Part III: Conservation and Management380
However, this model for expansion, and perhaps subse-
quent contractions, during the Pleistocene for wild boar in
South East Asia does not appear to be without its complications.
Mitochondrial DNA analyses hints that there may be a number
of distinct regions of wild boar diversity in South, South East,
and East Asia (Herrero-Medrano 2013). Moreover, studies on
nuclear genomes have revealed a complex distribution of vari-
ation. One that is particularly interesting is the distinct diver-
gence between wild boar of northeast Asia (northern China,
eastern Siberia, Korea, and parts of Japan), and south China.
This distinction is apparent from genome-wide marker data
(Groenen et al. 2012; Frantz et al. 2015a), but it is even more
pronounced when considering X- and Y-chromosome data. In
Japan, it is possible to find Y-chromosome haplotypes that are
more similar to European than to Chinese haplotypes (Ramírez
et al. 2009). Something similar is seen for the X chromosome.
In pigs, a large portion of the X chromosome, roughly 50 Mb,
that lies around the centromere (pericentromeric) has a very
low recombination frequency (Fernández et al. 2014). As a con-
sequence, X-chromosome haplotypes remain ‘unshuffled’ over
very long distances and thereby allow inference of philogeog-
raphy similar to what can be achieved with mitochondrial and
Y-chromosome haplotypes. It turns out that north Chinese wild
boar X-chromosome haplotypes are philogeographically much
closer to Europe than to south China (Ai et al. 2015). The dis-
tribution of the northern Chinese X-chromosome haplotype in
domesticated pigs is intriguing: it is found in all northern and
central Chinese pig breeds, which includes the region where
pigs were probably first domesticated in China. All south-
ern Chinese pig breeds, on the other hand, have the southern
Chinese X-chromosome haplotype (Ai et al. 2015). As an addi-
tional twist, the southern Chinese X-chromosome appears to be
closest related to those of Sus species from ISEA (Figure 34.2B).
Therefore, the northern Chinese and European X chromosomes
represent variation outside of the entire spectrum of autosomal
diversity found in Sus scrofa. This finding highlights two impor-
tant hypotheses that are not mutually exclusive. First, there may
have been other pigs present in Eurasia – corroborated by pale-
ontological evidence – that were mostly replaced by Sus scrofa as
it dispersed from South East Asia further north and westwards.
The X-chromosome haplotypes (Ai et al. 2015), and possibly
also Y-chromosome haplotypes (Ramírez et al. 2009), found in
the western part of Eurasia and (parts of ) northeast Asia, may
therefore represent genomic regions of a suid species that other-
wise became extinct (Frantz et al. 2015a). In addition, it suggests
that there may have been a northern dispersion route for wild
boar, i.e. north of the Himalayan plateau to western Eurasia.
This northern distribution area may have had glacial refugia
that remain to be identified. Nevertheless, the X-chromosome
haplotypes depict a far more discrete distribution of diversity
than genome-wide variation does. From an autosomal and
mitochondrial perspective, the northern Chinese wild boar
appears to be far more closely related to the southern Chinese
than to western wild boar, indicating that gene flow in East Asia
(from south to north) must have been really high at least during
the Holocene (Groenen et al. 2012; Frantz et al. 2013; Bosse et al.
2014c; Frantz et al. 2015a). The fact that, despite evidence of ahigh gene flow, X-chromosomal diversity between northern and
southern populations remained rather discrete hints at some as-
yet unidentified mechanism that enforces this pattern, such as
meiotic drive.
The high degree of divergence between east and west
Eurasian wild boar may be currently diminishing. In Europe,
recent admixture with pigs is occurring at high rates in some
wild boar populations (Goedbloed et al. 2013a,b; Iacolina et al.
2016). With regard to hybridization between eastern and west-
ern populations, it is important to note that the ensuing genomes
will become mosaics of these two different demographies. For
instance, this effect can be derived from demographic analyses
based on genomic variation. European domestic pigs display
an almost intermediate demographic history between those of
their western and eastern ancestors. Interestingly, if genomes are
sorted by the origin of haplotypes, these two discrete demogra-
phies can be disentangled (Bosse et al. 2014a). The mosaic nature
of the pig genome, with western and eastern components, also
has consequences on the observed variation within individuals
and populations (Bosse et al. 2014a,b) and, as noted earlier in
this paragraph, for the selection potential (Bosse et al. 2014b;
Goedbloed et al. 2015). A more general discussion on admixture
between pigs and wild boar is the focus of the next section.A Long History of Genetic Admixture
between Pigs and Wild Boar
Wild boar and pigs have coexisted during the last 10,000 years
and both share a broad geographic range. This situation con-
trasts strongly with that of other domesticates whose wild ances-
tors have become extinct (e.g. aurochs) or display a restricted
geographic distribution (e.g. bezoars and mouflons). In medi-
eval Europe, pigs roamed in the forests feeding on beech masts,
acorns, and chestnuts (White 2011). This traditional manage-
ment, called pannage, was practised for centuries, providing a
broad window of opportunity for the accidental hybridization
between pigs and wild boar. Indeed, pigs were not permanently
kept in sties until the seventeenth and eighteenth centuries,
when the extensive deforestation and the steady increase of
human population densities in the British Isles led to a major
revolution in pig breeding (White 2011). Nevertheless, the
intensification of pig production was not uniformly adopted
across Europe, and even nowadays certain breeds are raised
extensively. In Romania, a research performed in the commune
of Bârzava (Arad County, 2005–2009) revealed that as many as
25 per cent of pigs raised in extensive conditions had been intro-
gressed with wild boar (Matiuti et al. 2010).
Genomic methods have been essential in determining the
timing and magnitude of genetic exchanges between pigs and
wild boar. Genotyping of modern European wild boar and pig
populations with mitochondrial and microsatellite markers
provided the first clues about the impact of such admixture pro-
cesses, making it evident that at least 5–16 per cent of modern
wild boar have been introgressed, to a variable extent (80 per cent
in some cases), with domestic pig genes (Vernesi et al. 2003;
Scandura et al. 2008, 2011; Frantz et al. 2012). Similarly, the
genetic analysis of Ryukyu wild boar from the Japanese island.03612:55:56