Chapter 34: A genomic perspective about wild boar demography and evolution379
better understanding of the selective processes that were impor-
tant during breed formation around 200–250 years ago, and
more generally it provides a window into the genetic architec-
ture of complex traits (Bosse 2015).
The high divergence of domesticated pigs from Asia and
Europe is due to the independent domestication of wild boar
in the Western and Eastern parts of Eurasia, around 10,000
years ago, based on local wild boar populations (Larson et al.
2005, Frantz et al. 2015a). This strong genetic differentia-
tion has become apparent in mitochondrial, Y-chromosome,
and microsatellite marker studies (Larson et al. 2005; Megens
et al. 2008; Ramírez et al. 2009), and it has recently been high-
lighted in whole-genome resequencing studies (Bosse et al.
2012; Groenen et al. 2012). Pig divergence is reflected in the
wild boar populations of east and west Eurasia: over 1.2 million
variants were found to be fixed differences, i.e. not segregating
in one of the geographic subdivisions of Eurasia, between west
and east Eurasian wild boar. In western Eurasia, expansion of
farming from Anatolia into Europe at first involved the entry of
Anatolian pigs into this continent. Over time, local European
wild boar appear to have increasingly contributed to the gene
pool of local pigs (Larson et al. 2007; Ottoni et al. 2013).
The wild (and domesticated) pig populations of central and
south Eurasia have been somewhat poorly investigated, but a
cline in diversity from east to west across Eurasia appears to
provide an accurate representation of the actual distribution
of wild boar diversity (Larson et al. 2005; Groenen et al. 2012;
Frantz et al. 2015a). This cline is consistent with the westward
migration of wild boar out of South East Asia, around ~1 Ma
(Frantz et al. 2013; Frantz 2015). It is also consistent with a
stepping-stone model of dispersal, where the amount of varia-
tion declines as the species migrates further away from its cen-
tre of origin. For example, whole-genome sequences retrieved
from six wild boar that represented all the major biogeographic
regions of Europe yielded only around 6.4 million single nucle-
otide polymorphisms (SNPs), while approximately 11.5 million
SNPs were discovered by comparing genome sequences from
four East Asian wild boar (Groenen et al. 2012). Moreover,
these European and Asian pigs only shared ~ 2.2 million SNPs.
The low variation in the westernmost distribution range, and
associated drift and divergence from the source populations in
the east, appears furthermore related to population decline in
recent ice-age episodes (Groenen et al. 2012; Frantz et al. 2013).
During these cold periods, wild boar populations retracted
to southern Europe, where they were largely confined to the
Iberian, Italian, and Balkan Peninsulas (Scandura et al. 2008;
Iacolina et al. 2016). Since the advent of agriculture in Europe,
and at an accelerated pace in the past 1000 years, humans con-
tributed significantly to population decline in wild boar across
Europe, causing the extinction of this species in the British Isles
by the thirteenth century (Harris & Yalden 2008). Conversely,
late Pleistocene climatic fluctuations seem to have had a far
smaller effect on Asian wild boar, probably because in East Asia
this species was able to migrate southwards, reaching large,
wooded refugia that were probably connected to the Sunda
region (Frantz et al. 2013).Figure 34.3 Principle of admixture
mapping. The putative admixed
population (in this case, commercial
pigs belonging to the Large White
breed) were compared to western and
eastern pigs that presumably were
not admixed. By determining whether
genomic haplotypes (on a per-window
basis) of the Large White pigs were
more similar to the eastern or western
unadmixed Sus scrofa population, the
Large White haplotypes were ‘sorted’
into a ‘western’ and ‘eastern’ fraction.
Regions of the genome with a very
high frequency of ‘eastern’ haplotypes
were assumed to be enriched for loci
under selection, because the Asian
fraction in the Large White genome
was, overall, a minority (redrawn from
Bosse et al. 2014b)..03612:55:56