DOI: 10.5061/dryad.1rn8pk13b
title: Data from: Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction between peripheral populations and the main admixture zones in Europe

description: Genome-wide technologies open up new possibilities to clarify questions on
 genetic structure and phylogeographic history of taxa previously studied
 with microsatellite loci and mitochondrial sequences. Here, we used 736
 individual red deer (Cervus elaphus) samples genotyped at 35,701 single
 nucleotide polymorphism loci (SNPs) to assess the population structure of
 the species throughout Europe. The results identified 28 populations, with
 higher degrees of genetic distinction in peripheral compared to mainland
 populations. Iberian red deer show high genetic differentiation, with
 lineages in Western and Central Iberia maintaining their distinctiveness,
 which supports separate refugial ranges within Iberia along with little
 recent connection between Iberian and the remaining Western European
 populations. The Norwegian population exhibited the lowest variability and
 the largest allele frequency differences from mainland European
 populations, compatible with a history of bottlenecks and drift during
 postglacial colonization from southern refugia. Scottish populations
 showed a high genetic distance from the mainland but high levels of
 diversity. Hybrid zones were found between Eastern and Western European
 lineages in Central Europe as well as in the Pyrenees, where red deer from
 France are in close contact with Iberian red deer. Anthropogenic
 restocking has promoted the Pyrenean contact zone, admixture events in
 populations on the Isle of Rum and the Netherlands, and at least partly
 the admixture of the two main lineages in central-eastern Europe. Our
 analysis enabled detailed resolution of the population structure of a
 large mammal widely distributed throughout Europe and contributes to
 resolving the evolutionary history, which can also inform conservation and
 management policies.
description: We collected tissue samples (e.g., fragments of ears, internal
 organs, or muscles) from culled individuals, immediately kept at 4°C and
 then stored at -20°C until use. Genomic DNA was isolated from pieces of
 tissue using the commercial DNA purification kits DNeasy Blood and Tissue
 Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s
 protocol. Due to the number of analyses that had to be carried out on each
 sample and the minimum requirements needed, it was necessary to obtain
 high-quality DNA (in terms of high molecular weight, purity, and yield)
 and carry out quantity and quality controls. Extracted DNA was visualized
 for integrity and quantified in a 0.8% agarose gel: a 3 ml aliquot of each
 sample was loaded with 2 ml of Loading Dye. The integrity of DNA samples
 was verified by comparing them against a DNA Ladder Sibenzyme molecular
 weight marker (1 Kb). After that, two μl of genomic DNA were measured by
 NanoDropTM One (Thermo Fisher Scientific Inc, Waltham, Massachusetts,
 USA). If the purified DNA did not have the required degree of purity
 (Absorbance ratios of A260/A280 and A260/230 of 1.8 to 2), a second
 extraction was carried out. The individuals were genotyped using the
 cervine 50K Illumina Infinium iSelect HD Custom BeadChip that includes
 50,841 SNP markers.
description: # Data from: Genome-wide SNP assessment of contemporary European red deer
 genetic structure highlights the distinction between peripheral
 populations and the main admixture zones in Europe
 [https://doi.org/10.5061/dryad.1rn8pk13b](https://doi.org/10.5061/dryad.1rn8pk13b) Data including the genetic information from 490 European red deer at 50,841 SNPs. Populations are coded as in the primary article. To conduct the analyses included in the primary article, these data were combined with those from McFarlane et al. (2020) and de Jong et al. (2021). de Jong, J.F., et al. (2020). Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands. Frontiers in Ecology and Evolution, 8. https://doi.org/10.3389/fevo.2020.535715 McFarlane, S.E., et al. (2020). Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evolutionary Applications, 13(2), 432–441.  https://doi.org/10.1111/eva.12880 ## Description of the data and file structure The data (SNP genotypes of deer) are provided in three files .bed, .bim, and .fam. .bed file is the primary representation of genotype calls at biallelic variants. .bim is the extended variant information file accompanying a .bed binary genotype table. .fam is the sample information file accompanying a .bed binary genotype table. These files can be loaded in PLINK software (Purcell et al. 2007) with the --bfile command. See, for instance, the File format reference on the PLINK website (https://www.cog-genomics.org/plink/1.9/formats#fam).  Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. *The American Journal of Human Genetics, 81*(3), 559-575.