Part III: Conservation and Management378
taking place since the middle of the Pleistocene, at around
1.2–0.8 Ma (Frantz et al. 2013; Frantz 2015) resulting in the high
genetic differentiation between the Western and Eastern repre-
sentatives of wild Sus scrofa (Groenen et al. 2012).
Genetic differences between Eastern and Western Sus scrofa
were initially highlighted in mtDNA analyses (Giuffra et al. 2000).
These studies revealed that European domesticated pigs carried
mitochondrial haplotypes that represented two very distinct bio-
geographies. This is hardly surprising, as it is well documented
that European pigs were improved, in the eighteenth and nine-
teenth centuries, and possibly even before, by crossing them with
pigs of East Asian origin (Porter 1993). The origins of the mito-
chondrial haplotypes were also readily identified from analyses of
European and Chinese populations, and extensive comparisons
allowed tracing back the origins of these pigs mostly to south-
eastern Chinese coastal provinces (Fang & Andersson 2006).
What also became clear from these initial mtDNA studies was
the high degree (up to 80–100 per cent ) at which Far Eastern mito-
chondrial haplotypes are present in certain European/American
domestic pig populations, hinting at a likely very large contribu-
tion of Asian/Chinese swine, particularly in modern commercial
breeds (Fang & Andersson 2006). Substantial percentages of Asian
mitochondrial haplotypes are found in several non-commercial
European breeds, particularly in the ones with a British heritage,
which given that genetic improvement based on the importation
of Chinese pigs started in England should not be a surprise. An
interesting twist to the mitochondrial evidence for an Asian intro-
gression into European pigs is that Asian Y-chromosomal hap-
lotypes are actually very rare in Europe. Asian Y-chromosomes
have so far been found mainly in the English Tamworth breed,
and at lower frequencies in breeds that appear to trace their origin
back to Tamworth. It seems, therefore, that it was mainly sows
that were shipped from China to the United Kingdom in the
eighteenth and nineteenth centuries (Ramírez et al. 2009).
The total contribution of Chinese pigs to modern commer-
cial Western breeds has been impossible to infer from historicalsources. Recently, whole-genome resequencing has provided a
means to infer haplotype origins across the entire genome, indi-
cating that the Asian contribution to modern European breeds
is roughly one-quarter to one-third (Groenen et al. 2012; Bosse
et al. 2014a,b; Frantz et al. 2015a). In close resemblance with
Asian and European mitochondrial and Y-chromosomal haplo-
types, defining the origins of nuclear haplotypes is aided by the
high degree of divergence between Asian and European pigs.
In modern European pigs, subsequent recombination resulted
in chromosomes that are a complex mosaic of segments with
highly divergent origins. This mosaic can still be traced back to
its two individual Asian and European origins in much of the pig
genomes (Wilkinson et al. 2013; Bosse et al. 2014a,b), provided
the recombination rate is not too high. Such a feature is aided
by the fact that the Asian introgression into European breeds
was relatively recent (~250–200 years ago; Porter 1993; White
2011). Chinese pigs were chosen for improving local European
pigs for practical reasons, i.e. Asian pigs in the eighteenth cen-
tury were superior in traits, like fatness and prolificacy, deemed
as desirable in a rapidly changing world where urbanization and
industrialization were increasingly dictating economic realities.
In that world, where farming became more (capital) intensive,
increased production rates in controlled environments (sties) to
produce good-quality pork products (increased fat production)
was revolutionizing pig production (White 2011).
The introduction of Asian pigs in England, therefore,
favoured the selection for desirable traits such as an elevated
number of piglets and a high fat content, features that Chinese
pigs were renowned for. The selective introgression of Asian
variants of genes that underlie these traits in European pigs
has been demonstrated recently (Wilkinson et al. 2013; Bosse
et al. 2014b). For example, Asian variants of the AHR gene were
shown to increase the number of piglets (Bosse et al. 2014b).
Inferring the selective advantage of variants of genes that are
introgressed from a highly divergent source is called admixture
mapping (Figure 34.3). This strategy is now leveraged to obtain aFigure 34.2 (A) Phylogeny and timing of speciation (in millions of years) within the genus Sus based on the autosomes. Sus scrofa and the ISEA species form two
distinct, monophyletic groups. (B) Phylogeny in the genus Sus based on only the X chromosome. Note that European and North Chinese wild boars form a highly
divergent, separate clade. Redrawn from Frantz et al. (2016)..03612:55:56