Ecology, Conservation and Management of Wild Pigs and Peccaries

Chapter 34: A genomic perspective about wild boar demography and evolution

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of Irimote indicated that 12 per cent of the analysed individu-

als might be hybrids (Murakami et  al. 2014). The low genetic

differentiation observed between Iberian pigs and wild boar

also suggests the occurrence of past genetic exchanges (Ramírez

et al. 2009; Herrero-Medrano et al. 2013; Manunza et al. 2013), a

feature consistent with the extensive management of this breed.

The advent of the 60K Porcine SNP BeadChip (Ramos et al.

2009), a high-through put genotyping platform that allows the

simultaneous genotyping of ~62,000 SNPs, offered the oppor-

tunity to accurately estimate the magnitude of gene flow from

pigs to wild boar. Goedbloed et al. (2013a) used the 60K SNP

BeadChip to genotype 88 wild boar from northwest Europe and

observed an excess of rare SNPs, with frequencies between 0.5

and 3 per cent. Around 70 per cent of these SNPs were exclusively

found in nine individuals (~10 per cent of the total sample) that,

in a principal component analysis, occupied an intermediate

position between pigs and wild boar. Moreover, an allele fre-

quency spectrum analysis of genome-wide SNP data enabled a

reliable ascertainment of up to fifth-generation backcrosses in

several wild boar populations, and such results could be further

confirmed through the analysis of introgressed chromosomal

segments(Goedbloed et  al. 2013a). Substantial levels of por-

cine introgression (Figure 34.4) have been also detected when

examining a second sample of northwest European wild boar

(Goedbloed et  al. 2013b) as well as specimens from Sardinia

(Iacolina et al. 2016) and Romania (Manunza et al. 2016), sug-

gesting that this is a widespread phenomenon.

Genomic methods can be used not only to estimate the

amount of pig introgression in wild boar, but also to ascer-

tain when this process began. The analysis of 103 genomes of

European and Asian wild boar and pigs and the subsequent

comparison, through an approximate Bayesian computation

approach, of models with and without migration revealed that

the most likely model was the one with gene flow between wild

and domestic populations as well as between Asian and European

populations (Frantz et  al. 2015a). These results (Figure 34.5)

demonstrated that the wild and domestic forms did not

remain reproductively isolated during and after domestication

Figure 34.4 Population assignment proportions per individual based on an analysis with the Structure software (K = 7) of 645 wild boars from northwest Europe
(greyscale background) and a number of domestic pigs (white background) with genotypes for 351 single nucleotide polymorphisms. The different greyscale and
black areas indicate the proportion of the genome belonging to a partition. It can be seen that there are wild boars whose genetic background is a mixture of the
wild (greyscale) and domestic (white) gene pools, thus indicating that these individuals are hybrids. Figure retrieved from Goedbloed et al. (2013b) with permission
of the editors and authors. (A black and white version of this figure will appear in some formats. For the colour version, please refer to the plate section.)

Figure 34.5 (A) Relationship between genome sequences of Wild (W) and Domestic (D) pigs in Asia (AS) and Europe (EU), (Frantz et al. 2015a). Tree representation
using the neighbour-joining method and based on an identity-by-state (IBS) distance matrix. (B) Population model representing European wild boar (EUW),
European domestic pig (EUD), Asian wild boar (ASW), and Asian domestic pig (ASD) and parameters used in the analyses. The model considering the existence
of gene flow between domestic and wild populations received the highest support (posterior probability of 0.93) in comparison to other five models with no
gene flow or gene flow restricted to some of the populations. Mode estimates for the parameters under analysis were NEU = 1.833; NAS = 1.227; NEUW = –0.071; NEUD
= 0.313; NASW = 0.556; NASD = 0.414 (population sizes relative to the log of the ancestral population). T 0 = 54.849; T 1 = 0.152; T 2 = 0.354 (times in relation to 4 times the
ancestral population). Gene flow estimates (log scale of 4 times the ancestral population size per migration rate) were negative (that is, below 1 after logarithmic
transformation) except for ASW vs ASD, in both directions (0.551 and 0.798), and for EUW to EUD (0.657). This figure has been retrieved from Frantz et al. (2015a) with
permission of the editors and authors.

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