Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar - PubMed (original) (raw)

Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar

Daniel J Goedbloed et al. BMC Genet. 2013.

Abstract

Background: Population genetic studies focus on natural dispersal and isolation by landscape barriers as the main drivers of genetic population structure. However, anthropogenic factors such as reintroductions, translocations and wild x domestic hybridization may also have strong effects on genetic population structure. In this study we genotyped 351 Single Nucleotide Polymorphism markers evenly spread across the genome in 645 wild boar (Sus scrofa) from Northwest Europe to evaluate determinants of genetic population structure.

Results: We show that wild boar genetic population structure is influenced by historical reintroductions and by genetic introgression from domestic pigs. Six genetically distinct and geographically coherent wild boar clusters were identified in the Netherlands and Western Germany. The Dutch Veluwe cluster is known to be reintroduced, and three adjacent Dutch and German clusters are suspected to be a result of reintroduction, based on clustering results, low levels of heterozygosity and relatively high genetic distances to nearby populations. Recent wild x domestic hybrids were found geographically widespread across clusters and at low frequencies (average 3.9%). The relationship between pairwise kinship coefficients and geographic distance showed male-biased dispersal at the population genetic level.

Conclusions: Our results demonstrate that wildlife and landscape management by humans are shaping the genetic diversity of an iconic wildlife species. Historical reintroductions, translocation and recent restocking activities with farmed wild boar have all influenced wild boar genetic population structure. The current trend of wild boar population growth and range expansion has recently led to a number of contact zones between clusters, and further admixture between the different wild boar clusters is to be expected.

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Figures

Figure 1

Figure 1

Population assignment proportions per individual based on results from structure for K = 2-7. Recent wild x domestic hybrids, sampled in the field as wild boar, are delimited by vertical lines. Results for K = 5 were not ambiguous across runs. Majority rule results (n = 10) are presented here, but the inclusion of E-Rhine in Kirchhellen at K = 5 is not fully supported, as various alternative clustering patterns were also inferred. Evanno’s method favoured optimal partitioning at K = 7 (see Additional file 5).

Figure 2

Figure 2

PCA plot of the wild boar and a sample of domestic pigs, indicating genetic variation along the first two eigenvectors. Colours correspond to Figure 1. The 25 recent wild boar x domestic pig hybrids identified by

structure

(threshold assignment proportion 0.25) are indicated in dark grey and four additional advanced generation hybrids with introgressed pig alleles identified in a previous study [21] are indicated in light grey.

Figure 3

Figure 3

PCA plots indicating the first four eigenvectors of the wild boar data only. Colours indicate the six clusters identified by

structure

. Putative hybrids are not indicated in this figure. Eigenvectors 1–4 explain 43% of variance in the dataset.

Figure 4

Figure 4

Map of the study area indicating identified clusters. Country borders are indicated by black lines, forests are indicated in soft green and inland water features in light blue. Dots indicate wild boar sampling sites. The size of the dot is relative to the sample size. The colours indicate genetic clustering by

structure

and correspond to other Figures. Hybrids identified by

structure

(domestic cluster assignment proportion >0.25) are indicated in grey.

Figure 5

Figure 5

NeighborNetwork of six representative samples per wild boar cluster and one sample per domestic pig breed. The number of samples was chosen for optimal balance in information content and clarity of the figure. Distances are based on the uncorrected P (or Hamming) method.

Figure 6

Figure 6

Pairwise kinship coefficients of both sexes versus geographic distance. Results are based on local polynomial regression analysis. Females show relative site fidelity at pairwise distances less than 25 kilometres, and males show higher kinship coefficients at distances between 25 and 150 kilometres, indicating higher dispersal rates.

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