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Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population

Citation

Yildiz, Beril; Megens, Hendrik-Jan; Bosse, Mirte; Hvilsom, Christina (2022), Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population, Dryad, Dataset, https://doi.org/10.5061/dryad.905qfttnc

Abstract

Demographic events such as series of bottlenecks impact the genetic variation and adaptive potential of populations. European megafauna, such as wild boars (Sus scrofa), have experienced severe climatic and size fluctuations that have shaped their genetic variation. Habitat fragmentation as well as human-mediated translocations have further contributed to the complex demographic history of European wild boar. Danish wild boars represent an extreme case of a small and isolated population founded by four wild boars from Germany. Here, we explore the genetic composition of the Danish wild boar population in Klelund. We genotyped all 21 Danish wild boars that were recently transferred from the source population in Lille Vildmose into the Klelund Plantation to establish a novel wild boar population. We compared the Danish wild boars to high‐density single nucleotide polymorphism genotypes from a comprehensive reference set of 1263 wild and domesticated pigs, including 11 individuals from Ulm, one of two presumed founder locations in Germany. Our findings support the European wild background of the Danish population and no traces of gene flow with wild or domesticated pigs were found. The narrow genetic origin of the Danish wild boars is illustrated by extremely long and frequent runs of homozygous stretches in their genomes, indicative of recent inbreeding. This study provides the first insights into one of the most inbred wild boar populations globally established a century ago from a narrow base of only four founders. --

Methods

PLINK format genotypes

We used PAX gene blood samples that were collected from 21 wild boars in Klelund Plantation. Additionally, 11 tissue biopsies were collected from wild boars in Ulm, Germany as a part of the yearly population cull by hunters. The SNP genotyping was conducted using the Illumina Porcine 60K+iSelect Beadchip, and a total of 61,565 loci were screened for each individual. We filtered out SNPs with overall call rate less than 95%. Due to missing genotype data, 1576 SNPs were removed. The final dataset consisted of 48,227 SNPs.

We obtained the reference samples and genotype data from (Iacolina et al. 2016, 2018; Yang et al. 2017a), which contains 1263 wild boars across Eurasia as well as international commercial pig populations (Suppl. Table 4) (Ramos et al. 2009). We checked overlapping SNP markers, which corresponded to 47,325 variants in the combined dataset. From the combined dataset, a subset of only European wild boar populations consisting of 459 individuals was made to make more detailed comparisons. These datasets were used for population structure analyses (PCA and admixture).

 

Usage Notes

PLINK format genotypes; suppl Table 4 in the main manuscript contains additional information about the samples.

Funding

NWO, Award: 016.Veni.181.050