Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus)

Abstract

The objective of the study was to establish and refine a method for the genomic characterization of European hedgehogs in Denmark using the second-generation genotyping technique, genotyping by sequencing (GBS). Single nucleotide polymorphisms (SNPs) were filtered with a read coverage between 20 - 100 and a maximum number of missing data of 25 %. Individuals with > 25 % missing data were removed yielding a total of 2.4 million SNPs, and after filtering for Minor allele frequency (MAF) >1 %, 2902 SNPs remained. Approximately half of the individuals analysed contained less than 75% of the selected SNPs, and were removed, resulting in a sample size of 30. We estimated inbreeding coefficients (F), observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity and the percent of polymorphic loci (P%). We tested for deviations from Hardy-Weinberg equilibrium (HWE) and patterns of isolation by distance (IBD). We assessed the genetic structure of the sampled individuals based on a Bayesian clustering method, and tested for recent population expansion or decline. We found a P% = 94.5%, a uHE and HE of mean ± SE; 0.31 ± 0.04 and 0.30 ± 0.02, respectively and an HO of 0.290 ± 0.03. The heterozygosity deficiency was reflected in a positive F-value; 0.1 ± 0.01 and a significant deviation for HWE (p < 0.05). The Mantel test for association between the genetical and geographical distances of populations was not significant (b = 0.007, R = 0.145, p > 0.05). The significant and positive F-value found, was explained by inbreeding, genetic substructure and low effective population size (Ne) which are all consequences of habitat fragmentation. We failed to detect recent signs of a population bottleneck or expansion. Further studies on a larger scale are needed to obtain a general view of the conservation status of the Danish hedgehog population.