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

Sophie Lund Rasmussen, Erika Yashiro, Elsa Sverrisdóttir, Kåre Lehmann Nielsen, Mie Bech Lukassen, Jeppe Lund Nielsen, Torben Asp, Cino Pertoldi

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

2 Downloads (Pure)

Resumé

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
OriginalsprogEngelsk
TidsskriftGenetics and biodiversity Journal
Vol/bind3
Udgave nummer2
Sider (fra-til)78-86
StatusUdgivet - 2019

Fingeraftryk

Erinaceus europaeus
Erinaceidae
genotyping
single nucleotide polymorphism
genomics
heterozygosity
inbreeding coefficient
methodology
Denmark
habitat fragmentation
inbreeding
gene frequency
population size
loci
sampling

Citer dette

Rasmussen, S. L., Yashiro, E., Sverrisdóttir, E., Nielsen, K. L., Lukassen, M. B., Nielsen, J. L., ... Pertoldi, C. (2019). Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus). Genetics and biodiversity Journal, 3(2), 78-86.
Rasmussen, Sophie Lund ; Yashiro, Erika ; Sverrisdóttir, Elsa ; Nielsen, Kåre Lehmann ; Lukassen, Mie Bech ; Nielsen, Jeppe Lund ; Asp, Torben ; Pertoldi, Cino. / Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus). I: Genetics and biodiversity Journal. 2019 ; Bind 3, Nr. 2. s. 78-86.
@article{9b39dc4bc1ab45ca8db37ea4b97b0aec,
title = "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",
author = "Rasmussen, {Sophie Lund} and Erika Yashiro and Elsa Sverrisd{\'o}ttir and Nielsen, {K{\aa}re Lehmann} and Lukassen, {Mie Bech} and Nielsen, {Jeppe Lund} and Torben Asp and Cino Pertoldi",
year = "2019",
language = "English",
volume = "3",
pages = "78--86",
journal = "Genetics and biodiversity Journal",
number = "2",

}

Rasmussen, SL, Yashiro, E, Sverrisdóttir, E, Nielsen, KL, Lukassen, MB, Nielsen, JL, Asp, T & Pertoldi, C 2019, 'Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus)', Genetics and biodiversity Journal, bind 3, nr. 2, s. 78-86.

Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus). / Rasmussen, Sophie Lund; Yashiro, Erika; Sverrisdóttir, Elsa; Nielsen, Kåre Lehmann; Lukassen, Mie Bech; Nielsen, Jeppe Lund; Asp, Torben; Pertoldi, Cino.

I: Genetics and biodiversity Journal, Bind 3, Nr. 2, 2019, s. 78-86.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus)

AU - Rasmussen, Sophie Lund

AU - Yashiro, Erika

AU - Sverrisdóttir, Elsa

AU - Nielsen, Kåre Lehmann

AU - Lukassen, Mie Bech

AU - Nielsen, Jeppe Lund

AU - Asp, Torben

AU - Pertoldi, Cino

PY - 2019

Y1 - 2019

N2 - 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

AB - 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

M3 - Journal article

VL - 3

SP - 78

EP - 86

JO - Genetics and biodiversity Journal

JF - Genetics and biodiversity Journal

IS - 2

ER -