Ecology, Conservation and Management of Wild Pigs and Peccaries

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

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There is also evidence for ecological differentiation, presum-
ably as adaptations to local niches. For instance, Sus barbatus, a
species whose range does extend beyond ISEA but not beyond
Peninsular South East Asia, seems to be highly adapted to the
dipterocarp forest of the Sunda plateau.
Recent phylogenomic studies have provided a more subtle
picture. The differentiation of suids into different species in ISEA
seems very much driven by isolation (Frantz et al. 2013; Frantz
2015). For instance, the effective population size of S. cebifrons,
a species confined to just a few (relatively small) islands, is much
more reduced than that of other species that have been investi-
gated so far (Bosse et al. 2015).
While insular isolation certainly played a major role in
the speciation of suids in ISEA, that is only part of the story,
because the large islands on the Sunda plateau, i.e. Java, Borneo,
and Sumatra, were often connected by dry land during cold
periods. Migration and hybridization were therefore entirely pos-
sible and, as a matter of fact, evidence for hybridization has been
found in genomic studies. Hybridization has even been inferred
between species distributed on different landmasses that have
never been connected during the Pleistocene (Frantz et al. 2013).
South East Asia appears to be the area of highest diversity in
the genus Sus, which is evident from molecular genetic studies
(Larson et al. 2005; Amaral et al. 2008; Megens et al. 2008; Groenen
et al. 2012 ) and also, most likely, it is the area where Sus scrofa
originated (Frantz et al. 2015a; see also Figure 34.2A). Whether
the origin of Sus scrofa is indeed insular, peninsular, or main-
land South East Asian is currently unclear. Recent phylogenomic
analyses that included Sus scrofa from Sumatra (most likely the
endemic subspecies Sus scrofa vittatus recently elevated to spe-
cies status; Groves & Grubb 2011; see also Chapter 1 in this book)
demonstrate a basal position of this subspecies compared to all
mainland populations (Frantz 2015). While this is highly sugges-
tive of an insular or peninsular Sundaland origin for Sus scrofa,
the actual scenario seems to have been far more complex. Gene
flow between Sus scrofa from Sumatra and East Asia (Southern
China) was demonstrated to have been extensive (admixture
fraction between 9.5 and 11 per cent; Frantz et al. 2013), which

can be attributed to Sumatra and mainland South East Asia being

a single landmass during most of the middle and late Pleistocene.

Nevertheless, gene flow between Sus scrofa and insular Sus spe-

cies was significant too, albeit smaller (admixture fractions

1.3–4.2 per cent; Frantz et al. 2013). Because the geographic dis-

tance between Sus scrofa from Sumatra and East Asia (Southern

China) is much larger than between Sumatran Sus scrofa and other

island species of the genus Sus, there can be little dispute regard-

ing the species status of Sus scrofa. At the same time, it is clear that

there has been significant admixture between different suid spe-

cies, indicating that speciation is not a discrete but rather a gradual

process (Frantz et al. 2015a). These recent phylo genomic studies

clearly show that the ecological and biogeographic differentiation

of large mammals can be a protracted process.

The recurrent waxing and waning of sea levels has probably

been an important driver in Sus speciation by either enabling

or hindering it, as it likely has been to many tropical taxa in this

region of the world. Somewhat unique to pigs, perhaps, is that

humans have been interfering with this natural order of things,

certainly recently, but possibly for quite some time. It seems that

humans have been shipping pigs – wild and domesticated, and

of different suid species – around the ISEA archipelago, thereby

causing an increase in admixture (Frantz et al. 2013). The insight

that, even from prehistoric to early historic times, humans have

been engaged in changing the biogeography of the suids of South

East Asia is also an important lesson, in modern times, about the

menace that domesticated Sus scrofa can entail for maintaining

the genetic integrity of endangered Sus species, such as Sus ver-

rucosus and Sus cebifrons (Frantz et al. 2015a).

Highly Divergent Patterns of Diversity in

Western and Far Eastern Wild Boar Reveal an

Ancient Genetic Split in the Pleistocene

From its origin in the late Pliocene or early Pleistocene in South

East Asia, Sus scrofa further dispersed across the vast expanses

of the Eurasian landmass. This dispersion appears to have been

Eocene

33.9

Suoidae

Suidae Suinae

23

Oligocene Miocene

15.9 11.6 5.3 2.5 0 Ma

Pliocene Pleistocene

Tayassuidae

Babyrousinae

Hylochoerus meinertzhageni

Sus celebensis

Sus barbatus

Sus philippensis

Sus cebifrons

Sus verrucosus

Sus scrofa

Porcula salvania

Potamochoerus larvatus

Potamochoerus porcus

Phacochoerus aethiopicus

Phacochoerus africanus

Figure 34.1 Phylogeny and timing of

speciation in extant Suidae. Redrawn from

Frantz et al. (2016).

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