotype files

The red deer population inhabiting the north block of the Isle of Rum, Scotland (57°0’N, 6°20’W) has been studied at an individual level since 1971 and was the main focus of this study. After quality control 39,587 autosomal SNPs genotyped in 3046 individuals were retained for analysis. This study also used equivalent genotype data for 157 individuals from a mainland population of red deer from Argyll, Scotland. Data files are in plink readable format (.bed .bim .fam) and include a .txt file with estimated SNP positions in centimorgans (cM). If you plan to analyse the data, we request that you inform us, see README file for more information. , DNA was extracted from ear punches from calves captured soon after birth or darted adults, post-mortem tissue or cast antlers (See Huisman et al (2016) for full details). DNA samples were genotyped at 50,541 attempted SNP loci on the Cervine Illumina 50K BeadChip (Brauning, 2015). SNP genotypes were clustered and scored using Illumina GenomeStudio v2.0, and were subject to quality control with the following parameters: SNP minor allele frequency (MAF) > 0.001, ID genotyping success > 0.9, and SNP genotyping success > 0.99.
For the Argyll dataset details of sample collection and DNA extraction can be found in McFarlane et al (2020). Samples were genotyped as above and quality control was carried out by McFarlane et al (2020) as above with the exception of SNP genotyping success >0.9.,