Chapter 34: A genomic perspective about wild boar demography and evolution383
and (iv) the magnitude of linkage disequilibrium (selection is
associated with extended regions of strong linkage disequi-
librium). These approaches have been widely used to identify
positive selection in many loci related with stature, coat colour,
nervous system development, reproduction and behaviour that
probably played a key role in the process of pig domestication
(Rubin et al. 2012; Frantz et al. 2015b).
Unfortunately, selective sweep scans have been rarely applied
to elucidate the genetic consequences of selection on wild boar.
One of the few studies that has addressed this question was
published by Groenen et al. (2012). These authors analysed the
genomes of 10 European and Asian wild boar and identified as
much as 251 putative selective sweeps covering 1 per cent of the
pig genome. Within these positively selected regions, there was
an over-representation of loci related with RNA splicing and
processing, suggesting that the divergence of the European and
Asian lineages involved regulatory changes modifying tran-
script structure and expression. Measurement of the dN/dS ratio
also indicated that the impact of purifying selection on the pig
genome is similar to that reported in other mammal species,
and that immune genes show an accelerated evolutionary rate
(Groenen et al. 2012).
In another study, Li et al. (2013) performed a genome scan
for selection in Tibetan wild boar, which live at high altitudes
(4000 m a.s.l.), and Duroc pigs (Figure 34.7). They found that
215 genes had an excess of non-synonymous mutations in
Tibetan wild boar. Several of these positively selected genes
were related with the hypoxia response and cardiovascular sys-
tem categories. This finding agrees well with some anatomical
features of Tibetan wild boar (e.g. large lungs and heart) that
facilitate the adaptation to a mountainous environment with a
low oxygen concentration (Li et al. 2013). Furthermore, posi-
tive selection was demonstrated to target genes involved in DNA
repair and response to DNA damage in the Tibetan wild boar,
presumably to cope with the mutagenic effects of the increased
exposure to ultraviolet radiation at high altitudes. In the future,
selective sweep analyses of a broad variety of wild boar popu-
lations will provide further insights into the adaptation of this
species to highly divergent ecological niches.Causes and Consequences of the Reduced
Variability of European Wild Boar
In many countries, wild boar have experienced drastic declines
in population size that, in some instances, have resulted in the
local extinction of this species. According to the IUCN Red
List of Threatened Species (Oliver & Leus 2008), wild boar
have been wiped out from Egypt and Libya, and they haveFigure 34.7 Distribution of the
nucleotide diversity ratios (which
reflect the relative amount of
polymorphism in Chinese domestic
pigs vs Tibetan wild boars) and FST
values across all the genome, in 100-kb
windows sliding in 10-kb steps. The FST
coefficient provides an estimate of the
genetic differentiation between two
populations (FST = 0, no differentiation;
FST = 1, maximum differentiation). In
principle, regions under divergent
selection are expected to display high
FST values because alternative alleles
tend to be fixed in each population.
In this picture, data points in dark and
medium grey at the two extremes of
the normal distribution (see the central
plot) are candidate regions that have
been affected by selection in Chinese
domestic pigs and Tibetan wild boars,
respectively. Marginal distributions
at top and right of the main panel
represent the extreme 5% tail of values
for the nucleotide diversity ratio and
for the FST statistic, respectively. Figure
extracted from Li et al. (2013) with the
permission of the editors..03612:55:56