Genome‐wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

Abstract

Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

“…2005) to our STRUCTURE data would suggest K  = 2. However, the efficacy of the ΔK method for detecting hierarchical population structure is debatable (Gao et al., 2011; Goedbloed et al., 2013; Waples & Gaggiotti, 2006; Welch et al., 2012). Evidence of hierarchical structure in our dataset is demonstrated by the increasing likelihood values of our STRUTURE runs (Figure S3); as well by the geographic concordance of individual genetic assignments in relation to capture locations (Figure 3).…”

“…We opted for the plateau criterion because the ΔK method (Evanno et al. 2005) can be biased toward detection of the first structural level in the data, and miss fine‐scale structure (Gao, Bryc, & Bustamante, 2011; Goedbloed et al., 2013; Waples & Gaggiotti, 2006; Welch et al., 2012). …”

Mining the pig genome to investigate the domestication process

“…In fact, variability is higher in European domestic pigs (Bosse et al, 2012) mainly due to the intense admixture with Asian pigs and the selection of advantageous Asian mutations that has occurred in these lineages (Ojeda et al, 2011). In addition, historical admixture with wild boars may have also had a role until a few hundred years ago (White, 2011;Goedbloed et al, 2013;Manunza et al, 2013). Amaral et al (2011) observed a positive correlation between the level of variability and recombination (also observed in Badke et al, 2012;Bosse et al, 2012 andEsteve-Codina et al, 2013), suggesting that selection (positive or negative) has an active role in shaping the variability of Sus scrofa and that interference among genomic positions has an impact on variability.…”

“…In summary, a complex demographic pattern becomes apparent from genomic data with recent mixtures of commercial breeds between geographically distant locations and recurrent introgression events of commercial breeds into wild populations (Goedbloed et al, 2013). The intricate genetic relationship among domesticated populations suggests that complex breeding practices, including genetic exchange with wild animals and/or multiple origins of domestication, have had an important role in delineating the genealogical relationships within this species.…”

El problema de la caza visto por un genetista

“…Sí sabemos que hay quienes hibridan jabalíes con cerdo doméstico para conseguir animales híbridos de gran tamaño. Aunque no es difícil detectar hibridación de jabalí y cerdo, no tenemos idea de la magnitud de estas prácticas de hibridación ni de sus consecuencias en la naturaleza porque prácticamen-te no se hace ningún control genético (Goedbloed et al, 2013). Existe evidencia de hibridación de codorniz común (Coturnix coturnix) con codorniz japonesa de corral (Coturnix japonica) y que esta hibridación se ha producido artificialmente en granjas cinegéticas.…”