Part I: Evolution, Taxonomy, and Domestication4
Phylogenetic Relationships between Extant
Sub-Saharan African Suinae
Mitochondrial and nuclear DNA multilocus analyses show that
Hylochoerus and Phacochoerus group together as a sister clade to
Potamochoerus (Figure 1.2; Gongora et al. 2011a), and the sepa-
ration between these two generic groupings is well supported
by morphological studies (White & Harris 1977; Cooke 1978;
Pickford 2012). Gongora et al.’s (2011a) findings reveal that
African suids are phylogenetically distinct from Eurasian Sus
and Porcula. This contrasts with previous taxonomic hypoth-
eses, which maintained that Potamochoerus and/or Hylochoerus
were sister genera to Sus (Cooke 1978) to the exclusion of
Phacochoerus (Thenius 1970; Groves 1981; Groves & Grubb
1993). Morphological data indicate a resemblance between
Potamochoerus and Sus, specifically in the teeth (Herring 1971;
Cooke & Wilkinson 1978; Kingdon 1979; Geraads 2004), which
was also suggested in an unpublished thesis by Cuddahee
(2008). A possible explanation for these similarities is retention
of ancestral traits and/or convergent evolutionary adaptation
to selective dietary pressures associated with omnivory (Harris
& White 1979; Pickford & Morales 2003) rather than close
ancestry (Gongora et al. 2011a). Another unpublished doc-
toral thesis assessing geometric morphometrics of suid cranial
shape, comparing this to published DNA phylogenies, came to
a similar conclusion, suggesting that shared generalist omnivo-
rous behaviour led to a convergence in their cranial morphol-
ogy despite their distinct evolutionary histories, which is why
morphology alone fails to reveal the monophyly of sub-Saharan
African Suidae as suggested by DNA (Owen 2013).
Interestingly, mitochondrial and nuclear DNA analyses sug-
gest that the divergence between modern sub-Saharan African
genera from their common ancestor occurred ~7.36–14.45 Ma
(Gongora et al. 2011a). This may suggest two possible scenarios
as to where this divergence took place. The first is that the diver-
gence between extant sub-Saharan suids took place in Africa,
but earlier than so far supported by the fossil record. To date
there is no fossil evidence of Suinae in Africa before the Early
Pliocene (Cooke 1978; Pickford 1993; Brunet & White 2001).
The second scenario is that sub-Saharan African genera could
have diverged from their common ancestor outside Africa, in
Eurasia. Pickford (2012) suggested that the common ances-
tor (‘Sus provincialis’) of the Phacochoerus and Potamochoerus
lineages diverged outside Africa after which these two lineages
entered the continent ~4 Ma and ~1 Ma, respectively.Phylogenetic Relationships between Extant
Eurasian Suinae
The phylogenetic position of Porcula has been the subject of
debate. Phylogenetic analyses of three mtDNA loci (control-
region, cytochrome b, 16S) shows that Porcula clusters in a
separate clade within Suidae (Funk et al. 2007) and is likely
to be a sister lineage to Sus (Figure 1.2; Gongora et al. 2011a).
Porcula salvania, the pygmy hog of India, was originally placed
in its own genus, then assigned to the genus Sus based on mor-
phological analyses (Groves 1981), but subsequently the origi-
nal taxonomy was restored based largely on genetic evidence(Funk et al. 2007; Groves & Grubb 2011). Description of another,
now extinct, species of Porcula indicates that the genus was
widespread in Asia until the Late Pleistocene (Pickford 2013).
Within Asian Sus, contrasting phylogenetic relationships
have been proposed based on DNA. On the one hand, some
evidence shows that S. barbatus/S. verrucosus and S. scrofa/
S. celebensis cluster together as a sister clade of S. cebifrons/
S. philippensis (Figure 1.2; Gongora et al. 2011a), which is par-
tially consistent with early DNA studies (Randi et al. 2002),
whereas other DNA and morphological analyses show different
clades: S. cebifrons/S. celebensis, S. barbatus and S. verrucosus/
S. scrofa (Lucchini et al. 2005). It has been suggested that the
S. barbatus/S. verrucosus lineage entered Island South East
Asia ~ 2 Ma and coexisted with S. celebensis, and that S. scrofa
evolved out of this (Groves 1981), which is in part consistent
with DNA analyses by Gongora et al. (2011a). Morphological
studies of extant and extinct forms have grouped Sus into primi-
tive ‘scrofic’ and derived ‘verrucosic’ forms (van der Made &
Moya-Sola 1989) based on the contrasting shapes of the male’s
lower canine, in which the S. scrofa group differs from the other
species of the genus (Groves 1981; Genov 2004).
In addition, mtDNA data (Gongora et al. 2011a) indicate
that the position of S. celebensis is ambiguous between the
S. barbatus/S. verrucosus and S. scrofa groups. This contrasts with
morphological analyses which have clustered S. celebensis within
the S. scrofa and S. philippensis group (Groves 1997). Previous
mtDNA studies have also shown that when S. scrofa specimens
from Island South East Asia are included, S. scrofa, S. barbatus,
and S. celebensis fail to show mitochondrial differentiation
despite those species being morphologically well defined
(Larson et al. 2007a). This reflects some of the shortcomings
of mtDNA: classification based on maternally inherited DNA
markers alone cannot provide a comprehensive understanding
of the interspecies interactions and admixture that could
have occurred during the evolutionary history of species; the
evolutionary history of the genus Sus is better explained by a
reticulate process (Frantz et al. 2016). Where hybridization
occurs, genome sequence approaches have provided an in-depth
understanding of these inconsistencies and interactions
between species. This is the case for the evolutionary history of
Sus from a genomic perspective, which is discussed in Chapter
34 of this book and also in Frantz et al. (2013, 2016) and Groenen
et al. (2012).Tayassuidae
Diversification and Dispersal of New World
Tayassuidae
Having settled in North America ~36 Ma, Tayassuidae further
evolved into 20–25 genera including lineages with peculiar cheek-
bone forms in the Late Oligocene (Savage & Russell 1983; Stucky
1992; Wright 1993a, 1993b, 1998; Harris & Liu 2007; Prothero
2009, 2015; Prothero & Pollen 2013). Subsequently, most of them
became extinct, but the flat-headed (Platygonus) and long-nosed
(Mylohyus) peccary lineages, which had developed better adap-
tations for eating grasses and a more generalized omnivorous12:28:36